Genome-wide mapping of regulatory variants for temperature- and salinity-adaptive genes reveals genetic basis of genotype-by-environment interaction in Crassostrea ariakensis

doi:10.1016/j.envres.2023.116614

IOCAS-IR > 实验海洋生物学重点实验室

	Genome-wide mapping of regulatory variants for temperature- and salinity-adaptive genes reveals genetic basis of genotype-by-environment interaction in Crassostrea ariakensis
	Zhang, Kexin 1,2,4; Yang, Qi 1; Du, Mingyang 1,2,4; Zhang, Ziyan 1,2,4; Wang, Wei 1,3,5; Zhang, Guofan 1,2,5; Li, Ao 1,3,5; Li, Li 1,3,4,5,6,7
	2023-11-01
发表期刊	ENVIRONMENTAL RESEARCH
ISSN	0013-9351
卷号	236 页码:10
通讯作者	Li, Ao([email protected]) ; Li, Li([email protected])
摘要	Regulatory variants in gene expression serve as bridges linking genetic variation and phenotypic plasticity. Environmental conditions typically influence the effects of regulatory variants on phenotypic plasticity; however, such genotype-by-environment interactions (G x E) are poorly understood. This study aimed to investigate the genetic basis of G x E in estuarine oyster (Crassostrea ariakensis), which is an important model animal for studying environmental adaption owing to its high plasticity and large intraspecific divergence. Genome-wide mapping of expression quantitative trait loci (eQTLs) for 23 environmental adaptive genes was performed for 256 estuarine oysters. We identified 1194 eQTL single nucleotide polymorphisms (eSNPs), including 433 cis- eSNPs in four genes and 722 trans-eSNPs in eight genes. The expression variation explanation of cis-eSNPs (9.95%) was significantly higher than that of trans-eSNPs (9.15%). We specifically showed cis-and trans-eSNPs with high linkage disequilibrium (LD) for Traf7, Slc6a5, Ggt, and Dap3. For example, we identified a cis-regu-latory LD block containing 68 cis-eSNP and a trans-regulatory LD block, including 20 trans-eSNPs in Traf7. A high proportion (85%) of 40 vital eSNPs exhibited significant G x E effects. We identified crossing and nonparallel interactions of G x E, with the tag cis-eSNPs of Baat and Slc6a5 as representatives. Our results indicated that cis- eQTLs are highly conserved. This study provides insights into the understanding of adaptive evolutionary mechanisms and phenotypic response prediction to variable environments, as well as the genetic improvement for superior adaptive traits for genetic resource conservation and aquaculture.
关键词	Temperature and salinity Adaptation Genotype-by-environment interaction Gene expression Cis-andtrans-eQTL Crassostrea ariakensis
DOI	10.1016/j.envres.2023.116614
收录类别	SCI
语种	英语
资助项目	National Key R amp; D Program of China[2022YFD2400304]; Strategic Priority Research Program of the Chinese Academy of Sciences[XDA23050402]; Key Research and Development Program of Shandong[2022LZGC015]; National Natural Science Foundation of China[32101353]; Young Elite Scientists Sponsorship Program by China Association of Science and Technology[2021QNRC001]; Key Technology Research and Industrialization Demonstration Projects of Qingdao[22-3-3-hygg-2-hy]; China Agriculture Research System of MOF and MARA[CARS-49]
WOS研究方向	Environmental Sciences & Ecology ; Public, Environmental & Occupational Health
WOS类目	Environmental Sciences ; Public, Environmental & Occupational Health
WOS记录号	WOS:001051004500001
出版者	ACADEMIC PRESS INC ELSEVIER SCIENCE
WOS关键词	PHENOTYPIC PLASTICITY ; ECOLOGICAL GENOMICS ; TRANS-EQTL ; EXPRESSION ; EVOLUTION ; ADAPTATION ; CIS ; ASSOCIATION ; DIVERGENCE ; RESPONSES
引用统计	被引频次：3[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/182784
专题	实验海洋生物学重点实验室
通讯作者	Li, Ao; Li, Li
作者单位	1.Chinese Acad Sci, Inst Oceanol, Ctr Ocean Mega Sci, CAS & Shandong Prov Key Lab Expt Marine Biol, Qingdao 266071, Peoples R China 2.Pilot Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao 266237, Peoples R China 3.Chinese Acad Sci, Key Lab Breeding Biotechnol & Sustainable Aquacult, Wuhan 430072, Peoples R China 4.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 5.Natl & Local Joint Engn Lab Ecol Mariculture, Qingdao 266071, Peoples R China 6.Shandong Technol Innovat Ctr Oyster Seed Ind, Qingdao 266000, Peoples R China 7.Inst Oceanol Chinese Acad Sci, 7 Nanhai Rd, Qingdao, Peoples R China
第一作者单位	中国科学院海洋研究所
通讯作者单位	中国科学院海洋研究所
推荐引用方式 GB/T 7714	Zhang, Kexin,Yang, Qi,Du, Mingyang,et al. Genome-wide mapping of regulatory variants for temperature- and salinity-adaptive genes reveals genetic basis of genotype-by-environment interaction in Crassostrea ariakensis[J]. ENVIRONMENTAL RESEARCH,2023,236:10.
APA	Zhang, Kexin.,Yang, Qi.,Du, Mingyang.,Zhang, Ziyan.,Wang, Wei.,...&Li, Li.(2023).Genome-wide mapping of regulatory variants for temperature- and salinity-adaptive genes reveals genetic basis of genotype-by-environment interaction in Crassostrea ariakensis.ENVIRONMENTAL RESEARCH,236,10.
MLA	Zhang, Kexin,et al."Genome-wide mapping of regulatory variants for temperature- and salinity-adaptive genes reveals genetic basis of genotype-by-environment interaction in Crassostrea ariakensis".ENVIRONMENTAL RESEARCH 236(2023):10.

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