Submitted to: Plant and Animal Genome
Publication Type: Proceedings
Publication Acceptance Date: 12/15/2008
Publication Date: 1/10/2009
Citation: Agrama, H.A., Yan, W., Li, Y., Luo, D., Gao, F., Ren, G. 2009. Identifying molecular markers associated with stigma characteristics in rice. In: Proceedings of Plant and Animal Genome Conference XVII, January 10-14-2009, San Diego, CA. P238.
Technical Abstract: Stigma characteristics play essential roles in hybrid seed production of rice and marker-assisted breeding plays essential role because they are quantitatively inherited with single-flowered perfect spikelet. Ninety four accessions originated from 47 countries were selected from the USDA rice core collection after cluster analysis. Phenotyping for stigma exsertion and size and spikelet size was conducted in Sichuan, China and genotyping with 109 molecular markers in Arkansas, USA. Genetic diversity was analyzed by polymorphism information content and Rogers distance with PowerMarker. Association mapping was based on a mixed linear model through linkage disequilibrium with TASSEL, and population structure was analyzed using principal component analysis verified by optimal number of subpopulations identified by STRUCTURE. Marker-trait association was judged by false discovery rate <0.001 corrected from p-values. Markers associated with single, dual and total stigma exsertions were located on eight chromosomes. Two markers on chromosome 1 explained about than 30% of phenotypic variation for the dual stigma exertions. Four markers were associated with stigma size in accounting for 2.6 – 16.3% of variation, and five associated with spikelet size in accounting for 13.5 – 25.9% of variation.