The population genetics of structural variants in grapevine domestication

First author: Yongfeng Zhou; Affiliations: University of California, Irvine (加州大学欧文分校): CA, USA

Corresponding author: Brandon S. Gaut

Structural variants (SVs) are a largely unexplored feature of plant genomes. Little is known about the type and size of SVs, their distribution among individuals and, especially, their population dynamics. Understanding these dynamics is critical for understanding both the contributions of SVs to phenotypes and the likelihood of identifying them as causal genetic variants in genome-wide associations. Here, we identify SVs and study their evolutionary genomics in clonally propagated grapevine cultivars and their outcrossing wild progenitors. To catalogue SVs, we assembled the highly heterozygous Chardonnay genome, for which one in seven genes is hemizygous based on SVs. Using an integrative comparison between Chardonnay and Cabernet Sauvignon genomes by whole-genome, long-read and short-read alignment, we extended SV detection to population samples. We found that strong purifying selection acts against SVs but particularly against inversion and translocation events. SVs nonetheless accrue as recessive heterozygotes in clonally propagated lineages. They also define outlier regions of genomic divergence between wild and cultivated grapevines, suggesting roles in domestication. Outlier regions include the sex-determination region and the berry colour locus, where independent large, complex inversions have driven convergent phenotypic evolution.

结构变异（structural variant；SV）是植物基因组中未被广泛鉴定的一类特征。关于植物中结构变异的类型和大小、个体中的分布以及群体动态都不是很清楚。对于结构变异的深入研究将有助于我们进一步理解结构变异对于表型的影响以及通过全基因组关联分析鉴定其作为目的表型关键遗传因子的可能性。本文中，作者鉴定了通过无性繁殖的葡萄栽培种群体以及其异交野生祖先种中的结构变异，并研究了SV的演化基因组动态。作者组装了一个高度杂合的Chardonnay基因组，基于SV的结果发现Chardonnay基因组上大约有七分之一的基因属于半合子。通过全基因组长read和短read比对到Chardonnay和Cabernet Sauvignon参考基因组上，作者检测了尽可能多的SV。作者发现强烈的纯化选择作用于结构变异，但尤其针对倒置和易位事件。尽管如此，结构变异还是通过隐性杂合子的方式在无性繁殖的葡萄谱系中不断积累。同时，结构变异还区分了葡萄野生种和栽培种之间基因组分化的离群区域，说明其在驯化中的作用。这些离群区域中包括一个性别决定区域和葡萄浆果着色位点，独立的大片段、复杂倒置驱动了趋同的表型演化。

通讯：Brandon S. Gaut（https://gautlab.bio.uci.edu/people/)

个人简介：加州大学河滨分校，博士；北卡罗来纳州立大学，博士后。

研究方向：葡萄和北美砧木种群基因组学研究；植物基因组的表观与演化；大肠杆菌实验演化；驯化遗传学。

doi: https://doi.org/10.1038/s41477-019-0507-8

Journal: Nature Plants

Published online: September 09, 2019