Genome-wide association study reveals structural chromosome variations with phenotypic effects in wheat (Triticum aestivum L.).

Structural chromosome variations (SCVs) are large-scale genomic variations that can be detected by fluorescence in situ hybridization (FISH). SCVs have played important roles in the genome evolution of wheat (Triticum aestivum L.), but little is known about their genetic effects. In this study, a total of 543 wheat accessions from the Chinese wheat mini-core collection and the Shanxi Province wheat collection were used for chromosome analysis using oligonucleotide probe multiplex FISH. A total of 139 SCVs including translocations, pericentric inversions, presence/absence variations (PAVs), and copy number variations (CNVs) in heterochromatin were identified at 230 loci. The distribution frequency of SCVs varied between ecological regions and between landraces and modern cultivars. Structural analysis using SCVs as markers clearly divided the landraces and modern cultivars into different groups. There are very clear instances illustrating alien introgression and wide application of foreign germplasms improved the chromosome diversity of Chinese modern wheat cultivars. A genome-wide association study (GWAS) identified 29 SCVs associated with 12 phenotypic traits, and five (RT4AS•4AL-1DS/1DL•1DS-4AL, Mg2A-3, Mr3B-10, Mr7B-13, and Mr4A-7) of them were further validated using a doubled haploid population and advanced sib-lines, implying the potential value of these SCVs. Importantly, the number of favored SCVs that were associated with agronomic trait improvement was significantly higher in modern cultivars compared to landraces, indicating positive selection in wheat breeding. This study demonstrates the significant effects of SCVs during wheat breeding and provides an efficient method of mining favored SCVs in wheat and other crops.