Association mapping of yield and its components in rice cultivars

Authors: AGRAMA, HESHAM - UNIV. OF AR RREC; Eizenga, Georgia; Yan, Wengui

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/29/2006
Publication Date: 2/11/2007
Citation: Agrama, H.A., Eizenga, G.C., Yan, W. 2007. Association mapping of yield and its components in rice cultivars. Molecular Breeding 19:341-356.

Interpretive Summary: Plant breeders often use cultivars and breeding lines, called accessions, obtained from other countries to incorporate desirable genes for pest resistance, stress tolerance and yield enhancing characteristics into cultivars under development. This is especially true for U.S. rice breeding programs where several new genes for disease resistance and grain quality have been incorporated from rice accessions obtained outside the U.S. Using mathematical methods originally developed to understand human diseases, it is now possible to identify potentially useful genes associated with pest resistance, stress tolerance and yield by characterizing the relationship between DNA markers and the trait of interest with a diverse set of rice accessions. This method was illustrated in the present study with a diverse set of 92 blast resistant rice accessions from seven different geographic regions in Africa, Asia and Latin America, and eleven U.S. cultivars that were characterized with DNA markers and evaluated for yield and yield related characteristics. Analysis of the DNA marker data indicated these accessions came from seven different backgrounds and could be put into eight different groups based on how the accessions were related to each other. Also identified were DNA markers associated with yield and/or yield related characteristics in the same chromosome regions identified in earlier studies of rice. The method illustrated in this study is quicker and more cost effective than the methods presently being used to identify DNA markers associated with important agronomic traits. Information on the background and relatedness of the accessions will be extremely helpful for U.S. rice breeders deciding which accessions to use for improving yield in new cultivars currently under development. Ultimately, these new cultivars will benefit the U.S. rice industry.

Technical Abstract: 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 like yield. Ninety-two rice germplasm accessions recently introduced from seven geographic regions located in Africa, Asia and Latin America, and eleven U.S. 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 considerable drop in LD decay values between 20 and 30 cM, suggesting that 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 from the 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 previously were identified. In conclusion, association mapping in rice is a viable alternative to QTL mapping based on crosses between diverse lines.