Identification of Distant Regulatory Elements Using Expression Quantitative Trait Loci Mapping for Heat-Responsive Genes in Oysters
Many 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...
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ftchinacasciocas:oai:ir.qdio.ac.cn:337002/175793 2023-05-15T15:58:20+02:00 Identification of Distant Regulatory Elements Using Expression Quantitative Trait Loci Mapping for Heat-Responsive Genes in Oysters Zhang, Kexin Wang, Jinpeng Ding, Fangfang Shi, Ruihui Wang, Wei Zhang, Guofan Li, Li 2021-07-01 http://ir.qdio.ac.cn/handle/337002/175793 https://doi.org/10.3390/genes12071040 英语 eng MDPI GENES http://ir.qdio.ac.cn/handle/337002/175793 doi:10.3390/genes12071040 oyster thermal adaption heat-responsive gene expression quantitative trait loci (eQTL) mapping distant regulatory locus Genetics & Heredity CRASSOSTREA-GIGAS SUMMER MORTALITY PACIFIC OYSTER STRESS HSP70 EVOLUTION TRANS EQTL TEMPERATURE DIVERGENCE 期刊论文 2021 ftchinacasciocas https://doi.org/10.3390/genes12071040 2022-06-27T05:46:09Z Many 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. Report Crassostrea gigas Pacific oyster Institute of Oceanology, Chinese Academy of Sciences: IOCAS-IR Pacific Genes 12 7 1040 |
institution |
Open Polar |
collection |
Institute of Oceanology, Chinese Academy of Sciences: IOCAS-IR |
op_collection_id |
ftchinacasciocas |
language |
English |
topic |
oyster thermal adaption heat-responsive gene expression quantitative trait loci (eQTL) mapping distant regulatory locus Genetics & Heredity CRASSOSTREA-GIGAS SUMMER MORTALITY PACIFIC OYSTER STRESS HSP70 EVOLUTION TRANS EQTL TEMPERATURE DIVERGENCE |
spellingShingle |
oyster thermal adaption heat-responsive gene expression quantitative trait loci (eQTL) mapping distant regulatory locus Genetics & Heredity CRASSOSTREA-GIGAS SUMMER MORTALITY PACIFIC OYSTER STRESS HSP70 EVOLUTION TRANS EQTL TEMPERATURE DIVERGENCE Zhang, Kexin Wang, Jinpeng Ding, Fangfang Shi, Ruihui Wang, Wei Zhang, Guofan Li, Li Identification of Distant Regulatory Elements Using Expression Quantitative Trait Loci Mapping for Heat-Responsive Genes in Oysters |
topic_facet |
oyster thermal adaption heat-responsive gene expression quantitative trait loci (eQTL) mapping distant regulatory locus Genetics & Heredity CRASSOSTREA-GIGAS SUMMER MORTALITY PACIFIC OYSTER STRESS HSP70 EVOLUTION TRANS EQTL TEMPERATURE DIVERGENCE |
description |
Many 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. |
format |
Report |
author |
Zhang, Kexin Wang, Jinpeng Ding, Fangfang Shi, Ruihui Wang, Wei Zhang, Guofan Li, Li |
author_facet |
Zhang, Kexin Wang, Jinpeng Ding, Fangfang Shi, Ruihui Wang, Wei Zhang, Guofan Li, Li |
author_sort |
Zhang, Kexin |
title |
Identification of Distant Regulatory Elements Using Expression Quantitative Trait Loci Mapping for Heat-Responsive Genes in Oysters |
title_short |
Identification of Distant Regulatory Elements Using Expression Quantitative Trait Loci Mapping for Heat-Responsive Genes in Oysters |
title_full |
Identification of Distant Regulatory Elements Using Expression Quantitative Trait Loci Mapping for Heat-Responsive Genes in Oysters |
title_fullStr |
Identification of Distant Regulatory Elements Using Expression Quantitative Trait Loci Mapping for Heat-Responsive Genes in Oysters |
title_full_unstemmed |
Identification of Distant Regulatory Elements Using Expression Quantitative Trait Loci Mapping for Heat-Responsive Genes in Oysters |
title_sort |
identification of distant regulatory elements using expression quantitative trait loci mapping for heat-responsive genes in oysters |
publisher |
MDPI |
publishDate |
2021 |
url |
http://ir.qdio.ac.cn/handle/337002/175793 https://doi.org/10.3390/genes12071040 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_relation |
GENES http://ir.qdio.ac.cn/handle/337002/175793 doi:10.3390/genes12071040 |
op_doi |
https://doi.org/10.3390/genes12071040 |
container_title |
Genes |
container_volume |
12 |
container_issue |
7 |
container_start_page |
1040 |
_version_ |
1766394066076958720 |