Forum Conf 10 (MAS) - All of November 2003

[For further information on the Electronic Forum on Biotechnology in Food and Agriculture see Forum website.
Note, participants are assumed to be speaking on their own behalf, unless they state otherwise.]

-----Original Message-----
From: Biotech-Mod2
Sent: 17 November 2003 12:46
To: 'biotech-room2@mailserv.fao.org'
Subject: 1: MAS for crop improvement in developing countries

From Denis Murphy, Head of Biotechnology Unit, University of Glamorgan, UK. Researcher/consultant in crop biotechnology.

Marker-assisted selection (MAS) should be viewed dispassionately as a potential tool for crop improvement to be usefully deployed alongside conventional phenotype selection for certain crops and for certain characters. MAS is a downstream technology that can improve and accelerate selection of favourable traits in a crop population. As such it should not be regarded (as is some times stated) as a direct alternative to more upstream technologies like the various forms of transgenesis, mutagenesis (radiation, chemical or somaclonal), protoplast fusion or other forms of assisted wide crossing. These more upstream technologies serve to generate additional variation in plant populations. In contrast, MAS and conventional phenotype selection are all about selecting the optimal variants from a population that can number many thousands and where the trait(s) of interest may be either obvious or cryptic.

MAS can definitely play a part in the improvement of many crops in developing countries. However, as indicated in the Turin conference [proceedings available at http://www.fao.org/biotech/Torino.htm ...Moderator], not all crops will benefit equally from MAS, and even within a single crop some traits are more suitable for MAS than others. The development of molecular markers for crops in industrialised countries over the past two decades has involved extensive collaboration between industry and public sector research bodies. One example is our development in the UK of molecular markers and mapping populations for rapeseed.

Since developing countries are often interested in different crops, they will need to develop their own MAS-related tools and expertise. The above model of industry/public sector collaboration may not be appropriate, especially for non-cash, subsistence crops without a large traded market from where value can be extracted. Therefore, the establishment of MAS systems in developing countries would tend to become more of a public sector function.

This has advantages as well as drawbacks. In the short term, there is the obvious disadvantage that public funding is smaller and less focused than private sector funding. Also, it can be challenging to build up and retain an effective expertise base in the public sector. However, on the plus side, a public sector MAS program is much more amenable to international collaboration and resource sharing. This collaboration can be facilitated by global entities like FAO and the Consultative Group on International Agricultural Research (CGIAR), where much of the initial transfer of expertise and hardware may be from industrialised countries. The next stage may be the establishment of regional groupings, either virtual or "real", of developing countries focussed on particular crops and/or traits.

There are many other important and effective avenues to the improvement of crop yield/quality in developing countries that may initially have higher priority than relatively expensive (but getting cheaper) technologies like MAS. For example, in some cases, crop gains from improved management and infrastructure can dwarf those from improved breeding. In Brazil, crop exports are jeopardised by week-long traffic jams on roads to the main ports in the North East while, in Malaysia, the yield of oil palm has stagnated for a decade at 3.7 T/ha despite the availability of germplasm from public programs that yields 7.5 T/ha. In the short term, basic, and easily addressed (at least in theory) issues like management and infrastructure should be accorded equal or higher priority as they can produce rapid returns on public sector investment. In the medium term, however, it is vital that developing countries build up a public sector expertise base in MAS and other crop improvement technologies, both new and "traditional". This will enable them to make their own informed decisions on when and how to deploy such technologies in the future.

Denis Murphy,
Head of Biotechnology Unit,
University of Glamorgan,
United Kingdom.
dmurphy2 (at) glam.ac.uk

-----Original Message-----
From: Biotech-Mod2
Sent: 17 November 2003 15:53
To: 'biotech-room2@mailserv.fao.org'
Subject: 2: Economic Impact of MAS

From Daniel Gianola, University of Wisconsin-Madison, USA

It seems to me that something that is badly lacking is economic analysis of MAS versus conventional phenotype-based selection procedures. Irrespective of whether the program is in a developing or developed nation, it would be essential to have a range of the internal rates of return to be expected from the (possibly massive) investment in genotyping costs, etc.

I would appreciate it if somebody in the conference can direct me to well done economic analyses, especially in livestock.

Professor Daniel Gianola
Department of Animal Sciences
Department of Biostatistics and Medical Informatics
Department of Dairy Science
University of Wisconsin-Madison
USA
gianola (at) calshp.cals.wisc.edu

-----Original Message-----
From: Biotech-Mod2
Sent: 18 November 2003 10:35
To: 'biotech-room2@mailserv.fao.org'
Subject: 3: Re: MAS for crop improvement in developing countries

This is from Olusola B Sokkefun, Lagos, Nigeria.

The concepts of marker assisted selection and its potentials, as novel as they all seem, would elude the developing world.

It is only in a few universities for instance in Nigeria, where I am based, that you find enough facilities to extract DNA, to talk of being able to do further studies on the DNA. The laboratories where they exist are not equipped. Most African universities are theoretical universities especially the faculties of science.

The developed world must generally carry the developing world along in the cutting edge technologies. We at the centre look forward to partnerships with laboratories, institutes and institutions within and outside the several universities for partnership which can find commercial applications.

Olusola B Sokefun
Research Secretary
The Bioscience Research Centre, Lagos State University, Ojo
Lagos
Nigeria
Tel:+ 234 8033335175
osokefun (at) hotmail.com

-----Original Message-----
From: Biotech-Mod2
Sent: 18 November 2003 10:36
To: 'biotech-room2@mailserv.fao.org'
Subject: 4: Re: Economic Impact of MAS

In response to message 2 (17 November) by Daniel Gianola, I can refer you to both of my books:

In the first book, I consider the question of economic evaluation in more detail, and in the second book, I review the various studies that have attempted to predict the gains possible by MAS. With respect to the economic questions, MAS is no different from any other technology that increases rates of genetic gain, but also increases costs. In brief, investment in MAS can be "massive" but so can the potential economic gains over the long-term. A little bit of genetic gain is very valuable over the long-term. Your frame of reference is also very important. For example, are you considering gain to a single breeding company in competition with other companies, or the economic gain that can be accrued to the national economy?

Joel Ira Weller
Institute of Animal Sciences
A. R. O., The Volcani Center
P. O. Box 6
Bet Dagan 50250
Israel
E-mail: weller (at) agri.huji.ac.il
Phone : 972-8-9484430
Fax : 972-8-9470587
http://www.agri.huji.ac.il/~weller
http://www.agri.gov.il/People/JoelWeller.html

[Regarding economic comparisons of conventional and MAS breeding, two relevant articles were recently published from the the International Maize and Wheat Improvement Center (CIMMYT) in the April 2003 edition of the journal Molecular Breeding. The work was referred to in the Background Document to this conference. Because of their relevance to the discussion here, the abstracts of the articles are reproduced below - the journal website is at http://www.kluweronline.com/issn/1380-3743/current, the April 2003 edition currently seems to be freely available.

The abstract of the first article (Dreher, K. et al. 2003. Money matters (I): costs of field and laboratory procedures associated with conventional and marker-assisted maize breeding at CIMMYT. Molecular Breeding. 11: 221-234) says "This article presents selected results of a study carried out in Mexico at the International Maize and Wheat Improvement Center (CIMMYT) to compare the cost-effectiveness of conventional and marker-assisted maize breeding. Costs associated with use of conventional and marker-assisted selection (MAS) methods were estimated using a spreadsheet-based budgeting approach. This information was used to compare the cost of using conventional screening and MAS to achieve a well-defined breeding objective-identification of plants carrying a mutant recessive form of the opaque2 gene in maize that is associated with Quality Protein Maize (QPM). In addition to generating empirical cost information that will be of use to CIMMYT research managers, the study produced four important insights. First, for any given breeding project, detailed budget analysis will be needed to determine the cost-effectiveness of MAS relative to conventional selection. Second, direct comparisons of unit costs for MAS methods and conventional selection methods provide useful information for research managers, but factors other than cost are likely to play an important role in driving the choice of screening methods. Third, the choice between MAS and conventional selection may be complicated by the fact that the two are not always direct substitutes. Fourth, when used with empirical data from actual breeding programs, spreadsheet-based budgeting tools can be used by research managers to improve the efficiency of existing protocols and to inform decisions about future technology choices".

The abstract of the second article (Morris, M. et al. 2003. Money matters (II): costs of maize inbred line conversion schemes at CIMMYT using conventional and marker-assisted selection. Molecular Breeding 11: 235-247) reads "This article presents selected results of a study carried out in Mexico at the International Maize and Wheat Improvement Center (CIMMYT) to compare the cost-effectiveness of conventional and biotechnology-assisted maize breeding. Costs associated with the use of conventional and marker-assisted selection (MAS) methods at CIMMYT were estimated using a spreadsheet-based budgeting approach. This information was used to compare the costs of conventional and MAS methods for a particular breeding application: introgressing an elite allele at a single dominant gene into an elite maize line (line conversion). At CIMMYT, neither method shows clear superiority in terms of both cost and speed: conventional breeding schemes are less expensive, but MAS-based breeding schemes can be completed in less time. For applications involving tradeoffs between time and money, relative profitability can be evaluated using conventional investment theory. Using a simple model of a plant breeding program, we show that the optimal choice of a breeding technology depends on the availability of operating capital. If operating capital is abundantly available, the "best" breeding method will be the one that maximizes the net present value (i.e., MAS), but if operating capital is constrained, the "best" breeding method will be the one that maximizes the internal rate of return (i.e., conventional selection). This insight may help to explain why private firms tend to invest more aggressively in biotechnology than public breeding programs, which are more likely to face budgetary constraints"...Moderator].

-----Original Message-----
From: Biotech-Mod2
Sent: 18 November 2003 11:27
To: 'biotech-room2@mailserv.fao.org'
Subject: 5: Cost analysis of MAS vs conventional breeding

I am Hayde F. Galvez, a university researcher at the Molecular Genetics Laboratory of the Institute of Plant Breeding, University of the Philippines Los Baños. I am 70%, 20% and 10% involved in research, teaching and administrative functions. My research field of interest or specialization is in molecular genetics (particularly QTL-map based gene discovery) and molecular plant breeding.

So far the only satisfiable economic analysis I have read that compares the direct costs associated with MAS-breeding and with conventional breeding is the work of Dreher et al. (Molecular Breeding 11:221-234, 2003) in maize for quality protein. The study was done in a CGIAR (public sector) center, thus can be equated for MAS breeding to be undertaken in developing countries. However, there are other major factors other than cost (money matters) that need to be looked into in deciding the added-benefits of MAS - i.e. time, effectiveness etc. Also, should the development of the robust/reliable and simple (breeders friendly) DNA markers be included in the cost analysis? If it is, I don't think the use of molecular markers in breeding can be justifiable. For a breeding institute in a developing country, shuttle-research/collaboration with an established marker laboratory (e.g. CGIAR, FAO-affiliated centers) in the development of DNA markers for MAS is the most cost-effective means, especially if capacity in that laboratory has yet to be established. Furthermore, the benefits derived from MAS should be looked at in longer periods of time, say in three selection cycles of breeding, to verify the time-effectiveness of the 'tool'.

DNA markers tightly tagging important but difficult to evaluate characters of economically important crops are indeed valuable tools to be used in MAS breeding. The decision on when to use them, which characters and which crops, may have to be made by the breeders themselves. Never one method is better than the other, or the two methods being not always direct substitutes. Both MAS breeding and coventional breeding metohds should be continuously reviewed and advanced in answer to the evolving biotic and abiotic factors limiting crop productivity. Because at any one time either method may have to be opted depending on the breeding objectives and other 'breeding factors'. The field (conventional) and lab-based breeders should form a team and closely coordinate, from research planning to implementation, to ensure full benefits from the use of MAS.

Hayde F. Galvez
University Researcher
Institute of Plant Breeding
University of the Philippines Los Baños
College, Laguna
Philippines
hgalvez_4031 (at) yahoo.com

[In the recently published CIMMYT economic studies comparing MAS and conventional breeding, mentioned in Message 4 (November 18) and above (Dreher et al), the costs of developing molecular markers associated with the trait of interest were not considered, as it was assumed that they were already available...Moderator].

