Chinese Journal OF Rice Science

Chinese Journal OF Rice Science >

2014 , Vol. 28 >Issue 3: 243 - 257

DOI: https://doi.org/10.3969/j.issn.1001-7216.2014.03.004

Research Papers

Association Analysis of Rice Grain Traits with SSR Markers

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  • 1State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; 2College of Agronomy, Hue University of Agriculture and Forestry, Hue University, 102 Phung Hung Street, Hue City, Vietnam; 3 Jiangsu Hongqi Seed Company Ltd, Taizhou 225311, China;

Received date: 2013-10-23

  Revised date: 2013-12-25

  Online published: 2014-05-10

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Abstract

The genetic diversity, population structure and linkage disequilibrium of 540 rice varieties from different ecological regions were assessed with 262 pairs of simple sequence repeat (SSR) markers. The general linear model method in software of TASSEL was used to analyze the association between SSR markers and four grain traits. The main results were as follows: 1)the population was classified into seven subpopulations,with linkage disequilibrium at certain extent between SSR marker loci either intrachromosome or interchromosome within each subpopulation. 2)Among 45 grain lengthassociated SSR marker loci detected in all three years, RM5849 had the highest contribution rate (5286%), RM3766140 had the highest positive phenotypic effect, their carrier variety was Nongxiang 25. Among 7 grain widthassociated SSR marker loci, RM17 had the highest contribution rate (63.61%), RM17145 and RM573235 had the highest positive phenotypic effect, the  carrier varieties were Ningjinghui 338 and Zaoshirihuangdao, respectively. Among 11 grain thicknessassociated SSR marker loci, RM276 had the highest contribution rate (25.44%), RM508215 and RM7288205 had the highest positive phenotypic effect, carrier varieties were both Hongmangshajing. Among six 1000grain weightassociated SSR marker loci, RM17 had the highest contribution rate (32.17%), RM17145 had the highest positive phenotypic effect,  the carrier variety was Ningjinghui 338. Potential parental combinations for hybridization were predicted for improving grain traits by using the carrier varieties  screened. 

Key words： rice; grain traits; SSR molecular marker; association analysis; elite allele

Cite this article

TRAN Thi Thu Giang1,2, DANG Xiaojing1, LIU Qiangming1, ZHAO Kaiming1,3, WANG Hui1, HONG Delin1 ,* . Association Analysis of Rice Grain Traits with SSR Markers[J]. Chinese Journal OF Rice Science, 2014 , 28(3) : 243 -257 . DOI: 10.3969/j.issn.1001-7216.2014.03.004

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