Qi Xinshuai, An Hong, Ragsdale Aaron P, Hall Tara E, Gutenkunst Ryan N, Chris Pires J, Barker Michael S
Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
Division of Biological Sciences, University of Missouri, Columbia, MI, USA.
Mol Ecol. 2017 Jul;26(13):3373-3388. doi: 10.1111/mec.14131. Epub 2017 May 5.
Demographic modelling is often used with population genomic data to infer the relationships and ages among populations. However, relatively few analyses are able to validate these inferences with independent data. Here, we leverage written records that describe distinct Brassica rapa crops to corroborate demographic models of domestication. Brassica rapa crops are renowned for their outstanding morphological diversity, but the relationships and order of domestication remain unclear. We generated genomewide SNPs from 126 accessions collected globally using high-throughput transcriptome data. Analyses of more than 31,000 SNPs across the B. rapa genome revealed evidence for five distinct genetic groups and supported a European-Central Asian origin of B. rapa crops. Our results supported the traditionally recognized South Asian and East Asian B. rapa groups with evidence that pak choi, Chinese cabbage and yellow sarson are likely monophyletic groups. In contrast, the oil-type B. rapa subsp. oleifera and brown sarson were polyphyletic. We also found no evidence to support the contention that rapini is the wild type or the earliest domesticated subspecies of B. rapa. Demographic analyses suggested that B. rapa was introduced to Asia 2,400-4,100 years ago, and that Chinese cabbage originated 1,200-2,100 years ago via admixture of pak choi and European-Central Asian B. rapa. We also inferred significantly different levels of founder effect among the B. rapa subspecies. Written records from antiquity that document these crops are consistent with these inferences. The concordance between our age estimates of domestication events with historical records provides unique support for our demographic inferences.
人口统计学建模经常与群体基因组数据一起使用，以推断群体之间的关系和年龄。然而，相对较少的分析能够用独立数据验证这些推断。在这里，我们利用描述不同芜菁作物的书面记录来证实驯化的人口统计学模型。芜菁作物以其显著的形态多样性而闻名，但驯化的关系和顺序仍不清楚。我们使用高通量转录组数据从全球收集的126份材料中生成了全基因组单核苷酸多态性（SNP）。对整个芜菁基因组中超过31000个SNP的分析揭示了五个不同遗传群体的证据，并支持芜菁作物起源于欧洲-中亚地区。我们的结果支持了传统上公认的南亚和东亚芜菁群体，有证据表明小白菜、大白菜和黄薹可能是单系群体。相比之下，油用型芜菁亚种油用芜菁和褐薹是多系的。我们也没有找到证据支持苤蓝是芜菁野生型或最早驯化亚种的观点。人口统计学分析表明，芜菁在2400-4100年前被引入亚洲，大白菜在1200-2100年前通过小白菜与欧洲-中亚芜菁的混合起源。我们还推断出芜菁亚种之间的奠基者效应水平存在显著差异。记载这些作物的古代书面记录与这些推断是一致的。我们对驯化事件的年龄估计与历史记录之间的一致性为我们的人口统计学推断提供了独特的支持。
