Powerful one-dimensional scan to detect heterotic quantitative trait loci.

Abstract

To meet the growing global demand for food, increasing yields through heterosis in agriculture is crucial. A deep understanding of the genetic basis of heterosis has led to the development of a quantitative genetic framework that incorporates both dominance and epistatic effects. However, incorporating all pairwise epistatic interactions is computationally challenging due to the large sequencing depth and population sizes needed to uncover the genes behind complex traits. In this study, we develop hQTL-ODS, a one-dimensional scanning method that directly assesses the net contribution of each quantitative trait locus to heterosis. Simulations show that hQTL-ODS reduces computational time while offering higher power and lower false-positive rate. We apply this method to a population of 5243 wheat hybrids with whole-genome sequenced profile, revealing key epistatic hubs that play a critical role in determining heterosis.