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Sent: 01 December 2003 16:05
Subject: 57: Experiences with MAS so far - Netherlands, plants
My name is Wytze de Lange and I am policy officer genetechnologies for a non-governmental organization (NGO) called XminY Solidarityfunds in the Netherlands.
I have followed the conference with great interest so far and think the background documents and contributions are most interesting. Following the question of the Moderator about MAS-developed cultivars, I have made a small query among Dutch plant breeding companies about their experiences with MAS so far.
MAS breeding was highlighted, promoted and hyped here years ago as a new, very useful tool which would speed up plant breeding enormously. From the people I interviewed last week, I got a slightly different picture. Results of MAS have been moderate. It is of some use for single-gene traits but not for multi-gene traits. Most plant traits are multi-gene traits. The cost of MAS is a problem, even for rich plant breeding companies. (I was told that American companies use MAS more since they are not so much interested in cost efficiency, they just want to see if it works). One interviewee remarked that for, for example, rust resistance in grass you don't really need MAS since you see very clearly at the phenotypic level whether the grass is rust resistant and you can select that immediately. MAS breeding at best seems to make the art of throwing away in plant breeding a bit easier and thereby somewhat time-saving.
Overall, this seems yet another over-hyped gene technology. I really doubt whether it is a good idea to spend so much money on this technology even when it comes from international fundings etc. All this money seems to be much better used in other projects that poor, small farmers are really needing and which would help them far more than MAS will probably ever do. Even in this (financially) rich country, we can see the negative consequences of investing in genetic technologies and research which fails to deliver the hyped promises. How much worse will this be for poor to very poor countries.
Wytze de Lange
Policy officer genetechnologies
De Wittenstraat 43-45
wdl (at) xminy.nl
Sent: 02 December 2003 09:44
Subject: 58: Locally adapted technology
Hello, I'm Jasper Buijs again.
I'm writing in response to message 57 (December 1) by Wytze de Lange. He argues that the high cost associated with MAS technology could more wisely be spent through other development routes. I wish not to counter-argue that there are other (technological) alternatives available to help poor farmers. Indeed, I would stress that viewpoint. However, his message also notes that MAS seems to be "yet another over-hyped gene technology". This wording, in my opinion, is somewhat too dismissing. The 'hype' is created by pro-biotech parties as well as anti-biotech parties. Many of them selling lies or partial truths (I am especially referring to the discussions about the use of GM crops). I still don't know whether we should call such intense discussion the virtue or the sickness of this information age. Living with the reality of such hypes, this does not mean that gene technologies' potentials shouldn't be further explored and tapped.
As far as I can oversee, many technologies are more expensive in their early phases. Once a deeper insight and more experience is gained (a knowledge base), usually people find ways to adapt the technology and make it cheaper to use. Tissue culture, for instance, has once also been regarded as a highly expensive technology of the developed world. But now it is effectively being used in many developing countries with cheaper local resources, or as 'creolizations' with traditional multiplication techniques (for instance with grafting, or the use of tissue culture growth hormones in locally prepared vermiculture soil to let tree shoots directly develop roots). [Creolization describes the coming together of diverse cultural traits or elements to form new traits or elements. For example, in the context of linguistics, creolization occurs when two or more languages converge to form a new, indigenous language...Moderator].
Although recognizing that technologies such as MAS are indeed still very expensive to actively apply, it is of importance that developing countries be able to build research capacity (institutional and human) and establish a knowledge base to find ways to adapt the technology to their own needs and abilities. Such reinforced capacity might also be able to attract more foreign financial resources to kick-start new developments. In this way, MAS might become one of the tools that developing countries could opt for, without making a hype of it and forgetting about cheaper options.
At the end of my argumentation, I must admit that I am not a MAS specialist. I would therefore like to post a question: Do people (especially from developing countries) have ideas already about how MAS could be locally adapted for lower cost, creolization or combination with other, (low-cost) technologies/techniques?
MSc. Ing. Jasper Buijs
Associate Expert Agricultural Biotechnology
Crop Improvement and Genetic Resources Department
International Potato Center (CIP)
Apartado 1558, Lima 12,
telephone: 349 6017 ext. 3063
fax: 349 5326
email: j.buijs (at) cgiar.org
Sent: 02 December 2003 09:53
Subject: 59: Re: Experiences with MAS so far - Netherlands, plants
My name is Hugh Wallwork and I am a cereal pathologist working in South Australia but with responsibility for the development of molecular markers in wheat and barley in the Cooperative Research Centre for Molecular Plant Breeding (MPBCRC). I am also actively using MAS in germplasm development projects.
The value of MAS in general has been questioned on the grounds of cost and practicality (see in particular message 57, December 1, by Wytze de Lange). However, how MAS is used can make an enormous difference to how costly and beneficial it is and it would seem to me that many of the criticisms stem from poor strategies rather than an inherant problem with the technology.
Using it to screen for rust resistance is possibly not a good economic strategy. Neither would using it on early generation segregating lines be very wise. Using it for selection of backcross F1 seed, where the trait of interest cannot be selected until late generations, is one example where it is likely to be much more economical than carrying the very high cost of keeping large numbers of lines that will inevitably be thrown out at a later stage after much wasted selection for other traits. (Sorry about the long sentence!). Indeed it may make outcomes possible that could not have succeeded otherwise. For this reason, MAS is and will remain a reality and it is only therefore a question of how it is deployed and how any one country can access that technology rather than whether they should.
Some breeding programs with limited objectives based on simply inherited traits may have no need to use MAS. For many countries the most obvious avenue is through importing CIMMYT/ICARDA (The International Maize and Wheat Improvement Center/International Center for Agricultural Research in the Dry Areas) germplasm developed centrally using these techniques. Some countries may be able to make arrangements for other central laboratories to screen lines for them. Many developing countries already have access to MAS technologies although there may be internal problems of deploying this expertise locally for breeding programs. In due course, the costs of MAS will come down dramatically as will the ease of using them away from high technology labs.
Most of the costs involved in MAS are related to marker development work and much of this work is already in progress in a diversity of organisations such as ours. We, for example, in the MPBCRC are working on a wide range of disease and abiotic stress traits and, with both CIMMYT and ICARDA as partners, are interested in providing assistance to developing countries by working on traits relevant to them.
In summary, I would suggest that instead of taking a negative approach to a powerful and useful tool, that we focus on how we can best use this opportunity and how we can facilitate developing countries taking advantage of what it offers.
Cereal Pathology and Genetics
South Australian Research and Development Institute
Wallwork.Hugh (at) saugov.sa.gov.au
Sent: 02 December 2003 10:34
Subject: 60: Collaborative international research on MAS
My name is Daniel J. Fairbanks and I am a Professor of Plant and Animal Sciences at Brigham Young University (BYU) in Provo, Utah, USA.
BYU is a collaborative partner with the PROINPA Foundation in Bolivia conducting research on quinoa, an important but underutilized food crop in Andean South America, under sponsorship of the McKnight Foundation's Collaborative Crops Research Program (http://www.mcknight.org/science/cropresearch.asp). We are developing DNA markers for use in germplasm characterization, selection of genotypes for core-collection development, and MAS in quinoa in Bolivia. Our experience has provided us with several insights that are making MAS workable and cost-effective in Bolivia, and have overcome some of the limitations imposed by intellectual-property issues.
At our laboratories in the USA, we developed polymorphic DNA markers of various types in quinoa, including amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs, also called microsatellites), single nucleotide polymorphisms (SNPs) and random amplified polymorphic DNA (RAPDs), and from them constructed a genetic map of quinoa. However, not all of these markers can be used in a cost-effective manner in Bolivia because of the laboratory equipment required and the inflated cost of consumables in that country. Instead, we have developed mapped SSR markers that can be reliably amplified by polymerase chain reaction (PCR) and display polymorphic alleles that are readily detectable on horizontal agarose gels. Although development of SSR markers is expensive, the only equipment required for amplification and detection of these markers after they are developed is a thermal cycler and an agarose gel apparatus. The cost of consumables is relatively low, and the agarose can be recycled. Bolivian scientists then use these SSR markers for their breeding and germplasm conservation programs in the country at a relatively low cost.
This approach of marker development and mapping in the USA, and utilization of mapped, cost-effective markers in Bolivia overcomes many of the economic obstacles faced by scientists in developing countries. Moreover, we have managed to work within intellectual-property restrictions that impede the transfer of germplasm across international boundaries. By developing markers in the USA and sending selected markers to Bolivia, there is no need for the Bolivian germplasm collection, or for large amounts of breeding material, to leave the country for analysis.
