ARS | Publication request: What about the phenome?

Submitted to: International Symposium of Molecular Breeding of Forage Turf
Publication Type: Abstract Only
Publication Acceptance Date: January 15, 2010
Publication Date: March 15, 2010
Citation: Brummer, C., Casler, M.D. 2010. What about the phenome [abstract]?. International Symposium of Molecular Breeding of Forage Turf. p.15.

Technical Abstract: Scientific investigations of the genome, proteome, and metabolome have contributed to our understanding of the genetic basis of traits. But the key to all of these technologies being applied to plant breeding is an effective understanding of the phenome – the constellation of phenotypes a particular genotype can produce across a suite of target environments. The phenotype is ultimately all that matters to plant breeders; while interesting, the underlying genome is only relevant inasmuch as we can manipulate it to produce the phenotype we desire. We consider how further understanding of the phenome will impact our ability to use genomics technologies, especially genetic markers and mapping, in breeding programs. Using markers for selection requires accurate phenotyping; without robust phenotypic assays, genomics can do little to improve genetic gain. The genomics era has emphasized the Cartesian concept of nature as machine – by tinkering with individual genes or quantitative trait loci (QTL), we can build the optimal plant from first principles. This thinking has led to a renewed emphasis on ideotypes composed of genes found by deconstructing complex phenotypes into easily assayed components. The ideotype concept has limitations because the parts never act alone and because population sizes rapidly escalate as the number of desired components increases. Recent advances in genome-wide selection (GWS) take the whole-plant, systems biology view. Instead of focusing on individual component traits and the QTL that control them, GWS simply uses markers to assess breeding values of individuals, and selections are made on the basis of aggregate breeding value, similar to traditional selection methods. Integrating GWS into forage breeding programs faces some apparent hurdles, centered on marker numbers and population sizes. But with genotyping costs decreasing, GWS appears to be the best opportunity for accelerating genetic gain for complex traits. We discuss possible methods to capitalize on this opportunity.