-----Original Message-----
From: Biotech-Mod2
Sent: 18 November 2003 12:18
To: 'biotech-room2@mailserv.fao.org'
Subject: 6: Re: Economic Impact of MAS

This is from Daniel Gianola. I have already introduced myself, but forgot to state that my interests focus on applications of statistics to quantitative genetics and animal breeding.

I wish to thank Dr. Joel Weller (Message 4, November 18) for reminding us of his books. In his message, he states that even though the investments in a MAS program may be "massive" (my terms), so may be the genetic gains. Fair enough, but what are the internal rates of return? This is a certainly a question that the World Bank would ask, should a developing nation consider approaching the organization for assistance in the implementation of a MAS program. Also, what is the volatility of such an investment? What is the risk that big single nucleotide polymorphism (SNP) platforms for searching elusive quantitative trait loci (QTLs) will soon become white elephants in the light of advances in postgenomics?

Also, from a developing nation perspective, the resources are scarce, and an investment in MAS should clearly produce markedly superior returns, given the significant opportunity costs.

I agree with Joel Weller in that the perspective from which the economic analysis is undertaken is important.

[Some definitions may be useful. Cost-benefit analysis is a procedure for evaluating the desirability of a project by weighting benefits against costs. Results may be expressed in different ways, including internal rate of return (IRR), net present value (NPV) and benefit-cost ratio. The NPV of a project is defined as the difference between the present values of its future cash inflows and outflows. The IRR is the discount rate (i.e. the rate at which future values are discounted to the present) at which a stream of costs and benefits has a net present value of zero, i.e. the rate of return for which the project breaks even. Projects with a higher IRR would be preferred over those with a lower IRR. Opportunity cost is the economic value of an input in the best possible alternative use. For more on the basics of cost-benefit analysis, see e.g. http://europa.eu.int/comm/regional_policy/sources/docgener/guides/cost/pdf/3 _full_en.pdf ...Moderator].

-----Original Message-----
From: Biotech-Mod2
Sent: 18 November 2003 13:29
To: 'biotech-room2@mailserv.fao.org'
Subject: 7: MAS and forestry crops

I am E.M. Muralidharan from India and I work on different aspects of biotechnology of tropical forest species.

I hope to see some discussion on the potential of MAS techniques in the area of forestry and horticulture. I need hardly emphasize that in most tropical forest species, especially the trees that are either still wild or at early stages of domestication, MAS will eventually play a crucial role in accelerating genetic improvement. The long life cycles of these trees no longer appear to be a formidable impediment. I also anticipate that use of MAS will help in rapid domestication of several new tree crops in the near future adding to the diversity of artificial forests and agroforestry systems.

When contrasted with the criticism that transgenic organisms have to contend with today, MAS technology is one aspect of modern biotechnology that can be expected to find wider acceptability. I like to view it as an atavistic shift (albeit with refinement) to what the pioneer agriculturists initiated centuries back, i.e. searching and picking out from whatever variation that nature makes available. Of course, application of MAS will not be restricted to such relatively benign activities. While researchers working on transgenics have a long way to go (if ever) to reach a level of competence that will avoid criticism, MAS can, slow and steadily, find applications all along the way. For the same reason, it ought to attract support from a wider range of funding agencies and governments, whether developed or developing. I am arguing here for letting such technologies take precedence in the short to medium term planning and particularly for developing countries to build their capabilities.

I agree with Denis Murphy (Message 1, November 17) when he gives priority to management and infrastructure issues in developing countries. An appropriate mix of technologies and increased awareness among researchers of the potential and limitations of alternate technologies is the recipe for success in crop improvement and ensuring that the benefits reach the people who need it.

Dr. E.M. Muralidharan
Genetics Division
Kerala Forest Research Institute
Peechi, Thrissur, Kerala State
680653, India
Email: emmurali (at) kfri.org

-----Original Message-----
From: Biotech-Mod2
Sent: 19 November 2003 09:00
To: 'biotech-room2@mailserv.fao.org'
Subject: 8: Indicators of utility of MAS in plant breeding

This is from C.R. Bhatia, India. I am a plant geneticist and breeder by profession. I have used isozyme, protein and molecular markers in genetic studies. I was a co-author in an early review on marker-assisted selection in crop plants (Molecular Breeding 1997 Vol. 3: 87-103). I have retired from field and bench research but continue international and national consultancy in agricultural biotechnology.

Whenever a new tool or technique comes up a lot of hype is generated by the developer that often reflects the vendor bias. Among the users, some look at the new tool in a highly critical mode, others are over appreciative, and yet others wish to use it as a contemporary or "fashionable" tool. When resources are a constraint, as they are in most plant breeding programs, it is important to have "reality" check based on evidences or indicators. Of course, selection of the indicators could also be biased. The utility of a tool/technique in plant breeding can be judged on the following indicators at different stages of the breeding program:

Many participants would very much like to see evidence-based answers to the points raised above, also for the selections based on quantitative trait loci (QTLs). Colleagues from the developed countries who have used MAS for a longer period may share their experiences.

Another question often asked by the breeders is: Can the MAS-related analytical work (when the molecular markers are well established) be outsourced to a private laboratory? Related to the above is: Would private investment in a service laboratory providing marker analysis commercially generate adequate returns? Can the service be provided at a cost which breeders can afford to pay?

C. R. Bhatia
17 Rohini, Sector 9-A,
Vashi,
New Bombay - 400 703,
India
neil (at) bom7.vsnl.net.in

-----Original Message-----
From: Biotech-Mod2
Sent: 19 November 2003 09:06
To: 'biotech-room2@mailserv.fao.org'
Subject: 9: Cost of MAS - the biggest barrier

My name is Bert Collard. My background is in marker development for disease resistance traits in chickpea and wheat in Australia.

I think that the cost of MAS is the most important limitation for utilisation in developing countries. I completely agree with the previous contribution by Daniel Gianola (Message 6, November 18) that rigorous cost-benefit analysis is of the utmost importance before even considering to use markers for MAS (in any country), because this varies considerably for different species, traits, labour costs etc. Such planning should also be done from an interdisciplinary perspective: by plant breeders, molecular biologists, physiologists, pathologists and economists etc, which in my experience, is not done often enough (this was also mentioned by Hayde Galvez in Message 5 (November 18)). However, given the relatively cheap labour costs and high costs for reagents, consumable products and equipment for MAS in developing countries, I suspect that there would not be many cases where MAS would be cost effective. (I would be very grateful if anyone can suggest additional references on cost-benefit analysis).

I would also like to emphasise that the costs associated with developing markers can also be extremely high - far greater than the costs associated with MAS, yet this is often neglected in reports or discussions about MAS (even if equipment has already been obtained; if a lab requires the purchase of equipment, then the initial costs could truly be 'massive'). Furthermore, marker development can take a long period of time - probably longer than previously thought. This can offset major time-savings gained by using MAS compared to conventional breeding.

What follows on from the costs associated with marker development or MAS is where funding will come from, given that funding for agriculture in the public sector in developing countries is limited, and already stretched. Moreover, could these funds - obtained from governments or external funding bodies - maintain a marker development/MAS facility in the long term?

Unfortunately, in my opinion, I doubt that adequate funding could be provided in the majority of cases. Therefore, I question whether MAS is generally feasible in the majority of labs/plant breeding institutes in developing countries, with the exception of Consultative Group on International Agricultural Research (CGIAR) centres and some National Research Centres.

Perhaps another exception could be the use of publicly available markers, if these markers were associated with high priority traits for relevant crops in developing countries. However, this would only be possible in major crop species, and not possible with the majority of minor crop and vegetable species that are vital for many subsistence farmers (due to a complete lack of marker research in some species).

In response to a previous contribution, I have encountered the following papers that have conducted cost-benefit analysis of MAS in crop species:

[Abstract given at end of Message 4, November 18...Moderator].

Dr. Bertrand Collard
Postdoctoral Research Fellow
Department of Biological and Physical Sciences
University of Southern Queensland, Australia
Toowoomba 4350
Tel: +613 4631 2699
Fax: +613 4631 1530
collardb (at) usq.edu.au

-----Original Message-----
From: Biotech-Mod2
Sent: 19 November 2003 10:43
To: 'biotech-room2@mailserv.fao.org'
Subject: 10: MAS for tree crop improvement and transgenics

I agree with E.M. Muralidharan (Message 7, November 18) that MAS has best contribution for perennial crops like fruit trees. Generations of breeders may be needed before an improved forest tree cultivar could be released. In our coconut tree planting program, DNA markers have been successfully used to assist the selection of parental trees (seed nuts) for the nationwide coconut replanting.

I would like to add to message 7 that MAS is very well very useful also in the production/release of a trangenic crop variety. Starting from the verification of the transgene to molecular characterization of transgenic plants and establishment/introgression into other breeding materials, MAS is the only way possible to track the 'movement' of the transgene in the gene pool.

Hayde F. Galvez
Molecular Genetics Laboratory
Institute of Plant Breeding
University of the Philippines Los Baños
The Philippines
hgalvez_4031 (at) yahoo.com

-----Original Message-----
From: Biotech-Mod2
Sent: 19 November 2003 11:34
To: 'biotech-room2@mailserv.fao.org'
Subject: 11: Areas that need to be debated - Plant breeding

This is from P.M. Priyadarshan, a plant breeder at the Rubber Research Institute of India.

It is indeed heartening to note that FAO has taken the initiative for an e-mail conference on the current most relevant subject in plant breeding - MAS. MAS is indeed a technique that can assist plant improvement, especially when the population is large enough and when phenotypic selection becomes difficult. Also, in crops like rubber, where the gestation period is 7-8 years, MAS can help (at least theoretically) to have a quick and routine selection either for monogenic or polygenic traits. But there are areas that need to be debated falling under this purview:

1) As pointed out by Dr. Denis Murphy (Message 1, November 17), MAS cannot be considered as a direct alternative to upstream technologies.

2) It is widely believed that quantitative trait loci (QTLs) governing yield can be 'tied' through markers. Yield is a multi-channel end point and several genes, in conjunction with the environment, will lead to high or low yield. When we talk of yield, what about multitude of environments prevailing across a country?

3) We must understand/analyze pathogen strain production. Why have so many biotypes and pathotypes originated over the years? When agriculture began centuries back, there were not much causal organisms. Or, such organisms could not get hosts to grow with. Now, with large areas under monoculture, infectious organisms have their ride to live in. Remedy to this is only and only crop diversification in all agriculturally suitable environments.

4) Cost effectiveness of MAS compared to conventional breeding is yet another aspect that needs attention. If MAS is not getting cheaper, developing countries cannot use them judiciously. A centralized facility for routinely doing MAS, either under a global entity like CGIAR or at individual national level, shall be a remedy.

5) During the 1980s, the journals of plant breeding were dominated by papers on tissue culture. The 1990s witnessed an overwhelming amount of papers on RAPDs, RFLPs and microsatellites and towards 2000 and beyond the journals were flooded with papers on MAS and molecular linkage maps. Many more molecular techniques are to come. But sadly, these technologies have not come out in a big way to boost conventional plant breeding efforts, as against the popular expectations, and have largely remained in papers. Micropropagation in woody species is yet to boom, transgenic cotton in India faced a miserable equation, and the stories and reports are many that need to be analyzed to mitigate doubt in the public about the utilization of biotechnology.

6) In India, the financial outlay (annual) for biotech research is nearly Rs. 150 crores [roughly 33 million US dollars - 1 crore is 10 million rupees, roughly 45 rupees per US dollar...Moderator]. We have been actively pursuing research for over 17 years. Theoretically speaking, biotech as such, is expected to accelerate the pace of breeding new varieties. Yet, I am doubtful how many varieties have been developed and released to farmers.

7) Environmental sensitivity in expression of genes is a crucial factor governing the expression of genes identified. The expression of genes for resistance is highly environment sensitive.

8) Man cannot duplicate the job of nature, for the nature knows all and everything. Instead of competing with nature in its processes/selection, man should try more to understand and learn the intricacies of nature, and put them into practice. Learning more about nature will sustain us to live in sustenance. Let us ask the nature to undertake the selection process, for the nature only knows how, when and what to select.

