Horticulture Research

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Article|17 Oct 2023|OPEN

Genome resequencing reveals the evolutionary history of garlic reproduction traits

Haiping Wang¹ ^,† , Einat Shemesh-Mayer² ^,† , Jiangjiang Zhang³ ^,† , Song Gao⁴ ^,† , Zheng Zeng³ , Zemao Yang³ , Xueyu Zhang³ , Huixia Jia¹ , Yanzhou Wang^3,5 , Jiangping Song¹ , Xiaohui Zhang¹ , Wenlong Yang¹ , Qiaoyun He³ , Amir Sherman² , Lin Li⁶ and Rina Kamenetsky² ^, , Touming Liu,^4,5 ^,

¹State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
²Institute of Plant Sciences, Agricultural Research Organization—The Volcani Institute, Rishon LeZion, Israel
³Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
⁴College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
⁵Industrial Research Institute of garlic (IBFC-Jinxiang), Jinxiang, China
⁶College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
*Corresponding author. E-mail: vhrkamen@volcani.agri.gov.il,liutouming@caas.cn
^†Haiping Wang,Einat Shemesh-Mayer,Jiangjiang Zhang and Song Gao contributed equally to the study.

Horticulture Research 10,
Article number: uhad208 (2023)
doi: https://doi.org/10.1093/hr/uhad208
Views: 242

Received: 08 Jul 2023
Accepted: 11 Oct 2023
Published online: 17 Oct 2023

Abstract

The propagation of cultivated garlic relies on vegetative cloves, thus flowers become non-essential for reproduction in this species, driving the evolution of reproductive feature-derived traits. To obtain insights into the evolutionary alteration of reproductive traits in the clonally propagated garlic, the evolutionary histories of two main reproduction-related traits, bolting and flower differentiation, were explored by genome analyses using 134 accessions displaying wide diversity in these two traits. Resequencing identified 272.8 million variations in the garlic genome, 198.0 million of which represent novel variants. Population analysis identified five garlic groups that have evolved into two clades. Gene expression, single-cell transcriptome sequencing, and genome-wide trait association analyses have identified numerous candidates that correlate with reproductive transition and flower development, some of which display distinct selection signatures. Selective forces acting on the B-box zinc finger protein-encoding Asa2G00291.1, the global transcription factor group E protein-encoding Asa5G01527.1, and VERNALIZATION INSENSITIVE 3-like Asa3G03399.1 appear to be representative of the evolution of garlic bolting. Plenty of novel genomic variations and trait-related candidates represent valuable resources for biological studies of garlic. Numerous selective signatures from genes associated with the two chosen reproductive traits provide important insights into the evolutionary history of reproduction in this clonally propagated crop.