Epistatic interactions in crosses of Illinois high oil x Illinois low oil and of Illinois high protein x Illinois low protein corn strains

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) x Illinois Low Oil (ILO) and of Illinois High Protein (IHP) x Illinois Low Protein (ILP), 500 S-2 lines were developed. Each IHO x ILO line Was genotyped for 479 single nucleotide polymorphism (SNP) markers, and each IHP x ILP line was genotyped for 499 SNP markers. Per se and testcross progenies of each S-2 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.