Genome-wide analysis reveals the genetic basis of key agronomic traits and modern wheat breeding in Henan Province

Despite the continuous improvement of wheat cultivars in Henan Province, the largest Chinese wheat-producing area, there have been no reports of studies on their breeding advances in the past decades. This study aims to elucidate their genetic basis and breeding advances. A total of 351 landraces and 265 cultivars in Henan Province were employed in selective sweep studies and genome-wide association studies. All the wheat accessions were planted in five locations in Henan Province in 2016−2017, 2017−2018 and 2018−2019. Candidate genes were identified through differential expression, GO annotation, gene homology, and haplotype analyses. Breeding advances were summarized based on four breeding periods (1950s, 1960s−1970s, 1980s−1990s, and post−2000s) of all 265 cultivars. The results demonstrated that 263 known genes with selection signals were found to be associated with important traits. Around the detected quantitative trait loci, 51 genes had been previously reported, while 252 genes were identified as candidate genes. Of the 303 genes and loci identified, 80 genes and 50 loci contributed to the improvement of 12 traits like plant height, and 12 key candidate genes was verified by qRT-PCR, while superior haplotypes of 24 genes explained cultivar climate adaptation. The superior haplotypes of 164 genes are available for future breeding. Transmission of superior haplotypes in four varietal pedigrees revealed pyramiding of superior haplotypes in elite cultivars. The analysis of post−2000 cultivars suggests a broader range of germplasm resources should be considered in parental selection than only recent accessions. This study provides a genetic basis and guide for wheat improvement.