GWAS在葫芦科作物遗传改良中的研究进展

doi:10.11924/j.issn.1000-6850.casb2022-0697

中国农学通报 ›› 2023, Vol. 39 ›› Issue (22): 23-33.doi: 10.11924/j.issn.1000-6850.casb2022-0697

GWAS在葫芦科作物遗传改良中的研究进展

徐颖超¹(), 陆森¹^,², 张思程¹^,², 孟琦涛¹^,², 林惠境¹, 薛舒丹¹, 刘洪标¹, 郭汉权¹, 傅曼琴³, 宋东光²(), 钟玉娟¹()

¹ 广东省农业科学院蔬菜研究所/广东省蔬菜新技术研究重点实验室，广州 510640
² 佛山科学技术学院食品科学与工程学院，广东佛山 528231
³ 广东省农业科学院蚕业与农产品加工研究所/农业农村部功能食品重点实验室/广东省农产品加工重点实验室，广州 510610

收稿日期:2022-08-22 修回日期:2023-03-09 出版日期:2023-08-05 发布日期:2023-07-28
通讯作者: 宋东光，男，副教授，研究方向为遗传学。Tel：0757-82272751，E-mail：3dsong@163.com。钟玉娟，女，研究员，研究方向为蔬菜品质分子遗传研究。Tel：020-85161059，E-mail：zhongyujuan@gdaas.cn。
作者简介:
徐颖超，女，1994年出生，山东烟台人，助理研究员，博士，研究方向为蔬菜品质分子遗传研究。通信地址：510640 广东省广州市天河区金颖路66号广东省农业科学院蔬菜研究所，Tel：020-85161059，E-mail：xuyingchao@gdaas.cn。
基金资助:
广东省农业科学院协同创新中心课题项目“岭南特色果蔬多维品质数据库构建与应用及精深加工研究”(XT202226); 广东省农业科学院农业优势产业学科团队建设项目“优质高效瓜类产业研究”(202103TD); 国家自然科学基金面上基金“CmCCD7介导独脚金内酯合成调控中国南瓜果实类胡萝卜素积累和生长发育的分子机制”(32172604); 广东省现代农业产业技术体系项目“果蔬加工共性关键技术研究”(2022KJ117); 广东省农业科学院科技人才引进专项资金项目“优秀博士第三层次”(R2022YJ-YB3012); 广东省蔬菜新技术重点实验室开放基金“基于GWAS分析的中国南瓜碳水化合物相关性状关键基因挖掘与分子标记开发”(202201)

Progress of Genome-wide Association Studies in Genetic Improvement of Cucurbitaceae

XU Yingchao¹(), LU Sen¹^,², ZHANG Sicheng¹^,², MENG Qitao¹^,², LIN Huijing¹, XUE Shudan¹, LIU Hongbiao¹, GUO Hanquan¹, FU Manqin³, SONG Dongguang²(), ZHONG Yujuan¹()

¹ Vegetable Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640
² School of Food Science and Engineering, Foshan University of Science and Technology, Foshan, Guangdong 528231
³ Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou 510610

Received:2022-08-22 Revised:2023-03-09 Online:2023-08-05 Published:2023-07-28

摘要/Abstract

摘要：

为推进全基因组关联分析(GWAS，genome-wide association study)在葫芦科瓜类作物重要农艺性状关键遗传变异位点精准挖掘中的应用，文章介绍了GWAS的原理和统计模型，归纳了GWAS在鉴定群体中的遗传变异位点、解析植物代谢机制，并对其在实施精准遗传改良策略中体现出的优势进行了概述，系统梳理了GWAS在西瓜、甜瓜、黄瓜、南瓜等主要葫芦科瓜类作物遗传改良研究中的最新进展，同时对葫芦科作物育种研究中的多组学联合分析和数据库构建进行了展望，以期为葫芦科作物的遗传改良过程中提供更多的依据和参考。

关键词: GWAS, 葫芦科, 农艺性状, 单核苷酸多态性, 遗传改良, 基因定位

Abstract:

To advance the application of genome-wide association study (GWAS) in the precise mining of the key genetic variation loci associated with important agronomic traits in cucurbit crops, this paper introduced the principles and statistical models of GWAS, outlined the advantages of GWAS in identifying genetic variation loci in crops populations, studying plant metabolic mechanisms and implementing precise genetic improvement strategies. It also systematically reviewed the recent advances of GWAS in the genetic improvement of major cucurbit crops such as watermelon, melon, cucumber, pumpkin or other kinds of cucurbit crops. Furthermore, it provided an outlook on the joint multi-omics analysis and database in breeding research of cucurbit crops, giving a basis and reference in the process of genetic improvement of cucurbit crops.

