The genetic architecture of grain yield and related traits in Zea maize L. revealed by comparing intermated and conventional populations

Abstract

Using advanced intermated populations has been proposed as a way to increase the accuracy of mapping experiments. An F(3) population of 300 lines and an advanced intermated F(3) population of 322 lines, both derived from the same parental maize inbred lines, were jointly evaluated for dry grain yield (DGY), grain moisture (GM), and silking date (SD). Genetic variance for dry grain yield was significantly lower in the intermated population compared to the F(3) population. The confidence interval around a QTL was on average 2.31 times smaller in the intermated population compared to the F(3) population. One controversy surrounding QTL mapping is whether QTL identified in fact represent single loci. This study identifies two distinct loci for dry grain yield in the intermated population in coupling phase, while the F(3) identifies only a single locus. Surprisingly, fewer QTL were detected in the intermated population than the F(3) (21 vs. 30) and <50% of the detected QTL were shared among the two populations. Cross-validation showed that selection bias was more important in the intermated population than in the F(3) and that each detected QTL explained a lower percentage of the variance. This finding supports the hypothesis that QTL detected in conventional populations correspond mainly to clusters of linked QTL. The actual number of QTL involved in the genetic architecture of complex traits may be substantially larger, with effect sizes substantially smaller than in conventional populations.

Figure 1.—

Comparative linkage maps of F₃ (left) and intermated LHRF-F₃ (right) populations. Marker positions are in centimorgans (cM) for the conventional F₃ (using Haldane's function) and intermated centimorgans (IcM) (see text) for the intermated population. *0.05; **0.01; and ***0.001 indicate genotypic distortions at the respective levels of risk. Gray bars indicate regions where markers showed allelic bias at P = 0.001.

Figure 2.—

Specific examples of QTL detected in both populations after projection on the F₃ map. (A) One QTL for DGY on chromosome 4 detected in the F₃ population corresponds to two QTL in the LHRF-F₃ population. (B) A QTL for SD detected on chromosome 5 in the LHRE-F₃ population has a smaller CI than the corresponding QTL detected in the conventional population. In each case, only part of the chromosome is shown with the chromosome number above. Numbers in parentheses are marker positions along the chromosome in centimorgans. Dark lines indicate QTL detected in the F₃ population; gray lines indicate QTL detected in the intermated F₃ population.