P.M. Priyadarshan
Plant Breeder,
Rubber Research Institute of India,
Regional Station, AGARTALA - 799 006,
India
Tel: Off : 91-381-2355287/2355143 - Extn:205
Tel: Resi : 91-381-2354325
Fax: 91-381-2353149
pmpriyadarshan (at) hotmail.com
alternate e-mails: pmpriyadarshan (at) rediffmail.com pmpriyadarshan (at) yahoo.co.in
personal web page: www.freewebs.com/pmpriyadarshan/

-----Original Message-----
From: Biotech-Mod2
Sent: 19 November 2003 11:43
To: 'biotech-room2@mailserv.fao.org'
Subject: 12: Re: Indicators of utility of MAS in plant breeding

This is from P.B. Kirti. I am a Professor in the Department of Plant Sciences of the University of Hyderabad, interested in the genetic transformation of legumes for disease and insect resistance.

Of the so-far-received opinions on MAS, the opinion expressed in Message 8 (November 19) by Dr. C.R. Bhatia, Former Secretary, Department of Biotechnology, Government of India, appears to be highly pragmatic. MAS is a highly fashioned and expensive technique, that is supposed to improve the selection efficiency in breeding programs and shorten the time taken for attaining the expected goals. There is no comprehensive treatise available so far on MAS in terms of successful utilization of the technique in the development of new crop varieties or breeding material, that is undergoing active consideration. Such information is most welcome in arriving at a conclusion whether the technique under consideration is good to be pursued, particularly in plant breeding programs in developing countries.

P.B. Kirti,
Department of Plant Sciences
University of Hyderabad, Hyderabad 500046
India
E Mail: pbksl (at) uohyd.ernet.in

-----Original Message-----
From: Biotech-Mod2
Sent: 19 November 2003 13:34
To: 'biotech-room2@mailserv.fao.org'
Subject: 13: MAS for livestock in developing countries

From Dirk-Jan de Koning, Department of Genetics and Biometry at the Roslin Institute (Scotland, UK). My area of work is design and analysis of QTL experiments in livestock.

Improvement of livestock productivity in the developing world through breeding should be focused on animals that are tolerant against a variety of diseases and can cope with the environmental stress (heat, drought).

As a consideration for the cost-benefit analysis: for animal trypanosomosis, the annual cost of curative and preventative treatments for African livestock is estimated at 35 million US Dollars (USD) with a total annual cost exceeding one billion USD (Kristjanson et al. 1999. Agricultural Systems 59:79-89). At this moment, the lack of routine recording of production and health traits, alongside limited availability of molecular research facilities to individual countries (as pointed out by Olusola Sokefun in message 3, November 18), prohibits the implementation of any structural breeding program exploiting MAS. [Animal trypanosomosis, caused by trypanosomes, protozoan parasites, transmitted by the tsetse fly, is an important constraint, if not the most important constraint, to livestock and mixed crop-livestock farming in tropical Africa. The paper referred to is by P.M. Kristjanson et al, entitled "Measuring the costs of African animal trypanosomosis, the potential benefits of control and returns to research". Among other things, their results indicate that the potential benefits of improved trypanosomosis control, in terms of meat and milk productivity alone, are $700 million per year in Africa and that the disease costs livestock producers and consumers an estimated $1340 million annually, without including indirect livestock benefits such as manure and traction...Moderator].

However, MAS can be an important tool in the development of more robust breeds that can cope with the biotic and abiotic stresses of the (sub-)tropical climates in many developing countries. In agreement with previous messages, I feel that this should be done as large international collaborative efforts and not by individual countries. In such a scenario, existing breeds are assessed for their tolerance and production and subsequently a variety of experimental crosses can be made. QTL analysis followed by MAS would be used to derive a robust synthetic hybrid from the experimental crosses. Given the international nature of such an approach, any breeds would need to suit the particular challenges of each of the participating countries. The logistic and social issues related to introduction of a new hybrid breed for smallholder farms pose additional challenges for such an effort. International collaboration is a must for both the developed and developing world because studies by individual groups can suffer from limited statistical power, thus prohibiting a clear picture of the overall genetic architecture of the trait of interest.

The laboratory cost of MAS may be 'massive', but so is running a structured breeding program: At the workshop on MAS held in Turin on 17-18 October 2003 [proceedings available at http://www.fao.org/biotech/Torino.htm ...Moderator], we were told that the Italian government contributes annually about 93 million Euro towards the breeding value evaluations in Italian livestock. In plants, the development of a new cereal variety was estimated between 1 and 5 million Euro. Many developed and developing countries have large and efficient genotyping facilities available that could be targeted towards livestock improvement in an internationally coordinated program.

Dirk-Jan de Koning
Roslin Institute
Genetics and Biometry
Roslin, Midlothian, EH25 9PS
UK
phone:+44 (0)131 5274460
fax: +44 (0)131 4400434
e-mail: DJ.DeKoning (at) bbsrc.ac.uk

-----Original Message-----
From: Biotech-Mod2
Sent: 19 November 2003 13:56
To: 'biotech-room2@mailserv.fao.org'
Subject: 14: Crossing-over // false-positive markers

This is from Adilson Mota, a research molecular geneticist working at the National Dairy Cattle Research Center of Embrapa (Brazilian Agricultural Research Corporation), located in Juiz de Fora, state of Minas Gerais, Brazil. Recent research activities focus on functional genomics related to bovine mammary gland physiology and pathology.

I have read all messages so far with great interest. But I have other questions that I would like to address. Besides the economics/labor involved in MAS (regarding construction of reference population, genotyping, data collection, and analysis), the selected marker may even, at the end, be far enough from the QTL (or gene). In this case, crossing-over(s) in that region may cause chromosome recombination and selection based on the marker genotype (MAS) may not be effective. There is also the possibility of generating false-positive markers, depending on experimental design and analysis, for which MAS should be preceded of evaluating the marker in an independent population.

I would appreciate hearing the experiences/opinion of participants regarding these (and other) technical issues of MAS and get some recent references on these subjects. I also hope that, at some point, the discussions will consider MAS related to livestock genetics.

Adilson Mota, PhD
Embrapa Gado de Leite - Dairy Cattle Research Center
R. Eugenio do Nascimento, 610
Dom Bosco - Juiz de Fora - MG
36038-330 - BRAZIL
Phone (+55) (32) 3249-4825
Fax (+55) (32) 3249-4701
E.mail amota (at) cnpgl.embrapa.br
HTTP://WWW.CNPGL.EMBRAPA.BR
HTTP://WWW.EMBRAPA.BR

-----Original Message-----
From: Biotech-Mod2
Sent: 19 November 2003 15:57
To: 'biotech-room2@mailserv.fao.org'
Subject: 15: Re: Crossing-over // false-positive markers

Responding to Adilson Mota (Message 14, November 19), both problems you raised are important, and there are no easy answers. With respect to "false-positives", which is a hugh problem for whole genome scans, the best solution to date is the "false-discovery-rate" (FDR). The FDR does not give a definitive answer as to which effects are real, but you can at least get an indication if there is something really there. With respect to the question of QTL location with respect to the markers, confidence intervals will be large, unless both the QTL effect and sample size are large. Genotyping additional markers in the region of interest doesn't help much. Once you are down to a marker spacing of 10 cM, additional markers will not reduce the confidence interval.

Joel Ira Weller
Institute of Animal Sciences
A. R. O., The Volcani Center
P. O. Box 6
Bet Dagan 50250
ISRAEL
E-mail: weller (at) agri.huji.ac.il
Phone : 972-8-9484430
Fax : 972-8-9470587
http://www.agri.huji.ac.il/~weller
http://www.agri.gov.il/People/JoelWeller.html

-----Original Message-----
From: Biotech-Mod2
Sent: 19 November 2003 17:03
To: 'biotech-room2@mailserv.fao.org'
Subject: 16: Re: Crossing-over // false-positive markers

From Dirk-Jan de Koning, UK.

A very specific reply to Adilson Mota (Message 14, November 19) about false positives and MAS.

There is a very good paper on this issue by Hayes and Goddard (Livestock Production Science Volume 81, Issues 2-3, June 2003, Pages 197-211), entitled "Evaluation of marker assisted selection in pig enterprises". In a nutshell (at the risk of misrepresenting some of the article): When you use a very relaxed threshold for quantitative trait locus (QTL) detection, you detect (and use) many QTL that are false positives BUT you also detect most of the REAL QTL, hence increasing your genetic gain! The profit (yes, it includes a cost benefit analysis) becomes then a function of the QTL effects and the genotyping costs. I realise that Livestock Production Science is not widely available but you can always request a copy from one of the authors (ben.hayes (at) akvaforsk.nlh.no). To me, it was a refreshing read compared to all the literature claiming we need highly stringent genome-wide significant thresholds. I guess the latter depends on how damaging the detection of a false positive is. I agree with Joel Weller (Message 15, November 19) in his endorsement of the false-discovery-rate (FDR) for getting an idea on the expected number of false positives among your QTL.

Dirk-Jan de Koning
Roslin Institute
Genetics and Biometry
Roslin, Midlothian, EH25 9PS
UK
phone:+44 (0)131 5274460
fax: +44 (0)131 4400434
e-mail: DJ.DeKoning (at) bbsrc.ac.uk

-----Original Message-----
From: Biotech-Mod2
Sent: 20 November 2003 09:49
To: 'biotech-room2@mailserv.fao.org'
Subject: 17: Re: Cost of MAS - the biggest barrier

I am Paul Heisey, an economist at Economic Research Service, U.S. Department of Agriculture. From 1985-1998 I was an economist with The International Maize and Wheat Improvement Center (CIMMYT).

Another reference on the economics of MAS is:

Moreau, L., Lemarie, S., Charcosset, A. and Gallais, A. 2000. Economic efficiency of one cycle of marker-assisted selection. Crop Science 40:329-337. [Full text available from High WirePress, providing a large archive of free full-text science articles, at http://highwire.stanford.edu/ ...Moderator].

This is a synthetic, not an empirical study, I believe, covering a single cycle. But it is useful in outlining some of the analytical issues.

Paul Heisey
Economic Research Service, USDA
USDA Economic Research Service, 1800 M St., NW
Washington D.C. 20036-5831
U.S.A.
Tel. +1-202 694-5526
Fax: +1-202 694-5774
EMail: pheisey (at) ers.usda.gov

-----Original Message-----
From: Biotech-Mod2
Sent: 20 November 2003 09:59
To: 'biotech-room2@mailserv.fao.org'
Subject: 18: Re: MAS for livestock in developing countries

This is from Prof. Hugo Montaldo, Mexico. I have been interested in the evaluation of "new technologies" for the genetic improvement of animals.

I would be very adamant with respect to the need to build-up a sound breeding strategy and begin first using the so-called "traditional methodology" (recording of important traits and genealogy, Best Linear Unbiased Preduction (BLUP) etc.) as the only reasonable framework for using MAS in developing countries for improving animal populations. This has a very simple logic. MAS is very costly and its efficiency is still a matter of debate, moreover knowledge of the genetic control of important traits from a molecular perspective is very incomplete. Conversely, "traditional technology" is very well proven as cost effective and efficient.

This is to emphasize that use of MAS does not solve the need for choosing the right breeding objectives and does not solve the lack of reasonable breeding strategies involving breed utilization and within-breed selection. This is valid for typical productivity traits or disease resistance traits. Emphasis on MAS will be dictated by the economic importance of each trait and the probable contribution of comprehensive strategies involving MAS and other technology, including the traditional ones compared to simpler, and cheaper, options. Thus, MAS should not be regarded a a simple device in animal populations, but instead as an interacting part of much more complex strategies and decision-making processes. By sure, they are not only biological, but social, political and economic ones.

I think use of MAS due to extra costs involved should be done in a commercial framework of a national (regional) interest framework. Thus, we must clarify our perspective from the beginning, before general recommendations are made, by making case by case, comprehensive studies.

Prof. Hugo H Montaldo V
Jefe/Head
Departamento de Genética y Bioestadística
Facultad de Medicina Veterinaria y Zootecnia
Universidad Nacional Autónoma de México (UNAM)
Ciudad Universitaria, México 04510, D.F.
Tel./Fax 52 55 5622 5894
Fax. 52 55 5622 5956
e-mail: hmontald (at) fmvz.unam.mx hmontal2_s (at) hotmail.com

-----Original Message-----
From: Biotech-Mod2
Sent: 20 November 2003 10:11
To: 'biotech-room2@mailserv.fao.org'
Subject: 19: MAS in livestock - extension/traits

This is from Don Nicol, cattle breeding consultant based in Brisbane Australia but working in a number of countries. I have been associated with the commercialisation of DNA marker tests for a number of years with my client Genetic Solutions, an Australian based company that has released two beef quality direct marker tests to industry under the GeneSTAR product line.

