Genome-wide mapping of QTL associated with heterosis in the RIL-based NCIII design

Abstract

Heterosis represents one of the most revolutionary advancements in crop improvement. In the genetic dissection of heterosis, NCIII design is one of the most powerful and widely used mating schemes. However, the methodologies for quantitative trait loci (QTL) detection in the design were mostly based on composite interval mapping. Therefore, in this study, our purpose was to develop a statistical method for mapping epistatic QTL associated with heterosis in the RIL-based NCIII design. First, we derivated the expectations of two classical linear transformations, Z 1 and Z 2, while a quantitative trait was controlled by two QTL with digenic epistasis and arbitrary linkage under the F ∞ and F 2 metric models. Then, we constructed an epistatic genetic model that includes all markers on the whole genome simultaneously, and estimated all the parameters in the model by the empirical Bayes approach. Finally, a series of Monte Carlo simulation experiments was carried out to confirm the proposed approach. The results show that: (1) all the augmented genetic parameters for main-effect QTL could be rightly identified with satisfactory statistical power and precision; (2) the statistical powers in the detection of augmented epistatic effects were substantively affected by the signs of pure epistatic effects; (3) it is more difficult to detect epistatic QTL than to detect main-effect QTL; (4) statistical power is higher in the RIL-based NCIII design than in the F2-based NCIII design, especially in the detection of the augmented epistatic effect that consists of two pure epistatic effects in opposite directions. © 2012 The Author(s).