J Integr Plant Biol. ›› 2009, Vol. 51 ›› Issue (12): 1126-1137.DOI: 10.1111/j.1744-7909.2009.00883.x

• Molecular Physiology • Previous Articles     Next Articles

Association Analysis of the Amino Acid Contents in Rice

Weiguo Zhao1,2,3, Eun-Jin Park1, Jong-Wook Chung3, Yong-Jin Park3*, Ill-Min Chung1, Joung-Kuk Ahn1 and Gwang-Ho Kim1   

  1. 1Department of Applied Bioscience, Konkuk University, Seoul 143-701, Korea
    2Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Jiangsu University of Science and Technology, Zhenjiang 212018, China
    3Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 340-802, Korea
  • Received:2009-06-15 Accepted:2009-09-05 Published:2009-12-01
  • About author:
    *Author for correspondence Tel: +82 41 330 1201; Fax: +82 41 330 1209; E-mail: yjpark@kongju.ac.kr


The main objective of the present study was to identify simple sequence repeat (SSR) markers associated with the amino acid content of rice (Oryza sativa L.). SSR markers were selected by prescreening for the relationship to amino acid content. Eighty-four rice landrace accessions from Korea were evaluated for 16 kinds of amino acids in brown rice and genotyped with 25 SSR markers. Analysis of population structure revealed four subgroups in the population. Linkage disequilibrium (LD) patterns and distributions are of fundamental importance for genome-wide mapping associations. The mean r2 value for all intrachromosomal loci pairs was 0.033. LD between linked markers decreased with distance. Marker–trait associations were investigated using the unified mixed-model approach, considering both population structure (Q) and kinship (K). A total of 42 marker-trait associations with amino acids (P < 0.05) were identified using 15 different SSR markers covering three chromosomes and explaining more than 40% of the total variation. These results suggest that association analysis in rice is a viable alternative to quantitative trait loci mapping and should help rice breeders develop strategies for improving rice quality.

Zhao W, Park EJ, Chung JW, Park YJ, Chung IM, Ahn JK, Kim GH (2009). Association analysis of the amino acid contents in rice. J. Integr. Plant Biol. 51(12), 1126–1137.

Key words: Amino acid content, Association mapping, Linkage disequilibrium (LD), Population structure, Simple sequence repeats (SSRs).

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