1) The issue that I would raise is in respect of the extension to farmers of the value and use of these tests when they become available commercially. Extension agencies have traditionally supported the diffusion of genetic tools such as estimated breeding values (EBVs) and $ indexes. However, the case is different for marker tests. This is because of the complexity, "that's up to the commercialiser" arguments, perceived competition with quantitative genetic tools, faint praise or condemnation from quantitative geneticists etc etc. There is a huge educational challenge with these technologies. Who is likely to be the commercialiser of these tests in developing countries? Does extension capability exist to assist uptake and use?

2) What traits are being researched for the tropics? I am aware of work on cattle tick and internal parasite in tropical Australia, work on the slick coat gene in Florida USA. Is there a list?

P.S. I thought the background document very well written and want to know who to acknowledge. [The appropriate reference for the document is
FAO, 2003. Molecular marker assisted selection as a potential tool for genetic improvement of crops, forest trees, livestock and fish in developing countries. Background document to conference 10 of the FAO Biotechnology Forum. http://www.fao.org/biotech/C10doc.htm...Moderator].

Don Nicol
Brisbane
Australia
dnicol (at) b022.aone.net.au

-----Original Message-----
From: Biotech-Mod2
Sent: 20 November 2003 11:32
To: 'biotech-room2@mailserv.fao.org'
Subject: 20: Re: MAS for livestock in developing countries

From Dirk-Jan de Koning, UK.

The opinion expressed by Professor Montaldo (Message 18, November 20) differs quite a bit from what I put forward in my message (nr. 13, November 19), yet I agree with him on several points:

If you can organise routine recording of production and disease traits as well as pedigree information then you can implement 'traditional' breeding methods and subsequently evaluate, on a case by case basis, whether MAS has the potential to give additional benefit.

However, in the scenario that I put forward in my message, there would be no (reliable) routine recording and the livestock is mainly kept by smallholders with only a handful of animals. MAS could then be used in the development of 'robust' breed crosses that subsequently would be introduced to the smallholders. This is more similar to the MAS efforts of the Consultative Group on International Agricultural Research (CGIAR) in plants (or see, for example, the work on cotton by CIRAD in the Turin proceedings) where a large collaborative effort (including MAS) is made to develop more profitable crops for the developing world. [The paper referred to is by J-M Lacape et al. from the Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, available at http://www.fao.org/biotech/docs/Giband.pdf ...Moderator]

Hence the potential for MAS and the level at which it can be used depends on the local level of animal production. The developing countries represent a broad variety of climates and livestock systems, as well as social, economical and political agendas. Unfortunately, this conference does not allow us to look at MAS on a case by case basis and it is unavoidable that we have to resort to general statements that only apply to part of the developing countries. Rather than a commercial national/regional framework, I remain convinced that any form of MAS for the developing world will depend on heavily sponsored international collaborative efforts.

Dirk-Jan de Koning
Roslin Institute
Genetics and Biometry
Roslin, Midlothian, EH25 9PS
UK
phone:+44 (0)131 5274460
fax: +44 (0)131 4400434
e-mail: DJ.DeKoning (at) bbsrc.ac.uk

-----Original Message-----
From: Biotech-Mod2
Sent: 20 November 2003 14:00
To: 'biotech-room2@mailserv.fao.org'
Subject: 21: Suitability of MAS for livestock improvement in developing countries

I am Victor Olori, from Nigeria, working as a geneticist for the Irish Cattle Breeding Federation with lots of interest in livestock improvement in developing countries.

The discussion so far has been very relevant to the general question of the use or role of MAS in genetic improvement in general. There is no questioning the fact that successful application of MAS in a well structured breeding program in any developing country will yield the same benefits as in developed countries.

I find Dirk-Jan de Koning's first message (nr. 13, November 19) as particularly relevant to the question of using MAS in developing countries. As the background document to the conference indicates, using MAS in a structured breeding program is not synonymous with developing marker maps. The cooperation and links between labs and personnel in developing and developed countries is essential for the development of relevant maps for all species of interest but I think this form of cooperation is already taking place and should be encouraged irrespective of whether the technique will become widely used in the developing countries or not.

The major cost aspect in the application of MAS in a breeding program is in the genotyping of individuals, which is akin to recording under conventional breeding programs. The cost of recording is enormous and, under conventional breeding, much more animals may need to be recorded for the quantitative techniques to succeed. In straight comparison, I think the cost of genotyping the fewer animals (assuming a very effective marker is available) and the cost of recording and progeny testing (in dairy cattle, for example) will not be too far apart. My point therefore is that any developing country that can set up a successful breeding program with routine recording can, with little help, afford to introduce MAS for a few relevant traits. I agree with Dirk-Jan de Koning and others that MAS will be most relevant for some specific traits and can even be introduced in novel schemes without an elaborate breeding programs for specific traits. This is one way MAS will particularly benefit genetic improvement in the developing countries. It has potential for the integration of indigenous and exotic breeds without one polluting the good benefits of the other for both the developed and developing production environments.

So, because MAS may be a little bit more expensive should not be the only reason for thinking it is unsuitable in developing countries. Like any conventional breeding program or such endeavour, a cost benefit analysis is essential before embarking on MAS as an alternative.

So for me, the answer is YES to the question of the relevance of this technique in the developing countries. Perhaps the real question is 'can MAS speed up or jump start genetic improvement of livestock in the developing countries'. I ask this question because we still do not yet have the answer as to why, even with the well tested and trusted conventional breeding technique, genetic improvement of livestock species in the developing world is more of a myth than a reality. FAO has also been interested in this question and I believe that once we find a way to succeed in this regard, application of MAS, where it will be effective and most relevant, can also be introduced in developing countries. The absence of any real sense of the need for a genetic improvement program, especially for livestock, in most of these countries will further hinder the gains of MAS technique in these countries.

Dr. V.E. Olori
Irish Cattle Breeding Federation,
Shinagh House, Bandon,
Co. Cork,
Republic of Ireland.
Tel: +353 (23) 20220
Fax +353(23) 20229
E-Mail volori (at) icbf.com

[Regarding Victor's comments in the last paragraph concerning livestock genetic improvement programmes in developing countries, participants might be interested in looking at
1) the recommendations developed for, and finalised by, a symposium on "Realising sustainable breeding programmes in livestock production" conducted jointly by the World Congress on Genetics Applied to Livestock Production, and FAO on 22 August 2002 in Montpellier, France (http://dad.fao.org/en/refer/library/guidelin/7WCGALP.pdf).
2) proceedings of a workshop on "Developing breeding Strategies for lower input animal production environments", held on 22-25 September 1999 in Bella, Italy, organised by FAO and the International Committee for Animal Recording (http://dad.fao.org/en/refer/library/reports/bella.pdf) ...Moderator].

-----Original Message-----
From: Biotech-Mod2
Sent: 20 November 2003 15:21
To: 'biotech-room2@mailserv.fao.org'
Subject: 22: MAS and other ongoing research

This is Jasper Buijs. I am Associate Expert Agricultural Biotechnology at the International Potato Center in Lima, Peru. My work involves assessing deployment pathways for transgenic potato in developing countries, addressing connected socio-economic and environmental issues.

Addressing the high costs associated with the use of MAS - although not rejecting this reality - I think we should put these costs into the perspective of other ongoing research. Many developing countries are also in the process of setting up research and regulation capacities for the use of genetically modified organisms (GMOs). One of the important arguments given for these activities is that "developing countries should not be lagging behind in these developments" and "benefit from the technology". In that sense MAS, of course, is not different. Capacities built for the exploitation of MAS are, at least partly, a complement to capacities needed for the development of GMOs, and vice versa. With the further advantage that plant varieties or animals bred with the aid of MAS, do not need any further safety regulation (with its associated high costs). Moreover, I think that especially developing countries could benefit from MAS, as they would be able to generate new breeding products faster and in this way appropriate key knowledge and materials.

MSc. Ing. Jasper Buijs
Associate Expert Agricultural Biotechnology
Crop Improvement and Genetic Resources Department
International Potato Center (CIP)
Apartado 1558, Lima 12, Peru
telephone: 349 6017 ext. 3063
fax: 349 5326
email: j.buijs (at) cgiar.org
website: www.cipotato.org

-----Original Message-----
From: Biotech-Mod2
Sent: 20 November 2003 16:58
To: 'biotech-room2@mailserv.fao.org'
Subject: 23: Genetic conditions for MAS efficiency

This is from H.L. Dulieu. I worked in the Plant Breeding Station INRA-Dijon, until 1999. I was professor of Plant Biology and Genetics at the University of Burgundy; I am presently retired.

During at least five decades, several techniques were proposed to plant breeders to facilitate their work and to accelerate the selection procedures, particularly when the generation times are particularly long : radiation and chemical mutagenesis, in vitro techniques of multiplication and embryo rescue, genetic manipulations and, since almost ten years, marker assisted selection (MAS). Luckily, the breeders did not stop using their eyes and their scrutiny to continue their important work, particularly in developing countries. However, it seems normal to search for new applications of the tools offered by the advancing biological sciences.

MAS requires very particular conditions to be efficient: I will discuss only the genetic ones.

1. The genetic nature of the character to be selected among progenies must be clearly defined: monolocus versus multilocus status, additivity versus dominance (heritability), expressivity and penetrance. This implies traditional qualities of observer of the breeder and does not replace progeny tests over F1 and F2 generations.

2. It is necessary to cover the whole genetic map of a species both with molecular markers and traits. This has been done for a very few number of species of interest. This number is increasing, namely for molecular markers. It is relatively rapid to choose two different lines (if the genetic distance between them allows us to assume many molecular differences at many loci), to cross them and study the F2 or BC1s to map a set of markers. I doubt that the characters to be selected by breeding are incorporated in the map at the same rate. [The F1 is the initial hybrid generation resulting from a cross between two parents. The F2 is the second hybrid generation, produced either by intercrossing two F1 individuals, or by self-fertilizing an F1 individual. BC1 is the first backcross generation, produced by crossing an individual with one of its parents or with the genetically equivalent organism...Moderator].

3. The nature of the markers must allow their use in crosses different from those which led to the map. Then, the specificity of the primers must be assessed by many tests over the germplasm.

4. The degree of linkage between the character and the markers must be very high, at least at the very beginning of the selection, to avoid loss of genotypes by recombination, but in the next steps of the back-cross selection, it should be interesting to select recombinants. These requirements can lead to a compromise but reduce the efficiency of the procedure.

5. If the generation time is substantial, as in forest trees, the map must be performed at the existing population level, comparing natural progenies from identified maternal parents to possible pollen parents from the population. This requires also many analyses and mathematical treatments of molecular data.

As a conclusion, I would say that MAS must not be considered as a method able to replace easily traditional selection, even if MAS remains associated with phenotypic observations (macroscopic, quantitative measures, chemical analyses, comportment, etc.). Important preliminary work on the genetic variability of the species, at both levels (molecular and phenotypic) must be made and this must be balanced with the real costs of both classical versus MAS approaches. I remain convinced that in many species of interest for developing countries, which are relatively near the wild state by their population structures and genetic richness, the best and very efficient solution remains classical plant selection. Of course, this is not the case for species that are very intensively bred and selected during several decades, which have lost their polymorphism and, thanks to neighboring species, have been the object of dense molecular mapping.

If it often believed that MAS should be used both for saving time and to reduce the numbers of individuals. I think instead that, in many cases, it is a mirage. Moreover, it is also true that MAS offers the opportunity to mobilize a lot of money without warranty of success, especially when very precise preliminary studies are lacking.

H. D. Dulieu,
Geneticist,
6, rue des roses, 21 110-Genlis,
France
Email : hdulieu (at) u-bourgogne.fr

-----Original Message-----
From: Biotech-Mod2
Sent: 21 November 2003 08:51
To: 'biotech-room2@mailserv.fao.org'
Subject: 24: International collaborative efforts - MAS

This is from Daniel Gianola.

