QTL analysis for yield components and kernel-related traits in maize across multi-environments

Huangzaosi, Qi319, and Ye478 are foundation inbred lines widely used in maize breeding in China. To elucidate genetic base of yield components and kernel-related traits in these elite lines, two F2:3 populations derived from crosses Qi319 × Huangzaosi (Q/H, 230 families) and Ye478 × Huangzaosi (Y/H, 235 families), as well as their parents were evaluated in six environments including Henan, Beijing, and Xinjiang in 2007 and 2008. Correlation and hypergeometric probability function analyses showed the dependence of yield components on kernel-related traits. Three mapping procedures were used to identify quantitative trait loci (QTL) for each population: (1) analysis for each of the six environments, (2) joint analysis for each of the three locations across 2 years, and (3) joint analysis across all environments. For the eight traits measured, 90, 89, and 58 QTL for Q/H, and 72, 76, and 51 QTL for Y/H were detected by the three QTL mapping procedures, respectively. About 70% of the QTL from Q/H and 90% of the QTL from Y/H did not show significant QTL × environment interactions in the joint analysis across all environments. Most of the QTL for kernel traits exhibited high stability across 2 years at the same location, even across different locations. Seven major QTL detected under at least four environments were identified on chromosomes 1, 4, 6, 7, 9, and 10 in the populations. Moreover, QTL on chr. 1, chr. 4, and chr. 9 were detected in both populations. These chromosomal regions could be targets for marker-assisted selection, fine mapping, and map-based cloning in maize.