Genome-wide Analysis Reveals the Genetic Basis of Key Agronomic Traits and Modern Wheat Breeding in Henan Province

Although wheat cultivars and yields in Henan Province have improved continuously, there have been no systematic reports on breeding improvement in recent decades. This study aims to elucidate the genetic basis of these wheat cultivars and summarize their breeding advances across four breeding periods. A total of 351 landraces and 265 cultivars from Henan Province were used in selective sweep studies and planted at five locations within the province in 2016 - 2017, 2017 - 2018, and 2018 - 2019 for genome-wide association studies. Candidate genes were identified through differential expression, Gene Ontology (GO) annotation, gene homology, and haplotype analyses. The results demonstrated that 263 known genes with selection signals were associated with yield, quality, and resistance traits. Of the quantitative trait loci identified, 51 genes had been previously reported, whereas 252 genes were novel candidates; among these, 80 genes and 50 loci contributed to the improvement of 12 traits, such as plant height. Twelve key candidate genes were verified by quantitative reverse transcription PCR (qRT-PCR). Superior haplotypes of 24 and 164 genes, respectively, explain cultivar climate adaptation and are available for future breeding. Conversely, analyses of superior haplotypes in cultivars from the 2000s onward suggest that parental selection should consider a broader range of germplasm resources, rather than just recent accessions. The transmission of superior haplotypes in four varietal pedigrees revealed the pyramiding in elite cultivars. This study provides a genetic basis for wheat improvement and offers guidance for future genetic improvement.