Association Analysis of the Amino Acid Contents in Rice

doi:10.1111/j.1744-7909.2009.00883.x

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 Zhao^1,2,3, Eun-Jin Park¹, Jong-Wook Chung³, Yong-Jin Park^3*, Ill-Min Chung¹, Joung-Kuk Ahn¹ and Gwang-Ho Kim¹

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

Abstract

Abstract:

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).

Weiguo Zhao, Eun-Jin Park, Jong-Wook Chung, Yong-Jin Park, Ill-Min Chung, Joung-Kuk Ahn, and Gwang-Ho Kim. Association Analysis of the Amino Acid Contents in Rice[J]. J Integr Plant Biol., 2009, 51(12): 1126-1137.

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Association Analysis of the Amino Acid Contents in Rice

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