Daniel J. Fairbanks
Department of Plant and Animal Sciences
Brigham Young University
Provo, UT 84602,
df3 (at) email.byu.edu
[Since at least 3000 BC, if not longer, the seed of quinoa (Chenopodium quinoa) has been a vital part of the Andean diet, used as a grain in baking, as well as being served in numerous dishes prepared by Aymara, Quechua and other indigenous peoples throughout the Andean region...Moderator].
Sent: 03 December 2003 08:33
Subject: 61: Pedigree selection, plants
From Dr Kuldeep Singh, India.
I am happy to see the contribution of Hugh Wallwork (Message 59, December 2) who has taken a positive view of MAS. I fully agree with him that MAS is not required for traits that are easily scorable, like rust resistance in wheat, bacterial blight (BB) resistance in rice and many such diseases. Think of selection for insect resistance, viral resistance, drought etc. Even for easily scorable traits, like rust in wheat, MAS may have its own place like selecting for one gene or two genes (if the two genes in question show differential reaction to the prevalent races, even then MAS is not required; but if one intends to pyramid two genes for durable resistance then MAS is the only strategy).
Concerning cost vs strategy, it will depend on whether one intends to add some desirable genes in an already well-adapted variety through marker assisted backcrossing, or whether it is direct pedigree selection for developing new strains. For the first I have already contributed my viewpoint [Message 44, November 26...Moderator]. For the second approach, my viewpoint is as follows:
1. MAS should be an integral part of the breeding programme and not in isolation, as has been until now (this was necessary for technology development).
2. It is the breeder who should exercise selection first in his first segregation generartion (F2 or BC1F1) and only those plants should be analyzed for markers that are agronomically good. This approach of MAS is possible if rapid protocols are developed for isolating DNA from mature plants. This will reduce the MAS work considerably and it can be used in a large number of crosses. A breeder in general works with large populations - maybe 2,000 F2 plants per cross and several hundred crosses. The selection intensity in F2 is in general not more than 5%, on visual basis. However, if we are using MAS, then the plant breeders could select more plants and these plants can be analysed for desirable markers. In the next generation a plant breeder can carry only those plants which have the desirable genes. If this strategy is adopted, I am sure the cost of MAS will be even lower than the breeder incurs while carrying large junk until advanced generations.
Dr Kuldeep Singh
Dept. Genetics and Biotechnlogy
Punjab Agricultural University
Ludhiana 141 004,
Tel. +91-161-243 30 81 (R)
kuldeep35 (at) yahoo.com
Sent: 03 December 2003 08:57
Subject: 62: Developing countries can use information from developed countries
[While discussions have so far focused on MAS in crop and livestock improvement, there have been no views/experiences from participants on MAS in aquaculture and very few on applications in forestry. Does this mean (by the silence) that participants feel that MAS will be more appropriate or easily applicable in the crop and livestock sectors than in aquaculture or forestry in developing countries?...Moderator].
This is VLN Reddy from the Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India.
In my view, MAS should be used for few traits for which it is difficult to get phenotypic data, like quality traits i.e. amylose content, gel consistency etc. Then only is it economical in developing countries like India. Moreover, developing countries can use genetic and physical maps already prepared by developed countries. For example in rice, genetic and physical maps are available along with complete sequence of the rice genome. This information can be used by developing countries for MAS. Markers flanking the traits can be used straight away for MAS instead of going for mapping QTLs again.
Junior Research Fellow
Laboratory of Molecular Genetics
Centre for DNA Fingerprinting and Diagnostics
ECIL Road, Nacharam, Hyderabad-500 076,
Ph. # 27151344-1102
e-mail:vlnreddy (at) hotmail.com lax_gene (at) yahoo.com lax_gene (at) operamail.com
Sent: 04 December 2003 10:38
Subject: 63: Marker technologies aquaculture, some thoughts....
My name is Victor Martinez, from the Department of Animal Science, Faculty of Veterinary Sciences, University of Chile.
Application of markers and DNA technologies for improvement, I believe is still scarce in aquaculture, even in developed countries. I think that this is due, to some extent, to the lack of adequate integration between quantitative and molecular genetics in this area (see symposia of genetics in aquaculture). [I presume the reference is to the VIIIth International Symposium Genetics in Aquaculture, held in Puerto Varas, Chile, 9-15 November 2003 (http://www.genaqua.uchile.cl/). The proceedings will be published in the international journal Aquaculture, as a special issue...Moderator].
I think that the only succesful application of marker technology has been described previously by Miguel Toro (Message 50, November 27) in reference to the inference of parentage analysis for pedigree selection. But profit analysis of this technology compared to individual identification using passive integrated transponders are still scarce. [Passive integrated transponders (also called PIT tags) are implanted electronic devices allowing identification of individual fish as they pass by a transponder sensing device. PIT tags were developed initially to mark fish and since have been used to mark a range of wild and captive animal species...Moderator].
Despite all this, I do not think that the methods used for livestock regarding MAS or GAS (gene assisted selection) will depart significantly for aquaculture (see the paper of Villanueva et al 2001, methods and comparisons between BLUP, MAS and GAS). Our analyses (Martinez, 2003, PhD Thesis, University of Edinburgh) have shown that due to the extremely high fecundity rates, coupled with the use of chromosomal manipulations. novel and more powerful designs can be used in aquaculture compared to livestock. [The paper referred to above is Beatriz Villanueva et al. 2002. "Marker assisted selection with optimised contributions of the candidates to selection". Genetics Selection Evolution 34: 679-703, available at http://www.edpsciences.org/articles/gse/pdf/2002/06/03.pdf ...Moderator].
Victor Martinez MSc. PhD.
Department of Animal Science.
Faculty of Veterinary Sciences
University of Chile.
Phone 0056- 2 - 678 5597
Fax 0056 - 2 - 678 5611
vmartine (at) uchile.cl
Sent: 04 December 2003 10:56
Subject: 64: Fusion of soft and hard technologies
From Olusola Sokefun, Nigeria.
I have followed with interest all issues raised so far and would like to comment as such. I want to divide technology in the area of plants, animals etc. into two parts: the first being the soft technologies and the second being the hard technologies. This division is just for the purposes of being able to follow my line of thought.
The soft technologies I note are as old as manhood and the quest of man to conquer the vagaries of animal production/domestication, plant etc. They include the use of top of the lines to produce the next generation of offspring and modern science calls this selection. I remember in the village, my grandfather would say that a particular cock should not be allowed to mount a hen or that a particular hen has good mothering ability because it hatches maybe ten chicks and they were all cared for without loss.
Hard technologies would include MAS, which is the main issue in this conference. I would define it as technological types that tend to be out of the ordinary (all the definitions are mine).
I note rather importantly that there is no way the hard technologies would totally replace the soft technologies and that for the developing world and the developed, the best that we can have is a fusion of both to achieve the best of results.
Finally, maybe this is not the best place to put this, but please pardon me if I have erred in anyway. I just emerged from a meeting as part of a technical group which has as its focus the development of agriculture. We URGENTLY need firms or individuals that can assist on a fee for service basis in the following general and specific areas of agriculture: 1. plant propogation - food crops, ornamentals, cash crops etc. through tissue culture or any other more advanced means 2. animal propagation - micro and macro livestock, large and small ruminants, monogastrics etc. I would appreciate feedback on this urgently. [This conference IS not the appropriate place for it. Any responses on this should be addressed directly to Olusola...Moderator].
The Bioscience Research Centre,
Lagos State University, Ojo
PMB 1087 Apapa,
Tel: + 234 8033335175
osokefun (at) hotmail.com
Sent: 04 December 2003 14:37
Subject: 65: Participation of developing countries in MAS development
I am Victor Olori, again.
In response to the Moderator's half way message (1 December), I would like to address the question of "When should developing countries play an active role in the development of MAS technology (construction of molecular marker maps, detection of association between molecular markers and traits of interest etc.) or when, instead, should they aim to import the technology developed elsewhere?").
The answer to this question depends on exactly what we mean by 'developing countries'. I think individuals and institutions in developing countries are, and should be, playing active roles in the development of MAS right now. From the contributions to this conference received so far, there are many scientists from, and in, developing countries with experience in MAS techniques and many more are probably students or postdocs in laboratories across the world today. There are those in labs in the developing countries that are collaborating actively with others in developed countries. I call this active participation. Often times, this contribution is limited because of limited resources and perhaps to few institutions with extensive research capabilities and mandate. Places like ILRI (International Livestock Research Institute), IITA (International Institute of Tropical Agriculture) for example.
