Dissection of genetic loci modulating heading date in common wheat

1. A genome-wide recombination landscape consisting of 88 recombination hotspots regions (RHR) was constructed in common wheat. 2. Phenotype-based GWAS and linkage mapping identified 55 significant SNPs clusters and 21 QTLs associated with heading date and flowering date in wheat. 3. Expression-based GWAS identified 307 potential regulators and one candidate gene associated with heading date and flowering date in wheat. Heading date is one of the most important indicators to evaluate adaptation in wheat. In this study, we used three association panels to construct a genome-wide recombination landscape consisting of 97 recombination hotspots regions (RHR) in wheat. We further identified 1,043 RHR in six bi-parental populations, and 88 recombination hotspots overlapped with association panels. We next identified 2223 significant SNPs forming 55 clusters for heading date by phenotype-based genome-wide association studies (pGWAS), and 53 stable SNPs associated with 13 candidate genes were detected in at least two environments. Twenty-one QTLs were mapped in bi-parental populations and five QTL intervals overlapped RHR. By integration of collinearity analysis, recombination hotspots, and haplotype analysis, five homoeologous interval pairs were discovered, of which 7D_Hap1 advanced heading by 8.7 days. Further analysis showed that heading date-network genes were involved into transcription regulation and post-translational modification (PTM). Meanwhile, expression GWAS (eGWAS) on heading date regulatory core module identified 307 potential novel genes acting in heading date regulatory network. These findings provide new insights into wheat phenological adaptation and developed resources for developing climate-resilient wheat cultivars.