Genome-Wide Association Study Reveals PC4 as the Candidate Gene for Thermal Tolerance in Bay Scallop (Argopecten irradians irradians)
The increasing sea temperature caused by global warming has resulted in severe mortalities in maricultural scallops. Therefore, improving thermal tolerance has become an active research area in the scallop farming industry. Bay scallop (Argopecten irradians irradians) was introduced into China in 19...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2021-07-01
|
| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2021.650045/full |
| _version_ | 1818922345531703296 |
|---|---|
| author | Xinghai Zhu Pingping Liu Xiujiang Hou Junhao Zhang Jia Lv Wei Lu Qifan Zeng Xiaoting Huang Xiaoting Huang Qiang Xing Qiang Xing Zhenmin Bao Zhenmin Bao |
| author_facet | Xinghai Zhu Pingping Liu Xiujiang Hou Junhao Zhang Jia Lv Wei Lu Qifan Zeng Xiaoting Huang Xiaoting Huang Qiang Xing Qiang Xing Zhenmin Bao Zhenmin Bao |
| author_sort | Xinghai Zhu |
| collection | DOAJ |
| description | The increasing sea temperature caused by global warming has resulted in severe mortalities in maricultural scallops. Therefore, improving thermal tolerance has become an active research area in the scallop farming industry. Bay scallop (Argopecten irradians irradians) was introduced into China in 1982 and has developed into a vast aquaculture industry in northern China. To date, genetic studies on thermal tolerance in bay scallops are limited, and no systematic screening of thermal tolerance-related loci or genes has been conducted in this species. In the present study, we conducted a genome-wide association study (GWAS) for thermal tolerance using the Arrhenius break temperature (ABT) indicators of 435 bay scallops and 38,011 single nucleotide polymorphism (SNP) markers. The GWAS identified 1,906 significant thermal tolerance-associated SNPs located in 16 chromosomes of bay scallop. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses showed that 638 genes were enriched in 42 GO terms, while 549 annotated genes were enriched in aggregation pathways. Additionally, the SNP (15-5091-20379557-1) with the lowest P value was located in the transcriptional coactivator p15 (PC4) gene, which is involved in regulating DNA damage repair and stabilizing genome functions. Further analysis in another population identified two new thermal tolerance-associated SNPs in the first coding sequence of PC4 in bay scallops (AiPC4). Moreover, AiPC4 expression levels were significantly correlated (r = 0.675–0.962; P < 0.05) with the ABT values of the examined bay scallops. Our data suggest that AiPC4 might be a positive regulator of thermal tolerance and a potential candidate gene for molecular breeding in bay scallop aiming at thermal tolerance improvement. |
| first_indexed | 2024-12-20T01:52:04Z |
| format | Article |
| id | doaj.art-e086218980894d13a4c21c3382b55baf |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-20T01:52:04Z |
| publishDate | 2021-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-e086218980894d13a4c21c3382b55baf2022-12-21T19:57:37ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-07-011210.3389/fgene.2021.650045650045Genome-Wide Association Study Reveals PC4 as the Candidate Gene for Thermal Tolerance in Bay Scallop (Argopecten irradians irradians)Xinghai Zhu0Pingping Liu1Xiujiang Hou2Junhao Zhang3Jia Lv4Wei Lu5Qifan Zeng6Xiaoting Huang7Xiaoting Huang8Qiang Xing9Qiang Xing10Zhenmin Bao11Zhenmin Bao12MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, ChinaMOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, ChinaMOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, ChinaMOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, ChinaMOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, ChinaMOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, ChinaMOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, ChinaMOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, ChinaLaboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, ChinaMOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, ChinaLaboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, ChinaMOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, ChinaLaboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, ChinaThe increasing sea temperature caused by global warming has resulted in severe mortalities in maricultural scallops. Therefore, improving thermal tolerance has become an active research area in the scallop farming industry. Bay scallop (Argopecten irradians irradians) was introduced into China in 1982 and has developed into a vast aquaculture industry in northern China. To date, genetic studies on thermal tolerance in bay scallops are limited, and no systematic screening of thermal tolerance-related loci or genes has been conducted in this species. In the present study, we conducted a genome-wide association study (GWAS) for thermal tolerance using the Arrhenius break temperature (ABT) indicators of 435 bay scallops and 38,011 single nucleotide polymorphism (SNP) markers. The GWAS identified 1,906 significant thermal tolerance-associated SNPs located in 16 chromosomes of bay scallop. