J Genomics 2014; 2:20-30. doi:10.7150/jgen.4089 This volume

Research Paper

Analysis of Diversity and Linkage Disequilibrium Mapping of Agronomic Traits on B-Genome of Wheat

Haixia Yu, Zhiying Deng, Changfen Xiang, Jichun Tian

State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong, China

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Yu H, Deng Z, Xiang C, Tian J. Analysis of Diversity and Linkage Disequilibrium Mapping of Agronomic Traits on B-Genome of Wheat. J Genomics 2014; 2:20-30. doi:10.7150/jgen.4089. Available from https://www.jgenomics.com/v02p0020.htm

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Association mapping is an efficient method to test the association between molecular markers and quantitative trait loci (QTL) based on linkage disequilibrium (LD). In this study, 13 agronomic traits of 109 wheat accessions were evaluated at Tai'an of China in 2006-2010. Genetic diversity, population structure, and LD were investigated using Diversity Array Technology (DArT) markers. The extent of LD on B-genome (chromosomes 1B, 2B, 3B, 4B, 5B, 6B and 7B) was about 18-27 cM. The polymorphism information content (PIC) value of markers in the LD blocks was often lower than the mean value of each chromosome. Analysis of the phenotypic diversity of the 13 traits showed that the population structure accounted for an average of 5.82% of the phenotypic variation. Association of 139 DArT markers on chromosome 1B-7B with the 13 traits was analyzed with a mixed linear model. A total of 84 significant marker trait associations (MTAs) were found and some of the associated markers were located in the QTL region detected in previous linkage mapping studies. Combined with hitchhiking effects, we identified five important markers for future analysis, such as wPt-1708(4B, 93.8cM), wPt-3457(5B, 92.3cM), wPt-9613(5B, 94.4cM), wPt-4858(6B, 66.1cM) and wPt-8598(7B, 142.4cM). The information obtained in this study should be useful for marker-assisted selection in wheat breeding programs.

Keywords: Association mapping, Agronomic traits, Linkage disequilibrium, DArT markers, hitchhiking effects