If by "developing countries", we are referring to getting governments to purposely fund direct research and application of MAS, then the answer is different and perhaps that is the whole purpose of this conference. I think MAS would have to be seen to be possible, efficient and required before these countries can commit and justify the required huge resources. My understanding of the discussion so far is that;1) MAS is possible and will be useful in developing countries.
Under these circumstances, I would suggest that developing countries should at present be putting the building blocks for MAS in place. Application of MAS requires first and foremost the training of personnel. One thing developing countries and the governments of these countries can do right now is to fund Educational Institutions to put in place the required facilities and training programs to support research in biotechnology and particularly genetics research. I see these institutions as the sustainable units that will nurture the culture of breed improvement and the introduction of 'hard technologies' (as Olusola Sokefun in message 64 (December 4) describes technologies like MAS) into structured breeding programs. The role of educational and research institutions in the developed countries in this regard cannot be over emphasised and, whether MAS eventually becomes the panacea for plant and livestock improvement in these countries or not, the facilities and personnel will always be useful for other purposes and as such are an asset. Also, it is easy to justify funding for education, and development of MAS can be a residual of such educational development. This will also allow them to "import the technology" when it can be justified.
Dr. V.E. Olori
Irish Cattle Breeding Federation,
Shinagh House, Bandon,
Republic of Ireland.
Tel: +353 (23) 20220
Fax +353(23) 20229
E-Mail volori (at) icbf.com
Sent: 04 December 2003 16:40
Subject: 66: Is MAS a little luxurious for developing countries?
This is Nazimi Acikgoz from Turkey. I am a rice breeder and moderator of a monthly, bilingual agricultural biotechnology newsletter: (http://www.agbiyotek.ege.edu.tr).
Recent drops in "yearly yield increase" indicate that plant breeding is approaching its theoretical limits. But quality seems to be focused more intensively on the future. This is valid only for the developed world. Can we claim the same for developing countries? I'm afraid we cannot say that - there is not enough suitable varieties improved for every micro-ecology yet. The main reason is an organizational issue. Agricultural research in developing countries is not well coordinated and many scientists lean towards biotechnology, especially MAS studies. Scientists are forced to cut back on field work for a number of reasons (including limited sources, caused by national coordination defect) and tend to work in laboratories.
We had the same paradox 20-30 years ago. The "population genetics" studies were quite popular. I just wonder whether my "correlated response studies on rice" have contributed to my released varieties! How did those academic studies effect "to the new cultivars hunger" agriculture? (in Turkey a cultivar namely TOKAK, released in 1937, is still in the seed market). [Some additional information has been provided by Nazimi Acikgoz about this. He adds "Where "Genotype by Environment" interaction is existing, we have to provide a new cultivar to those environments. Every agricultural micro ecology is in need of a new genotype. I’m afraid we did not conduct any proper yield trial in such micro ecology yet. In Italy, for a single macro ecology (Po valley), there are more than 40 rice cultivars. In Turkey, we grow rice in 12 macro ecologies and we have only 15 released varieties. For some special micro ecologies we have to improve new genotypes...Moderator].
Now, concerning Dirk-Jan de Koning's message (number 20, November 20): "Rather than a commercial national/regional framework, I remain convinced that any form of MAS for the developing world will depend heavily on sponsored international collaborative efforts", this MAS issue seems to be quite a luxury for developing countries.
I wish that FAO should focus on the effective use of plant breeding activities in national or regional level, in the first place. Coordinated and collaborative research organization attempts should be considered before basic scientific issues.
Breeding of new varieties to meet the needs of recently established consumption systems (frozen food industry; bakery, pickles, jam, paste, etc...) or changing agricultural conditions force all plant scientists to first find out the desired genes. The success story of the "Clearfield system" starts with mutant resistance genes proving that even developed countries are in need of classical breeding activities. Characterization of existing genetic material has been neglected not only in developing countries. Proper organization of "agricultural research systems" in least developed countries (LDCs) should have priority for FAO. This luxurious MAS occupation keeps scientists, especially plant breeders in developing countries, from doing their real job. Because some scientists without any traditional breeding programs enter directly into MAS. [Clearfield varieties display herbicide-tolerance and were developed through a breeding technique known as seed mutagenesis...Moderator].
Prof. Dr. Nazimi Acikgoz
Ege Uni. Seed Technology Center
nacikgoz (at) ziraat.ege.edu.tr
Sent: 04 December 2003 16:56
Subject: 67: Costs of genotyping
I am Miguel Toro again.
With respect to the cost of genotyping, the figure that many people quote is about 1 dollar (or euro) per microsatellite and individual (this means that the genotying of 1,000 individuals for 20 markers will cost $ 20,000, a considerable amount of money). Is this value correct? I have also heard that new technologies are coming that could reduce the cost to about $ 0.25. If that is the case, the prospective for using MAS will certainly increase.
Finally, I think that the genotyping task hardly can be considered a research task. Are there companies that offer to do the genotyping (of which species?) at a reasonable cost? I am thinking of using markers as a source of information without bothering too much about gene detection (along the line suggested by Lande and Thompson, Hayes and Goddard etc). Probably the most sensible thing to do is to carry on with mapping projects using research funds (and on a collaborative basis) and promote companies that do the large scale genotyping at competitive prices.
Miguel Angel Toro Ibanez
Departamento de Mejora Genetica Animal
Instituto Nacional de Investigacion y Tecnologia Agraria y Agroalimentaria (INIA)
Carretera La Coruna km. 7
Telf: 34 913476807
Fax: 34 913572293
e-mail: toro (at) inia.es
Sent: 05 December 2003 09:24
Subject: 68: Role of developing countries in MAS
This is from Delphin Koudande, researcher at the National Agricultural Research Institute of Benin.
I am going to comment on the following question from Section 6 of the Background Document: "When should developing countries play an active role in the development of MAS technology (construction of molecular marker maps, detection of association between molecular markers and traits of interest etc.) or when, instead, should they aim to import the technology developed elsewhere?".
I think that developing countries have been playing so far a key role in the development of MAS technologies. Just take a look around the world in many laboratories in USA and Europe, you may find about one tenth of the people working in the lab originate from the so-called developing countries. When it comes to finding out what is being done in developing countries, let us say in Africa, I would rather ask what is the priority in these countries? Given the economics of those countries, we can imagine the part of the budget that is devoted to the whole research programs and the one to MAS. There has been a lot of argument during this conference on the cost of genotyping and what could be the benefit of that compared to the traditional selection program. In developed countries, most of applied MAS in breeding is held by companies. Which companies in Africa are wealthy enough to support equipment and functioning cost in a laboratory to develop MAS? Do we need at present to develop markers or to try hunting for genes or QTLs? How sustainable will such research be in countries where the priority is how to survive?
I think [where?...Moderator] many researchers have been trained in developed countries there is possibility to use markers designed elsewhere. There are areas in which markers can be applied for immediate use like diagnosis or biodiversity assessment. In Africa, I have suggested to tackle research in marker technology on a regional basis or in international institutions like ILRI (International Livestock Research Institute, in Kenya), CIRDES (Centre international de Recherche-Developpement sur l'elevage en zone subhumide, in Burkina Faso) and ITC (International Trypanotolerance Centre, in The Gambia). In my point of view, we can still keep on importing markers from elsewhere.
The major constraints for agricultural production in Africa are water management, conserving soil fertility and pest management.
National Agricultural Research Institute of Benin
01 BP 884 Cotonou
dkoud2002 (at) yahoo.fr
Sent: 05 December 2003 09:30
Subject: 69: Flanking markers // Patenting
My name is Rosan Ganunga and I am working towards my doctoral degree in Plant Breeding and Genetics at Texas A and M University, Texas, USA.
My first contribution is on MAS regarding the message 42 (November 26) by Prof H. Dulieu. My point is to emphasize that when you have you have flanking markers on both sides of the gene of interest, the ability to select for that trait is increased compared to using a single marker. In addition, if the marker is part of the gene of interest, then your chance of selecting for the trait is also greatly improved compared to using a single marker.
My second contribution is on patenting genetic products or inventions. I guess it is not right to oversimplify the cost of patenting genetic products. It requires huge amounts of investment, amounting to thousands of US Dollars, to patent an innovation and it involves so many players. Therefore, for developing countries to go into patenting their products, they must have adequate investments starting from genetic map construction, to patenting the final products. Potential markets for the product must be properly anticipated to make sure of returns to the investment. But are small scale farmers in developing countries ready to pay for the high cost of patented products?