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses showed that 638 genes were enriched in 42 GO terms, while 549 annotated genes were enriched in aggregation pathways. Additionally, the SNP (15-5091-20379557-1) with the lowest P value was located in the transcriptional coactivator p15 (PC4) gene, which is involved in regulating DNA damage repair and stabilizing genome functions. Further analysis in another population identified two new thermal tolerance-associated SNPs in the first coding sequence of PC4 in bay scallops (AiPC4). Moreover, AiPC4 expression levels were significantly correlated (r = 0.675–0.962; P < 0.05) with the ABT values of the examined bay scallops. Our data suggest that AiPC4 might be a positive regulator of thermal tolerance and a potential candidate gene for molecular breeding in bay scallop aiming at thermal tolerance improvement.https://www.frontiersin.org/articles/10.3389/fgene.2021.650045/fullgenome-wide association studyArgopecten irradians irradiansthermal tolerancesingle nucleotide polymorphismtranscriptional coactivator p15 |
| spellingShingle | Xinghai Zhu Pingping Liu Xiujiang Hou Junhao Zhang Jia Lv Wei Lu Qifan Zeng Xiaoting Huang Xiaoting Huang Qiang Xing Qiang Xing Zhenmin Bao Zhenmin Bao Genome-Wide Association Study Reveals PC4 as the Candidate Gene for Thermal Tolerance in Bay Scallop (Argopecten irradians irradians) Frontiers in Genetics genome-wide association study Argopecten irradians irradians thermal tolerance single nucleotide polymorphism transcriptional coactivator p15 |
| title | Genome-Wide Association Study Reveals PC4 as the Candidate Gene for Thermal Tolerance in Bay Scallop (Argopecten irradians irradians) |
| title_full | Genome-Wide Association Study Reveals PC4 as the Candidate Gene for Thermal Tolerance in Bay Scallop (Argopecten irradians irradians) |
| title_fullStr | Genome-Wide Association Study Reveals PC4 as the Candidate Gene for Thermal Tolerance in Bay Scallop (Argopecten irradians irradians) |
| title_full_unstemmed | Genome-Wide Association Study Reveals PC4 as the Candidate Gene for Thermal Tolerance in Bay Scallop (Argopecten irradians irradians) |
| title_short | Genome-Wide Association Study Reveals PC4 as the Candidate Gene for Thermal Tolerance in Bay Scallop (Argopecten irradians irradians) |
| title_sort | genome wide association study reveals pc4 as the candidate gene for thermal tolerance in bay scallop argopecten irradians irradians |
| topic | genome-wide association study Argopecten irradians irradians thermal tolerance single nucleotide polymorphism transcriptional coactivator p15 |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2021.650045/full |
| work_keys_str_mv | AT xinghaizhu genomewideassociationstudyrevealspc4asthecandidategeneforthermaltoleranceinbayscallopargopectenirradiansirradians AT pingpingliu genomewideassociationstudyrevealspc4asthecandidategeneforthermaltoleranceinbayscallopargopectenirradiansirradians AT xiujianghou genomewideassociationstudyrevealspc4asthecandidategeneforthermaltoleranceinbayscallopargopectenirradiansirradians AT junhaozhang genomewideassociationstudyrevealspc4asthecandidategeneforthermaltoleranceinbayscallopargopectenirradiansirradians AT jialv genomewideassociationstudyrevealspc4asthecandidategeneforthermaltoleranceinbayscallopargopectenirradiansirradians AT weilu genomewideassociationstudyrevealspc4asthecandidategeneforthermaltoleranceinbayscallopargopectenirradiansirradians AT qifanzeng genomewideassociationstudyrevealspc4asthecandidategeneforthermaltoleranceinbayscallopargopectenirradiansirradians AT xiaotinghuang genomewideassociationstudyrevealspc4asthecandidategeneforthermaltoleranceinbayscallopargopectenirradiansirradians AT xiaotinghuang genomewideassociationstudyrevealspc4asthecandidategeneforthermaltoleranceinbayscallopargopectenirradiansirradians AT qiangxing genomewideassociationstudyrevealspc4asthecandidategeneforthermaltoleranceinbayscallopargopectenirradiansirradians AT qiangxing genomewideassociationstudyrevealspc4asthecandidategeneforthermaltoleranceinbayscallopargopectenirradiansirradians AT zhenminbao genomewideassociationstudyrevealspc4asthecandidategeneforthermaltoleranceinbayscallopargopectenirradiansirradians AT zhenminbao genomewideassociationstudyrevealspc4asthecandidategeneforthermaltoleranceinbayscallopargopectenirradiansirradians |