| Correlation analysis was carried out on the natural mixed population composed of the main domestic varieties and materials preserved in our laboratory on the basis of genetic diversity analysis and linkage disequilibrium analysis after a field investigation on 20 target characters in order to mine the molecular markers associated with target traits.The main results are as follows:1.Phenotypic diversity analysis showed that the coefficient of variation of target characters ranged from 10.00% to 45.30%,which demonstrated that there was an rich phenotypic diversity in the population.2.When the square of the Euclidean distance equaled to 20,the population was clustered into three groups using the seven principal components as variables which were extracted based on principal component analysis of phenotypic data with a cumulative contribution rate of 87.72%.3.154 allelic variation was detected with 39 pairs of polymorphic SSR primers with an average of four allelic variation each marker,ranging from 2 to 8.The MAF value ranged from 0.1788 to 0.8214 with a mean of 0.547,the value of heterozygosity ranged from 0.0275 to 0.6732 with a mean of 0.1921,the value of genetic diversity ranged from 0.3076 to 0.8645 with a mean of 0.5694 and the PIC value ranged from 0.2838 to 0.8492 with a mean of 0.5021,which indicated that a high genetic diversity were existed in this population.4.There were 741 kinds of loci combinations among 39 pairs of polymorphic markers,632 of them were with linkage disequilibrium,which accounted for the total number of 85.29%.D’ values ranged from 0.0793 to 0.849964 with an average of 0.35144.Linkage disequilibrium existed among 466 and 391 combinations under the statistical probability of p<0.05 and p<0.01 respectively.Linkage disequilibrium of high degree(D ’> 0.5)existed among 103 pairs of loci combination.5.Thecoefficient ΔK occurred the biggest turning point at the K value of 2,so that the population could be divided into two subgroups.86.98 % of the materials were divided into appropriate groups when the Q value ≥0.70,however,25 materials were not included in these two subpopulations other than defined as mixed subpopulations.6.Plant height,main spike height,stem diameter,main spike length,stem wax layer,capsule size and the length,width and thickness of main spike seed were associated with 8 marker loci at a significant level of p <0.001,the phenotypic variation explained by each marker ranged from 0.0747 to 0.2461.the primers RCM1341,RCM1727 and RCM583 associated with two or more traits significantly.17 phenotypic traits were associated with18 marker loci at a significant level of p <0.01,the phenotypic variation explained by each marker ranged from 0.045 to 0.1902,Among which 9 primers associated with two or more phenotypic traits simultaneously.It was found that 18 of 20 phenotypic traits investigated associated with marker loci and 22 of 39 SSR markers associated with phenotypic variation highly significant or significantly,which indicated that the high efficiency of SSR markers in association analysis. |
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