PhD Student in Plant Breeding and Genetics
Texas A and M University,
College Station, Texas, 77845-2474
Email:lawson (at) neo.tamu.edu
Sent: 05 December 2003 17:46
Subject: 70: Marker applications - wheat, maize
[Many thanks to Dr. Manilal William for this message, which raises many interesting issues. We ask participants to try and restrict messages to 600 words...Moderator].
My name is Manilal William, Geneticist, Applied Biotechnology Centre at CIMMYT (International Maize and Wheat Improvement Centre) - Mexico.
As Kevin Williams (message 37 and 51...Moderator] and others pointed out previously, utilization of markers has helped tremendously in the understanding of complex traits in many cultivated species - for example how many loci control a particular trait of importance and the genomic location of those genes etc. However, the practical applications of molecular markers in any crop species (for MAS) is limited although it is not zero. Many contributors mentioned the limitations; costs, lack of infrastructure etc. in the developing world in order that MAS be used effectively. Some also mentioned the "hype" that biotechnologists had used to promote marker technologies with very limited results. [Message 57, December 1 by Wytze de Lange...Moderator]. All these comments in my view are valid comments to make.
If we take the view that molecular markers are "tools" that plant breeders may use to enhance their efforts, it is a bit naive (and reflects the lack of understanding that some have) for some to question about the acreages planted using MAS technologies because MAS can only be used as tools to select for certain key traits rather than whole plant phenotype which is planted in the field. Part of the reason that some think that there is 'hype' associated with markers is undoubtedly due to unrealistic promises in the form of their potential applications that biotechnologists have promoted over the past couple of decades but it is also possible that plant breeders have misunderstood (at least to a certain degree) what is being discussed in the biotechnology community.
Since CIMMYT works with wheat and maize, my comments are based on our experience and efforts in these two crops. The wheat-related MAS activities are conducted within the Cooperative Research Centre for Molecular Plant Breeding (MPBCRC) that links CIMMYT with several key research centers in Australia. [Mentioned in Message 37, November 25 by Kevin Williams...Moderator].
Wheat is considered by biotechnologists as a species that is difficult to work with - mainly due to its large genome size and the number of linkage groups (with 21 basic chromosomes). It shows very limited levels of polymorphisms at the marker level, making marker development more challenging and therefore more resource intensive. But it has the tremendous advantage that it can be crossed with its wild relatives relatively easily and a number of chromosomal translocations are available that contain many agronomically important genes. When such translocations with desirable traits can be identified, marker development is relatively easy and regardless of the linkage between the marker and the gene, the translocations can be introgressed into different wheats using the marker since there is very little, if any, chromosome pairing between wheat chromosomes and alien translocations. Several major genes conferring resistance to important fungal and viral diseases have thus been transferred to wheat by breeders and markers made available by biotechnologists. At CIMMYT, we are using markers to transfer an alien chromosome segments carrying resistance to barley yellow dwarf virus and a segment of chromosome from Aegilops ventricosa that carries a set of genes for resistance to leaf rust, yellow rust and nematodes. Another area where we are applying markers is to improve root health in wheat (a robust root system would benefit wheat in drought-prone regions of the world). Some of these markers are diagnostic (no recombination between the marker and the gene of interest) and some others have close linkages. When markers are used, we use the approach of screening early generations to make sure of the capture of the gene of interest in segregating material. When diagnostic markers are not available, markers with close linkages are used to increase the allele frequency for the gene of interest in segregating progeny. Without the markers, it would be challenging to screen for certain root diseases in our breeding stations in Mexico due to lack of screening facilities.
Experiments have shown that markers can be effectively used in maize for backcross (BC) breeding. AT CIMMYT, we are using markers (diagnostic ones) located within the opaque 2 mutant (that gives high lysine and tryptophan maize - or quality protein maize, also known as QPM). When a donor (containing opaque2) is used in crosses with several recurrent parents in line conversion activities, markers are effectively used to identify the heterozygotes to be used in crosses in the next BC generation. Protein assays are quite expensive compared to marker assays.
In a crop such as maize, where extensive SSR (microsatellite) maps are available, markers can also be used in backcross breeding not only to select for the target trait but also to select for the genotype of the recurrent parent. Simulation studies have shown that the recurrent parent genotype can be recovered in less than two years using MAS (Ribaut and Hoisington, 1998). For the private industry, where the saved time in releasing a line may have positive financial implications, these approaches can be used effectively although there is considerable investment in using markers to select for the recurrent parent genotype. These approaches also can be used in transferring a desirable transgene such as Bt from one cultivar to another since diagnostic markers for the inserted gene is available when a GMO is available.
In order to support the 'service' activities, that is to provide the services to the maize and wheat breeders at CIMMYT, we have set up a service laboratory. A pre-requisite for these type of laboratories is the capacity to perform large number of DNA extractions in a relatively short period of time and also the capacity for high throughput PCR assays. Obviously, there is a capital cost involved in setting up such a facility but the running operational costs of marker assays that we are performing at CIMMYT is quite low and is cost effective compared to other alternatives. In maize, the service lab conducts approximately 4000 marker assays in helping the maize breeders in QPM line conversion activities and in wheat approximately 5000 assays are conducted for various traits annually.
Another key aspect of marker applications and utilization of markers in the breeding programs is the need for close collaboration between the field personnel such as pathologists, entomologists, breeders with the personnel working in the laboratories. There has to be acceptance by the plant breeders about the utility of markers at least for some key traits that they would like to integrate into the breeding activities as well as there has to be willingness for laboratory personnel to make the extra effort to have better communication with breeders and other field personnel in order to convince them about the utility of markers.
For many third world countries, setting up 'marker laboratories' and running them can pose significant challenges. A marker laboratory, although not prohibitively expensive to set up and operate in the industrialized world, can be challenging in developing countries due to declining financial support for agricultural research from the host governments as well as from the donor community. The objectives and the scale of activity have to depend on the needs of individual situations as well as on the resources available - both human and financial.
One other complication in promoting MAS is the desire or the tendency that even the public sector researchers show in having some intellectual property (IP) rights for markers developed in different research groups. As many have commented, development of a useful marker is a significant challenge. However, even when some markers are available, if their use is restricted due to IP or other ownership related issues, their use would be really limited.
Apologies offered for making a long message.
Reference: Ribaut Jean-Marcel and D. Hoisington (1998) Trends in Plant Science. 3: 236-239.
Dr. Manilal William
Applied biotechnology Centre
m.william (at) cgiar.org
Sent: 08 December 2003 10:27
Subject: 71: MAS, new crops and developing countries
This is P.M. Priyadarshan again.
I fully agree with the points raised by Nazimi Acikgoz (Message 66, December 4). Derivation of varieties for a micro-environment is very important, especially when excessive and under-utilized agricultural land is available.
I have the following points:
1) The current world population of 6 billion is estimated to reach 7 billion in 7 years (by 2010) and even 8 -10 billion by 2025. The demand will be to produce 40-50% more food and fiber by 2025. This is a formidable challenge, in view of the fact that plant breeding might have reached the "theoretical limits". One option for this is to utilize the maximum available area with higher yielding varieties.
2) Of the estimated 350,000 plant species in the world, 80,000 are edible. Only 150 species are actively cultivated for food, feed, fiber and fuel. Of these, 30 produce 95% of the human calories and proteins. Half of our food derivatives come from only four species - wheat, rice, maize and potato. What about utilizing the under-exploited species? Now, the question will be how to change the 'taste of the mouth'. Again, back to MAS for changing quality traits!
3) I am unaware whether FAO or CGIAR have a programme to popularize under-utilized species. If not, I would suggest that some activity in this direction is essential. Crop diversification will also reduce disease/pest insurgence. A consortium of FAO and CGIAR (with active IPGRI participation) can bring out some useful results on the description of under-utilized species. [One recent initiative that might be mentioned here is the release in November 2003 by The Global Facilitation Unit for Underutilized Species (GFU) of its web site on underutilized species (http://www.underutilized-species.org/index.htm). Initially covering only plants, there are plans to extend its scope in future. On the initiative of GFAR (Global Forum on Agricultural Research), an informal group of representatives from FAO, IPGRI (International Plant Genetic Resources Institute), ICUC (International Centre for Underutilized Crops), IFAD (International Fund for Agricultural Development) and BMZ (German Federal Ministry for Economic Cooperation and Development) developed the concept of the GFU. For more information, contact i.zeledon (at) cgiar.org...Moderator].
