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Article|22 Feb 2023|OPEN
Large-scale population structure and genetic architecture of agronomic traits of garlic 
Huixia Jia1 , Qing Zhao1 , Jiangping Song1 , Xiaohui Zhang1 , Wenlong Yang1 , Zhenzhen Du1 , Yue Zhu1 and Haiping Wang,1 ,
1State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
*Corresponding author. E-mail: wanghaiping@caas.cn

Horticulture Research 10,
Article number: uhad034 (2023)
doi: https://doi.org/10.1093/hr/uhad034
Views: 311

Received: 12 Sep 2022
Accepted: 16 Feb 2023
Published online: 22 Feb 2023

Abstract

Garlic, an asexually propagated crop, is the second important bulb crop after the onion and is used as a vegetable and medicinal plant. Abundant and diverse garlic resources have been formed over thousands of years of cultivation. However, genome variation, population structure and genetic architecture of garlic agronomic traits were still not well elucidated. Here, 1 100 258 single nucleotide polymorphisms (SNPs) were identified using genotyping-by-sequencing in 606 garlic accessions collected from 43 countries. Population structure, principal component and phylogenetic analysis showed that these accessions were divided into five subpopulations. Twenty agronomic traits, including above-ground growth traits, bulb-related and bolt-related traits in two consecutive years were implemented in a genome-wide association study. In total, 542 SNPs were associated with these agronomic traits, among which 188 SNPs were repeatedly associated with more than two traits. One SNP (chr6: 1896135972) was repeatedly associated with ten traits. These associated SNPs were located within or near 858 genes, 56 of which were transcription factors. Interestingly, one non-synonymous SNP (Chr4: 166524085) in ribosomal protein S5 was repeatedly associated with above-ground growth and bulb-related traits. Additionally, gene ontology enrichment analysis of candidate genes for genomic selection regions between complete-bolting and non-bolting accessions showed that these genes were significantly enriched in ‘vegetative to reproductive phase transition of meristem’, ‘shoot system development’, ‘reproductive process’, etc. These results provide valuable information for the reliable and efficient selection of candidate genes to achieve garlic genetic improvement and superior varieties.