| In this study, STRUCTRE software used to evaluate population structure of the target groups that composed of 261 wheat varieties germplasm lines, including a female sterile line XND126, by the 41 polymorphic markers. The association relationship were tested between the 41 polymorphic markers and two fertility phenotype value of female fertility D.F. (domestic fertility) and I.F. (international fertility) in wheat by the GLM model in software TASSEL, identify to selected SSR markers, and then analyzed linkage groups that selected marker is located on it, to find the SSR markers which is more closely associated with female fertility in wheat. We used three populations of different sizes to carry through the linkage disequilibrium analysis with 9 SSR markers which closely linked with loci taf1 on 2DS linkage group and flanking markers of them. The following results:(1) The results of assessment of population structure showed that there were three sub-populations in the target groups.(2) The association analysis results showed that molecular markers Xcfd36 and Xcfd88 were associated with the two female fertility phenotype values in wheat, their genetic effects of the two markers on D.F. and I.F., respectively, are 0.1585, 0.113 and 0.087, 0.0596.(3) 18, 30, 19 markers on 2AL, 2DS and 4AL linkage groups were used for further association analysis because of Xcfd36 and Xcfd88 on it, we found that the markers Xwmc25(2DS), Xgwm71(2DS)and Xwmc232(4AL)more closely associated with female fertility in wheat, effect of the three markers were 0.5833, 0.5824 and 0.2841, respectively, and none associate marker was found on 2AL linkage group.(4) The study for markers on 2DS linkage group in three different sizes populations found that the markers of Xgwm296, Xgdm35, Xbrac95 and so on which were located from linkage analysis have strong linkage disequilibrium between locus taf1,and found the markers of Xgwm71, Xwmc25, Xgwm515 which have the same large LD values as Xgdm35.
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