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Association mapping of yield and its components in rice 2007.pdf

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Association mapping of yield and its components in rice 2007

Association mapping of yield and its components in rice cultivars H. A. Agrama ? G. C. Eizenga ? W. Yan Received: 23 April 2006 / Accepted: 29 October 2006 / Published online: 11 February 2007 Springer Science+Business Media B.V. 2007 Abstract To make advances in rice breeding it is important to understand the relatedness and ancestry of introduced rice accessions, and iden- tify SSR markers associated with agronomically important phenotypic traits, for example yield. Ninety-two rice germplasm accessions recently introduced from seven geographic regions of Africa, Asia, and Latin America, and eleven US cultivars, included as checks, were evaluated for yield and kernel characteristics, and genotyped with 123 SSR markers. The SSR markers were highly polymorphic across all accessions. Popu- lation structure analysis identified eight main clusters for the accessions which corresponded to the major geographic regions, indicating agree- ment between genetic and predefined popula- tions. Linkage disequilibrium (LD) patterns and distributions are of fundamental importance for genome-wide mapping association. LD between linked markers decreased with distance and with a substantial drop in LD decay values between 20 and 30 cM, suggesting it should be possible to achieve resolution down to the 25 cM level. For the 103 cultivars, the complex traits yield, kernel width, kernel length, kernel width/length ratio, and 1000-kernel weight, were estimated by analysis of variety trial data. The mixed linear model method was used to disclose marker-trait associations. Many of the associated markers were located in regions where QTL had previ- ously been identified. In conclusion, association mapping in rice is a viable alternative to QTL mapping based on crosses between different lines. Keywords Linkage disequilibrium Unified mixed-model method Population structure Kinship coefficient Relatedness Abbreviations SSR Simple sequence repeat QTL Quantitative trait loci cM CentiMorg