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Note, participants are assumed to be speaking on their own behalf, unless they state otherwise.]

-----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 & 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 biotechnology projects by various national agencies in various universities and government institutions in India, in addition to massive funding by the international agencies that has flowed in with which the laboratory facilities have been created in many centers, the observation by Kevin Williams (Message 37, November 25) that MAS is not expensive may hold true. But, perhaps, difficulties in supporting and implementing result-oriented well-conceived projects might come in the way of realizing the benefits. Kevin Williams has also pointed out the fact that MAS has the potential to increase the rate of genetic gain when used in conjunction with traditional breeding. Certainly, this might explain the small success story that has been achieved by us at the Central Rice Research Institute (CRRI) (Message 35, November 24) utilizing the major opportunity of international collaboration.

Some difficulties in getting the MAS products successfully have been expressed by some of the participants. I would like to draw attention to the following steps drawn up by Dr. John Bennett, Senior Molecular Biologist of the International Rice Research Institute, for successful implementation of a MAS programme in rice. This may hold good for other crops as well.

Finally, to sum up, project formulation with clear objectives, constitution of the research team, international collaboration with the International Rice Research Institute, setting up the laboratory facilities and selection of materials, and implementation of the programme explains how the success described in Message 35 (November 24) was achieved by us at CRRI, India.

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,
India
URL: http://personal.vsnl.com/rangasri/
rangsridhar (at) yahoo.com

-----Original Message-----
From: Biotech-Mod2
Sent: 27 November 2003 11:46
To: 'biotech-room2@mailserv.fao.org'
Subject: 49: Applying MAS in indigenous tropical African tree species

This is from Alice Muchugi, Kenya. I am a PhD candidate at Kenyatta University, Kenya, and a research fellow at the World Agroforestry Centre (ICRAF). I am interested in the application of molecular markers in the conservation of indigenous tropical African tree species.

I agree with the sentiments voiced by several participants on the economics and successful utilization of the MAS technique in the development of new crop varieties or breeding material. However, I feel that as voiced by several participants too, MAS is still a best placed technique in selection and upgrading of planting material, especially for the tropical tree species where first fruiting may be as long as 20 years. So far, in Kenya, molecular markers have been employed to guide conservation and utilisation strategies of important tree species such as Mellia volkensii, Molinga oleifera, Prunus africana, Sesbania sesban, Sclerocarya birrea, Vitex keniensis, among others. However, the question of neutral markers as revealed in RAPDs, which have been widely used in these studies, makes the selection questionable as far as traits of interest (such as medicinal components and growth rate) are concerned. We therefore look forward to collaborative research with you researchers out there in the use of MAS to improve the selection efficiency in breeding programs of indigenous species where little of the genomes are known but store great wealth. This is especially important for the medicinal species, which have gained a lot of popularity in the last ten years.

Alice Muchugi
PhD Research Fellow,
Germplasm Resource Unit
World Agroforestry Centre
United Nations Avenue
PO Box 30677-00100
Nairobi,
Kenya
Email: a.muchugi (at) cgiar.org
Tel: +254-20-524000 ext 4273
Fax: +254-20-524001
http://www.worldagroforestrycentre.org

-----Original Message-----
From: Biotech-Mod2
Sent: 27 November 2003 15:02
To: 'biotech-room2@mailserv.fao.org'
Subject: 50: Pedigree - Linkage disequilibrium

I am Miguel Toro from Spain.

1) As pointed out by several people, molecular markers can be useful in breeding besides MAS. One of them is as a tool to implement classical genetic improvement programmes. In some fields, mainly tree and fish breeding, one of the problems in doing Best Linear Unbiased Preduction (BLUP) evaluations and for controlling inbreeding is the lack of pedigree information. Then, an alternative could be to construct the pedigree using molecular markers.

In fish, for example, 4-6 microsatellites will be enough to allow paternity assignment with high precision. Then, at the moment of evaluation (when the fish is weighed) we can take a small portion of the tail and use markers to assign it to the father and the mother. In trees, I supect, there are situations where we cannot distinguish between full- and half-sibs. With molecular markers we can solve the problem and, as a consequence, improve BLUP evaluations.

Are there practical breeding programmes, either in fish or trees, that are using molecular markers just to reconstruct or improve the pedigree information and, as a consequence, to improve genetic evaluations?

2) I think that we use the term MAS to refer to two types of actions. One of them (that some people call GAS, gene-assisted selection) is to use markers to locate genes of interest (QTLs), usually from some experimental design (F1, backcross, etc). Once we have found a gene of interest, we go to the commercial population and we try to use this information either by introgression or by selection of the desired allele, etc.

The other course of action, that I consider MAS in a strict sense, is to use markers as a source of information, in the framework of selection index theory. This was, I believe, the idea underlying the seminal paper of Lande and Thompson. In that case, the usefullness of a marker depends on the linkage disequilibrium of the marker with the polygenes that control the productive trait. For example, a marker could be informative if it presents such disequilibrium even if it is located on another chromosome.

Although the first approach seems to be more atractive, it has some drawbacks. The main one is that to go from the marker to the causal gene could be very hard work (or not, it depends mainly on luck). However, the second approach always works and it is amenable to a cost-benefit analysis. Furthermore, as marker genotyping will get more cheap and robotizable, it could be the more practical way of doing MAS for economically important traits.

Miguel Angel Toro Ibanez
Departamento de Mejora Genetica Animal
Instituto Nacional de Investigacion y Tecnologia Agraria y Agroalimentaria (INIA)
Carretera La Coruna km. 7
28040 Madrid
Spain
Telf: 34 913476807
Fax: 34 913572293
e-mail: toro (at) inia.es

[The paper referred to is R. Lande and R. Thompson, 1990. Efficiency of Marker-Assisted Selection in the Improvement of Quantitative Traits. Genetics 124, 743-756, available free at http://www.genetics.org/cgi/reprint/124/3/743.pdf. Their approach is based on linkage disequilibrium (LD, i.e. statistical associations between alleles at the marker loci and quantitative trait loci (QTLs)), where selection across the whole population is possible. With the availability of large numbers of DNA markers, LD between QTLs and closely linked markers can be detected, even in outbreeding populations. This LD is, however, eroded over time by recombination. They suggest that the most potent mechanism for generating LD is occasional hybridisation between genetically differentiated lines...Moderator].