DataSheet1_Genetic Diversity, Structure, and Selective Sweeps in Spinacia turkestanica Associated With the Domestication of Cultivated Spinach.xlsx

Genotype-by-sequencing (GBS) was used to explore the genetic diversity and structure of Spinacia turkestanica, and the selective sweeps involved in domestication of cultivated spinach, S. oleracea, from S. turkestanica. A total 7,065 single nucleotide polymorphisms (SNPs) generated for 16 Spinacia oleracea and 76 S. turkestanica accessions placed the S. oleracea accessions in one group, Q1, and the 76 S. turkestanica accessions, which originated from Central Asia, in two distinct groups, Q2 and Q3. The Q2 group shared greater genetic identity with the S. oleracea accessions, Q1, than the Q3 S. turkestanica group. Likewise, the S. oleracea Q1 group had a smaller Fst (0.008) with the Q2 group than with the Q3 group (Fst = 0.012), and a greater gene flow (Nm = 30.13) with the Q2 group than with the Q3 group (Nm = 21.83). The Q2 accessions originated primarily from Uzbekistan while the Q3 accessions originated mostly from Tajikistan. The Zarafshan Mountain Range appears to have served as a physical barrier that largely separated members of the Q2 and Q3 groups of S. turkestanica. Accessions with admixtures of Q2 and Q3 were collected primarily from lower elevations at the southern end of the Zarafshan Mountain Range in Uzbekistan. Selective sweep regions identified at 32, 49, and 52 Mb on chromosomes 1, 2, and 3, respectively, appear to have played a vital role in the domestication of S. oleracea as they are correlated with important domestication traits, including day length sensitivity for bolting (flowering). High XP-CLR scores at the 52 Mb genomic region of chromosome three suggest that a selective sweep at this region was responsible for early differentiation of S. turkestanica into two groups in Central Asia.

本研究采用基因型测序（Genotype-by-sequencing, GBS）技术，探究了突厥菠菜（Spinacia turkestanica）的遗传多样性与群体结构，以及栽培菠菜（S. oleracea）由突厥菠菜驯化过程中所涉及的选择性清除（selective sweeps）事件。本研究为16份栽培菠菜与76份突厥菠菜种质材料共鉴定得到7065个单核苷酸多态性（single nucleotide polymorphisms, SNPs）。基于这些SNP标记，可将栽培菠菜种质材料聚为单一类群Q1；而76份源自中亚的突厥菠菜种质材料则分为两个显著分化的类群Q2与Q3。相较于Q3类群，Q2类群与栽培菠菜类群Q1的遗传一致性更高。同样地，Q1类群与Q2类群间的遗传分化系数（Fst）为0.008，显著低于其与Q3类群间的Fst值（0.012）；同时Q1与Q2间的基因流（Nm=30.13）也高于其与Q3间的基因流（Nm=21.83）。Q2类群的种质材料主要采集自乌兹别克斯坦，而Q3类群则主要源自塔吉克斯坦。扎拉夫尚山脉似乎作为物理屏障，极大程度上分隔了突厥菠菜的Q2与Q3类群。同时携带Q2与Q3类群遗传背景的混合种质材料，主要采集自乌兹别克斯坦境内扎拉夫尚山脉南端的低海拔区域。研究在1号、2号、3号染色体上分别于32 Mb、49 Mb、52 Mb区间鉴定到选择性清除区域，这些区域与包括抽薹（bolting，开花）光周期敏感性在内的重要驯化性状显著相关，推测其在栽培菠菜的驯化过程中发挥了关键作用。对3号染色体52 Mb基因组区域的XP-CLR评分较高，表明该区域的选择性清除事件是突厥菠菜在中亚分化为两个类群的早期驱动因素。