Concerning Dr. de Koning's optimism and his final statement (in Message 20, November 20):

"...Rather than a commercial national/regional framework, I remain convinced that any form of MAS for the developing world will depend on heavily sponsored international collaborative efforts".

May I ask why is it reasonable to expect that developed nations would be interested in sponsoring something like this, other than for the purpose of discovering gene products that have biomedical application, leading to patentable outputs, say (pharmacogenomics)?

-----Original Message-----
From: Biotech-Mod2
Sent: 21 November 2003 09:03
To: 'biotech-room2@mailserv.fao.org'
Subject: 25: Use of MAS and related technologies in livestock improvement

I am David Notter, Professor of Animal Science at Virginia Tech in the USA. My area of work is the genetic improvement of livestock and the development of breeding systems.

I would like to add a few thoughts to the discussion of use of MAS and related technologies in livestock improvement.

First, I agree with Hugh Montaldo's comments (Message 18, November 20) that ANY effective livestock improvement program will likely require an associated capacity for animal recording and use of traditional genetic improvement methods, such as Best Linear Unbiased Prediction (BLUP) evaluations. Application of MAS still requires, in most cases, accurate pedigree information. Even the determination of ancestry by DNA testing requires a substantial element of animal control and regular interactions with a testing service. Further, since much of the available additive genetic variation remains in the polygenic component, long-term sustained improvement would seem to require attention to this component. And finally, successful animal improvement programs require day-to-day attention to, and understanding of, animal performance levels that can only be attained by some sort of animal recording. Experience with the implementation of genetic evaluation programs for new traits such as parasite resistance in small ruminants or ultrasonic meat yield traits suggest that much of the overall advantages of such programs comes from better understanding of what is happening in the herd or flock on both genetic and nongenetic levels. Measurement of performance confers understanding and improves management, in addition to allowing genetic improvement. It is not always clear which (better management or genetic improvement) is the most important outcome.

I would perhaps disagree with Hugh Montaldo that animal recording has to be put into place BEFORE MAS could be implemented. Perhaps MAS or related technologies are the lever we use to promote the implementation of animal recording. But I think they must at least be implemented together. MAS without recording is unlikely to be very beneficial for most traits.

I will grant that detection of quantitative trait loci (not markers, which may differ in linkage phase among families) for important traits such as disease resistance (see comments on trypanosomiasis by Dirk-Jan de Koning, Message 13, November 19) might impact populations independently of animal recording. Opportunities to screen populations for animals carrying favorable QTL for such traits might hasten development of lines that would reliably possess a subset of favorable genetic characteristics. Interest in selective elimination of genotypes that are susceptible to scrapie in sheep in Europe would be an example. But this is not MAS, and also raises important questions about the genetic diversity that might be lost in the process of fixing a subset of desirable alleles.

This brings us to Dirk-Jan de Koning's comments on how and where program using MAS might be established. I agree that substantial resources will be required to implement MAS and that nucleus populations of some sort should be the model of choice. But the history of publicly funded genetic improvement programs in the developing world is not good, as Victor Olori commented (Message 21, November 20). Some successes in publicly funded initiatives in plant breeding for developing countries through the CGIAR system can be identified, but comparable successes in animal breeding are rare. I believe the problem lies in the sustainability of large, publicly funded animal breeding projects and in their greater complexity. I could relatively easily design a project to create a productive composite breed of some species for a specific region. With adequate resources, I suspect success in developing productive, useful animals would be quite likely. At this level, Dirk-Jan's comments make great sense. But I don't know how to organize the ongoing genetic improvement over multiple generations or how to distribute and properly test the germplasm over multiple production environments. To do this properly, in my opinion, still requires animal recording to document the value of the improved type in different places and production systems. And to maintain and disseminate the genetic improvement widely, requires a system of private breeders acting initially as multipliers and eventually as independent centers of genetic improvement.

In my opinion, the most significant limitation to genetic improvement of livestock in the developing countries has been the failure to establish private breeders whose livelihood is linked to the production and marketing of genetically superior animals. Public institutions have not been shown to be adequate substitutes, since sustained funding is rarely available. And the establishment of private suppliers of improved animals also requires a commercial sector (of either small or large farms) that recognizes the value of these animals and is willing to pay a premium for genetically superior commercial stock. MAS is not particularly likely to change this picture or remove these limitations unless coupled with expanded animal recording and better documentation of benefits (which again can only be achieved by some sort of recording, even if on a limited scale). It is here that plant breeding (with more commercial marketing of seeds by private concerns at all levels of production) and animal breeding seem to diverge most in the developing world.

So, in my mind the necessity is to establish a structure for developing sustainable centers for genetic improvement of livestock, for documentation of benefits from the use of the resulting animals, and for the distribution of improved animals through private multipliers. To date, I see little likelihood that can be achieved by relying on government farms or public initiatives, except as supporting institutions (where their role can be very important). However, as such a structure evolves, MAS can be implemented as appropriate, along with other useful technologies. IF (and perhaps only if) MAS can hasten development of such structures, then it will make a substantial contribution.

David R. Notter
Department of Animal and Poultry Sciences
Virginia Polytechnic Institute and State University
Blacksburg, VA 24061-0306
U.S.A.
Phone: 1(US)-540-231-5135
Fax: 1(US)-540-231-3010
E-mail: drnotter (at) vt.edu

-----Original Message-----
From: Biotech-Mod2
Sent: 21 November 2003 12:26
To: 'biotech-room2@mailserv.fao.org'
Subject: 26: Re: Use of MAS and related technologies in livestock improvement

This is from Ashok Seth, UK. After a career in the private sector (research and development of crop protection chemicals for multinational corporation) and international development (career in the World Bank as agriculture and rural development specialist) I now work as an independent consultant.

Thank you David Notter (Message 25, November 21) for your clear, logically laid out incisive observations. I totally agree with your comments. Only thing I would add is the need for a robust priority setting mechanism at the start of research programs/projects so that scarce resources (financial and human) are only allocated to issues that really matter in the context of the national agricultural economy. Research managers/administrators must insist on a greater role for social scientists in deciding priorities. Thereafter, biologists should employ tool and techniques (including MAS) that are most likely to provide cost effective results in the shortest possible time.

Ashok Seth
ARD Consultants Ltd
98 Whitedown Lane
Alton
Hampshire, UK GU34 1QR
AKSth1 (at) aol.com

-----Original Message-----
From: Biotech-Mod2
Sent: 21 November 2003 14:11
To: 'biotech-room2@mailserv.fao.org'
Subject: 27: Re: Use of MAS and related technologies in livestock improvement

Victor Olori again.

With regards to Ashok Seth's message (No. 26, November 21) and David Notter's earlier comment (Message 25, November 21), I would like to refer to the 'DECIDE' tool that was under development by FAO. I am hoping the moderator can point us to the latest on this. Last year there was a workshop to evaluate this tool which is aimed at helping those interested in setting up a genetic improvement program especially for low input production systems in developing countries. The prototype we evaluated was very versatile and all inclusive and, if used, will allow the setting up of programs that are sustainable and hopefully successful. The good thing for me was that this decision making tool can be used by individuals as well as organisations responsible in any capacity in either formulating policy, advising government or NGOs or actually setting up the program. This tool draws the attention of such individual or individuals to all aspects (scientific, economic and social) which must be covered in order to set up a successful and sustainable program that will be readily adopted. I would like to know the state of this web based tool and how it can fit into the use of MAS as being discussed in this forum.

Dr. V.E. Olori
Irish Cattle Breeding Federation,
Shinagh House, Bandon,
Co. Cork,
Republic of Ireland.
Tel: +353 (23) 20220
Fax +353(23) 20229
E-Mail volori (at) icbf.com

[Work on this tool has been stopped due to the retirement of the Senior Officer (Breeding) in FAO's Animal Production and Health Division. The tool is approximately 40% ready but needs further work on content and user interface. A new officer will join FAO early next year and will develop the tool during 2004...Moderator].

-----Original Message-----
From: Biotech-Mod2
Sent: 21 November 2003 15:30
To: 'biotech-room2@mailserv.fao.org'
Subject: 28: Utility of MAS in tropical trees for small-holders

Greetings from Kenya. I am Tony Simons, responsible for the conservation, characterization and improvement of tree genetic resources at our institute. The World Agroforestry Centre (ICRAF) is engaged in research for development to increase the stability, productivity and profitability of trees on small-holder farms in the tropics, and has 400 staff based in 27 countries in Latin America, Asia and Africa. We focus on timber, fruit, medicinal, fodder and fertilizer trees and currently undertake work on over 200 species.

Echoing the sentiments outlined earlier in the conference, I would like to hear from those engaged in MAS about their utility in tropical trees for small-holders. We have a number of problems we face including dioecy, undocumented origins, uncertainty of genetic control of various traits, need to accelerate vegetative and sexual tree improvement, less resources per species to allocate than mainstream taxa, etc.

Tony Simons, PhD
Principal Tree Scientist
World Agroforestry Centre (ICRAF)
PO Box 30677-00100
Nairobi, Kenya
tel: +254-20-524151
fax: +254-20-524255
email: t.simons (at) cgiar.org
http://www.worldagroforestrycentre.org

-----Original Message-----
From: Biotech-Mod2
Sent: 21 November 2003 16:49
To: 'biotech-room2@mailserv.fao.org'
Subject: 29: Use of licensed genomic technology

I am Pablo Corva, Assistant Professor of animal breeding and genetics at the University of Mar del Plata, Argentina.

I've been following with great interest the discussion about potential application of MAS strategies in developing countries.

I would like to hear from other participants in this conference, about the use of licensed genomic technology by public institutions, especially those in developing countries.

A growing number of new polymorphisms affecting economically important traits in beef or dairy cattle are being described in the scientific literature. Soon after that, many of those new markers appear in the market with a fantasy name and protected by patent agreements. Unfortunately, that's another proof that we are most of the time "one step behind" in research and development (R and D) of genomic technology.

I wonder if we people working at the university would be allowed to use those tests in validation experiments, for example. If we target a given mutation (let's say a single nucleotide polymorphism (SNP)) that has been described in the literature with a given experimental protocol (maybe not the same one reported in the original paper), are we violating proprietary rights of the companies that are now marketing the test?

This is a very important issue for us, because there are more tests on the market every day. Cattlemen have heard about them and now are asking for advice on the matter.

Pablo M. Corva, PhD
Assistant Professor
Dept. Anim. Science
University of Mar del Plata
CC 276
7620 Balcarce
Argentina
pcorva (at) balcarce.inta.gov.ar

-----Original Message-----
From: Biotech-Mod2
Sent: 24 November 2003 10:32
To: 'biotech-room2@mailserv.fao.org'
Subject: 30: Re: Use of licensed genomic technology

In response to Pablo Corva (Message 29, November 21):

Also I am not a lawyer, I do know a little bit about patents, and there are several misconceptions in your note.

- First, patents only apply to the country in which they were granted. That is unless a patent was granted in your country (Argentina) you can do whatever you want within your country with a gene that was patented in the US.

- Second, a patent is a "negative" right, and only refers to profit from the patent. As long as you are only doing research, and not making money from the patent you are OK, even if there is a patent in your country.

- Third, in most cases with respect to genes, the patent has been filed, but has not been granted yet. It takes at least several years for the patent to be granted, and this procedure is far from automatic. However, if the patent is granted, then it becomes effective retroactively.

Again, I am not a lawyer, and I would appreciate it if someone who knows more about this topic would also respond.

[This message and the next two (nrs. 31 and 32) follow up on the theme of patenting and intellectual property rights in the context of marker assisted selction in developing countries, raised by Pablo Corva in message 29. We would also appreciate some viewpoints/experiences from conference subscribers working in the private sector, including multinational companies, on this issue, as the private sector is obviously a key player here...Moderator].

-----Original Message-----
From: Biotech-Mod2
Sent: 24 November 2003 10:32
To: 'biotech-room2@mailserv.fao.org'
Subject: 31: Re: Use of licensed genomic technology

I am S. Saravanan working towards the doctoral degree in plant breeding and genetics at Tamil Nadu Agricultural University, Coimbatore, India.

