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| Genetic Diversity, Population Structure, and Linkage Disequilibrium in Chinese Winter Wheat (Triticum aestivum L.) |
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Abstract In order to identify simple sequence repeat (SSR) markers which associated with yield or quality characters, this study was conducted to investigate polymorphism analysis of locis、cluster analysis based on unweight pair method using arithmetic averages、population structure analysis based on mathematic model and linkage disquilibrium analysis among 91 wheat (Triticum aestivum L.) cultivars and breeding lines using 88 wheat SSR markers distributed throughout the wheat genome. A total of 883 alleles were detected, with 2 to 30 alleles per locus and a mean genetic richness of 10.03. The average genetic diversity index was 0.703, with a range from 0.160 to 0.932. The mean PIC value was 0.667, ranging from 0.148 to 0.929. These results indicated that the genetic diversity of the 91 Chinese winter wheat cultivars was low. Further analysis showed that B genome had the highest genetic diversity and D genome had the lowest genetic diversity, significant differences were observed between these 2 genomes (P＜0.01). The collection of winter wheats could be divided into 3 and 4 subgroups based on UPGMA (unweight pair method using arithmetic averages) and STRUCTURE analyses, respectively. The results of clustering had no obvious relationship with the geographic eco-type, but partly correlated to some extent with pedigrees. The results of clustering and population structure analyses could complement and confirm each other, making the results more reliable. Results of AMOVA (analysis of molecular variance) indicated that the majority genetic variation occurred in different individuals within a population. Furthermore, gene flow proved that there was some high frequency of gene intercommunication among different subpopulations. The baseline of linkage disequilibrium (LD) decay for genome was r2=0.028 7 and the mean LD decay distance of the whole genome was 4.3 cM, while the mean LD decay distance of A, B and D genome was 3.7, 1.0 and 4.1 cM, respectively. The LD decay distance and rate of B genome was shorter and faster than A and D genomes. The results of this study were expected to provide valuable information for future association analysis. Evaluating the genetic diversity, population structure and LD of Chinese winter wheat will provide useful information support for enhancing the efficiency of further breeding, molecular assisted selection (MAS) and association analysis.
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Received: 27 October 2014
Published: 13 May 2015
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