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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)