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Moderated conference on Genomics in Food and Agriculture

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Biotech-Mod3 <[log in to unmask]>
Mon, 18 Mar 2013 14:45:56 +0100
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My name is Wayne Parrott, and I run a soybean genetics program at the University of Georgia, United States. To begin with, I want to thank the organizers of the conference.

Beatrix Tappeser (Message 24) gave a really great overview of the current state of genomic applications to breeding. Yet, although the use of marker assisted selection (MAS) is routine and widespread in a few crops, such as maize and soybean, the bottom line is that the technology is still in its infancy. I want to share my experience in soybean, and as well as where I see this technology going, because there is no reason why these developments cannot apply to other crops. Genomic breeding is evolving at an amazing speed. Furthermore, the cost of the technology is going down so rapidly, that I hope these techniques will be universally available to all crops within a decade- as long as appropriate research funding and training is in place.

MAS technology in soybean has evolved from restriction fragment length polymorphisms (RFLPs) to simple sequence repeat (SSRs) and now to single nucleotide polymorphisms (SNPs) and chips, with a greater abundance of markers and greater levels of automation at each step. We have several soybean genomes sequenced now, and their availability has made it possible to identify millions of SNP markers. In addition, 50,000 of these markers - spread every 16 centiMorgan or so apart in the genome, have been placed on a chip, making it possible to monitor the entire genome during the breeding process!

The use of recombinant inbred lines, combined with a genomic sequence, is making it possible to clone both classical monogenic traits and an ever-increasing number of quantitative trait loci (QTLs). Once the genes are identified, it is possible to develop allele-specific markers for each gene/QTL. Whereas before we had to monitor markers flanking the gene or QTL of interest, now we are starting to be able to track the gene itself. I envision that soybean DNA chips of future will be designed with allele-specific SNPs, rather than evenly spaced markers. [Recombinant inbred lines are formed by crossing two inbred strains followed by repeated selfing or sibling mating to create a new inbred line whose genome is a mosaic of the parental genomes (from K.W. Broman. 2005. The genomes of recombinant inbred lines. Genetics, 169, 1133-1146, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449115/ ...Moderator].

What does all this mean? It means that:

- Breeders can monitor multiple traits during a breeding program
- Any gene can be backcrossed in just 3 generations
- Traits with the same phenotype (e.g. disease resistance) can be stacked together
- Phenotyping for several traits can be omitted during the intermediate breeding stages
- Traits from unadapted germplasms can be deployed effectively without linkage drag

The same genomic tools that are contributing to breeding efficiency are also giving greater insights into the plant genome. Accordingly, I no longer agree with the statement in Message 24 that "in genetically uniform populations, evolutionary changes which are the basis of biodiversity development and maintenance are impossible". For example, see Rasmussen and Phillips (1997) and Fasoula and Boerma (2007). A review of the various sources of genomic variability in otherwise uniform crops can be found in Weber et al (2012).

For that matter, I do not really view genetic uniformity in any given field as a problem. First, modern cultivars are not analogous to growing a landrace across a wide area - they have a broad genetic base, with traits incorporated from dozens of parents. Secondly, the most useful place for diversity is between fields - soybeans adapted for my region don't do well in other regions. Thus, having different genetically distinct varieties for different regions ensures diversity is deployed where it does the most good. Finally, there is still a tremendous amount of diversity in old varieties, landraces, and feral relatives that has yet to be used in breeding. With genomic tools, it is becoming possible to identify this diversity and breed it into new varieties, thus increasing their genetic base and increasing the diversity between fields.

The topic of GM crops has come up in Messages 24 and 33. Although I view GMOs and genomic breeding as two different things, I agree with Message 24 that there will always be traits that MAS cannot achieve, and therefore must be moved in from other sources. Furthermore, the two approaches are complementary. Probably over 99.99% of breeding effort will be conventional, and it is conventional breeding that is used to move transgenes into dozens if not hundreds of different varieties. Ultimately, the most durable and stable quality and resistance traits are probably best achieved by stacking native genes with transgenes. Time will tell.

Finally, as DNA chips and computers play greater roles in the breeding process, the human element is irreplaceable. As has been pointed out before in this conference, traits still need to be linked to genes. And, most importantly, only a human can evaluate a cultivar's intended use and determine which are the important traits to breed for in that cultivar.

Wayne Parrott
Department of Crop and Soil Sciences,
University of Georgia,
Athens, GA 30602
United States
wparrott (at) uga.edu

References
- Fasoula, V.A. and H.R. Boerma. 2007. Intra-cultivar variation for seed weight and other agronomic traits within three elite soybean cultivars. Crop Science, 47: 367-373.  
- Rasmussen, D.C. and R.L. Phillips. 1997. Plant breeding progress and genetic diversity from de novo variation and elevated epistasis. Crop Science 37: 303-310. 
- Weber N, Halpin C, Hannah LC, Jez JM, Kough J, Parrott W. 2012. Editor's choice: Crop genome plasticity and its relevance to food and feed safety of genetically engineered breeding stacks. Plant Physiol., 160: 1842-53.

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