Molecular Breeding

, Volume 19, Issue 4, pp 341–356 | Cite as

Association mapping of yield and its components in rice cultivars

  • H. A. AgramaEmail author
  • G. C. Eizenga
  • W. Yan
Original Paper


To make advances in rice breeding it is important to understand the relatedness and ancestry of introduced rice accessions, and identify 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. Population structure analysis identified eight main clusters for the accessions which corresponded to the major geographic regions, indicating agreement between genetic and predefined populations. 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 previously been identified. In conclusion, association mapping in rice is a viable alternative to QTL mapping based on crosses between different lines.


Linkage disequilibrium Unified mixed-model method Population structure Kinship coefficient Relatedness 



Simple sequence repeat


Quantitative trait loci





The authors acknowledge the support of H. Raeann Refeld and Dr Hesham A. Agrama from the Arkansas Rice Research and Promotion Board. Technical contributions to this research were made by H. Raeann Refeld and Quynh P. Ho. Contributions of Melissa H. Jia, Gordon H. Miller and the late Mark A. Redus of the DB NRRC Genomics Core Facility also are acknowledged.


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Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  1. 1.University of Arkansas Rice Research and Extension CenterStuttgartUSA
  2. 2.United States Department of Agriculture – Agricultural Research ServiceDale Bumpers National Rice Research CenterStuttgartUSA

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