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Genome-wide mapping of regulatory variants for temperature- and salinity-adaptive genes reveals genetic basis of genotype-by-environment interaction in Crassostrea ariakensis
Zhang, Kexin1,2,4; Yang, Qi1; Du, Mingyang1,2,4; Zhang, Ziyan1,2,4; Wang, Wei1,3,5; Zhang, Guofan1,2,5; Li, Ao1,3,5; Li, Li1,3,4,5,6,7
2023-11-01
Source PublicationENVIRONMENTAL RESEARCH
ISSN0013-9351
Volume236Pages:10
Corresponding AuthorLi, Ao(ali@qdio.ac.cn) ; Li, Li(lili@qdio.ac.cn)
AbstractRegulatory 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.
KeywordTemperature and salinity Adaptation Genotype-by-environment interaction Gene expression Cis-andtrans-eQTL Crassostrea ariakensis
DOI10.1016/j.envres.2023.116614
Indexed BySCI
Language英语
Funding ProjectNational 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 Research AreaEnvironmental Sciences & Ecology ; Public, Environmental & Occupational Health
WOS SubjectEnvironmental Sciences ; Public, Environmental & Occupational Health
WOS IDWOS:001051004500001
PublisherACADEMIC PRESS INC ELSEVIER SCIENCE
WOS KeywordPHENOTYPIC PLASTICITY ; ECOLOGICAL GENOMICS ; TRANS-EQTL ; EXPRESSION ; EVOLUTION ; ADAPTATION ; CIS ; ASSOCIATION ; DIVERGENCE ; RESPONSES
Citation statistics
Cited Times:2[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.qdio.ac.cn/handle/337002/182784
Collection实验海洋生物学重点实验室
Corresponding AuthorLi, Ao; Li, Li
Affiliation1.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
First Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Corresponding Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Recommended Citation
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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