Genetic Dissection of Wheat Heterosis Identifies Candidate Genes in Biparental and Diverse Hybrid Populations

Understanding how numerous heterotic quantitative trait loci (hQTL) shape heterosis and shifting from hQTL to candidate genes are central challenges. To address these challenges, we performed a systematic, genome-wide mapping in a biparental population and a population of diverse hybrids. Leveraging both a triple testcross and immortalized F₂ designs, we examined the genetic basis of the heterosis of the wheat hybrid Piko × Hermann. We detected a major hQTL on chromosome 4B, primarily driven by epistasis. This region contains the Green Revolution gene Rht-B1 as the primary candidate gene. Then, we used a population of ~6000 wheat hybrids, derived from crosses between diverse Central European inbred lines, to perform a one-dimensional scan for hQTL. This scan identified 174 hQTL for grain yield, 70 for heading date, and 166 for plant height. Further dissection of these hQTL revealed that epistatic interactions predominantly contribute to heterosis. We discovered an epistatic hub at the distal end of chromosome 4A coinciding with an alien introgression region from emmer wheat. A data-driven, integrative analysis combining high-resolution SNP data, sequence variant annotation, and hQTL signals from the population uncovered TraesCS7B03G1341000 as the candidate gene underlying grain yield heterosis. Our findings deepen the understanding of the genetic architecture of heterosis in wheat by shifting from hQTL to candidate genes and provide insights into their application in hybrid wheat breeding.