With regard to message 29 (November 21) of Pablo Corva, I submit to state that any of the technological inventions that are directly and indirectly effecting mankind welfare projects should be very well allowed to be utilized freely. Anyhow, any biotechnological tool should have been patented for security point of view. I suggest that the patent laws should impose a restriction to patented material only at the market level and not at the research level. Research is a continuous and cyclic process, any new finding will form a base towards the next finding. Hence, patenting of biotechnological tools should stand only at the marketing level and not the research level. Any biotechnology tools should be allowed to be used freely by researchers for their new findings so that it will pay the way for further developments in the society.

S. Saravanan
Centre for Plant Breeding and Genetics
Tamil Nadu Agricultural University
Coimbatore 3
India
sarapbg2002 (at) yahoo.co.in

-----Original Message-----
From: Biotech-Mod2
Sent: 24 November 2003 10:32
To: 'biotech-room2@mailserv.fao.org'
Subject: 32: Corporate patents on particular genes

I'm Eric Storlie from the University of Southern Queensland, Australia, where I'm working as a project officer for a collaborative wheat breeding project with Chinese scientists.

After reading a few of the messages posted so far, I feel scientists in developing countries are worried about lagging behind a blossoming technology. The farmers, especially, of these countries probably have something to worry about. I don't think they need to worry about missing out on miraculous offerings of the technology, but conversely, they may become constrained by corporate patents on particular genes, which may require a company's authorization for possession and use.

Growing food is basic to the livelihoods of humans; if we have plants, animals, soil, water and air, people all over the world can take care of themselves. We will have trouble improving on the agricultural accomplishments of the past. I think we easily forget that the germplasm we cherish was developed long before the development of modern technologies and methodologies, and the people who have most recently inherited these landraces etc... have not insisted on patent rights to their heritage.

I don't think we should justify biotechnology on a desire to "help" other people or countries, nor should it be advocated as a panacea, because I don't think this is true. It is simply a tool that may expedite an existing potential. I think we overlook the possibility that we may make things worse.

Eric Storlie
Faculty of Science
University of Southern Qld
Toowoomba, Qld 4350
Australia
storlie (at) usq.edu.au

-----Original Message-----
From: Biotech-Mod2
Sent: 24 November 2003 10:44
To: 'biotech-room2@mailserv.fao.org'
Subject: 33: MAS and animal breeding

I am Juan F. Chavez from Peru. I work with animal genetic resources in my country, specially the native ones.

I would like to place the following question: Have the studies realized until now, about the economical advantages of MAS compared to conventional artificial selection, taken into account the magnitude of their effects on reduction of reproductive performance due to variability shortage of the gene pools? I think one not-addressed advantage of MAS could be, besides more rapid responses to selection, its less harmful effect on reproductive traits because of more precise targetting to the desirable alleles we are looking for.

Related to the use or not of MAS for improving our livestock, I think it all depends on the goals we want to achieve. Within our "Criollo" cattle there are some valuable genes related to traits that could be in demand from countries with well developed livestock industries (i.e. dairy cattle). These genes could be identified and concentrated by MAS into a breed developed from Criollo cattle and become a "live library" of desirable genes that could be offered to anyone interested in "reshaping" the make-up of their cattle overseas.

Now we have other priorities related to animal breeding. More than 80% of our livestock is owned by small farmers, who have very low levels of education; they raise their animals on natural pastures which have low nutritional value. They are poor and besides their own traditional selection systems, there is no possibility for them to pay for MAS. Under these circumstances, more rapid responses to genetic improvement (genotype) could be reached by selecting and interchanging males among small farmers flocks, within and among communities. Also we need to help them to educate, organize and integrate with the industry and commerce as part of Chains of Value.

Juan F. Chavez
Calle Las Copaibas 145. Urb. Remanso II
La Molina. Lima,
Peru
chavram (at) terra.com.pe

[Regarding the first paragraph, to my knowledge there is no evidence that MAS, per se, will have a less (or more) harmful effect on reproductive traits and reproductive performance then conventional selection. Also, whether selection (be it MAS or conventional) might reduce reproductive performance depends on the selection programme, the traits selected etc. etc. (e.g. if the trait selected for is increased fertility, neither MAS nor conventional selection are likely to result in reduced reproductive performance...Moderator].

-----Original Message-----
From: Biotech-Mod2
Sent: 24 November 2003 10:49
To: 'biotech-room2@mailserv.fao.org'
Subject: 34: cost effectiveness of MAS

This is from P.M. Priyadarshan again. I am a plant breeder by profession, with 20 years of experience on spices and rubber. Actively involved in breeding rubber for non-traditional areas especially with stresses like low temperature, wind and diseases. Currently working at the Regional Research Station, Rubber Research Institute of India, Agartala, India.

I must fully agree with the opinions of Ashok Seth (Message 26, November 21) on the cost effectiveness of MAS. Developing countries, in many cases, cannot afford to keep apart their financial resources for MAS, since the money spent so far for related studies, I am doubtful whether it has yielded appreciable results.

P.M. Priyadarshan
Rubber Research Institute of India,
Regional Station, AGARTALA - 799 006,
India
Tel: Off : 91-381-2355287/2355143 - Extn:205
Tel: Resi : 91-381-2354325
Fax: 91-381-2353149
pmpriyadarshan (at) hotmail.com
alternate e-mails: pmpriyadarshan (at) rediffmail.com pmpriyadarshan (at) yahoo.co.in
personal web page: www.freewebs.com/pmpriyadarshan/

-----Original Message-----
From: Biotech-Mod2
Sent: 24 November 2003 10:58
To: 'biotech-room2@mailserv.fao.org'
Subject: 35: MAS approach yields disease resistant rice lines

This message is from Dr. R. Sridhar former Principal Scientist, Central Rice Research Institute, Cuttack, 753006, India. I have retired from the services and continue as an independent researcher to keep my association with science.

During the past decade, I was leading a project aimed at developing disease resistant rice lines at the Central Rice Research Institute (CRRI). The following message describes a success story of MAS which touches some of the points raised by participants of this conference. (The results are yet to be published in journals).

In the absence of any chemicals effective against bacterial leaf blight of rice, the only way to minimize the losses caused by this disease is the use of resistant varieties. At the Central Rice Research Institute in Cuttack, attempts were made in a collaborative venture with the International Rice Research Institute in the Philippines (a programme under the Asian Rice Biotechnology Network supported by the Asian Development Bank, the Rockefeller Foundation and the Indian Council of Agricultural Research) to understand the population structure of the bacterial leaf blight pathogen occurring in eastern India using molecular tools for fingerprinting them combined with the conventional technique for analysing the virulence patterns of the pathogen strains and evaluation of the resistance genes in disease trap nursery. This led to the assessment of the usefulness of the bacterial blight resistance genes singly and in different combinations. This is primarily essential for meaningful deployment of the resistance genes.

The next step was to move the genes of interest (xa5, xa13 and Xa21 conferring resistance to bacterial leaf blight) to two popular commercial rice varieties, IR 64 and Swarna, which are susceptible to the disease. This was achieved employing MAS in conjunction with the conventional back cross breeding strategy. Assessing resistance of plants by artificially inoculating with the pathogen is particularly complicated when more than one resistance gene is transferred together, as it is not possible to inoculate the same plant with two different strains of the pathogen. This approach finally resulted in the development of 50 lines in the background of IR 64 and 95 lines in the background of Swarna carrying three bacterial blight resistance genes singly and in different combinations to the above rice varieties. Although lines with single genes are resistant to specific strains of the pathogen, lines carrying two genes in different combinations and three genes are resistant to a wide spectrum of the pathogen strains, thus enhancing the durability of resistance to the disease. These lines have been evaluated for disease resistance and yield in on-station trials and a select set of them are in on-farm trials in farmers' fields. These have a high potential for replacing the bacterial leaf blight susceptible IR 64 and Swarna being grown by the farmers, without having much difficulty of their acceptance as the grain qualities and yield potential of these lines are quite similar to the original varieties.

The CRRI's approach of improving the existing varieties for their resistance to bacterial leaf blight offers promise for transferring other desired traits to popular varieties which otherwise lack them resulting in decreased yield. This also points out the need for sustained involvement of a team of researchers with expertise in conventional and molecular biology as it blends both these approaches for realizing the ultimate goal of crop improvement.

Dr. R. Sridhar
Flat 5, Rajparis Kings Castle
(Old No. 19), New No. 11, First Main Road
I-Block, Anna Nagar East, Chennai 600 102
Tamil Nadu,
India
rangsridhar (at) yahoo.com
Website: http://personal.vsnl.com/rangasri/

-----Original Message-----
From: Biotech-Mod2
Sent: 24 November 2003 11:30
To: 'biotech-room2@mailserv.fao.org'
Subject: 36: When the marker is the gene

From Adilson Mota, Brazil.

I see now that we have participants from many countries and different backgrounds (I would suggest the moderator informs us how many participants are attending the conference). Many ones work on livestock, express their opinions from developing countries, and may (as well as I am) be concerned about advantages and pitfalls of MAS, specifically for developing countries. [Over 600 people have registered for the conference so far, coming from a wide range of countries and work situations. We encourage you all to participate actively...Moderator].

I must repeat from the introduction of the background document to the conference when it stated: "despite the considerable resources that have been invested in this field and despite the enormous potential it still represents, MAS, with few exceptions, has not yet delivered its expected benefits in commercial breeding programmes for crops, animals, forest trees or farmed fish in the developed world".

In my previous message (Message 14, November 19), I attempted to raise questions that a funding agency from a developing country might ask in case a proposal containing MAS is submitted. I am absolutely in favour of MAS research and technology, in the whole sense. But I am not convinced about using DNA "markers" in marker assisted selection (MAS) for genetic improvement of animals within breeding programs in developing countries. Unless the marker is the gene !

I will try to explain this important distinction. Let us keep up with the background document, where it mentions the reference of Dekker (2003) (Section 2.2 - From markers to MAS). If the situation is the first kind of relationship therein described between the marker and the gene of interest (i.e. "complete linkage"), then selection of an animal with the favorable alleles of the marker will represent selection of the favorable alleles of the gene. In the other situation, there is "linkage disequilibrium" between marker and gene, and selection of favorable genotypes of the marker does NOT always represent selection of superior animals. The rate of success depends on the distance and phase between marker and gene.

I also underline Joel Weller's words (Message 15, November 19) that properly stated: "Genotyping additional markers in the region of interest doesn't help much. Once you are down to a marker spacing of 10 cM, additional markers will not reduce the confidence interval."

In conclusion, developing countries may consider MAS in their breeding programs, BUT solely in the case of absolute agreement between the marker and the gene. Otherwise, developing countries will be asked to adopt technology that will bring up costs (a major concern), as they will have to buy genotyping equipment, reagents, and technology to achieve information that is not absolute guarantee of selecting superior animals. And additional markers and genotyping may not represent significant progress.

This situation is opposed to straight selection of superior animals when there is "complete linkage". In this case, it is even possible to identify heterozygotes carrying unfavorable alleles (i.e., for health traits). Estimates are also available for production levels, depending on the genotypes, and can be used by the developing country to evaluate costs vs. benefits of genotyping. This way, scarce resources (financial and human) from developing countries are allocated to issues that will certainly represent development in the context of its national agricultural economy.

Besides breeding programs, MAS can be recommended for developing countries, regardless of evaluating "linkage" situation between gene and marker, in research activities. This may be carried out by international collaborative networks proposed to accelerate discovery (towards the "complete linkage" situations), depending on the interest of not being left behind with respect to strategic discoveries and/or technologies. Collaborative projects may also consider investments in studies with candidate genes in the putative chromosome region(s) presenting significant marker association.

I used here an example with livestock, because of its economical importance for Brazil, but it may very well represent other agricultural sectors.

-----Original Message-----
From: Biotech-Mod2
Sent: 25 November 2003 11:49
To: 'biotech-room2@mailserv.fao.org'
Subject: 37: Successful use of MAS - cereal crops

This message is from Dr Kevin Williams, Molecular Geneticist at the South Australian Research and Development Institute. I am involved in developing marker-trait associations in several crops, both major and minor, and also conduct MAS for the development of disease resistant germplasm in my laboratory.

