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

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. E...

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Published in:Genome Biology 2022-09, Vol.23 (1), p.1-188, Article 188
Main Authors: Li, Ningyang, Zhang, Xueyu, Sun, Xiudong, Zhu, Siyuan, Cheng, Yi, Liu, Meng, Gao, Song, Zhang, Jiangjiang, Wang, Yanzhou, Yang, Xiai, Chen, Jianrong, Li, Fu, He, Qiaoyun, Zeng, Zheng, Yuan, Xiaoge, Zhou, Zhiman, Ma, Longchuan, Wang, Taotao, Li, Xiang, Liu, Hanqiang, Pan, Yupeng, Zhou, Mengyan, Gao, Chunsheng, Zhou, Gang, Han, Zhenlin, Liu, Shiqi, Su, Jianguang, Cheng, Zhihui, Tian, Shilin, Liu, Touming
Format: Article
Language:English
Subjects:
Domestication
Evolutionary genetics
Garlic
Genetic diversity
Genomes
Genomics
History
Morphology
Phylogenetics
Plant breeding
Population
Transcriptomics
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Summary: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.
ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-022-02756-1