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Moderated conference on Genomics in Food and Agriculture

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Biotech-Mod3 <[log in to unmask]>
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Date:
Thu, 14 Mar 2013 22:07:05 +0100
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This is Rajeev Varshney, working for two Consultative Group on International Agricultural Research (CGIAR) organizations, namely the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT, www.icrisat.org) and the Generation Challenge Programme (www.generationcp.org). 

I have been following very useful discussions and submissions from a large number of colleagues. I am very excited to see contributions from both young as well as senior colleagues. It is clear from ongoing discussions that genomics has an important role in crop, forestry, livestock, fishery and agro-industry sectors. While we have success stories not only in crops, but in other sectors as well, we all realize that the majority of genomics applications in breeding (referred to as genomics-assisted breeding) happened/are happening in either developed countries or in private sectors. 

Although success stories have started to come from developing countries, there are still challenges (as mentioned for instance by John Gibson in Message 17) for full realization of genomics-assisted breeding in developing countries. If we just talk about the crop sector in developing countries, quality phenotyping, infrastructure, expertise, cost on genotyping, availability of appropriate and breeders-friendly decision support tools amongst many others are still serious constraints. It is also important to mention here that genotyping (markers or sequencing based) work in developed countries and private sector is centralized or being availed through outsourcing, several colleagues in developing countries still feel that they should be able to undertake genomics-assisted breeding only if they are involved in generation of genotyping data. As sequencing and genotyping technologies are changing (evolving) continuously, I don't think that majority of national programmes in developing countries are ready to keep on buying/upgrading those machines. Economy of the scale is the other important factor when we do centralize genotyping/sequencing. 

The most important aspects where we need to emphasize/invest for enhancing adoption of genomics-assisted breeding in developing countries are: (a) improve infrastructure and expertise in field-based phenotyping, (b) decision support tools (e.g. Integrated Breeding Platform  https://www.integratedbreeding.net/ ), (c) improve expertise in making the use (instead of generation) of genotyping data, and (d) long-term investment (instead of project-based genomics-assisted breeding experiments). Some of these issues were discussed in an opinion piece published as an Open Access article we wrote in Nature Biotechnology in 2012 ('Can genomics boost productivity of orphan crops?', http://www.nature.com/nbt/journal/v30/n12/full/nbt.2440.html). 

In the last, coming to decision support tools especially in the case of genomic selection for calculating genomic-estimated breeding values (GEBVs), though we may not have the perfect tools/models, we should not just wait to have the perfect tools/programme for deploying genomic selection. Of course we need to continue to improve the tools/models. Challenges are always there, (being optimistic) one should avail the existing opportunities to tackle those challenges and continue to work towards enhancing genetic gain in crop/livestock/forestry/fishery improvement programmes.

Rajeev K. Varshney, PhD, FNAAS
Principal Scientist (Applied Genomics) &
Director, Centre of Excellence in Genomics, ICRISAT; 
Adjunct Professor (Plant Biology), University of Western Australia; and             
Theme Leader, CGIAR Generation Challenge Program 

Mailing Address: 
Centre of Excellence in Genomics (CEG), Building # 300
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)
Patancheru - 502 324, Greater Hyderabad, 
India 
Tel: 0091 40 30713305; Fax: 0091 40 3071 3074/ 3075
e-mail: varshney.raj (at) gmail.com

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