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Moderated conference on Genomics in Food and Agriculture

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This is Uche Godfrey Okeke again.

I strongly agree with Humberto Peralta's opinion (Message 27) on viewing agriculture as a complex system. Microbes, especially fungi and bacteria, are having profound interactions with especially the plant roots for different purposes including nutrient exchange, nutrient recycling and transfer, reduction of elements into that which can be utilized by plants, warding off pathogenic organisms, forming complex matrices for structural adaptation, aiding in plant signal transduction for adaptation in their environment and so much more. 

Previously, a lot of these interactions have been skipped by breeders. It occurs to me that these elements may contribute to the Gene-by-environment (GXE) interaction that we notice in plant breeding especially. However these interactions are not easy to measure especially if they are to be included in selection indices.

Interestingly, metagenomics offers an approach to view crop production and plant-microbe interactions systematically. The next generation sequencing technologies, especially the combination of PacBio and Illumina platforms, offer an opportunity for in-depth whole metagenome sequencing allowing for a deep view of the entire microbial community interacting with a crop in the rhizosphere. [The rhizosphere is the soil region in the immediate vicinity of growing plant roots...Moderator].

However as breeders, clear phenotypes is the prime interest. This has led to the concept of the microbial core (describing the taxa of organisms that occur frequently in many sequenced samples especially in the human and animal microbiomes). Most studies aiming for reduced greenhouse gases (GHG) emissions in the bovine rumen are trying to see a common microbial core implicated in less GHG emission genotypes so as to devise simpler indicators for measurement. If we imagine how complex the microbial community in the rumen is, then how complex will the rhizosphere be?

Although there is a huge challenge in trying to harmonize metagenomics experiments and especially in using them as phenotypes for breeding, I believe that this is a learning phase and things will unfold sooner or later. I am convinced that agriculture is more complex than we thought but am very optimistic especially for the applications genomics is offering. Old knowledge and new tools will be tested and as time goes by, we will understand more and more what genomics is offering us. I am very hopeful that with the genomic selection technology, different traits that have been previously neglected or under-utilized will surface again and usher in novel agricultural products that we have been sitting on for a long period of time.

In conclusion, I will strongly agree with Dr. V.M. Okoro (Message 26) that strong mutualistic collaborations are needed not just for genomic selection in the developing world, but also for same in the developed world. We are increasingly seeing that we are more linked to each other than we thought. A great pool of genotypic and phenotypic data will be needed for genetic improvement (via genomics) of different plant and livestock species existing today.

Uche Godfrey Okeke.
DNA sequencing & Genomics Lab
Institute of Biotech
University of Helsinki, 
Finland
Skype: urchgene
Email: urchgene (at) gmail.com , urchgene (at) yahoo.com

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