A Guide to QTL Mapping with R/qtl by BROMAN, K. W. and SEN, S

Genome-wide identification of agronomically important genes in outcrossing crops using OutcrossSeq

Many important crops (e.g., tuber, root, and tree crops) are cross-pollinating. For these crops, no inbred lines are available for genetic study and breeding because they are self-incompatible, clonally propagated, or have a long generation time, making the identification of agronomically important genes difficult, particularly in crops with a complex autopolyploid genome. In this study, we developed a method, OutcrossSeq, for mapping agronomically important loci in outcrossing crops based on whole-genome low-coverage resequencing of a large genetic population, and designed three computation algorithms in OutcrossSeq for different types of outcrossing populations. We applied OutcrossSeq to a tuberous root crop (sweet potato, autopolyploid), a tree crop (walnut tree, highly heterozygous diploid), and hybrid crops (double-cross populations) to generate high-density genotype maps for the outcrossing populations, which enable precise identification of genomic loci underlying important agronomic traits. Candidate causative genes at these loci were detected based on functional clues. Taken together, our results indicate that OutcrossSeq is a robust and powerful method for identifying agronomically important genes in heterozygous species, including polyploids, in a cost-efficient way. The OutcrossSeq software and its instruction manual are available for downloading at www.xhhuanglab.cn/tool/OutcrossSeq.html.

The complex genetic architecture of male mate choice evolution between Drosophila species

Mate choice behaviors are among the most important reproductive isolating barriers in many animals. Little is known about the genetic basis of reproductively isolating behaviors, but examples to date provide evidence that they can have a simple genetic basis. However, it is unclear if these results indicate that individual genes with large effects are common, or are instead due to ascertainment biases. Here, we present the results of a QTL mapping study for the most important behavioral isolating barrier between Drosophila simulans and D. sechellia: male mate choice. Our QTL results initially suggested that differences in male mate choice may be due to a couple loci with large effects. However, as we divided the largest-effect QTL using stable introgression strains, we found evidence of multiple interacting loci. We further find that separate regions of the genome control different aspects of male choice. Taken together, our results suggest that the genetic architecture of mate choice behavior, in this case, is more complex than QTL mapping suggested, highlighting potential challenges to future mapping studies. We discuss the implications of these results as they relate to signal-receiver coevolution, mate choice, and reproductive isolation.