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Moderated conference on Genomics in Food and Agriculture

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Biotech-Mod3 <[log in to unmask]>
Mon, 4 Mar 2013 16:14:58 +0100
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[Thanks to Professor PK Gupta from India for sending in the first message of this FAO e-mail conference on the "Impacts of genomics and other 'omics' for the crop, forestry, livestock, fishery and agro-industry sectors in developing countries". All messages will be numbered chronologically. If during the conference you notice that you are missing any messages, just contact me at [log in to unmask] ...Moderator].

I am Pushpendra Kumar Gupta, Emeritus Professor, Department of Genetics & Plant Breeding, CCS University, Meerut, India. At Meerut, as a group, we have been involved in crop biotechnology research for more than 20 years now. More particularly, we have been involved in the development and use of molecular markers in wheat (a cereal) and jute (a fibre crop). We have also been involved in QTL interval mapping and association studies in wheat and jute, followed by use of marker-trait associations for marker-assisted selection (MAS) for wheat breeding.

During the last 10 years, I have come across the phrase "genomics-based crop improvement", which I have not been able to appreciate, since genomics research has not been directly used (and will not be used in future) for crop improvement, although it is relevant to crop improvement programs, since it helps us in the discovery of genes and markers, which are subsequently used for crop improvement either through the development of transgenics or using MAS. Genome sequences or transcriptomes, proteomes or metabolomes cannot be directly used for crop improvement programs, although this information may indirectly prove useful for crop improvement. Therefore, I don't see any direct impact of genomics and other 'omics' research on crop improvement in developing countries. Under these circumstances, in this conference, we need to discuss if there are examples of an indirect impact of genomics and other 'omics' research on crop improvement. The participants should enumerate examples, if any, where this research had a direct impact. If not, we should discuss indirect impact through development of markers and discovery of genes. There are also hardly any examples where genomics or other 'omics' disciplines were first used for development and use of markers or for the discovery of genes, which later led to the development of improved cultivars, which can be traced back to genomics or other 'omics' research. If there are examples, I would myself like to be educated.

Under the above circumstances, we should give-up using the phrase "genomics-based crop improvement" (which is misleading), because crop improvement programs make use of markers, rather than genome or transcriptome sequences. These genomics and other 'omics' research areas generate knowledge and resources, which can then be used to develop resources that are directly used for crop improvement programs.

Notwithstanding the above, 'whole genome resequencing' (WGS) has been used for quantitative trait locus (QTL) interval mapping and association mapping studies, leading to identification of single nucleotide polymorphisms (SNPs), which may prove useful for crop improvement, but there are no examples where this has actually been achieved successfully. Perhaps only in future this may be done successfully. In our own laboratory, we are trying to identify wheat orthologues using available genes and sequences for traits like nitrogen/phosphorus use efficiency (NUE & PUE) and water-use efficiency (WUE), and then design polymerase chain reaction (PCR) primers for these orthologues to be used for study of polymorphism in the available wheat germplasm. This will perhaps give us markers to be used for crop improvement programs. This will be the future area of research, where genome sequences will be used for crop improvement. Also expressed sequence tag (EST) databases have already been extensively used for development of simple sequence repeat (SSR) and SNP markers in a number of crops, but this is also an indirect use of transcriptome data for crop improvement.

I would like the above issues to be addressed in this e-conference.

Professor PK Gupta
Hon. Emeritus Professor & NASI Senior Scientist
Meerut University, Meerut, 
India
Residence: F-119, Shastri Nagar, Meerut 250004
Telephone: 121-2762505 (R); 121-2768195 (Office); 9411619105 (M)
Web: http://molbiolabccsumrt.webs.com/founder.htm
e-mail: pkgupta36 (at) gmail.com

[Orthologues, mentioned above, are genes derived from a common ancestor through vertical descent (or speciation) and can be thought of as the direct evolutionary counterpart. In contrast, paralogues are genes within the same genome that have evolved by duplication. (Source: Ensembl glossary (http://useast.ensembl.org/info/website/glossary.html) ...Moderator].

[To contribute to this conference, send your message to [log in to unmask] For further information on this FAO Biotechnology Forum, see http://www.fao.org/biotech/biotech-forum/ ]

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