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Identification of Distant Regulatory Elements Using Expression Quantitative Trait Loci Mapping for Heat-Responsive Genes in Oysters
Zhang, Kexin1,2,3; Wang, Jinpeng1,2,3,4; Ding, Fangfang1,2,3; Shi, Ruihui1,2,3; Wang, Wei1,5,6; Zhang, Guofan1,2,6; Li, Li1,3,5,6
2021-07-01
Source PublicationGENES
Volume12Issue:7Pages:12
Corresponding AuthorLi, Li(lili@qdio.ac.cn)
AbstractMany marine ectotherms, especially those inhabiting highly variable intertidal zones, develop high phenotypic plasticity in response to rapid climate change by modulating gene expression levels. Herein, we examined the regulatory architecture of heat-responsive gene expression plasticity in oysters using expression quantitative trait loci (eQTL) analysis. Using a backcross family of Crassostrea gigas and its sister species Crassostrea angulata under acute stress, 56 distant regulatory regions accounting for 6-26.6% of the gene expression variation were identified for 19 heat-responsive genes. In total, 831 genes and 164 single nucleotide polymorphisms (SNPs) that could potentially regulate expression of the target genes were screened in the eQTL region. The association between three SNPs and the corresponding target genes was verified in an independent family. Specifically, Marker13973 was identified for heat shock protein (HSP) family A member 9 (HspA9). Ribosomal protein L10a (RPL10A) was detected approximately 2 kb downstream of the distant regulatory SNP. Further, Marker14346-48 and Marker14346-85 were in complete linkage disequilibrium and identified for autophagy-related gene 7 (ATG7). Nuclear respiratory factor 1 (NRF1) was detected approximately 3 kb upstream of the two SNPs. These results suggested regulatory relationships between RPL10A and HSPA9 and between NRF1 and ATG7. Our findings indicate that distant regulatory mutations play an important role in the regulation of gene expression plasticity by altering upstream regulatory factors in response to heat stress. The identified eQTLs provide candidate biomarkers for predicting the persistence of oysters under future climate change scenarios.
Keywordoyster thermal adaption heat-responsive gene expression quantitative trait loci (eQTL) mapping distant regulatory locus
DOI10.3390/genes12071040
Indexed BySCI
Language英语
Funding ProjectNational Key R&D Program of China[2018YFD0900304] ; Strategic Priority Research Program of the Chinese Academy of Sciences[XDA23050402] ; Key Deployment Project of the Centre for Ocean Mega-Research of Science, Chinese Academy of Sciences[COMS2019Q06] ; Distinguished Young Scientists Research Fund of the Key Laboratory of Experimental Marine Biology, Chinese Academy of Sciences[KLEMB-DYS04] ; Blue Life Breakthrough Program of LMBB of Qingdao National Laboratory for Marine Science and Technology[MS2018NO02] ; Technology and the Modern Agroindustry Technology Research System[CARS-49]
WOS Research AreaGenetics & Heredity
WOS SubjectGenetics & Heredity
WOS IDWOS:000676497500001
PublisherMDPI
Citation statistics
Document Type期刊论文
Identifierhttp://ir.qdio.ac.cn/handle/337002/175795
Collection实验海洋生物学重点实验室
Corresponding AuthorLi, Li
Affiliation1.Chinese Acad Sci, Ctr Ocean Megasci, Inst Oceanol, 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.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
4.Shandong Acad Agr Sci, Inst Anim Sci & Vet Med, Jinan 250100, Peoples R China
5.Pilot Natl Lab Marine Sci & Technol, Lab Marine Fisheries Sci & Food Prod Proc, Qingdao 266237, Peoples R China
6.Natl & Local Joint Engn Lab Ecol Mariculture, Qingdao 266071, Peoples R China
First Author AffilicationCenter for Ocean Mega-Science, Chinese Academy of Sciences
Corresponding Author AffilicationCenter for Ocean Mega-Science, Chinese Academy of Sciences
Recommended Citation
GB/T 7714
Zhang, Kexin,Wang, Jinpeng,Ding, Fangfang,et al. Identification of Distant Regulatory Elements Using Expression Quantitative Trait Loci Mapping for Heat-Responsive Genes in Oysters[J]. GENES,2021,12(7):12.
APA Zhang, Kexin.,Wang, Jinpeng.,Ding, Fangfang.,Shi, Ruihui.,Wang, Wei.,...&Li, Li.(2021).Identification of Distant Regulatory Elements Using Expression Quantitative Trait Loci Mapping for Heat-Responsive Genes in Oysters.GENES,12(7),12.
MLA Zhang, Kexin,et al."Identification of Distant Regulatory Elements Using Expression Quantitative Trait Loci Mapping for Heat-Responsive Genes in Oysters".GENES 12.7(2021):12.
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