Data from: The genetics of extreme microgeographic adaptation: an integrated approach identifies a major locus underlying leaf trichome divergence in Yellowstone Mimulus guttatus

Microgeographic adaptation provides a particularly interesting context for understanding the genetic basis of phenotypic divergence, and may also present unique empirical challenges. In particular, plant adaptation to extreme soil mosaics may generate barriers to gene flow or shifts in mating system that confound simple genomic scans for adaptive loci. Here, we combine three approaches - QTL mapping of candidate intervals in controlled crosses, population resequencing (PoolSeq), and analyses of wild recombinant individuals - to investigate one trait associated with Mimulus guttatus (yellow monkeyflower) adaptation to geothermal soils in Yellowstone National Park. We mapped a major QTL causing dense leaf trichomes in thermally-adapted plants to a < 50kb region of Linkage Group 14 (Tr14) previously implicated in trichome divergence between independent M. guttatus populations. A PoolSeq scan of Tr14 region revealed a cluster of six genes, co-incident with the inferred QTL peak, with high allele frequency differences sufficient to explain observed phenotypic differentiation. One of these, the R2R3 MYB transcription factor Migut.N02661, is a plausible functional candidate, and was also strongly-associated (r2 = 0.27) with trichome phenotype in analyses of wild-collected admixed individuals. Although functional analyses will be necessary to definitively link molecular variants in Tr14 with trichome divergence, our analyses are a major step in that direction. They point to a simple, and parallel, genetic basis for one axis of Mimulus guttatus adaptation to an extreme habitat, suggest a broadly conserved genetic basis for trichome variation across flowering plants, and pave the way for further investigations of this challenging case of microgeographic incipient speciation.

微地理适应（microgeographic adaptation）为解析表型分化的遗传基础提供了极具研究价值的视角，同时也带来了独特的实证研究挑战。具体而言，植物对极端土壤镶嵌生境的适应可能引发基因流障碍或交配系统偏移，进而干扰针对适应性位点的简易基因组扫描分析。本研究结合三种研究手段——控制杂交候选区间的数量性状位点（QTL）定位、群体重测序（PoolSeq）以及野生重组个体分析——，探究了黄花沟酸浆（Mimulus guttatus，俗称黄色猴面花）适应黄石国家公园地热土壤的相关性状。我们将导致热适应植株叶片密被表皮毛的主效QTL定位至连锁群14（Linkage Group 14，Tr14）上一段小于50kb的区域，该区域此前已被证实与独立黄花沟酸浆种群间的表皮毛分化相关。对Tr14区域的PoolSeq扫描结果显示，与推断的QTL峰值重合的区域内存在6个基因簇，其等位基因频率差异显著，足以解释观测到的表型分化。其中，R2R3型MYB转录因子Migut.N02661是极具说服力的功能候选基因；在对野生混合个体的分析中，该基因与表皮毛表型也呈现出强相关性（r²=0.27）。尽管后续仍需开展功能分析才能明确Tr14区域的分子变异与表皮毛分化之间的直接关联，但本研究已朝着该目标迈出了关键一步。本研究结果表明，黄花沟酸浆适应极端生境的某一性状轴拥有简洁且趋同的遗传基础，同时也提示开花植物的表皮毛变异存在广泛保守的遗传机制，并为进一步探究这一极具挑战性的微地理初期物种形成案例铺平了研究道路。