4) Scientists, especially those of developing countries, despite being given perks and incentives are scaring away from working under new environments. Lack of social facilities is one reason. One option is to have young, talented and capable personnel on a contract basis for 3-5 years. The International Center for Agricultural Research in the Dry Areas (ICARDA, a CGIAR centre in Syria) is successfully following this option, especially for rejuvenating agriculture in war-torn Afghanistan. This is an excellent example of sheer determination and confidence. Developing countries must follow the example set by ICARDA.
5) But, if plant breeding is approaching the "theoretical limits", then the situation is worrisome. When we think of a new area of operation for a specific crop, it largely depends on how scientists make themselves available for working in that environment. Often, not a lack of resources but lack of skilled manpower is the constraint that developing countries face (maybe due to lack of fair selection!). As Nazimi Acikgoz pointed out, it is easy to do laboratory work at the cost of valuable fieldwork. The latter is invaluable, directly contributing to the derivation of varieties.
6) Developing countries can experiment with MAS on crops where a linkage map has been developed and the DNA sequence analysis completed (e.g. rice and, to a large extent, tomato).
7) Aquaculture needs a great deal of emphasis. Seafood is more nutritious than anything else; and sea resources are exploited to the minimum. (Rightly, the Moderator says participation from the aquaculture specialists is minimum in this conference)! I would look forward to see active participation from the World Fish Center (a CGIAR center).
Rubber Research Institute of India,
Regional Station, AGARTALA - 799 006,
Tel: Off : 91-381-2355287/2355143 - Extn:205
Tel: Resi : 91-381-2354325
pmpriyadarshan (at) hotmail.com
alternate e-mails: pmpriyadarshan (at) rediffmail.com pmpriyadarshan (at) yahoo.co.in
personal web page: www.freewebs.com/pmpriyadarshan/
Sent: 08 December 2003 10:48
Subject: 72: MAS technology
My name is T. Gopalakrishna, a research scientist involved mainly with blackgram and groundnut crops.
I feel that there is no "exact time" as to when developing countries should develop MAS technology as this would depend on the particular crop in question. For example, in the case of blackgram (Vigna mungo), a relative of mungbean (Vigna radiata), the interest would be mainly in India as it is extensively grown in India. As far as traits are concerned, MAS would be most appropriate (as many have mentioned earlier) for "difficult to score visually" traits as well as in gene pyramiding.
Dr. T. Gopalakrishna
Nuclear Agriculture and Biotechnology Division
Bhabha Atomic Research Centre
Mumbai 400 085
tgk (at) apsara.barc.ernet.in
Sent: 09 December 2003 08:59
Subject: 73: Active role in the development of MAS technology
This is S. Saravanan, India, again.
Regarding the question "When should developing countries play an active role in the development of MAS technology", my suggestion is that a collaborative effort needs to be organized for the successful running of a MAS programme in developing countries. Many developing countries often fall into severe financial difficulties that stop any scientific development activities. My statement here is that the developed countries should find their place in the developing countries for investment in any scientific programme. This may enhance the application of MAS in developing countries too.
Centre for Plant Breeding and Genetics
Tamil Nadu Agricultural University
sarapbg2002 (at) yahoo.co.in
Sent: 09 December 2003 13:59
Subject: 74: Costs of MAS
This is E.M. Muralidharan from India again.
I was wondering if the participants who discussed the costs of MAS technology vis-à-vis developing countries, had seriously considered the near certainty of technology improving and getting cheaper in the future, mainly due to automation/robotics and other refinements of current techniques and software. Miguel Toro (Message 67, December 4) did mention about competitive prices that might be offered by companies. I feel the costs will then become a non-issue.
If the trends in development of expertise and infrastructure in a country like India is any indication, then such services will probably be available at a fraction of the costs of that in the developed nations. Currently, much of the resources in India are anyway getting superfluous as more and more research centers are investing in facilities that could have ideally been shared. The emphasis of funding agencies should shift to the use of MAS technology as a part of a structured comprehensive crop improvement programme. Considering that the same crop is being studied by several laboratories, efforts at coordination by national or international agencies (FAO) is very essential.
Dr. E.M. Muralidharan
Kerala Forest Research Institute
Peechi, Thrissur, Kerala State
Email: emmurali (at) kfri.org
Sent: 10 December 2003 09:13
Subject: 75: Costs of alternative MAS - fish, animals
[Thanks to Antti Krause, from Finland, for this message which looks at four different ways of applying marker information in genetic selection programmes and the implications they might have for costs of MAS. The last day for submitting messages to the conference is December 14. In the remaining days, we would especially like to get some additional input about MAS in the forestry sector and, secondly, to hear the views/perspectives from some of the many participants from the private sector that have subscribed to the conference...Moderator].
My name is Antti Kause from MTT Agrifood Research Finland. I work mainly with fish breeding but I am also exposed to some work on farm animals.
I want to draw your attention to the very different costs of alternative ways of using molecular marker information in selection. This has relevance for the applicability of different type of MAS schemes.
Case A. One way of performing MAS is that we are working with a quantitative trait (or traits) which is determined simultaneously by few major genes and many genes with a small effect. And the idea is to increase the frequency of favourable alleles coding for the trait(s). Finding the several, hopefully population-wide, QTLs (or the genes) is laborious and costly. And to perform MAS in a sophisticated manner, one needs to combine the marker information with the breeding values for the trait(s) to create an appropriate selection index. Performing efficient MAS may here requires genotyping of many individuals, which again is costly.
Case B. In some cases, we have in a population a detrimental allele with only a simple major effect, making the trait an almost all-or-none trait (i.e. a qualitative trait). Such a case is, for example, an immotile short tail sperm defect in pigs and, perhaps, the halothane gene influencing meat quality in pigs. Here, the idea is that we want to get rid of the allele and there is a simple gene test available to do this. The gene test for the sperm defect, for instance, can be done on a limited number of animals (sires to be used for artificial insemination). It is obvious that in these cases, performing MAS is much more cheaper and simple.
Case C. Moreover, one may perform normal breeding value estimation first, and then use specific markers, for example to decide which of the full-sibs should be used in mating. In breeding value estimation, full sibs tend to get very similar breeding values for traits which cannot be measured directly on breeding candidates themselves but information comes from their sibs (e.g., disease challenge tests in fish). In this way, only certain full-sib groups need to be analysed using markers.
Case D. Finally, an example in which molecular marker information can be directly used to reduce the costs of a breeding program. In fish, we need to make back-up copies of the nucleus breeding population and the back-up fish are transferred to the other side of the country to another fish farm. Traditionally, each year we individually tag (a small electronic chip is injected into the body cavity) the back-up fish from all the families made during that year. In this way, we can always connect the back-up fish to the pedigree, and use them if the nucleus is destroyed. This makes thousands of extra tagged fish each year. This is time consuming and costly (though we can recycle most of the tags). Most of these costs can be avoided simply by taking, each year, tissue samples from the sires and dams used in the mating, and storing the samples. We can then send many untagged fish from all the families to the back-up fish farm. We need to proceed with the molecular genetic assignment of the parentage only if the nucleus is destroyed. If this does not happen, the cost of parentage assignment of the back-up fish is never realized. Thus, we are saving money by relaying on molecular markers here.
MTT Agrifood Research Finland
Animal Production Research
work tel: 358-3-41883608
work fax: 358-3-41883618
email: Antti.Kause (at) mtt.fi
Sent: 10 December 2003 09:32
Subject: 76: MAS for developing nations
This is from R. Sridhar, India.
This is in response to the Moderator's observation on areas which still need to be discussed.
The conference has clearly brought out the fact that MAS is an effective strategy for any crop improvement programme that aims at moving genes governing resistance/tolerance to stress factors which are difficult to phenotype. This would include even combining (pyramiding) more than one gene to enhance the durability of resistance especially to biotic stress-inducing agents. Therefore, the usefulness of MAS for developing countries cannot be less emphasized and they cannot afford postponing its use in their programmes.
However, effective use of MAS needs the involvement of a team of researchers and strong networking. For example, in a developing country like India, the trained manpower and the biotechnology facilities are spread in different institutions, comprising national research institutes and universities. The expertise both for molecular and non-molecular components (see my message 48, November 27) for MAS available in these institutions may also vary considerably. Teams consisting of breeders, pathologists, entomologists, agronomists, soil scientists and physiologists (as the objective of the project demands) need to work together. Again, marker development and application of MAS need to be integrated between institutions through effective networking for achieving the goal. In this, the CGIAR institutes like IRRI (International Rice Research Institute) and CIMMYT (The International Maize and Wheat Improvement Center) have demonstrated the strength of this aspect. This experience should encourage the national centers to develop similar networks. Some attempts have been made in this direction. Nevertheless, more has to be learnt to share information and materials with the laboratories sprinkled across the country for achieving common goals.
