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

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

Abstract

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

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.

Figures/Tables 1

References 91

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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]