Accumulation of beneficial haplotypes in the Huang-Huai-Hai wheat region and its application in molecular breeding

The Huang-Huai-Hai wheat region (HHHR) is characterized by the largest cultivation area and highest yield among all the major wheat-producing regions in China. Over the past 70 years, significant advances in wheat breeding have been achieved in this region, resulting in high and stable yields as well as improved disease resistance. However, a notable deficiency remains in the systematic molecular-level analyses of wheat breeding advantages in HHHR. To bridge this gap, we used a Wheat 55K SNP array to evaluate 384 accessions from a core collection of wheat germplasms across China, and then systematically analyzed the distribution patterns of beneficial haplotypes associated with traits related to yield and powdery mildew resistance specific to HHHR. The findings indicate that varieties from HHHR demonstrate significantly superior performance in terms of yield-related traits and powdery mildew resistance compared to those from other wheat regions. A genome-wide association study (GWAS) analysis identified the quantitative trait nucleotides (QTNs) associated with both grain yield and powdery mildew resistance. Importantly, beneficial haplotypes were found at significantly higher frequencies in the HHHR than in other wheat-growing regions. Based on these haplotypes, the MFP-a gene was identified as potentially regulating jasmonic acid synthesis while also playing a role in grain development and conferring powdery mildew resistance. Furthermore, identity by descent (IBD) analysis revealed specific conserved genomic segments that have become fixed through selective breeding practices in HHHR, which may serve as valuable resources for the targeted enhancement of yield and disease resistance traits in other wheat-growing areas. Finally, the Aimengniu breeding lineage was used as a case study to elucidate the genetic basis underlying the key founder parental formations utilized in breeding programs. This study not only provides essential references and guidance for future molecular breeding initiatives in China but also has implications for enhancing wheat production worldwide.