It is needless to say that to implement the above and experience the realities of MAS in crop improvement, meaningful breeding programmes and knowledge on usefulness of the genes to be deployed generated over the basic foundation of proper unbiased priority setting are essential.
For MAS, although it is slower than genetic transformation, a sustained effort would bring benefits as the latter technology, which is faster in providing its fruits, is yet to free itself from the debates against it.
Dr. R. Sridhar
Flat 5, Rajparis Kings Castle
(Old No.19), New No. 11, First Main Road
I-Block, Anna Nagar east 60102, Chennai, Tamil Nadu,
rangsridhar (at) yahoo.com
Sent: 10 December 2003 16:02
Subject: 77: Some of the main topics for discussion
[Thanks to Ismahane ElOuafi, Syria, for directly addressing some of the topics mentioned in Section 6 of the Background Document...Moderator].
I believe that asking such question for only developing countries is unfair to research institutions and scientists in these countries. Asking about "when is it appropriate for developing countries to use MAS", is like asking if they need to use a computer? I believe that with the developed technologies and with the great information unlocked in various plant and animal genomes, MAS is becoming a necessity in any breeding program. Protein markers, for example, have been used for the last decade for quality selection in wheat in developed and developing countries. Isn't it a kind of MAS?
"Should the previous establishment of a successful conventional breeding program be a prerequisite"? Sure, either in a developing or developed country. The means are not the main issue, rather the genetic material and the breeding strategies you are working with. If you are unable to choose your genotypes and the kind of crosses with conventional methods, you will not be able to do it also with advanced biotech tools.
The usefulness of MAS as a tool for genetic improvement is not anymore questioned (at least in my mind). When we talk about MAS, it means that the marker/gene is already identified and/or isolated; it means a marker has been developed to trace it back in the genome. I think at this stage, and especially if we are talking about difficult characters to measure, using genetic screening instead of the phenotypic one is an advantage. There are a lot of ways and means to substitute some chemicals with others in order to reduce the costs. At our MAS durum lab at ICARDA (International Center for Agricultural Research in the Dry Areas), we were able to bring down the cost of 1 SSR (microsatellite) to less than 0.2$/sample. I believe once the information is obtained, using it becomes very rewarding and cost effective. Whereas developing the marker itself is still expensive, even though it is getting cheaper.
Indeed, while developing markers, developing countries should take part in it with developed countries. As one of the key issues in QTL identification, for example, is 1) the phenotypic data in the adequate environments e.g. drought, heat, cold... 2) used genotypes holding genes of interest for the stresses mentioned above. In addition, most of the genetic biodiversity for food crops is found in developing countries, e.g. the Fertile Crescent.
As for the limiting factors for use of MAS in developing countries, I think the availability of information and chemical products is a major one. Most of the international companies are not located in these countries and whenever they have representatives, their prices are much higher than in the developed countries. In fact, it should have been the other way around.
Ismahane ElOuafi, Ph.D.
Germplasm Program, ICARDA,
P.O. Box 5466, Aleppo,
Fax: (+963)-21- 2213490
USA Direct: (+1)-650-833-6680
USA Fax: (+1)-650-833-6681
E-mail: i.elouafi (at) cgiar.org
ICARDA homepage: http://www.cgiar.org/icarda
ICARDA is one of the 16 centers supported by Consultative Group on International Agricultural Research (CGIAR)
Sent: 11 December 2003 10:38
Subject: 78: When MAS should be used in a developing country
This is from Rakotonjanahary Xavier, plant breeder in FOFIFA (National Center of Applied Research for Rural Development), Madagascar. My area is mainly rice but I work also on groundnut.
So far, I followed with interest all the discussions about MAS and my interest is to know which are the types of MAS currently used and which types of traits are linked to these (although molecular markers usually should not have any biological effect). I find some good examples from the messages, and I understand that few molecular markers are till now found for some traits and in some crops. However, I am personally convinced that MAS is efficient for selection and it should speed up selection with reduction in time and effort (cost and labor).
In a developing country like Madagascar, resources for research, both financial and manpower, are scarce. However, breeders should release in the shortest time superior lines both in tolerance to biotic and abiotic stresses and productivity, as well as more nutritious lines to ensure the consumption need of the population. We are obliged to use the most rapid way within our reach, that is mainly visual selection based on physiological traits. DNA collection, genotyping and analysis, and developing molecular markers will require undoubtedly a longer time and it is more costly.
I would contribute for discussion on five points:1. MAS should be used when conventional breeding cannot identify directly the individuals to be used for breeding (i.e parent or individual carrying the genes of interest).
BP 1690, Antananarivo 101,
r.xavier (at) simicro.mg
Sent: 11 December 2003 10:46
Subject: 79: Re: Costs of genotyping
[Upon request, Miguel Toro has provided some additional input to his message 67 (December 4), when he wrote "I am thinking of using markers as a source of information without bothering too much about gene detection (along the line suggested by Lande and Thompson, Hayes and Goddard etc)"...Moderator].
Even if the genetic basis of economic traits is only polygenic, you can get some benefit from using MAS. The reason is that you can use markers as a source of information in a selection index. As long as markers explain some of the additive variance (in a regression framework for example) you will benefit from including them in the index. Obviously, the benefits will increase as the number of genes that affect the trait decreases.
Hayes and Goddard (2003, Livestock Production Science 81: 197-211) consider MAS in a commercial pig enterprise (with a 100 sow nucleus, 1000 sow multiplier and 10,000 sow commercial tier). Using computer simulation, they assume four traits (growth, prolificacy, meat quality and feed intake) and that 7 markers for each of 18 chromosomes can explain 30% of the additive variance. In such a situation, the gain in the index was about 17%. But the cost would be high (1000 progeny x 18 chromosomes x 7 markers x 4$ marker = 504,000 $). However, if the cost decreases to about 0.5 $ they conclude that could be profitable.
Miguel Angel Toro Ibanez
Departamento de Mejora Genetica Animal
Instituto Nacional de Investigacion y Tecnologia Agraria y Agroalimentaria (INIA)
Carretera La Coruna km. 7
Telf: 34 913476807
Fax: 34 913572293
e-mail: toro (at) inia.es
Sent: 12 December 2003 10:11
Subject: 80: MAI from wild species, other issues
This is from N. Sarla, Principal Scientist, Directorate of Rice Research, India. I am working on identification and introgression of yield-enhancing QTLs from wild species of rice.
My comments are on marker aided introgression from wild species and some of the 11 issues put up for discussion. [refers to Section 6 of the Background Document to the conference...Moderator].
1. Marker aided introgression of QTLs for complex traits from close wild relatives to crops would be useful for developing countries as the genetic gains (e.g. high yield, drought tolerance, etc.) are enormous. Such QTLs, stable over different genetic backgrounds and environments, have been reported. The advanced backcross (BC) method for identifying QTLs from the wild species helps save time. I might add that it is possible to get plants looking like the recurrent parent in BC2 itself (all the chromosomes may not undergo recombination in each meiotic cycle) from elite cultivar x wild species crosses.
2. Marker-aided allele mining (for specific traits or QTLs) from the vast germplasm is also a distinct possibility. Assuming synteny (colinearity) one can look for beneficial alleles in the germplasm using markers for specific traits. Since many developing countries have large germplasm resources, it will be useful to develop competency in these areas for accelerating utilization of germplasm by breeders. FAO can play a catalytic role in the process.
3. As long as all information on mapping and marker development is kept in the public domain, benefits are sure to follow, either in the form of reduced costs or time saved to researchers in developing countries. To give an example, working with limited resources we were trying to introgress, map and identify QTLs for yield from a wild species O.rufipogon using the advanced backcross method. Knowing that certain chromosomes have more QTL-rich regions than others, the mapping work was then confined to polymorphic SSR markers on 5 chromosomes (instead of 12, cost cutting!) and getting a dense linkage map to increase the likelihood of identifying significant QTLs in these chromosomes. We thus mapped a QTL with significant effects on yield on chromosome 2. Secondly, inclusion of some unmapped multilocus markers (RAPDs, ISSRs which are cheaper to use) along with mapped SSR markers (which are costlier, if proprietary) in mapping studies helps in placing cheaper (per polymorphism) markers on maps. [Inter-simple sequence repeat (ISSR) techniques are nearly identical to random amplified polymorphic DNA (RAPD) techniques, except that ISSR primer sequences are designed from microsatellite regions and the annealing temperatures used are higher than those used for RAPD markers. SSR markers are also called microsatellites...Moderator].
