QTL identification and characterization of the recombination landscape of the mountain pine beetle (Dendroctonus ponderosae)

Abstract

Insect pests can rapidly accumulate in number and thrive in diverse environments, making them valuable models for studying phenotypic plasticity and the genetic basis of local adaptation. The mountain pine beetle (Dendroctonus ponderosae) is a major forest pest and adult body size and generation time are two traits that vary among populations and directly influence reproductive success and outbreak dynamics. To identify regions of the genome linked to these two traits, we generated ddRAD sequencing data from an F2 intercross, using populations from two Y haplogroups with phenotypic and genetic differences in these traits. A high-density linkage map was generated and QTL analyses performed. We identified a single large effect QTL for generation time, associated with an adult diapause. The QTL spans the entire X chromosome, peaking over the evolutionarily conserved portion of the X. We were unable to detect a significant QTL for body size. Our linkage map identified putative inversions shared by parents that are absent in the published reference genome, with three putative inversions on chromosomes 2, 3, and the X. We also detected extensive regions of low recombination that were associated with low gene density, indicative of large pericentromeric regions. Surprisingly, we found that in our cross, F2 males inherited X chromosomes with significantly fewer crossover events than F2 females. Our findings provide information about the recombination landscape, the sex-biased inheritance of recombined Xs, and the genomic location of a key trait in a major forest pest.