Genomic insights into the evolutionary history and diversification of bulb traits in garlic.

IF 12.3 1区生物学 Q1 Agricultural and Biological Sciences Genome Biology Pub Date : 2022-09-07 DOI:10.1186/s13059-022-02756-1

Ningyang Li, Xueyu Zhang, Xiudong Sun, Siyuan Zhu, Yi Cheng, Meng Liu, Song Gao, Jiangjiang Zhang, Yanzhou Wang, Xiai Yang, Jianrong Chen, Fu Li, Qiaoyun He, Zheng Zeng, Xiaoge Yuan, Zhiman Zhou, Longchuan Ma, Taotao Wang, Xiang Li, Hanqiang Liu, Yupeng Pan, Mengyan Zhou, Chunsheng Gao, Gang Zhou, Zhenlin Han, Shiqi Liu, Jianguang Su, Zhihui Cheng, Shilin Tian, Touming Liu

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引用次数: 3

Abstract

Background: Garlic is an entirely sterile crop with important value as a vegetable, condiment, and medicine. However, the evolutionary history of garlic remains largely unknown.

Results: Here we report a comprehensive map of garlic genomic variation, consisting of amazingly 129.4 million variations. Evolutionary analysis indicates that the garlic population diverged at least 100,000 years ago, and the two groups cultivated in China were domesticated from two independent routes. Consequently, 15.0 and 17.5% of genes underwent an expression change in two cultivated groups, causing a reshaping of their transcriptomic architecture. Furthermore, we find independent domestication leads to few overlaps of deleterious substitutions in these two groups due to separate accumulation and selection-based removal. By analysis of selective sweeps, genome-wide trait associations and associated transcriptomic analysis, we uncover differential selections for the bulb traits in these two garlic groups during their domestication.

Conclusions: This study provides valuable resources for garlic genomics-based breeding, and comprehensive insights into the evolutionary history of this clonal-propagated crop.

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大蒜鳞茎性状的进化历史和多样化的基因组见解。

背景:大蒜是一种完全不育的作物，具有重要的蔬菜、调味品和药用价值。然而，大蒜的进化史在很大程度上仍然未知。结果:在这里，我们报告了大蒜基因组变异的综合地图，包括惊人的1.294亿个变异。进化分析表明，大蒜种群至少在10万年前就分化了，在中国种植的两个群体是从两条独立的路线驯化的。因此，15.0%和17.5%的基因在两个培养组中经历了表达变化，导致其转录组结构的重塑。此外，我们发现在这两个群体中，由于单独的积累和基于选择的去除，独立驯化导致有害取代很少重叠。通过选择性扫描分析、全基因组性状关联和相关转录组分析，我们揭示了这两个大蒜群体在驯化过程中球茎性状的差异选择。结论:本研究为大蒜基因组育种提供了宝贵的资源，并对大蒜无性系繁殖作物的进化历史有了全面的了解。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Genome Biology BIOTECHNOLOGY & APPLIED MICROBIOLOGY-GENETICS & HEREDITY

CiteScore

25.50

自引率

3.30%

发文量

审稿时长

14 weeks

期刊介绍： Genome Biology is a leading research journal that focuses on the study of biology and biomedicine from a genomic and post-genomic standpoint. The journal consistently publishes outstanding research across various areas within these fields. With an impressive impact factor of 12.3 (2022), Genome Biology has earned its place as the 3rd highest-ranked research journal in the Genetics and Heredity category, according to Thomson Reuters. Additionally, it is ranked 2nd among research journals in the Biotechnology and Applied Microbiology category. It is important to note that Genome Biology is the top-ranking open access journal in this category. In summary, Genome Biology sets a high standard for scientific publications in the field, showcasing cutting-edge research and earning recognition among its peers.