Effects of random mating on marker-QTL associations in the cross of the Illinois High Protein X Illinois Low Protein maize strains

The effects of random mating on population performance and identification of marker-quantitative trait loci (QTL) associations were studied in the cross of the Illinois High Protein (IHP) and Illinois Low Protein (ILP) maize (Zea mays L.) strains. The F, was randomly mated to produce the Syn0 and Syn4 generations. Two hundred Syn0 S-1 and 200 Syn4 S, lines were crossed to two inbred testers. The S, lines per se and the testerosses (TCs) were evaluated for grain protein, starch, and oil concentrations in four environments. Genetic variance for protein and starch was reduced from the Syn0 to the Syn4 and genetic variance for the S-1 lines per se was greater than for the TCs. Heritability was similar in the Syn0 and Syn4. With single factor (SF) analysis, the number of significant marker-QTL associations for protein and starch in the Syn4 was drastically reduced from the number found in the Syn0. Multiple regression (MR) analysis supported this result. Very few significant marker-QTL associations for oil were found in either the Syn0 or Syn4. Agreement between the testers and the S, lines per se for chromosomal regions identified as associated with QTL for starch and protein was high. Genotypic correlations of starch with protein ranged from -0.96 to -0.98. However, three markers had the same sign and significant additive effects for both starch and protein in the S, progeny and both TCs. Such markers should be useful for simultaneous selection for high starch and high protein.