4. The limiting factors for successful application of MAS in some developing countries may not be costs alone. The cost of mapping, marker development, and their use is coming down. Simpler, quicker and high throughput methods of DNA extraction are being reported. Use of multiplex PCR (polymerase chain reaction), multiplex PAGE (polyacrylamide gel electrophoresis), cheaper staining methods may cut costs further. The application requires a close synergy between the user of MAS and the developer of markers, the need and value of MAS should be obvious to both. Successful conventional breeding programs should be linked right from the beginning of a MAS program.
5. The issue raised by Dr Williams regarding communication between breeders and lab personnel is significant. From my earlier experience as faculty of Genetics at Indian Agricultural Research Institute, New Delhi, I would say PhD students who work with both and appreciate both are an asset. They could help "bridge the gap", so to say. FAO could provide PhD scholarships for MAS application studies especially in crops of regional importance, which are nutritionally important but may not attract much funds otherwise. [The messages referred to is message 70 (December 5) by Manilal William, who wrote "Another key aspect of marker applications and utilization of markers in the breeding programs is the need for close collaboration between the field personnel such as pathologists, entomologists, breeders with the personnel working in the laboratories"...Moderator].
Tanksley SD, Nelson JC, 1996. Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding line. Theoretical and Applied Genetics 92, 191-203
Tanksley SD and SR McCouch, 1997. Seed banks and molecular maps: Unlocking genetic potential from the wild. Science 277: 1063-1066
N Sarla PhD
Crop Improvement Section
Directorate of Rice Research
Hyderabad 500 030
email: sarlan (at) operamail.com
Sent: 12 December 2003 11:16
Subject: 81: MAS and bioinformatics for developing countries
This is from Alberto Davila, molecular biologist and bioinformatician, from Instituto Oswaldo Cruz-Fiocruz, Brazil.
I have followed with great interest the discussion about MAS and developing countries. Some points that have not been addressed are:
a) While MAS could be a bit expensive for some developing countries, it is something that can be done without major problems in "less" poor countries such as Brazil, for example. So, ideally we could use countries like Brazil (and others, of course) to help with MAS development in other developing countries. This refers to the concept of "South-South collaborations".
b) Nobody (as far as I know) has talked about bioinformatics. How do you analyze your markers? In a recent IAEA meeting (DNA-based techonologies), it was proposed to the plenary to help with the establishment of a working group in bioinformatics. As you know, bioinformatics is one of the disciplines that can be developed with success in developing countries. The World Health Organization (WHO) has recognized its importance and created 3 centers for "Bioinformatics and applied genomics": http://www.who.int/tdr/grants/awards/bioinformatics-10-01.htm. [The meeting referred to is the international symposium on "Applications of gene-based technologies for improving animal production and health in developing countries", held on 6-10 October 2003 in in Vienna, Austria, jointly organized by the International Atomic Energy Agency (IAEA) and FAO. The book of extended synopses from the meeting is available at http://www.iaea.org/programmes/nafa/d3/mtc/synopses.pdf or contact h.makkar (at) iaea.org for more details...Moderator].
I have not seen anything similar in the livestock research field, especially for developing countries.
So, my suggestion is to promote the establishment of the working group on bioinformatics (in developing countries) for livestock research having, as the main goal, the development of that discipline in developing countries.
Alberto M. R. Davila, PhD
Kinetoplastid Biology and Disease (Biomed Central)
DBBM / Instituto Oswaldo Cruz / FIOCRUZ
Av. Brasil 4365
Rio de Janeiro, RJ, Brasil
Email: davila (at) fiocruz.br amrdavila (at) yahoo.com
Phone: 55-21-3865-8229 / 3865-8206
Centralized Trypanosome Resources: http://www.trypanosome.com
Sent: 13 December 2003 11:03
Subject: 82: Re: MAS and bioinformatics for developing countries
I am Rajeev Varshney from the Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany. At IPK I am working in the area of development of gene-derived molecular markers, especially microsatellites or simple sequence repeats (SSRs) in barley. During my Ph.D. I was engaged in development and identification of molecular (microsatellite) markers for some traits like grain protein content, preharvest sprouting tolerance, grain yield (1000 grain weight), etc. in bread wheat in India.
First of all I should mention that I really enjoyed the reading of messages from different people about MAS and role of developing countries. In fact the recent message (no. 81, December 12) from Alberto Davila prompted me to post the following message.
(1) I agree with Alberto Davila that integration of bioinformatics with MAS will prove very useful not only for development of molecular markers but also for effective utilization of MAS for crop improvement programmes. For instance, people have already started to use bioinformatics by writing some perl scripts or computer programmes to identify the microsatellites in the EST (expressed sequence tag) sequences (e.g. Kantety et al. 2002; Varshney et al. 2002). Thus development of microsatellite markers has become very inexpensive as compared to earlier techniques (Gupta and Varshney, 2000). Moreover, since these markers are derived from the ESTs/genes, they hold better potential for their applications across the species (Thiel et al. 2003). Furthermore, it has been advocated that the 'functional' markers are better resources for their use in breeding since they have developed from the expressed part of the genome and directly from the genes affecting a particular trait (Anderson and Lueberstadt, 2003). I am sure that many of the rice geneticists and breeders are already aware of the use of bioinformatics to saturate the map of rice with about 2200 SSR markers (McCouch et al. 2002).
In my opinion the availability of draft sequence of rice genome and its annotation can be a target for bioinformaticsts to identify the gene(s) which can be used as markers (like SSR, STS, CAPS or SNP, etc.) in breeding programmes of not only of rice, but also in other cereal species because of conservation of synteny of rice with other cereals. I would also argue to use those genes, identified for different traits (like abiotic stress, etc.) by using cDNA or microarray technology, as markers (of course, after converting them in appropriate marker systems, as mentioned above) in breeding programmes. So, I think that it is the time to go one step ahead from MAS to 'GAB' i.e. Genomics-Assisted Breeding.
(2) Generation of databases for storing the marker data, their protocols, etc. is also a task for bioinformaticists so that the available information can be disseminated successfully and duplication of similar efforts can also be avoided/minimized. In this direction, the USDA-IFAFS (Initiative for Future Agricultural and Food Systems) sponsored project MASWheat (http://maswheat.ucdavis.edu/) is an example, and there is a need to generate more databases for other crops, livestocks, etc.
I am sorry for the long message but I hope that it would inspire geneticists, breeders and bioinformaticsts to co-ordinate the efforts in the area of MAS or GAB aimed for crop improvement programmes.
Andersen JR, Lubberstadt T (2003) Functional markers in plants. Trends in Plant Sciences 11:555-560
Gupta PK, Varshney RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with special emphasis on bread wheat. Euphytica 113: 163-185
Kantety RV, Rota ML, Matthews DE, Sorrells ME (2002) Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol 48:501-510
McCouch SR,Teytelman L, Xu Y, Lobos KB, Clare K, Walton K, Fu B, Maghirang R, Li Z, Xing Y, et al (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res. 9: 199-207
Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development of cDNA derived microsatellite markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411-422
Varshney RK, Thiel T, Stein N, Langridge P, Graner A (2002) In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell Mol Biol Lett 7: 537-546
Rajeev Kumar VARSHNEY, Ph.D.
Molecular Markers Group, Plant Genome Resource Centre,
Institute of Plant Genetics and Crop Plant Research (IPK)
D 06466 GATERSLEBEN
Tel: ++ 49 39482 5594(off.),5231 (lab) Fax: ++ 49 39482 5595
E-mail: rajeev (at) ipk-gatersleben.de / rajeevkvarshney (at) hotmail.com
Web : http://www.ipk-gatersleben.de/en/ ; http://pgrc.ipk-gatersleben.de/
Sent: 13 December 2003 11:14
Subject: 83: Integration of molecular markers with plant breeding
From David Reece, United Kingdom.
Several people have indicated that it is both difficult and important to integrate molecular markers with plant breeding programmes if the maximum benefits are to be realised. I would be very interested in hearing experiences and opinions about what constitutes "good practice" in achieving this kind of integration, and about the kind of difficulties that need to be overcome.
