The transfer to and functional annotation of alien alleles in advanced wheat lines derived from synthetic hexaploid wheat

The abundant genetic diversity in synthetic hexaploid wheat (SHW) can achieve breakthroughs in wheat genetic improvement, but little is known of the genetic mechanisms involved. In this study, three populations of advanced lines (totaling 284 individuals), derived from three top-crosses of SHW-L1 with different common wheat cultivars, followed by ten generations of artificial selection, were used to evaluate the transfer of alien alleles with 24872 Diversity Arrays Technology (DArT) markers. Only 1824, 1786 and 1514 DArT markers were needed to distinguish the alleles from SHW-L1 and the other common wheat parent in the populations SCPD, SS7M and SSYZ, respectively. The data clearly showed that all the advanced lines contained alien alleles from SHW-L1. The lowest percentage of alien alleles was 6.97% in an advanced line in population SSYZ, while the biggest was 30.41% in a SCPD advanced lines. The percentages of alien alleles at each locus ranged from 0% to 100% in all three populations. Forty-four alien alleles did not exist in all advanced lines, while two alien alleles were present in all advanced lines. Two of the 100% alien alleles were associated with thousand-grain weight and leaf rust resistance. Thirteen alien alleles were associated with grain yield, grain thickness and width, thousand-grain weight, grain weight/ear, plant height, grain weight, grain number, powdery mildew resistance, spikelet number per spike or yellow rust resistance. The research provided direct evidence of the existence of alien alleles in advanced lines and detected a number of valuable alleles related to wheat yield or disease resistance. More research is needed to analyze the functional mechanisms of these alleles, and to use these materials and alleles in wheat improvement.