Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 1/1/2009
Publication Date: 1/12/2009
Citation: Agrama, H.A., Yan, W., Li, Y., Luo, D., Gao, F., Lu, X., Ren, G. 2009. Associating mapping of stigma characteristics using the USDA rice core collection. Plant and Animal Genome.
Technical Abstract: A mini-core from the USDA rice core collection was phenotyped for nine traits of stigma and spikelet and genotyped with 109 DNA markers. Marker-trait association mapping was used to identify the regions associated with the nine traits. Resulting associations were adjusted using false discovery rate (FDR) technique. We identified 34 marker-trait associations involving 22 SSR markers for eight of these traits. Four markers were associated with single stigma exsertion (SStgE), six with dual exsertion (DStgE) and five with total exsertion. RM5_Chr1 played major role and explained 35% of phenotypic variation for DStgE and 17% for SStgE. Four markers were associated with spikelet length, three with width and seven with L/W ratio. Numerous markers were co-associated with multiple traits that were phenotypically correlated, i.e. RM12521_Chr2 associated with all three correlated spikelet traits. These correspondences between trait-trait correlation and trait-marker association confirmed the associations.