Large-scale population structure and genetic architecture of agronomic traits of garlic.
Large-scale population structure and genetic architecture of agronomic traits of garlic.
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大蒜大尺度群体结构及农艺性状遗传结构
DOI：
10.1093/hr/uhad034
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发表时间：
2023-04
影响因子：
8.7
通讯作者：
中科院分区：
文献类型：
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摘要 大蒜是一种无性繁殖作物，是继洋葱之后第二重要的球茎作物，用作蔬菜和药用植物。经过数千年的栽培，形成了丰富多样的大蒜资源。然而，大蒜农艺性状的基因组变异、群体结构和遗传结构仍未得到很好的阐明。在这里，通过测序基因分型在从 43 个国家收集的 606 个大蒜品种中鉴定出了 1~100~258 个单核苷酸多态性 (SNP)。群体结构、主成分和系统发育分析表明，这些材料分为5个亚群体。连续两年对20个农艺性状进行了全基因组关联研究，包括地上生长性状、球茎相关性状和螺栓相关性状。总共有542个SNP与这些农艺性状相关，其中188个SNP与两个以上性状重复相关。一个 SNP（chr6：1896135972）与 10 个性状重复相关。这些相关的 SNP 位于 858 个基因内或附近，其中 56 个是转录因子。有趣的是，核糖体蛋白 S5 中的一个非同义 SNP（Chr4：166524085）反复与地上生长和鳞茎相关性状相关。此外，对全抽苔和非抽苔材料基因组选择区候选基因的基因本体富集分析表明，这些基因在“分生组织营养向生殖相变”、“芽系统发育”、“生殖过程”等方面显着富集。这些结果为可靠、高效地选择候选基因以实现大蒜遗传改良和优良品种提供了有价值的信息。
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.
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影响因子：
13.8
作者：
Han K;Lee HY;Ro NY;Hur OS;Lee JH;Kwon JK;Kang BC
通讯作者：
Kang BC
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Sham PC
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通讯作者：
Buszczak, Michael
影响因子：
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作者：
Kamenetsky, R;Rabinowitch, HD
通讯作者：
Rabinowitch, HD