Data from: Adaptation to climate through flowering phenology: a case study in Medicago truncatula

Local climatic conditions likely constitute an important selective pressure on genes underlying important fitness-related traits such as flowering time and in many species flowering phenology and climatic gradients strongly covary. To test whether climate shapes genetic variation on flowering time genes and to identify candidate flowering genes involved in the adaptation to environmental heterogeneity, we used a large M. truncatula core collection to examine the association between nucleotide polymorphisms at 224 candidate genes and both climate variables and flowering phenotypes. Unlike genome-wide studies, candidate gene approaches are expected to enrich for the number of meaningful trait associations because they specifically target genes that are known to affect the trait of interest. We found that flowering time mediates adaptation to climatic conditions mainly by variation at genes located upstream in the flowering pathways, close to the environmental stimuli. Variables related to the annual precipitation regime reflected selective constraints on flowering time genes better than the other variables tested (temperature, altitude, latitude or longitude). By comparing phenotype and climate associations, we identified 12 flowering genes as the most promising candidates responsible for phenological adaptation to climate. Four of these genes were located in the known flowering time QTL region on chromosome 7. However, climate and flowering associations also highlighted largely distinct gene sets, suggesting different genetic architectures for adaptation to climate and flowering onset.局地气候条件可能对与适合度相关的重要性状（如开花时间）背后的基因构成重要选择压力；在诸多物种中，开花物候与气候梯度呈现显著共变关系。为验证气候是否塑造开花时间基因的遗传变异，并鉴定参与环境异质性适应的候选开花基因，本研究利用大型蒺藜苜蓿（Medicago truncatula）核心种质集，分析224个候选基因的核苷酸多态性与气候变量及开花表型之间的关联。与全基因组研究不同，候选基因策略可富集有意义的性状关联结果，因其靶向的均为已知会影响目标性状的基因。本研究发现，开花时间主要通过开花通路上游、紧邻环境刺激位点的基因变异，介导植物对气候条件的适应。相较于本次测试的温度、海拔、纬度与经度等变量，与年降水格局相关的变量更能反映开花时间基因所承受的选择约束。通过对比表型与气候的关联分析，本研究鉴定出12个开花基因，作为介导气候适应的物候适应最具潜力的候选基因。其中4个基因位于已报道的7号染色体上的开花时间数量性状位点（quantitative trait locus, QTL）区域。然而，气候关联与开花关联所指向的基因集存在显著差异，这表明气候适应与开花起始的遗传调控架构存在差异。