I would like to give a view on MAS from a country where the technology is well advanced in the major cereal crops wheat and barley. Australia has industry-funded national molecular marker programs for these crops, which fund phenotyping and genotyping of segregating populations and also contributes to the validation of markers and implementation of MAS in many breeding programs. There is also the Cooperative Research Centre for Molecular Plant Breeding, which includes South Australian, Victorian and Western Australian agriculture departments and universities, as well as the International Maize and Wheat Improvement Center (CIMMYT). These groupings have been instrumental in ensuring that the large amount of research conducted (see special issues of Australian Journal of Agricultural Research vols 52:11 and 12 and 54:11 and 12 for examples) is actually translated into outcomes for plant breeders. Many tens of thousands of marker assays for a wide range of loci are conducted in wheat and barley breeding programs annually. [It is obviously important that MAS research eventually results in useful germplasm for the breeder. Are figures available (precise or estimated), for any country, on the amount of hecterage cultivated with varieties developed using MAS - referring to Message 8 (November 19) of C.R. Bhatia who suggested that the area covered by the cultivar(s) developed using MAS would be the ultimate indicator of the utility of MAS in plant breeding...Moderator].

Many of the concerns of previous correspondents about the limitations of MAS are valid and, although I am not a plant breeder, I would like to contribute several observations from six years of active research in this field with both major crops and also with breeders of minor crops wanting to access the technology cheaply.

1. Molecular markers have many uses in addition to MAS. They can be used to verify the identity of lines, investigate heterogeneity and assess diversity of germplasm. Anonymous markers, with low development costs, can be used for these purposes.

2. Molecular markers have the greatest benefit when selecting for loci controlling traits of high value which are difficult and expensive to phenotype. Root nematodes are a classic example in Australia. Phenotyping is time-consuming and variable, so molecular markers have been widely used in wheat and barley breeding, and barley cultivars bred using MAS for nematode resistance are being commercialised. Interestingly, as the highest cost of MAS in plants is DNA extraction and extra markers can be assessed at low marginal cost, once the DNA is available, breeders will also often ask for additional marker assays for a wide range of loci with lower value, but still important in selection decisions. Importantly, MAS can produce outcomes not easily achieved by traditional breeding, such as strategically selecting for resistance to exotic pests, pyramiding of race-specific resistance genes for potential durable resistance, and selection for multiple traits from single plants such as BCF1's rather than later segregating populations. [Gene pyramiding is the combination of target genes identified in different parents into a single genotype...Moderator].

3. Intuitively, recombination between markers and the gene of interest seems important. However, in practice we have found that lack of marker polymorphism is a far greater limitation than the distance between marker and gene. Many theoretical studies are done using wide crosses to improve the polymorphism level, but a breeding program will often have closely related material showing low polymorphism. The feedback that I receive from breeders is that any marker within 10 cM is useful at present, as their main aim is to increase the frequency of favourable alleles in a large population at the lowest cost.

4. MAS need not be expensive. The recent huge increase in the public availability of genomic resources such as expressed sequence tags (ESTs) for a wide range of species has greatly reduced the cost of the development of markers such as simple sequence repeats (SSRs) which can often be identified in model species and transferred to minor crop species. [SSRs are also known as microsatellites...Moderator]. MAS itself need not use sophisticated infrastructure. SSR analysis for MAS in my laboratory uses a thermal cycler, vertical gel tanks, UV transilluminator and camera, total cost US$10,000. By far the largest operating cost is labour, and although I have access to automated systems or could outsource genotyping, a small team of technical officers is still the most efficient set-up for the varied demands of MAS throughout the season.

In summary, in contrast to those who question the effectiveness of MAS, I have no doubt that MAS has the potential to increase the rate of genetic gain when used in conjunction with traditional breeding, and the adoption of MAS by cereal breeders in Australia and the subsequent commercialisation of cultivars bred using MAS is testimony to this.

Dr Kevin Williams
Senior Research Scientist-Molecular Genetics
South Australian Research and Development Institute
PO Box 397
Adelaide SA 5001
Australia
Phone +61 8 8303 9369
Fax +61 8 8303 9393
williams.kevin (at) saugov.sa.gov.au
http://www.sardi.sa.gov.au/field_crops/pathology_quarantine/cereal_molecular/cereal_molecular.htm

-----Original Message-----
From: Biotech-Mod2
Sent: 25 November 2003 11:59
To: 'biotech-room2@mailserv.fao.org'
Subject: 38: Re: When the marker is the gene

This is Hayde Galvez again from the Philippines.

This is in reply to message 36 (November 24) from Adilson Mota about the necessity for 'complete linkage' of the marker to the gene for effective use in MAS breeding.

I strongly agree with this. In fact this should be a general rule for MAS application in animals, crops etc. However, complete linkage means the marker is within the gene sequence itself and getting (isolating) the whole gene sequenced/characterized is not a 1-2-3 process - map-based or direct PCR-based isolation etc. The developing countries may not be financially ready to do this themselves. So again [see message 5, November 18...Moderator], I maintain my opinion that international (or external fund source) collaboration is needed to develop markers for MAS for the developing countries, i.e. shuttle research. Targeting major genes (genes involved in major resistance/biochemical pathways - e.g. resistance gene analog-derived) may give more return as the markers can be applied across a wide range of populations (even species), environments and pathogens.

Another point is that the marker may not be "completely linked (0 cM)" to the gene/trait but still effective for MAS breeding. As actual gene identification and isolation/sequencing takes much longer time than in theory, a certain degree of recombination between the marker and the gene can be acceptable as long as the breeder takes this into consideration in the selection process. It is still much much better than using a pure morphological marker that may end up totally dis-associated from the desired trait or target gene. But how much 'dis-linkage' can be allowed that will still give REAL economic advantage of employing MAS in breeding programs remains to be studied, worryingly in a case-to-case basis. Anyone who can give relevant references on this aspect is much appreciated.

Hayde F. Galvez
University Researcher
Institute of Plant Breeding
University of the Philippines Los Baños
College, Laguna
Philippines
hgalvez_4031 (at) yahoo.com

-----Original Message-----
From: Biotech-Mod2
Sent: 25 November 2003 12:04
To: 'biotech-room2@mailserv.fao.org'
Subject: 39: Re: When the marker is the gene

Regarding message 36 (November 24) from Adilson Mota:

When the marker is the gene, then the most cost effective way of diffusing the gene is by artificial insemination using sires homozygous for the favourable allele that also have merit for other traits of economic importance.

Don Nicol,
Brisbane
Australia
dnicol (at) b022.aone.net.au

-----Original Message-----
From: Biotech-Mod2
Sent: 25 November 2003 12:17
To: 'biotech-room2@mailserv.fao.org'
Subject: 40: Re: MAS and animal breeding

I am Miguel Toro from Spain. I work on quantitative genetics and QTL detection.

With repect to message 33 (November 24) from Juan Chavez, I cannot see why MAS will have a "less harmful effect on reproductive traits because of more precise targetting to the desirable alleles we are looking for". Is there a general consensus on this opinion? I would think just the opposite. When people find a big QTL at intermediate frequency in a breed selected for growth, they are usually reluctant to use it because they are afraid that the gene will have adverse effects on fitness (if this was not the case, why is the gene still segregating despite selection pressure favouring it?). On the other hand, a very 'precise targetting' could be transgenesis with not very good results with respect to fitness...

I will rather support the more classical ideas on selection and fitness. Both standard selection and MAS could deteriorate fitness. There are two courses of action. The first is to evaluate also the fitness traits and then calculate the effect of markers on both production and fitness traits. The other action (also valid in classical selection and MAS) is to keep the inbreeding below certain levels. There is a very well developed theory on optimisation of selection response with restricted inbreeding.

With respect to a second point by Juan Chavez: "Within our "Criollo" cattle there are some valuable genes related to traits that could be in demand from countries with well developed livestock industries (i.e. dairy cattle). These genes could be identified and concentrated by MAS into a breed developed from Criollo cattle and become a "live library" of desirable genes". I do not undertand the point. There COULD BE valuable genes.., but the problem is that we do not know them. In such circumstances, I cannot see how to accummulate them in a live library.

It seems that in plants, genetic resources from developing countries have been useful to improve commercial populations but in animals I think that the situation is not as clear. Is there examples? [This seems to me to be also the case. Use of genetic resources from developing countries to improve commercial populations in developed countries seems to have been more limited in animals. One example, would be the introduction of genetic material from the fat, but highly prolific, Meishan pig (from China) into lean commercial pig breeding lines...Moderator].

Miguel Angel Toro Ibañez
Departamento de Mejora Genética Animal
Instituto Nacional de Investigación y Tecnología Agraria y Agroalimentaria (INIA)
Carretera La Coruña km. 7
28040 Madrid
ESPAÑA
Telf: 34 913476807
Fax: 34 913572293
e-mail: toro (at) inia.es

-----Original Message-----
From: Biotech-Mod2
Sent: 25 November 2003 13:53
To: 'biotech-room2@mailserv.fao.org'
Subject: 41: Crops - India

This is from Dr Kuldeep Singh. I am primarily a plant breeder and now use the molecular biology techniques for rice and wheat improvement. We at Punjab Agricultural University, Ludhiana, are among the first who used MAS for pyramiding bacterial blight resistance genes in two of our popular rice varieties.

The conference has raised many issues and I would like to talk on a few issues and these are based on my experience and knowledge in the context of Indian agriculture.

During the last decade the emphasis was on training manpower and the Rockefeller Foundation, Asian Development Bank (ADB) and international agricultural research centres (especially the International Rice Research Institute (IRRI), in relation to rice) primarily contributed to this. Now I feel sufficient people are trained and who can train more people in molecular marker technology.

The feasibilty of MAS has been demonstrated, especially for pyramiding disease resistance genes, not only at one place but at several institutes in India like PAU, CRRI, UAS, IGAU, TNAU (as was mentioned by Dr R. Sridhar (message 35, November 24) as well). This was achieved more or less independent of plant breeders and mostly in well adapted varieties. Plant breeders simultaneously came up with new varieties that may be higher yielding, hence the pyramid lines may not find their way to the farmers` fields (although the newly developed pyramid lines yield at par with the recurrent parents). The MAS was adapted for disease resistance that plant breeders feel are relatively simple traits to work with and even single genes can do the job (an issue that is debatable).

The question now arises how to make MAS operational in the developing world. My opinion is:

1. Since MAS is expensive and breeding programmes are mostly funded by the local governments, the federal governments may start some pilot MAS projects with committed funding. In India, for example, the Indian Council of Agricultural Research (ICAR) can identify a few universities/institutes and identify the key traits, like quality, for which MAS can be started. This must be an integral part of the breeding programme and may not be the backcross programme. Once successful it can be extended to other institutes and finally the local governments can take over.

2. Breeders are not much thrilled about MAS for simply inherited traits, and not many QTL (especially the productivity related ones) with tightly linked markers are available. This I believe may take some more time, especially the productivity related QTL from the wild species germplasm, to become available to breeders. Any QTL mapped in one environment will need validation before it is involved in MAS.

3. QTL for abiotic stresses are available and MAS can be used for their incorporation but unfortunately the areas where abiotic stresses are more prevalent are poor as well and it may not be possible for institutes from this regions to begin MAS without funding from the federal governments or the international funding agencies.

Finally, as a student of plant breeding, I foresee a good scope for MAS for several traits.

Dr Kuldeep Singh
Molecular Geneticist
Dept. Genetics and Biotechnlogy
Punjab Agricultural University
Ludhiana 141 004,
India
Tel. +91-161-243 30 81 (R)
kuldeep35 (at) yahoo.com

-----Original Message-----
From: Biotech-Mod2
Sent: 26 November 2003 10:12
To: 'biotech-room2@mailserv.fao.org'
Subject: 42: Re: When the marker is the gene

From Prof. H. Dulieu, again. I worked in the Plant Breeding Station INRA-Dijon until 1999. I was professor of plant biology and genetics at the University of Burgundy. I am presently retired.

Several participants - Adison Mota (Message 36, November 24), Hayde Galvez (Message 38, November 25), Don Nicol (message 39, November 25) - discussed the case of complete linkage (0 cM!) between the marker and the gene (trait) to be selected. Of course, if selection is made on the marker which has its allelic form completely associated with the allelic form of the trait, the probability of selecting for the trait (gene) rises to a maximum. However, it must not be neglected that a complete linkage group (one chromosome) is associated with the trait, then you perform a simple Mendelian experiment!

