Data from: Signatures of soft sweeps across the Dt1 locus underlying determinate growth habit in soybean [Glycine max (L.) Merr.]

Determinate growth habit is an agronomically important trait associated with domestication in soybean. Previous studies have demonstrated that the emergence of determinacy is correlated with artificial selection on four non-synonymous mutations in the Dt1 gene. To better understand the signatures of the soft sweeps across the Dt1 locus and track the origins of the determinate alleles, we examined patterns of nucleotide variation in Dt1 and the surrounding genomic region of approximately 800 kb. Four local, asymmetrical hard sweeps on four determinate alleles, sized approximately 660, 120, 220 and 150 kb were identified, which constitute the soft sweeps for the adaptation. These variable-sized sweeps substantially reflected the strength and timing of selection, and indicated that the selection on the alleles had been completed rapidly within half a century. Statistics of EHH, iHS, H12 and H2/H1 based on haplotype data had the power to detect the soft sweeps, revealing distinct signatures of extensive long-range LD and haplotype homozygosity, and multiple frequent adaptive haplotypes. A haplotype network constructed for Dt1 and a phylogenetic tree based on its extended haplotype block implied independent sources of the adaptive alleles through de novo mutations or rare standing variation in quick succession during the selective phase, strongly supporting multiple origins of the determinacy. We propose that the adaptation of soybean determinacy is guided by a model of soft sweeps and that this model might be indispensable during crop domestication or evolution.

有限结荚习性（Determinate growth habit）是与大豆驯化相关的重要农艺性状。既往研究表明，有限结荚习性的起源与Dt1基因（Dt1）上4个非同义突变（non-synonymous mutations）的人工选择存在显著关联。为了更好地解析Dt1基因座的软选择扫描（soft sweeps）特征，并追溯有限结荚等位基因的起源，我们对Dt1及其上下游约800 kb的基因组区域的核苷酸变异（nucleotide variation）模式进行了分析。本研究鉴定到与4种有限结荚等位基因相关的4处局部不对称硬选择扫描（hard sweeps），其基因组跨度分别约660 kb、120 kb、220 kb与150 kb；上述扫描共同构成了适配适应过程的软选择扫描信号。这些跨度各异的选择扫描清晰反映了选择作用的强度与发生时序，并表明针对这些等位基因的选择在半个世纪内便已快速完成。基于单倍型（haplotype）数据计算的延伸单倍型纯合性（Extended Haplotype Homozygosity, EHH）、整合单倍型得分（integrated Haplotype Score, iHS）、H12与H2/H1统计量均具备检测软选择扫描的效能，其结果揭示了广泛的长程连锁不平衡（linkage disequilibrium, LD）、单倍型纯合性以及多种高频适应性单倍型的典型特征。针对Dt1基因构建的单倍型网络（haplotype network），以及基于其延伸单倍型区块（haplotype block）的系统发育树（phylogenetic tree）均显示，适应性等位基因在选择阶段通过新发突变（de novo mutations）或罕见现存遗传变异（standing variation）快速独立起源，有力支持了有限结荚习性的多起源假说。我们提出，大豆有限结荚习性的适应性演化遵循软选择扫描模型，且该模型可能在作物驯化与演化过程中不可或缺。