Genome Selection Sweep and Association Analysis Shed Light on Future Breeding by Design in Wheat

Two sets of bread wheat (Triticum aestivum L.) varieties and their respective founder parents (St2422/464 and Abbondanza) in China were genotyped at 481 microsatellite loci. The selection sweeps detected almost completely overlapped with one another across the two sets on the 21 chromosomes although a cluster analysis showed that they do represent distinct subpopulations with F-st = 0.0734 (minor allele frequency [MAF] = 0.1, log(10)p = 5). About 38.7% of the loci appeared to have experienced some selection sweep. Important agronomic traits were usually associated with these selection sweep valleys. The alleles present at key loci in these valleys were often in common between the two founders. Marker trait association based on three seasons of field data suggested the association of one, four, and six loci with, respectively, the number of fertile tillers per plant, grain number per spike, and thousand grain weight. Five, 14, and 21 loci were associated with the three yield components in two of the three seasons. We suggest that the breeding potential of a line can be predicted from its allelic state at certain critical marker loci, which represent major targets for breeding by design in wheat. Genotypic descriptions of major cultivars and the analytical approach we have described here provide a path toward the a priori selection of favorable breeding parents.