Key words: genome-wide association study, Cucurbitaceae, agronomic traits, single nucleotide polymorphism, genetic improvement, gene mapping

徐颖超, 陆森, 张思程, 孟琦涛, 林惠境, 薛舒丹, 刘洪标, 郭汉权, 傅曼琴, 宋东光, 钟玉娟. GWAS在葫芦科作物遗传改良中的研究进展[J]. 中国农学通报, 2023, 39(22): 23-33.

XU Yingchao, LU Sen, ZHANG Sicheng, MENG Qitao, LIN Huijing, XUE Shudan, LIU Hongbiao, GUO Hanquan, FU Manqin, SONG Dongguang, ZHONG Yujuan. Progress of Genome-wide Association Studies in Genetic Improvement of Cucurbitaceae[J]. Chinese Agricultural Science Bulletin, 2023, 39(22): 23-33.

图/表 1

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物种		变异检测手段	模型算法	群体结构分析		亲缘关系		文献
西瓜		重测序	FaST-LMM	STRUCTURE		—		[13]
西瓜		GBS	EMMAX	PCA、STRUCTURE		K矩阵		[35]
西瓜		SRAP、RAPD、ISSR	GLM	STRUCTURE		UPGMA估计		[36]
西瓜		BSA-seq	MLM	PCA		K矩阵		[37]
西瓜		USDA提供重测序数据	EMMAX	PCA		K矩阵		[19]
西瓜		重测序数据	MLM+Q+K、GLM+Q	PCA		K矩阵		[38]
甜瓜		重测序	MLM、GML	ADMIXTURE		—		[39]
甜瓜		GBS	MLM	PCA		K矩阵		[40]
甜瓜		SSR CAPS	GLM、MLM	STRUCTURE		—		[41]
甜瓜	数据库+GBS		EMMAX		—		EMMAX内置的功能估计亲缘关系	[42]
甜瓜	BSA-seq mapping		GLM、MLM		PCA		K矩阵	[43]
黄瓜	GBS		FaST-LMM		STRUCTURE		—	[44]
黄瓜	GBS		GLM		—		K 矩阵	[45]
黄瓜	GBS		EMMA(GAPIT)		STRUCTURE		—	[46]
南瓜	GBS		BLINK、FarmCPU、CMLMM		PCA		K矩阵	[47]
葫芦瓜	RAD sequencing		MLM(PCA+Kin)、MLM(Q+K)、(TASSEL)		PCA、ADMIXTURE		K矩阵	[48]

物种		变异检测手段	模型算法	群体结构分析		亲缘关系		文献
西瓜		重测序	FaST-LMM	STRUCTURE		—		[13]
西瓜		GBS	EMMAX	PCA、STRUCTURE		K矩阵		[35]
西瓜		SRAP、RAPD、ISSR	GLM	STRUCTURE		UPGMA估计		[36]
西瓜		BSA-seq	MLM	PCA		K矩阵		[37]
西瓜		USDA提供重测序数据	EMMAX	PCA		K矩阵		[19]
西瓜		重测序数据	MLM+Q+K、GLM+Q	PCA		K矩阵		[38]
甜瓜		重测序	MLM、GML	ADMIXTURE		—		[39]
甜瓜		GBS	MLM	PCA		K矩阵		[40]
甜瓜		SSR CAPS	GLM、MLM	STRUCTURE		—		[41]
甜瓜	数据库+GBS		EMMAX		—		EMMAX内置的功能估计亲缘关系	[42]
甜瓜	BSA-seq mapping		GLM、MLM		PCA		K矩阵	[43]
黄瓜	GBS		FaST-LMM		STRUCTURE		—	[44]
黄瓜	GBS		GLM		—		K 矩阵	[45]
黄瓜	GBS		EMMA(GAPIT)		STRUCTURE		—	[46]
南瓜	GBS		BLINK、FarmCPU、CMLMM		PCA		K矩阵	[47]
葫芦瓜	RAD sequencing		MLM(PCA+Kin)、MLM(Q+K)、(TASSEL)		PCA、ADMIXTURE		K矩阵	[48]

GWAS在葫芦科作物遗传改良中的研究进展

Progress of Genome-wide Association Studies in Genetic Improvement of Cucurbitaceae

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