Epistatic Interactions in Crosses of Illinois High Oil × Illinois Low Oil and of Illinois High Protein × Illinois Low Protein Corn Strains

Abstract

Epistasis has been proposed as a possible explanation for the long continued progress from selection in the Illinois long‐term corn (Zea mays L.) selection strains. From the crosses of Illinois High Oil (IHO) × Illinois Low Oil (ILO) and of Illinois High Protein (IHP) × Illinois Low Protein (ILP), 500 S2 lines were developed. Each IHO×ILO line was genotyped for 479 single nucleotide polymorphism (SNP) markers, and each IHP×ILP line was genotyped for 499 SNP markers. Per se and testcross progenies of each S2 line were evaluated for oil, protein, and starch. A large number of QTL were found to control these traits. The objective of this paper is to report the results of analysis of these crosses for two‐way epistatic interactions. More epistatic interactions were significant than expected by chance. The proportion of significant interactions that involved a marker significant in a single marker analysis (SMA) was no greater than expected by chance. The number of markers associated only with significant epistatic effects ranged from 46.3 to 72.2% of the total number of markers significant for either an interaction effect or from SMA. The number of QTL controlling a trait is much greater than will be found by analyzing for significant QTL main effects. Thus, epistasis could contribute to the long continued response to selection in the Illinois long‐term selection strains and also may help explain the continued success of commercial corn breeding.