Genome-wide analysis with additive and epistasis effects reveals growth-related loci and candidate genes in hybrid Argopecten scallops

doi:10.1016/j.aquaculture.2024.741018

	Genome-wide analysis with additive and epistasis effects reveals growth-related loci and candidate genes in hybrid Argopecten scallops
	Song, Xinyu 1,4; Ning, Junhao 1; Wang, Quanchao 1; Liu, Guilong 5; Xu, Xin 5; Wang, Chunde 1,3,6; Lu, Xia2,7
发表期刊	AQUACULTURE
ISSN	0044-8486
	2024-08-30
卷号	589 页码:14
关键词	Argopecten scallops Hybridization Genome-wide association study (GWAS) Growth -related traits Additive and epistatic effects
DOI	10.1016/j.aquaculture.2024.741018
通讯作者	Wang, Chunde([email protected]) ; Lu, Xia([email protected])
英文摘要	The first filial (F1) generation from the successful hybridization of bay scallops (Argopecten irradians) and Peruvian scallops (A. purpuratus) exhibits significant heterosis, playing a crucial role in enhancing the germplasm and increasing yields of the scallops. However, there is significant variation in the growth traits of the F1 hybrid population, and there is little information concerning its hereditary basis. To unravel the heterosis mechanism and identify key loci and genes contributing to superhybrids, genome-wide association study (GWAS) with additive and epistasis models were conducted for six growth-related traits in the F1 hybrid scallop population in this study. In total, 18,789,547 single nucleotide polymorphisms (SNPs) were identified after filtering from 198 hybrid individuals, comprising 63.5% of maternal loci and 36.5% of paternal loci. The additive model revealed 2768 associated SNPs and 14 candidate genes, with most of the loci associated with the body mass traits. The additive-additive epistatic model identified 133,094 SNP interaction pairs and 20 candidate gene pairs with exon region SNPs, which were predominantly associated with shell morphology traits. Almost all the SNP pairs associated with body mass traits were maternal-maternal interactions, but the shell morphology traits had the most maternal-paternal and maternal-maternal interactions, suggesting that body mass traits might be affected mainly by maternal effects and that parental interaction effects mainly contributed to the shell size of the hybrid scallops. Both in the shell morphology and the body mass traits, multiple loci participate in epistasis, interacting with more than one locus and forming high-order epistatic interactions, which could be critical factors contributing to the heterosis observed in hybrid scallops. The identified associated loci and candidate genes not only constitute valuable resources for the molecular breeding of hybrid scallops, contributing to the improvement of growth-related traits, but also revealed mechanisms underlying heterosis in aquatic species, providing insights into the advantages of heterosis and paving the way for future research on hybridization in aquatic organisms.
资助机构	National Key Research and Development Program of China ; National Natural Science Foundation of China ; Scientific and Technological Project of Yantai, Shandong Province ; Earmarked Fund for Shandong Modern Agro- Industry Technology Research System
收录类别	SCI
语种	英语
关键词[WOS]	TRIGLYCERIDE TRANSFER PROTEIN ; BAY SCALLOP ; LINES REVEALS ; BODY-WEIGHT ; HETEROSIS ; TRAITS ; QTL ; ASSOCIATION ; DOMINANCE ; YIELD
研究领域[WOS]	Fisheries ; Marine & Freshwater Biology
WOS记录号	WOS:001237277600002
引用统计
文献类型	期刊论文
条目标识符	http://ir.yic.ac.cn/handle/133337/36005
专题	海岸带生物学与生物资源利用重点实验室海岸带生物学与生物资源利用重点实验室_海岸带生物资源高效利用研究与发展中心
通讯作者	Wang, Chunde; Lu, Xia
作者单位	1.Chinese Acad Sci, Yantai Inst Coastal Zone Res, Res & Dev Ctr Efficient Utilizat Coastal Bioresour, Yantai 264003, Shandong, Peoples R China 2.Yantai Univ, Sch Oceang, Yantai 264005, Shandong, Peoples R China 3.Qingdao Agr Univ, Coll Marine Sci & Engn, Qingdao 266109, Shandong, Peoples R China 4.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 5.Yantai Spring Sea AquaSeed Ltd, Yantai 264006, Peoples R China 6.17 Chunhui Rd, Yantai 264003, Peoples R China 7.30 Qingquan Rd, Yantai 264005, Peoples R China
推荐引用方式 GB/T 7714	Song, Xinyu,Ning, Junhao,Wang, Quanchao,et al. Genome-wide analysis with additive and epistasis effects reveals growth-related loci and candidate genes in hybrid Argopecten scallops[J]. AQUACULTURE,2024,589:14.
APA	Song, Xinyu.,Ning, Junhao.,Wang, Quanchao.,Liu, Guilong.,Xu, Xin.,...&Lu, Xia.(2024).Genome-wide analysis with additive and epistasis effects reveals growth-related loci and candidate genes in hybrid Argopecten scallops.AQUACULTURE,589,14.
MLA	Song, Xinyu,et al."Genome-wide analysis with additive and epistasis effects reveals growth-related loci and candidate genes in hybrid Argopecten scallops".AQUACULTURE 589(2024):14.