Incidentally, I recently gave a conference paper on this subject: the text version is not yet ready, but will shortly appear on our website at www.ex.ac.uk/egenis. I would appreciate comments from members of this conference. Unfortunately, the paper will not appear until after the end of the conference, but people can contact me directly.
Egenis (the ESRC Centre for Genomics in Society)
University of Exeter,
J.D.Reece (at) exeter.ac.uk
Sent: 15 December 2003 12:54
Subject: 84: Re: Integration of molecular markers with plant breeding
This is from Dionysia Fasoula, Agricultural Research Institute, Cyprus.
It has been very interesting to follow the thoughts shared by colleagues from many countries during this FAO conference, culminating with the recent message from David Reece (no. 83, December 13), which also prompted the following contribution:
The issue of integrating molecular markers with plant breeding activities is essential. An inherent limitation remains the fact that while molecular analysis, by its very nature, has the capacity to focus on and evaluate the individual genome, conventional plant breeding evaluation works not at the level of the individual plant, but at the level of multiplant plots. The possibility to use a breeding methodology that enables the breeder to establish the individual plant as the unit of evaluation and selection from the earliest segregating generations in the actual fields of his or her choice, can enhance the efforts to identify useful markers.
In this regard, it is helpful to consider the essence of honeycomb breeding, which is a breeding methodology conceived to evaluate individual plants at distances that minimize the CV (coefficient of variation) of individual plant yields, while maximizing the yield per plant, in the arrangement of one of the several so-called honeycomb designs.
Following are some points that I believe will be of value to participants seeking to enhance their relevant programs, both in developing as well as in developed countries: What is needed for marker development and validation, as well as for successful QTL studies, is the most accurate phenotyping possible, particularly for traits that have economic impact (e.g. yield, stability of performance, tolerance to density and the various biotic and abiotic stresses, responsiveness to inputs). These traits are usually inherited in a polygenic manner, and therefore, are difficult to score reliably with conventional field or greenhouse techniques. Reliable phenotyping for the above traits is possible in all segregating generations in honeycomb trials, which are designed for accurate phenotypic (not visual) evaluation and place equal emphasis on selection both among and within the progeny lines.
Our experience with the honeycomb trials so far indicates that, encouragingly, success in plant breeding may not approach its theoretical limit yet, once we have methodologies to exploit the ability of the genome for self-restructuring.
Accordingly, developing countries can play an active role in the development of MAS, particularly in the detection of associations between molecular markers and traits of interest. These countries can develop their own dual-purpose honeycomb breeding programs, which will lead to the release of superior breeding germplasm or end-cultivars, and at the same time produce accurate phenotypic data to be used for the development of molecular markers, in collaboration settings. This will also produce useful information on the range of the validity of various markers across the different production environments.
Details about the construction of the appropriate honeycomb designs and the establishment of honeycomb trials are found in: Fasoulas, A.C. and V.A. Fasoula, 1995. Honeycomb selection designs. Plant Breeding Reviews 13:87-139. This article provides also illustrations of several honeycomb designs.
The rationale and the benefits stemming from the coupling of molecular breeding activities with the capabilities of the honeycomb breeding are found in: Fasoula, V.A. and D.A. Fasoula, 2000. Honeycomb breeding: Principles and applications. Plant Breeding Reviews 18:177-250.
The concept and the criteria for whole genome phenotypic evaluation are found in: Fasoula, V.A. and D.A. Fasoula, 2002. Principles underlying genetic improvement for high and stable crop yield potential. Field Crops Research: 191-209. It also presents a unifying genetic basis connecting vigor, degeneration and response to selection.
Dionysia A. Fasoula
Molecular Genetics and Breeding
Agricultural Research Institute
P.O. Box 22016
e-mail: dfasoula (at) arinet.ari.gov.cy dionysia_fasoula (at) yahoo.com
Sent: 15 December 2003 12:56
Subject: 85: marker assisted introgression in cattle
From Delphin Koudande, Benin.
I sent a reflection on 12 December, starting by approving comment by Ismahane ElOuafi (message 77, December 10), but unfortunately my connection to internet did not work. I have now about ten minutes, so I will just sumarise what I wrote:
Marker assisted introgression (MAI) in cattle should be thought deeply before implementation because:- QTL can be lost during the backcross process,
National Agricultural Research Institute of Benin
01 BP 884 Cotonou
dkoud2002 (at) yahoo.fr
[Thanks very much for these comments about MAI. Delphin's PhD from
Wageningen University, Netherlands in 2000, entitled "Introgression of
trypanotolerance genes" is highly relevant in this context. The abstract is
"Trypanosomosis is the most widespread parasitic disease of great importance in Africa affecting human and animals. There are breeds of cattle that are trypanotolerant. Trypanotolerance is an ability of these breeds to withstand the effects of trypanosome infections. The disease impedes production in Sub-Saharan Africa. In this thesis, the main focus is on marker-assisted breeding to improve trypanotolerance and mouse is used as model organism for cattle. We have concentrated on the opportunities to exploit individual genes (QTL) that affect trypanotolerance. We have shown how the size of a breeding experiment increases with the number and the size of the QTL region to introgress. Biological factors to be considered when estimating the required size of an introgression experiment are also highlighted. Strategies to optimize designs for introgression show that selecting two lines each carrying two of the donor's QTL allele during the backcross (when intogressing three QTL) is more advantageous than monitoring simultaneously the three QTL in terms of number of animals to maintain, number of genotyping and costs involved. An experiment in mice shows that QTL introgression is feasible and successful, and that the background genotype is an important factor to be considered when analyzing the results of such an experiment. This experiment is unique. The general discussion focuses on the introgression of trypanotolerance genes is cattle with an emphasis on Sub-Saharan zones of Africa. The introduction of trypanotolerant cattle in the humid and sub-humid zones of Africa, however, should be done with care to avoid damage to the environment and bio-diversity"...Moderator].
Sent: 15 December 2003 13:05
Subject: End of FAO conference on Marker Assisted Selection
The last message (number 85), from Delphin Koudande, has been posted so Conference 10 of the FAO Biotechnology Forum is now officially closed.
FAO established the Biotechnology Forum in the year 2000 with the aim of providing quality balanced information on agricultural biotechnology in developing countries and to make a neutral platform available for people to exchange views and experiences on this subject. We hope that this conference on "Molecular marker assisted selection as a potential tool for genetic improvement of crops, forest trees, livestock and fish in developing countries" has been both interesting and of value to you.
For your information, we can provide some figures about the conference. It ran for four weeks, from 17 November to 14 December 2003, and a total of 627 people subscribed, the highest number for any of the Biotechnology Forum conferences held so far.
Of the 627 people, 52 (i.e. 8 %) submitted at least one message. Messages were received from all major regions of the world - 28 of the 85 messages posted (i.e. 33%) came from participants in Asia, 26% from Europe, 14% from Latin America and the Caribbean, 9% each from Africa and Oceania and 8% from North America.
Messages came from people living in 26 different countries - the greatest proportion by far was from participants in India (25%), followed by Australia (9%), United States (8%), United Kingdom (7%) and Peru (6%). A total of 50 messages (i.e. 59%) were from participants in developing countries and 35 (41%) from participants in developed countries.
The great majority of messages came from people working in research centres, including CGIAR centres, (52%) and in universities (33%). The remainder worked as consultants, development agencies, farmer organisations, government agencies, NGOs or UN organisations.
[Note that figures about the relative contributions of the developing versus developed world or of the different world regions to the conference are only approximate - people from developing countries may be currently living in developed countries (and vice versa). Similarily, results on participants workplaces are only an approximation - people may have several roles at any one time].
If, in the future, you use material from the conference for your decision-making or refer to it in articles or use it as reference material we would be happy to be know about it (at firstname.lastname@example.org). All the messages posted will remain on the Forum website for future reference, at http://www.fao.org/biotech/logs/c10logs.htm. As is standard practice with conferences in the Biotechnology Forum, we will prepare a Summary Document in the future to provide a summary of the main arguments and concerns discussed during the conference, based on the messages posted by the participants.
Finally, a very special and sincere thanks to all of the 52 individuals who submitted messages and who devoted their time and effort to this excellent exchange of views, insights and experiences about MAS in developing countries.John
John Ruane, PhD
FAO Working Group on Biotechnology,
Moderator, Conference 10
e-mail: biotech-mod2 (at) fao.org
FAO website http://www.fao.org
Forum website http://www.fao.org/biotech/forum.asp
FAO Biotechnology website http://www.fao.org/biotech/index.asp