ARS | Publication request: Using association genetics to study rice end-use quality

Submitted to: American Association of Cereal Chemists Meetings
Publication Type: Abstract Only
Publication Acceptance Date: September 1, 2007
Publication Date: October 7, 2007
Citation: Bergman, C.J., Fjellstrom, R.G., Chen, M.H. 2007. Using association genetics to study rice end-use quality. [abstract] American Association of Cereal Chemists, October 7-10, 2007, San Antonio, TX. Paper 52:A16.

Technical Abstract: Most crop end-use quality characteristics are complex traits under multi-gene control. Improvement of such traits is challenging due to the reliance on time consuming phenotyping methods and data that is confounded by environmental effects. Marker assisted methods lessen the challenges of breeding by providing data for selection purposes that are not influenced by the environment. Historically, genetic markers have been identified by first creating a progeny population segregating for the trait of interest. The population is phenotyped, scored for genetic markers placed throughout the genome, and associations between the two are identified by mapping the proportions of phenotypic variation explained by the markers. The power of this method, known as quantitative trait loci analysis, is limited due to the multiple years required for population development and the restricted number of genetic recombinations that are typically present in mapping populations. Association genetic analyses can overcome these constraints by using germplasm that is unrelated and contains a high degree of phenotypic variation, and which normally has more genetic recombinations between markers and traits compared to mapping populations. Thus, lengthy population development is avoided. A mapping type approach can be performed by genotyping markers across the genome for each accession and then identifying associations between markers and the trait of interest. Also, mutations in candidate genes can be identified, genotyping of the accessions performed and associations between the mutations and phenotypes evaluated. Both approaches have been used to a limited degree to identify genetic markers associated with end-use quality traits of cereal grains. This presentation will focus on the use of the candidate gene approach to association genetics as related to several rice starch traits.