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Zhu X, Ni P, Sturrock M, Wang Y, Ding J, Chang Y, Hu J, Bao Z. Fine-mapping and association analysis of candidate genes for papilla number in sea cucumber, Apostichopus japonicus. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:343-355. [PMID: 37073167 PMCID: PMC10077181 DOI: 10.1007/s42995-022-00139-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 06/03/2022] [Indexed: 05/03/2023]
Abstract
The papilla number is one of the most economically important traits of sea cucumber in the China marketing trade. However, the genetic basis for papilla number diversity in holothurians is still scarce. In the present study, we conducted genome-wide association studies (GWAS) for the trait papilla number of sea cucumbers utilizing a set of 400,186 high-quality SNPs derived from 200 sea cucumbers. Two significant trait-associated SNPs that passed Bonferroni correction (P < 1.25E-7) were located in the intergenic region near PATS1 and the genic region of EIF4G, which were reported to play a pivotal role in cell growth and proliferation. The fine-mapping regions around the top two lead SNPs provided precise causative loci/genes related to papilla formation and cellular activity, including PPP2R3C, GBP1, and BCAS3. Potential SNPs with P < 1E-4 were acquired for the following GO and KEGG enrichment analysis. Moreover, the two lead SNPs were verified in another population of sea cucumber, and the expressive detection of three potential candidate genes PATS1, PPP2R3C, and EIF4G that near or cover the two lead SNPs was conducted in papilla tissue of TG (Top papilla number group) and BG (Bottom papilla number group) by qRT-PCR. We found the significantly higher expression profile of PATS1 (3.34-fold), PPP2R3C (4.90-fold), and EIF4G (4.23-fold) in TG, implying their potential function in papilla polymorphism. The present results provide valuable information to decipher the phenotype differences of the papilla trait and will provide a scientific basis for selective breeding in sea cucumbers. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-022-00139-w.
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Affiliation(s)
- Xinghai Zhu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Ping Ni
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Marc Sturrock
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, D02 YN77 Ireland
| | - Yangfan Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Jun Ding
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023 China
| | - Yaqing Chang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023 China
| | - Jingjie Hu
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya, 572000 China
| | - Zhenmin Bao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
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Liu A, Hou X, Zhang J, Wang W, Dong X, Li J, Zhu X, Xing Q, Huang X, Hu J, Bao Z. Tissue-Specific and Time-Dependent Expressions of PC4s in Bay Scallop ( Argopecten irradians irradians) Reveal Function Allocation in Thermal Response. Genes (Basel) 2022; 13:genes13061057. [PMID: 35741819 PMCID: PMC9223095 DOI: 10.3390/genes13061057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/10/2022] [Accepted: 06/10/2022] [Indexed: 12/10/2022] Open
Abstract
Transcriptional coactivator p15 (PC4) encodes a structurally conserved but functionally diverse protein that plays crucial roles in RNAP-II-mediated transcription, DNA replication and damage repair. Although structures and functions of PC4 have been reported in most vertebrates and some invertebrates, the PC4 genes were less systematically identified and characterized in the bay scallop Argopecten irradians irradians. In this study, five PC4 genes (AiPC4s) were successfully identified in bay scallops via whole-genome scanning through in silico analysis. Protein structure and phylogenetic analyses of AiPC4s were conducted to determine the identities and evolutionary relationships of these genes. Expression levels of AiPC4s were assessed in embryos/larvae at all developmental stages, in healthy adult tissues and in different tissues (mantles, gills, hemocytes and hearts) being processed under 32 °C stress with different time durations (0 h, 6 h, 12 h, 24 h, 3 d, 6 d and 10 d). Spatiotemporal expression profiles of AiPC4s suggested the functional roles of the genes in embryos/larvae at all developmental stages and in healthy adult tissues in bay scallop. Expression regulations (up- and down-) of AiPC4s under high-temperature stress displayed both tissue-specific and time-dependent patterns with function allocations, revealing that AiPC4s performed differentiated functions in response to thermal stress. This work provides clues of molecular function allocation of PC4 in scallops in response to thermal stress and helps in illustrating how marine bivalves resist elevated seawater temperature.
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Affiliation(s)
- Ancheng Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
| | - Xiujiang Hou
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
| | - Junhao Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
| | - Wen Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
| | - Xuecheng Dong
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
| | - Jianshu Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
| | - Xinghai Zhu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
| | - Qiang Xing
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Correspondence: ; Tel.: +86-532-82031969
| | - Xiaoting Huang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China (SOI-OUC), Sanya 572000, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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