Quantifying novel sequence variation and selective advantage in synthetic hexaploid wheats and their backcross-derived lines using SSR markers

Synthetic hexaploid wheats (SHWs) and synthetic backcross-derived lines (SBLs) obtained from them are novel sources of useful traits for broadening the diversity in breeding germplasm of hexaploid bread wheat (Triticum aestivum). Fifty-one EST-derived and 39 genomic-derived microsatellite markers (SSRs) covering the A, B, and D genomes were used to assess the genetic diversity present in 11 SHWs, their backcross derived families, and their durum and bread wheat parents and to test for the selective advantage of SHW alleles in SBL families after several generations of selection. The 90 SSR markers amplified 91 loci with 474 alleles across all genotypes. In many of the SHWs, novel alleles were observed which were stably inherited in the SBL families. Gene diversity, the average number of alleles per locus, cluster analysis, and principal coordinate analysis revealed a high level of genetic diversity in the Aegilops tauschii and durum parents of the SHWs, and also in the SBLs. In the latter, alleles from the SHW parent had a selective advantage for six SSR markers. This indicates that SHWs and SBLs are a valuable resource for broadening the genetic base of elite wheat breeding germplasm. Fingerprinting of SBLs and their corresponding SHW and bread wheat parents, and testing for selective advantage of SHWs alleles promises to be a useful method for detecting chromosomal regions of interest for bread wheat improvement.