The influence of QTL allelic diversity on QTL detection in multi-parent populations: a simulation study in sugar beet

Abstract

Multi-parent populations (MPPs) are important resources for studying plant genetic architecture and detecting quantitative trait loci (QTLs). In MPPs, the QTL effects can show various levels of allelic diversity, which is an important factor influencing the detection of QTLs. In MPPs, the allelic effects can be more or less specific. They can depend on an ancestor, a parent or the combination of parents in a cross. In this paper, we evaluated the effect of QTL allelic diversity on the QTL detection power in MPPs.We simulated: a) cross-specific QTLs; b) parental and ancestral QTLs; and c) bi-allelic QTLs. Inspired by a real application, we tested different MPP designs (diallel, chessboard, factorial, and NAM) derived from five or nine parents to explore the ability to sample genetic diversity and detect QTLs. Using a fixed total population size, the QTL detection power was larger in MPPs with fewer but larger crosses derived from a reduced number of parents. The use of a larger set of parents was useful to detect rare alleles with a large phenotypic effect. The benefit of using a larger set of parents was however conditioned on an increase of the total population size. We also determined empirical confidence intervals for QTL location to compare the resolution of different designs. For QTLs representing 6% of the phenotypic variation, using 1600 offspring individuals, we found 95% empirical confidence intervals of 50 and 26 cM for cross-specific and bi-allelic QTLs, respectively.MPPs derived from less parents with few but large crosses generally increased the QTL detection power. Using a larger set of parents to cover a wider genetic diversity can be useful to detect QTLs with a reduced minor allele frequency when the QTL effect is large and when the total population size is increased. 1The influence of QTL allelic diversity in MPPs due to a better control over the population structure [1]. Here, we focus on MPPs composed of bi-parental crosses without further intercrossing. This definition does not cover MPPs like the multi-parent advanced generation inter-cross (MAGIC) populations [2]. Different statistical procedures exist to detect QTLs in MPPs but generally those methods, like the one adapting models used in genome-wide association studies [3,4], do not model properly the diversity of allelic effects present in MPPs. Similarly, most of the MPPs simulation studies have not simulated the wide range of QTL allelic effects present in those populations. Therefore, we investigated the QTL detection power in MPPs using scenarios that accounted better for the MPP QTL allelic diversity. We also determined empirical confidence intervals for the detected QTLs, which is an essential information for marker assisted selection (MAS) [5]. To the extent of our knowledge, no article provides such information in MPPs composed of crosses. MPP designMany MPP designs have been evaluated through simulation studies [3,6,7,8]. The nested association mapping (NAM) design is a collection of crosses between a central parent and peripher...

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