Abstract：Synthetic hexaploid wheat (SHW) is known to be an excellent vehicle for transferring genetic variations especially many traits present in the D genome of Aegilops tauschii Cosson accessions (2n=2x=14, DD) to cultivated wheat (Triticum aestivum)(2n=6x=42, AABBDD) for improving its quality. The objective of this study was to identify 102 simple sequence repeat (SSR) markers associated with 4 important agronomic traits (plant height (PH), top internode length (TIL), spike number per plant (SNPP) and spike length (SL)) in a natural population (86 SHWs and 42 common wheats). A total of 660 alleles were identified; the number of alleles per locus varied from 3 to 11 with an average of 4.6. The polymorphism information content (PIC) value ranged from 0.247 7 to 0.897 1 with an average of 0.723 5. The maximum and minimum values of PIC values were WMS174 and GWM601, respectively. BARC241, GWM498a, GWM495, GWM359b, GWM273a and GWM508 had relative larger PIC values. The tested materials consisted of three subpopulations by the population structure analysis and cluster analysis, the two results were basically the same. There were slight differences, these may have been due to their complex genetic backgrounds. Additionally, the result of cluster analysis using unweighted pair-group with arithmetic mean (UPGMA) was in accordance with the model based analysis, except for V023 and V072; these were observed to cluster in another subgroup. However, there was a clear distinction between SHWs and common wheats, indicating that the genetic background of most SHW varieties varies greatly compared to common wheat varieties. Association analysis between traits and simple sequence repeat (SSR) markers was performed using the generalized linear model (GLM) approach. 20 and 17 loci were found to be associated with the above-mentioned traits in 2015 and 2016, respectively (P＜0.01). In 2015, 10 loci were found to be associated with more than one trait. WMC702 was associated with both SNPP and SL; WMS408 was related with PH, TIL and SL; the explanation rate ranged from 0.039 8 to 0.247 2; the maximum and minimum rates were for GWM-111, and WMS-174, respectively. In 2016, 12 loci were detected to be associated with more than one trait. GWM570b had significant association with both TIL and SL; GWM41 were associated with PH and TIL. The explanation rates range from 0.063 9 to 0.191 3, with the maximum and minimum values observed for GWM508 and WMS408, respectively. These tested significant markers may broaden our knowledge for how to harness genetic diversity and provide resource for further wheat molecular marker assisted breeding.
