ARS | Publication request: Characterization of a core collection of rice germplasm and elite breeding lines in the US with genetic markers associated with cooking quality

Submitted to: Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: November 1, 2004
Publication Date: December 1, 2004
Citation: McClung, A.M., Chen, M., Bockelman, H.E., Bryant, R.J., Yan, W., Fjellstrom, R.G. 2004. Characterization of a core collection of rice germplasm and elite breeding lines in the US with genetic markers associated with cooking quality. Proceedings, 2nd International Rice Functional Genomics Conference, Tucson, Arizona. p. 127.

Technical Abstract: Rice molecular markers have been developed in the granule bound starch synthase gene (Waxy) that controls grain amylose content and the soluble starch synthase IIa (Alk) gene that controls alkali spreading value (ASV). Both of these factors are considered the major determinants of rice cooking quality and texture. This set of markers is now being routinely used by US breeding programs to expedite the development of improved rice cultivars that meet rice cooking quality standards as determined by the US rice industry. For the first time, these markers have been used to characterize a core subset of rice germplasm that is maintained by the USDA-ARS National Small Grains Collection. There are over 17,000 accessions in the rice NSGC collection with about 10 percent of the selections being represented in the core subset. This core of some 1600 accessions, derived from over 100 countries, were grown in Stuttgart, AR during 2002 for phenotypic and genotypic evaluation. Two single nucleotide polymorphism (SNP) markers associated with amylose content, one SNP marker associated with starch pasting properties, an intragenic microsatellite (RM 190) in the Waxy gene, and two SNP markers in the Alk gene, associated with ASV, were scored. Fourteen microsatellite alleles for RM 190 were identified; eight of which were rare, each being found in less than 5% of the accessions. SNP genotypes were highly correlated with amylose content and ASV phenotypic results. A combination of SNPs in Exon 1 and Exon 6 of Waxy clearly differentiated low (4-19%), intermediate (20-22%), and high (>22%) amylose classes. Eight percent of the core accessions were found to be heterogeneous for RM 190. These results demonstrate that molecular marker evaluation provides a valuable method for characterizing world germplasm that is not skewed by environmental error, reveals sample heterogeneity that may be obscured in phenotypic evaluation, and clearly identifies novel alleles within a continuous spectrum of phenotypes.