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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ftdoajarticles:oai:doaj.org/article:bbd726e83c5447fdb7db1b5fc955f7d3 2023-05-15T15:58:56+02:00 Identification of Distant Regulatory Elements Using Expression Quantitative Trait Loci Mapping for Heat-Responsive Genes in Oysters Kexin Zhang Jinpeng Wang Fangfang Ding Ruihui Shi Wei Wang Guofan Zhang Li Li 2021-07-01T00:00:00Z https://doi.org/10.3390/genes12071040 https://doaj.org/article/bbd726e83c5447fdb7db1b5fc955f7d3 EN eng MDPI AG https://www.mdpi.com/2073-4425/12/7/1040 https://doaj.org/toc/2073-4425 doi:10.3390/genes12071040 2073-4425 https://doaj.org/article/bbd726e83c5447fdb7db1b5fc955f7d3 Genes, Vol 12, Iss 1040, p 1040 (2021) oyster thermal adaption heat-responsive gene expression quantitative trait loci (eQTL) mapping distant regulatory locus Genetics QH426-470 article 2021 ftdoajarticles https://doi.org/10.3390/genes12071040 2022-12-31T10:25:22Z 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 angulat a 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. Article in Journal/Newspaper Crassostrea gigas Directory of Open Access Journals: DOAJ Articles Genes 12 7 1040 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
oyster thermal adaption heat-responsive gene expression quantitative trait loci (eQTL) mapping distant regulatory locus Genetics QH426-470 |
spellingShingle |
oyster thermal adaption heat-responsive gene expression quantitative trait loci (eQTL) mapping distant regulatory locus Genetics QH426-470 Kexin Zhang Jinpeng Wang Fangfang Ding Ruihui Shi Wei Wang Guofan Zhang 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 QH426-470 |
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 angulat a 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 |
Article in Journal/Newspaper |
author |
Kexin Zhang Jinpeng Wang Fangfang Ding Ruihui Shi Wei Wang Guofan Zhang Li Li |
author_facet |
Kexin Zhang Jinpeng Wang Fangfang Ding Ruihui Shi Wei Wang Guofan Zhang Li Li |
author_sort |
Kexin Zhang |
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 AG |
publishDate |
2021 |
url |
https://doi.org/10.3390/genes12071040 https://doaj.org/article/bbd726e83c5447fdb7db1b5fc955f7d3 |
genre |
Crassostrea gigas |
genre_facet |
Crassostrea gigas |
op_source |
Genes, Vol 12, Iss 1040, p 1040 (2021) |
op_relation |
https://www.mdpi.com/2073-4425/12/7/1040 https://doaj.org/toc/2073-4425 doi:10.3390/genes12071040 2073-4425 https://doaj.org/article/bbd726e83c5447fdb7db1b5fc955f7d3 |
op_doi |
https://doi.org/10.3390/genes12071040 |
container_title |
Genes |
container_volume |
12 |
container_issue |
7 |
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1040 |
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1766394717470195712 |