Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.
Shandong Agricultural University, Tai'an, 271018, China.
Genome Biol. 2022 Sep 7;23(1):188. doi: 10.1186/s13059-022-02756-1.
Garlic is an entirely sterile crop with important value as a vegetable, condiment, and medicine. However, the evolutionary history of garlic remains largely unknown.
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.
This study provides valuable resources for garlic genomics-based breeding, and comprehensive insights into the evolutionary history of this clonal-propagated crop.
大蒜是一种完全无菌的作物，具有蔬菜、调味品和药用的重要价值。然而，大蒜的进化历史在很大程度上仍然未知。
在这里，我们报告了大蒜基因组变异的综合图谱，其中包含惊人的 1.294 亿个变异。进化分析表明，大蒜种群至少在 10 万年前就已经分化，而在中国种植的两个群体是从两个独立的途径驯化而来的。因此，在两个栽培群体中，有 15.0%和 17.5%的基因发生了表达变化，导致其转录组结构发生了重塑。此外，我们发现由于独立的积累和基于选择的去除，这两个群体中的有害替换很少有重叠。通过对选择清扫、全基因组性状关联和相关转录组分析的研究，我们发现了这两个大蒜群体在驯化过程中对鳞茎性状的不同选择。
本研究为基于大蒜基因组学的育种提供了有价值的资源，并全面了解了这种无性繁殖作物的进化历史。
