Stetter Markus G, Müller Thomas, Schmid Karl J
Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Fruwirthstraße 21, D-70599, Stuttgart, Germany.
Mol Ecol. 2017 Feb;26(3):871-886. doi: 10.1111/mec.13974. Epub 2017 Jan 27.
The domestication syndrome 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 colour 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 and A. quitensis. Genotyping 119 accessions of the three species from the Andean region using genotyping by sequencing (GBS) resulted in 9485 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 assignment 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 colour, A. caudatus shows a weak genomic and phenotypic domestication syndrome and proposes that it is 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.
驯化综合征包括使作物与其野生祖先区分开来的表型变化。我们比较了籽粒苋（Amaranthus caudatus）的两个假定驯化性状种子大小和种子颜色的基因组变异和表型分化，籽粒苋是南美洲的一种古老作物，以及它的两个近缘野生近缘种和假定祖先——杂种苋（A. hybridus）和昆氏苋（A. quitensis）。通过测序基因分型（GBS）对来自安第斯地区的这三个物种的119份材料进行基因分型，得到了9485个单核苷酸多态性（SNP），这些SNP揭示了栽培的籽粒苋与其两个近缘种之间存在强烈的遗传分化。昆氏苋和杂种苋的材料并没有按照物种分类聚类，而是分别根据它们在厄瓜多尔和秘鲁的地理起源形成了混合群体。籽粒苋的遗传多样性高于其近缘种，并且与其野生近缘种共享了高比例的多态性，这与不存在强烈瓶颈效应或近期高水平基因流一致。籽粒苋与其近缘种之间的基因组大小和种子大小没有显著差异，尽管来自玻利维亚的一组遗传上不同的籽粒苋种子明显更大。我们得出结论，尽管人类对白色籽粒颜色进行了长期的栽培和选择，但籽粒苋表现出较弱的基因组和表型驯化综合征，并提出它是一种未完全驯化的作物物种，要么是因为选择较弱，要么是因为来自其同域分布的近缘未驯化近缘种的高水平基因流抵消了关键驯化性状的固定。
