Data from: Application of a dense genetic map for assessment of genomic responses to selection and inbreeding in Heliothis virescens

Adaptation of pest species to laboratory conditions and selection for resistance to toxins in the laboratory are expected to cause inbreeding and genetic bottlenecks that reduce genetic variation. Heliothis virescens, a major cotton pest, has been colonized in the laboratory many times, and a few laboratory colonies have been selected for Bacillus thuringiensis (Bt) resistance. We developed 350-bp double-digest restriction-site associated DNA-sequencing (ddRAD-seq) molecular markers to examine and compare changes in genetic variation associated with laboratory adaptation, artificial selection and inbreeding in this nonmodel insect species. We found that allelic and nucleotide diversity declined dramatically in laboratory-reared H. virescens as compared with field-collected populations. The declines were primarily a result of the loss of low frequency alleles present in field-collected H. virescens. A further, albeit modest decline in genetic diversity was observed in a Bt-selected population. The greatest decline was seen in H. virescens that were sib-mated for 10 generations, in which more than 80% of loci were fixed for a single allele. To determine which regions of the genome were resistant to fixation in our sib-mated line, we generated a dense intraspecific linkage map containing three PCR-based and 659 ddRAD-seq markers. Markers that retained polymorphism were observed in small clusters spread over multiple linkage groups, but this clustering was not statistically significant. Overall, we have confirmed and extended the general expectations for reduced genetic diversity in laboratory colonies, provided tools for further genomic analyses and produced highly homozygous genomic DNA for future whole genome sequencing of H. virescens.害虫物种对实验室环境的适应，以及实验室中针对毒素抗性的选育，通常会引发近交与遗传瓶颈效应，进而降低种群遗传多样性。作为主要棉花害虫的棉铃实夜蛾（Heliothis virescens），已多次在实验室中被定植培养，且已有数个实验室种群经选育获得了苏云金芽孢杆菌（Bacillus thuringiensis, Bt）抗性。本研究针对这一非模式昆虫物种，开发了350bp双酶切限制性位点关联DNA测序（double-digest restriction-site associated DNA-sequencing, ddRAD-seq）分子标记，用以检测并对比实验室适应、人工选育与近交过程伴随的遗传变异变化。研究发现，与野外采集的种群相比，实验室饲养的棉铃实夜蛾的等位基因多样性与核苷酸多样性均出现显著下降。这种下降主要源于野外种群中存在的低频等位基因的丢失。经Bt选育的种群中还出现了进一步的、尽管幅度较小的遗传多样性下降。下降幅度最大的是经过10代同胞交配的棉铃实夜蛾种群，其中超过80%的基因座仅固定为单一等位基因。为了明确同胞交配品系中哪些基因组区域未发生等位基因固定，本研究构建了一张包含3个PCR标记与659个ddRAD-seq标记的高密度种内连锁图谱。保留多态性的标记呈小簇状分布于多个连锁群上，但这种簇状分布未达到统计学显著性。综上，本研究验证并拓展了关于实验室种群遗传多样性降低的普遍预期，为后续基因组分析提供了研究工具，并制备了高纯合度的基因组DNA，可用于棉铃实夜蛾的全基因组测序研究。