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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MDPI AG
2021-07-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/12/7/1040 |
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| 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 |
| collection | DOAJ |
| 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 <i>Crassostrea gigas</i> and its sister species <i>Crassostrea angulat</i><i>a</i> 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 (<i>HspA9</i>). Ribosomal protein L10a (<i>RPL10A</i>) 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 (<i>ATG7</i>). Nuclear respiratory factor 1 (<i>NRF1</i>) was detected approximately 3 kb upstream of the two SNPs. These results suggested regulatory relationships between <i>RPL10A</i> and <i>HSPA9</i> and between <i>NRF1</i> and <i>ATG7</i>. 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. |
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| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T09:38:33Z |
| publishDate | 2021-07-01 |
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| series | Genes |
| spelling | doaj.art-bbd726e83c5447fdb7db1b5fc955f7d32023-11-22T03:50:42ZengMDPI AGGenes2073-44252021-07-01127104010.3390/genes12071040Identification of Distant Regulatory Elements Using Expression Quantitative Trait Loci Mapping for Heat-Responsive Genes in OystersKexin Zhang0Jinpeng Wang1Fangfang Ding2Ruihui Shi3Wei Wang4Guofan Zhang5Li Li6CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, ChinaCAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, ChinaCAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, ChinaCAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, ChinaCAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, ChinaCAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, ChinaCAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, ChinaMany 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 <i>Crassostrea gigas</i> and its sister species <i>Crassostrea angulat</i><i>a</i> 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 (<i>HspA9</i>). Ribosomal protein L10a (<i>RPL10A</i>) 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 (<i>ATG7</i>). Nuclear respiratory factor 1 (<i>NRF1</i>) was detected approximately 3 kb upstream of the two SNPs. These results suggested regulatory relationships between <i>RPL10A</i> and <i>HSPA9</i> and between <i>NRF1</i> and <i>ATG7</i>. 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.https://www.mdpi.com/2073-4425/12/7/1040oysterthermal adaptionheat-responsive geneexpression quantitative trait loci (eQTL) mappingdistant regulatory locus |
| spellingShingle | 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 Genes oyster thermal adaption heat-responsive gene expression quantitative trait loci (eQTL) mapping distant regulatory locus |
| title | 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_short | 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 |
| topic | oyster thermal adaption heat-responsive gene expression quantitative trait loci (eQTL) mapping distant regulatory locus |
| url | https://www.mdpi.com/2073-4425/12/7/1040 |
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