Title: Transformation of the approach to breeding using genomics: Vison of USDA-ARS Authors
Submitted to: Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: June 15, 2009
Publication Date: August 11, 2009
Citation: Mcclung, A.M. 2009. Transformation of the approach to breeding using genomics: Vison of USDA-ARS. In: VIth Congresso Brasileiro de Arroz Irrigado, Porto Alegre, RS - Brasil, August 11-14, 2009. pp. 580-583. Technical Abstract: Traditional rice breeding methods have proven to be very successful with significant improvements in yield, grain quality, and resistances to biotic and abiotic stresses being seen in new cultivar releases every year. Research conducted by USDA ARS scientists at Stuttgart, Arkansas and Beaumont, Texas along with numerous university collaborators has focused on the use of basic genomic technologies to address applied aspects of rice breeding. Our initial approach was to develop genetic markers for simply inherited traits that were of economic importance to most breeding programs, traits that were labor intensive to determine, phenotyping methods that were not robust, relatively large amounts of seed were required for evaluation, or, for grain quality traits, could not be measured until after harvest. This research led to the successful development of genetic markers that are linked with grain amylose content, starch gelatinization temperature, grain aroma, starch pasting properties, and major blast resistance genes. Expanding genetic markers to traits that are quantitatively inherited is an on-going endeavor. An example of recent success comes from a multi-institution research project funded by the USDA CSREES National Research Initiative, “RiceCAP”, which identified a major QTL on chromosome 9 which explains over 20% of the variation in sheath blight disease resistance. However, our progress on developing markers linked with milling quality has been slower. Having efficient and repeatable phenotyping methods is one of the major bottlenecks for extending marker assisted selection to both simply and complexly inherited traits. In addition to using mapping populations to identify QTL, we have been successful in using a core collection of the USDA rice collection of over 18,000 rice accessions in association mapping studies. Putative regions on chromosomes 5 and 12 have been associated with the physiological disorder called straighthead. The core collection has recently been screened for ability to germinate under cold temperatures then will be used for association analysis. Although there is a wealth of genetic diversity within the world collection of Oryza sativa accessions, researchers are also pursuing the use of wild relatives of rice for gene discovery and cultivar improvement. In research conducted in collaboration with Susan McCouch’s lab at Cornell University, we have been successful in identifying chromosomal regions from O. rufipogon that are associated with enhanced yield potential. Recent work has suggested that wild species of rice may offer opportunities for improving rice cultivars to respond to increasing CO2 levels as a result of climate change. Having access to genomic information will facilitate the use of such unadapted germplasm to incorporate targeted introgressions from wild species into new cultivars. The US rice breeding community has embraced the use of microsatellite markers to assist in the development of improved cultivars. As a next step, the US rice research community is supporting the development of SNP technology for use in breeding. In addition, over one dozen key US cultivars are being completely sequenced in an effort to identify SNP markers in germplasm that is fundamental to all US breeding programs. It is hoped that this will lead to continued genomic discoveries within the elite genepool that US geneticists have been refining during the last century of rice breeding.