In many examples of crops or animals, the variety or breed to be improved has been previously selected and maintained, due to its high productivity or performance. A back-cross selection must then be performed over several generations to incorporate the trait(s) of a "donor" genotype into the existing variety which must recover its qualities. This implies selection over several generations, partially depending on the number of linkage groups (chromosomes). The genes located on the same chromosome as the trait must be recovered from the recurrent genotype (the receiver of the trait) by recombination. This is the reason why I considered (message 23, November 20) it important to have a map available with many molecular markers over all linkage groups. These markers are to be used also for counterselecting the regions of the donor genotype which must be replaced by the resident genes from the existing variety.

Theoretically, the ideal situation is to select the trait indirectly by molecular markers at a short distance (say 5 cM), to the left and right of the trait locus. The "false positives" should then be very reduced in expected frequency (p1*p2= 0.0025) because they must result from double crossing-over, where the trait locus ends up between the allelic forms of the markers of the receiving line. Then, for these reasons, I think that selection based on a single marker, even strictly associated with the trait, is not efficient as compared to phenotypic selection on the trait itself, especially if the breeder does not help the return to the existing variety with MAS applied to other markers located on different chromosomes, including the chromosome where the trait has been mapped!

Prof. H.Dulieu,
Plant genetics and Biology,
University of Burgundy,
France
hdulieu (at) u_bourgogne.fr

[Having a marker on either side of the gene of interest (Q) provides greater precision than having a single marker when following inheritance of Q from one generation to another. Consider a situation where a parent has the marker allele M1 and the allele Q1 on the same chromosome and the rate of recombination (crossing over) between M and Q is r (e.g. 0.05). If an offspring receives the allele M1 from the parent, there is a 0.95 probability it has also received Q1. With flanking markers, consider now that there is an additional marker N on the other side of Q, such that Q is midway between M and N and r is 0.05 between M and Q and between Q and N. Now, if a parent has the alleles M1, Q1 and N1 on the same chromosome, if an offspring receives the marker alleles M1 and N1 from the parent, there is a 0.997 probability it has also received Q1...Moderator].

-----Original Message-----
From: Biotech-Mod2
Sent: 26 November 2003 10:36
To: 'biotech-room2@mailserv.fao.org'
Subject: 43: Re: MAS and animal breeding

This is Juan Chavez again. I work for the Instituto Interamericano de Cooperacon para la Agricultura (IICA) in Peru and teach animal breeding at the National Agrarian University, La Molina.

Regarding message 40 (november 25) from Miguel Toro, I will ask the question: Is it not true that MAS gives more advantage when someone wants to identify with more precision a desirable allele? If not, then what are the advantages of MAS? I think with MAS the rest of the genome that does not code for the selected trait will remain less altered, compared to the less precise conventional artificial selection. Maybe the confusion arises when we do not take into account that mostly the responses of reproduction and fitness come from dominance and epistatic effects (combinatory effects) rather than to a specific allele. I understand this is the reason why, today, dairy cattle breeders are studying the responses of crossing dairy cattle breeds in order to improve the reproductive traits. Furthermore, regarding their precision, I believe MAS is closer to trangenesis than to classical artificial selection because with transgenesis it is possible to replace a specific gene without affecting the other parts of the genome. Maybe the problems of applying new technologies like MAS and transgenesis, which have to be better developed, is creating some "confounded effects" between what belongs to genetics and what belongs to the problems that arise from the application of the new tools of biotechnology.

Any type of artificial selection (focused on alleles coding for a specific response regarding a trait of interest) will affect fitness or the capacity of the population to be plastic to environmental changes. Genetic homeostasis and the limits of selection are close related with this underlying principle. I think fitness will always be reduced by artificial selection when traits other than reproductive traits are selected. Then, it is not necessary to study the detrimental effects of conventional or MAS artificial selection of a medium or a high heritable trait (i.e. fleece weight or live yearling weight) on reproductive performance, because we know, from a huge quantity of research, that this mostly always happen.

I agree that we Peruvians have to do research in order to identify the most valuable alleles, but that does not invalidate my point. I think any allele is valuable if it is different enough in its effects from others. And also, any allele with "detrimetal effects" in a given enviroment could have "selective advantages" in another environment. I am sure that our "Criollo" animals have valuable alleles because they live in very harsh conditions (high level of parasites, dry seasons with low nutritional inputs, freezing temperatures, low pressure of oxygen etc.). Regarding this, I am also sure that it could not be asserted that NATURAL SELECTION DOES NOT MAKE THE DIFFERENCE between almost 500 years of adaptation of Criollo livestock to the highlands of Peru (3000-5000 metres above sea level), since the sheep, goats, horses, cattle, poultry and pigs were brought by the Spaniards to our country. Finally, I think, any allele, any race, any species is valuable, more if we do not know what would be the future demands of we human beings.

Juan F. Chavez
IICA-Peru
Professor of Animal Breeding of National Agrarian University at La Molina
Lima
Peru
chavram (at) terra.com.pe

-----Original Message-----
From: Biotech-Mod2
Sent: 26 November 2003 13:06
To: 'biotech-room2@mailserv.fao.org'
Subject: 44: Marker assisted backcrossing

This is in response to message 42 (November 26) from Prof H. Dulieu.

Having experience with MAS, I strongly feel that marker assisted backcrossing for transferring one or more genes to a widely adapted variety, may not require larger number of backcrosses. Anything beyond two backcrosses may not stay economical and competitive. Our experience shows that selection based only on markers may not help in recovering the recurrent genotype. We suggest growing a larger BC1 population, rejecting about 50-60% of plants on a visual basis and analyzing the remaining 40-50% plants for markers and selecting 1-2 plants (with the desired marker and phenotype more closer to the recurrent parent) and backcrossing it to the recurrent parent. The same strategy can be followed in BC2. Again, growing a large BC2F2 population is important, wherein visual selection should be practiced prior to marker analysis. This will save a lot of time.

Dr Kuldeep Singh
Molecular Geneticist
Dept. Genetics and Biotechnlogy
Punjab Agricultural University
Ludhiana 141 004,
India
Tel. +91-161-243 30 81 (R)
kuldeep35 (at) yahoo.com

[Some definitions: Crossing 2 parents (P1 and P2) results in the F1 generation. Crossing F1 with P2 produces BC1 (also called BC1F1). Crossing BC1 with P2 results in the BC2 generation (also called BC2F1). Crossing BC2 with BC2 produces the BC2F2 generation...Moderator].

-----Original Message-----
From: Biotech-Mod2
Sent: 27 November 2003 09:54
To: 'biotech-room2@mailserv.fao.org'
Subject: 45: Investment makes MAS feasible in developed countries

Bert Collard here again.

I would like to respond to the contribution by Kevin Williams (Message 37, November 25).

I think there are several reasons as to why MAS has been successful in cereal crops in Australia (although from my experience, I do not know of many actual examples of MAS-derived cultivars grown in Australia, despite many publications from Australian institutions). However, there is a fundamental difference between Australia and developing countries, that must be emphasized if MAS is to be evaluated as a potential tool for crop improvement in developing countries: there is a large investment in research and development in Australia, and other developed countries.

Cereal production in Australia is largely export driven and there are well-established organizations in place for research and development and long-term strategic planning for the grains industry (for example, the Grains Research and Development Corporation (GRDC), see http://www.grdc.com.au). The GRDC's mission is to invest in research and development for the greatest benefit to its stakeholders (i.e. farmers) and provides funds for research and development through a levy on farmers. As mentioned by Kevin Williams, there are also Cooperative Research Centres (CRCs), but these centres have strong government and industry support.

In contrast, many developing countries are net importers of cereal grains and generally, do not have such organisations or available government funds to invest in capital-intensive research. A levy on poor farmers would be impossible in developing countries since their top priority is whether they have enough food and money for survival.

I think that scientists in developed countries such as Australia must understand that costing for MAS in developing countries is different. The laboratory in which I currently work has the standard equipment (e.g. thermal cyclers, gel apparatuses, gel scanning equipment, centrifuges) all of which are very expensive even in Australian dollars. But the costs of consumable products (chemicals/kits and consumable plastics for DNA extraction, Taq DNA polymerase, ethidium bromide/silver stain reagents, agarose/polyacrylamide gel ingredients, pipetters, pipette tips and PCR reaction tubes) and infrastructure (waste disposal, provision of electricity for freezers) cannot be neglected for the medium-long term application of MAS, especially after currency conversion. Perhaps in some cases, even the acquisition of essential ingredients cannot be taken for granted (e.g. infrastructure - adequate storage after overseas importation and roads to rural Universities/Plant Breeding stations).

Bertrand Collard
Department of Biological and Physical Sciences
University of Southern Queensland, Australia
Toowoomba 4350
Tel: +613 4631 2699
Fax: +613 4631 1530
collardb (at) usq.edu.au

-----Original Message-----
From: Biotech-Mod2
Sent: 27 November 2003 09:59
To: 'biotech-room2@mailserv.fao.org'
Subject: 46: Polyploid crops

This is Anjali Bhagwat from India and my research interests include molecular markers in plants.

MAS is universally accepted as being useful in faster introgression of traits from wild to cultivated and from cultivated to newer genotypes. And so should be useful in breeding of polyploid crops just as well as in diploid crops. However, I want to raise the basic question of whether polyploid genomes reveal less molecular polymorphism as compared to diploid ones. Since they have multiple copies of alleles, even if few are polymorphic does the presence of others mask the polymorphic sites, especially in the case of PCR-based markers? Two major polyploid crops of my interest are wheat (6X), a major cereal, and groundnut (4X), which is a very important oilseed crop. Sugarcane is another polyploid.

Dr Anjali Bhagwat
Plant Biochemical Genetics Section
Nuclear Agriculture and Biotechnology Division
Bhabha Atomic Research Centre
Trombay, Mumbai-400 085
INDIA
E mail: asb (at) magnum.barc.ernet.in anjubhagwat (at) yahoo.com

-----Original Message-----
From: Biotech-Mod2
Sent: 27 November 2003 10:06
To: 'biotech-room2@mailserv.fao.org'
Subject: 47: Tropical fruit breeding

This is from Dr Aisha, A. Badr, Tropical fruit division, Sabahia Horticultural Research Station, Alexandria, Egypt, working in research of tropical fruit breeding for 35 years and after spending most of my life waiting for F1 and F2 in most research to evaluate fruits of selection (fruit trees bear fruit after more than 4 years), so I continued breeding using new biotechnology to save time and to distribute my selections.

I agree with most contributers on the efficiency of MAS in breeding programs and with Kuldeep Singh (message 44, November 26) about marker assisted backcrossing for transferring one or more genes to a widely adapted variety. But we have only way to see real fruit which has genes we want is to graft on fruiting tree to reduce the time needed for fruiting because of the lack of research in this field, and research is more in papaya, which gives fruit after 8 months while other species need more.

Dr Aisha, A. Badr,
Tropical fruit division,
Sabahia Horticultural Research Station,
Alexandria
Egypt.
momidic (at) hotmail.com

-----Original Message-----
From: Biotech-Mod2
Sent: 27 November 2003 11:36
To: 'biotech-room2@mailserv.fao.org'
Subject: 48: Re: Successful use of MAS - cereal crops

This is from Dr. R.Sridhar, India.

It has been suggested that the area covered by the cultivar(s) developed using MAS or alternatively the number of cultivars approved for commercial cultivation and/or the number of lines entered into national evaluation trials be used as a yardstick for measuring the success of MAS research (Message 8, November 19, of C.R. Bhatia). This has also been emphasized by the Moderator in his note appended to Message 37 (November 25). Undoubtedly, this is the final determining factor for the success of MAS products. In India, most MAS products would still be in the hands of the research institutes undergoing final evaluation. I am afraid that presenting data on coverage of MAS products in the farmers' fields may have to wait till the products reach the clients (farmers).

For expediting this, MAS products need a 'fast track' evaluation system wherever MAS has been applied to improve well-adapted popular commercial cultivars (that have already passed once through the stringent evaluation procedures). This should relax certain initial evaluations. The absence of such a fast track approach might become a hurdle, temporarily or permanently, for the MAS products to reach the farmers. Such a system has been accepted in principle in the case of rice (but not documented properly and firmly). However, the maiden Indian experience has exposed certain weaknesses/teething problems in implementing the system. This should draw the attention of the research policy makers for smoothening/rectifying the system for delivering the fruits of biotechnology to the farmers.

Considering the magnitude of funding biotec