Identifying genetic variants responsible for phenotypic variation under selective pressure has the potential to enable productive gains in natural resource conservation and management. Despite this potential, identifying adaptive candidate loci is not trivial, and linking genotype to phenotype is a major challenge in contemporary genetics. Many of the population genetic approaches commonly used to identify adaptive candidates will simultaneously detect false positives, particularly in nonmodel species, where experimental evidence is seldom provided for putative roles of the adaptive candidates identified by outlier approaches. In this study, we use outcomes from population genetics, phenotype association, and gene expression analyses as multiple lines of evidence to validate candidate genes. Using lodgepole and jack pine as our nonmodel study species, we analyzed 17 adaptive candidate loci together with 78 putatively neutral loci at 58 locations across Canada (N > 800) to determine whether relationships could be established between these candidate loci and phenotype related to mountain pine beetle susceptibility. We identified two candidate loci that were significant across all population genetic tests, and demonstrated significant changes in transcript abundance in trees subjected to wounding or inoculation with the mountain pine beetle fungal associate Grosmannia clavigera. Both candidates are involved in central physiological processes that are likely to be invoked in a trees response to stress. One of these two candidate loci showed a significant association with mountain pine beetle attack status in lodgepole pine. The spatial distribution of the attack‐associated allele further coincides with other indicators of susceptibility in lodgepole pine. These analyses, in which population genetics was combined with laboratory and field experimental validation approaches, represent first steps toward linking genetic variation to the phenotype of mountain pine beetle susceptibility in lodgepole and jack pine, and provide a roadmap for more comprehensive analyses.

中文翻译：

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将基因型与表型联系起来，以确定与山松甲虫系统中宿主易感性相关的遗传变异。

识别在选择压力下导致表型变异的遗传变异有可能在自然资源保护和管理方面实现生产力收益。尽管有这种潜力，但识别适应性候选基因座并非易事，将基因型与表型联系起来是当代遗传学的一个重大挑战。许多常用于识别适应性候选者的群体遗传方法会同时检测到误报，特别是在非模式物种中，很少为通过离群值方法识别的适应性候选者的假定作用提供实验证据。在这项研究中，我们使用群体遗传学、表型关联和基因表达分析的结果作为验证候选基因的多重证据。我们使用黑松和短叶松作为我们的非模式研究物种，分析了加拿大 58 个地点的 17 个适应性候选基因座以及 78 个假定的中性基因座 ( N  > 800)，以确定这些候选基因座和与山松相关的表型之间是否可以建立关系甲虫的敏感性。我们确定了两个在所有种群遗传测试中都很重要的候选基因座，并证明了在受到伤害或接种山松甲虫真菌相关Grosmannia clavigera的树木中转录本丰度发生显着变化。两位候选人都参与了树木对压力的反应可能会被调用的核心生理过程。这两个候选基因座之一显示与黑松中山松甲虫的攻击状态显着相关。攻击相关等位基因的空间分布进一步与黑松易感性的其他指标一致。这些分析将群体遗传学与实验室和现场实验验证方法相结合，代表了将遗传变异与黑松和短叶松山松甲虫易感性表型联系起来的第一步，并为更全面的分析提供了路线图。