Data from: Genomic and phenotypic evidence for an incomplete domestication of South American grain amaranth (Amaranthus caudatus)

The domestication syndrom comprises phenotypic changes that differentiate crops from their wild ancestors. We compared the genomic variation and phenotypic differentiation of the two putative domestication traits seed size and seed color of the grain amaranth Amaranthus caudatus, which is an ancient crop of South America, and its two close wild relatives and putative ancestors A. hybridus or A. quitensis. Genotyping 119 accessions of the three species from the Andean region using genotyping-by-sequencing (GBS) resulted in 9,485 SNPs that revealed a strong genetic differentiation of cultivated A. caudatus from its two relatives. A. quitensis and A. hybridus accessions did not cluster by their species assigment but formed mixed groups according to their geographic origin in Ecuador and Peru, respectively. A. caudatus had a higher genetic diversity than its close relatives and shared a high proportion of polymorphisms with their wild relatives consistent with the absence of a strong bottleneck or a high level of recent gene flow. Genome sizes and seed sizes were not significantly different between A. caudatus and its relatives, although a genetically distinct group of A. caudatus from Bolivia had significantly larger seeds. We conclude that despite a long history of human cultivation and selection for white grain color, A. caudatus shows a weak genomic and phenotypic domestication syndrome and propose that it an incompletely domesticated crop species either because of weak selection or high levels of gene flow from its sympatric close undomesticated relatives that counteracted the fixation of key domestication traits.

驯化综合征（domestication syndrome）指区分栽培作物与其野生祖先的表型变化集合。本研究针对南美古老栽培作物尾穗苋（Amaranthus caudatus）及其两个近缘野生类群（推定其为祖先种，分别为A. hybridus与A. quitensis）的两个推定驯化性状——籽粒大小与籽粒颜色，比较了二者的基因组变异与表型分化。本研究通过测序分型技术（genotyping-by-sequencing, GBS）对安第斯地区3个物种的119份种质资源（accessions）进行基因分型，共获得9485个单核苷酸多态性（single nucleotide polymorphisms, SNPs）位点，结果显示栽培尾穗苋与其近缘类群存在显著的遗传分化。A. quitensis与A. hybridus的种质资源并未按照物种鉴定结果聚类，而是分别按照其地理起源——厄瓜多尔与秘鲁——形成了混合类群。尾穗苋的遗传多样性高于其近缘类群，且与其野生近缘类群共享了极高比例的多态性位点，这与未经历强烈瓶颈效应或近期存在高水平基因流的推论相符。尾穗苋与其近缘类群的基因组大小（genome size）与籽粒大小均无显著差异，但来自玻利维亚的一个遗传分化显著的尾穗苋类群拥有显著更大的籽粒。本研究得出结论：尽管尾穗苋已有悠久的人类栽培历史，且针对白色籽粒性状进行了选择，但其仍表现出较弱的基因组与表型驯化综合征特征。我们推测，尾穗苋属于未完全驯化的栽培物种，其原因可能是选择强度较弱，或是来自同域分布的近缘野生类群的高水平基因流抵消了关键驯化性状的等位基因固定过程。