Ecological genetics of local adaptation in Arabidopsis: an 8-year field experiment

There is considerable evidence for local adaptation in nature, yet important questions remain regarding its genetic basis. How many loci are involved? What are their effect sizes? What is the relative importance of conditional neutrality vs. genetic trade-offs?  Here we address these questions in the self-pollinating, annual plant Arabidopsis thaliana. We used 400 recombinant inbred lines (RIL) derived from two locally adapted populations in Italy and Sweden, grew the RILs and parents at the parental locations, and mapped quantitative trait loci (QTL) for mean fitness (fruits/seedling planted). We previously published results from the first three years of the study, and here add five additional years, providing a unique opportunity to assess how temporal variation in selection might affect QTL detection and classification. We found ten adaptive and one maladaptive QTL in Italy, and six adaptive and four maladaptive QTL in Sweden. The discovery of maladaptive QTL at both sites suggests that even locally adapted populations are not always at their genotypic optimum. Mean effect sizes for adaptive QTL, 0.97 and 0.55 fruits in Italy and Sweden respectively, were large relative to the mean fitness of the RILs (approximately 8 fruits/seedling planted at both sites). Both genetic trade-offs (four cases) and conditional neutrality (seven cases) contribute to local adaptation in this system. The eight-year dataset provided greater power to detect QTL and to estimate their locations compared to our previous three-year study, identifying one new genetic trade-off and reclassifying one QTL from genetic trade-off to conditionally neutral.

尽管已有大量证据表明自然界中存在局部适应性（local adaptation），但其遗传基础仍留存诸多关键待解问题：涉及多少个基因座（locus，复数形式loci）？各基因座的效应量（effect size）如何？条件中性（conditional neutrality）与遗传权衡（genetic trade-off）二者对局部适应性的相对重要性分别为何？

本研究以自花授粉的一年生植物拟南芥（Arabidopsis thaliana）为研究对象，旨在解答上述问题。我们使用了源自意大利与瑞典两个局部适应性种群的400个重组自交系（recombinant inbred line，RIL），将这些RIL及其亲本分别种植于种群原产地，并针对平均适合度（fitness，每定植幼苗所结果实数）定位数量性状基因座（quantitative trait locus，QTL）。

我们此前已发表该研究前三年的实验结果，本次补充了额外五年的观测数据，这为探究选择压力的时间变异如何影响QTL的检测与分类提供了独特的研究契机。我们在意大利试验位点检测到10个适应性QTL（adaptive QTL）与1个非适应性QTL（maladaptive QTL），在瑞典试验位点则检测到6个适应性QTL与4个非适应性QTL。两个位点均检出非适应性QTL的结果表明，即便已形成局部适应性的种群，其基因型也未必始终处于最优状态。

适应性QTL的平均效应量在意大利与瑞典分别为0.97个果实与0.55个果实，相较于重组自交系的平均适合度（两个试验位点均约为每定植幼苗结8个果实）而言，效应量较大。本研究体系中，遗传权衡（共4例）与条件中性（共7例）均对局部适应性具有贡献。相较于此前的三年研究数据，本研究的八年数据集拥有更强的QTL检测效力与基因座定位精度，新发现了1例遗传权衡事件，并将1个QTL从遗传权衡重新归类为条件中性类型。