Nature of the Genetic Variation in an Elite Maize Breeding Cross

Maize (Zea mays L.) breeders through selec- tion have had profound impacts on the maize genome. In this study we examine one aspect of this intense selection pressure, the extent and nature of genetic variation present in an elite maize breeding cross. Specifi cally genetic variation is examined with regards to genotype × environment interactions (G × E), magnitude of the genetic variance (Vg) estimates, and the underlying grain yield quantitative trait loci (QTL). Using two elite Iodent sister-lines that are 64% identical by descent, 128 recombinant inbred lines (RILs) were generated and testcrossed to a Stiff Stalk inbred line (CG102). Hybrid RILs were grown in 24 trials encompassing 4 yr, three locations, and three planting densities. Addi- tive main effects and multiplicative interaction analysis resolved the trials into eight unique patterns of G × E. Smaller Vg estimates were associated with the more frequently observed patterns of G × E. Nine single-effect QTL and four epistatic interactions were detected across seven of the G × E patterns; however, the single- effect QTL and epistatic interactions were, in general, specifi c to a G × E pattern. In summary, we found extensive linkage disequilibrium (LD), reduced Vg in the more commonly occurring G × E patterns, and genetic variation due to larger effect epistatic interactions and smaller single effect QTL specifi c to the G × E pattern. Conse- quences of the genetic variation are discussed in relation to modern maize breeding programs.