Data from: Heterogeneity of genetic architecture of body size traits in a free-living population

Knowledge of the underlying genetic architecture of quantitative traits could aid in understanding how they evolve. In wild populations, it is still largely unknown whether complex traits are polygenic or influenced by few loci with major effect, due to often small sample sizes and low resolution of marker panels. Here, we examine the genetic architecture of five adult body size traits in a free-living population of Soay sheep on St Kilda using 37 037 polymorphic SNPs. Two traits (jaw and weight) show classical signs of a polygenic trait: the proportion of variance explained by a chromosome was proportional to its length, multiple chromosomes and genomic regions explained significant amounts of phenotypic variance, but no SNPs were associated with trait variance when using GWAS. In comparison, genetic variance for leg length traits (foreleg, hindleg and metacarpal) was disproportionately explained by two SNPs on chromosomes 16 (s23172.1) and 19 (s74894.1), which each explained >10% of the additive genetic variance. After controlling for environmental differences, females heterozygous for s74894.1 produced more lambs and recruits during their lifetime than females homozygous for the common allele conferring long legs. We also demonstrate that alleles conferring shorter legs have likely entered the population through a historic admixture event with the Dunface sheep. In summary, we show that different proxies for body size can have very different genetic architecture and that dense SNP helps in understanding both the mode of selection and the evolutionary history at loci underlying quantitative traits in natural populations.对数量性状潜在遗传架构的认知，有助于解析其演化机制。在野生种群中，由于样本规模通常偏小且基因标记分型面板分辨率不足，复杂性状究竟属于多基因调控，还是受少数效应显著的基因座影响，这一问题迄今仍未得到充分解答。本研究基于圣基尔达（St Kilda）群岛上自由栖息的索艾羊（Soay sheep）种群的37037个多态性单核苷酸多态性（single nucleotide polymorphism，SNP）位点，剖析了5种成体体型性状的遗传架构。其中两项性状（颌骨长度与体重）表现出多基因性状的典型特征：染色体所解释的性状方差比例与其长度呈正相关，多条染色体及多个基因组区域均可解释显著的表型方差，但通过全基因组关联分析（genome-wide association study，GWAS）未检测到与该性状变异显著关联的单核苷酸多态性位点。相较而言，腿部长度相关性状（前肢、后肢与掌骨长度）的遗传方差却不成比例地由16号染色体上的s23172.1和19号染色体上的s74894.1两个单核苷酸多态性位点所解释，每个位点均可解释超过10%的加性遗传方差。在控制环境差异后，相较于携带长腿相关常见等位基因的纯合母羊，携带s74894.1杂合基因型的母羊终生产羔数及终生产下的存活后代数均更高。本研究还证实，短腿相关等位基因极有可能通过与邓弗斯羊（Dunface sheep）的历史杂交渗入事件引入该种群。综上，本研究表明，体型的不同衡量指标可拥有截然不同的遗传架构，而高密度单核苷酸多态性分型技术有助于解析自然种群中数量性状位点的选择模式与演化历史。