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Moderated conference on Genomics in Food and Agriculture

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Date:
Fri, 22 Mar 2013 15:57:06 +0100
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Let me introduce myself: my name is Michel Naves, from the french Institut National de la Recherche Agronomique (INRA) and I work in animal breeding and genetics of local animal breeds in French West Indies. I am really greatly interested by this conference as I am involved in a research program on the improvement and management of the local tropical breeds, mainly on Creole cattle. Other colleagues in my team work on small ruminants and pigs. In our work, we tackle the use of genomic tools (and other -omics), for i) the identification and quantification of variability within/between breeds, ii) the link with production and adaptation traits, and iii) the mechanisms involved in adaptation.

Since very few messages concern livestock this week, I wanted to follow up the discussion on the special issues of genomics for livestock in tropical countries.

Concerning livestock, great efforts and very effective results have been obtained in dairy cattle in developed countries, and these examples raised enthusiastic hopes of a "revolution" in genetic improvement in all species and breeds, especially in tropical countries (for example, see Message 10). 

Indeed, genomic selection improved the efficacy of selection in dairy cattle, in northern taurine breeds, in various points of view: time and money spent, accuracy of estimated breeding value (EBV), conservation of genetic variability,...  But I think we have to pay great attention to the conditions that made this progress possible: existence of great economic interest in the milk industry and dairy cattle genetics, strong and accurate record keeping systems, large pedigree information, dense markers available across the whole genome,... And very strong limitations have also arisen, especially for the application of genomics tools for genetic evaluation, across breed, in multibreed or in crossbreeding.

I really doubt the same conditions that contribute to the development of genomic selection in dairy cattle could be easily found in developing countries. Several messages (19, 22, 23 for instance) pointed out this effective and dramatic "bottleneck" for genetic improvement of livestock in developing countries. Does that mean that we cannot afford the use of genomic tools in livestock breeding in tropical countries? I don't think so, but special organisational, methodological, and technological issues should be addressed in order to fill this gap and make possible the same transition in tropical livestock, as pointed out by John Gibson (Message 17). 

In another way, generalisation of such methodology is not trivial: the technology is one thing that is easy to manage (however with a cost still unaffordable for developing country scientists)  but conditions of its application have to be considered with special attention. For example, SNP chips available in cattle at the moment (9K, 54K or 777K) have a very bad coverage in tropical breeds, with about 50-60% of informative SNP in african taurine or zebu, in comparison to the 80% of informative SNP in european taurine. Next generation sequencing (NGS) technology would allow the identification of new polymorphisms in tropical breeds, and the evaluation of the variability available between breeds, but efforts in this domain are still weak however. 

In tropical countries, reproductive, adaptation and resistance traits play a major role in livestock systems. Such traits are difficult to address (particularly resistance to infectious disease or drought, as an example), and may have a complex determinism (for example, tens of quantitative trait loci (QTL) for tick resistance have been cited in the literature). Genomic tools may help for their improvement, but results in this field are not yet very convincing. One difficulty is to how to identify the relationship of these traits with genetic markers, when phenotypes are not well defined, measurement is not easy, and reference population are lacking? Also the genetic background of these traits may also vary according to the breed. For example, the same SNP in the HSP70 gene is linked to higher fertility in Brahman (Rosenkrans et al, 2010), and to lower embryo heat tolerance in Holstein (Basirico et al, 2011), and I guess other examples may be found. 

As far as the technology is applied with tremendous results in great dairy taurine breeds, and large breeding or technological private companies are engaged in large programs, the impact of genomic tools and especially genomic selection in local breeds, farming systems and societies in developing countries may be dramatic if not controlled by public policies, driven with common interest in mind, and advocated by highlighted advice. In particular, I am not sure we have really a good appraisal of the consequences on local genetic resources, which have a great patrimonial value. This will probably be the challenge for future research in this field, and for livestock improvement of tropical breeds.

At the present time, a lot of private efforts are developed in the market of "-omics" technology, with clear economic private interest (Message 15 gave such example in Brazil), but very sparce efforts are made in a public domain, in a "global thinking approach" as deemed by David Steane (Message 8). Some recent messages (42 and 48) call for more partnership and exchange of information on these issues and I agree with these statements, which are very important to answer such a goal for benefits of the whole human community. 

Michel Naves
Ingénieur de Recherches/Researcher
Unité de Recherches Zootechniques
INRA Antilles-Guyane 
Domaine Duclos 97170 Petit-Bourg 
Guadeloupe
Tèl. : 0590 25 59 31 
Mobile : 0690 56 52 55  
Fax : 0590 25 59 36  
www.antilles.inra.fr
transfaire.antilles.inra.fr
e-mail; michel.naves (at) antilles.inra.fr 

References:
- Basirico L, Morera P, Primi V, Lacetera N, Nardone A, Bernabucci U. 2011. Cellular thermotolerance is associated with heat shock protein 70.1 genetic polymorphisms in Holstein lactating cows. Cell stress & chaperones 16:441-448
- Rosenkrans C, Jr., Banks A, Reiter S, Looper M. 2010. Calving traits of crossbred Brahman cows are associated with Heat Shock Protein 70 genetic polymorphisms. Anim Reprod Sci 119:178-182.

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