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Zhou B, Ling L, Wang B, Yang F, Hou M, Liu F, Li Y, Luo H, He W, Ye H. Hepatopancreas Transcriptome Analysis of Spinibarbus sinensis to Reveal Different Growth-Related Genes. Genes (Basel) 2024; 15:949. [PMID: 39062728 PMCID: PMC11276559 DOI: 10.3390/genes15070949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/15/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
Spinibarbus sinensis, also known as Qingbo, is an important economic fish in China. However, the detailed mechanisms underlying its growth are still unknown. To excavate the genes and signaling pathways related to its growth, we compared the transcriptome profiles of the hepatopancreas tissues of S. sinensis, with two groups of growth rate for evaluation. An average of 66,304,909 and 68,739,585 clean reads were obtained in the fast growth (FG) and slow growth (SG) group, respectively. The differential gene expression analysis results showed that 272 differentially expressed genes (DEGs) were screened between the FG and SG groups, including 101 up-regulated genes and 171 down-regulated genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis results showed that GO terms related to metabolic process, organic substance metabolic process, and catalytic activity were enriched, pathway signals related to steroid biosynthesis and protein digestion and absorption were also detected. Meanwhile, the potential key regulatory genes sst2, fndc4, and cckra related to the growth of S. sinensis were screened. Reverse transcript fluorescence quantitative PCR (RT-qPCR) validation of 18 DEGs associated with growth differences showed that the RT-qPCR results were consistent with RNA-seq analysis, and nine genes, stk31, gpr149, angptl1, fstl1, sik1, ror2, nlrc3, pdlim2, and nav2 were significantly expressed in the FG group. bmp1, stc1, gpatch8, sstrt2, s100a1, ktf6, cckar6, sync1, bhlha15, a total of nine genes were significantly expressed in the SG group. This study provides basic information for improving the growth characteristics of S. sinensis and the functional research of candidate genes.
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Affiliation(s)
- Bo Zhou
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Yibin 644000, China; (B.Z.); (B.W.); (F.Y.)
| | - Leyan Ling
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China; (L.L.); (M.H.); (F.L.); (Y.L.); (H.L.); (W.H.)
| | - Bin Wang
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Yibin 644000, China; (B.Z.); (B.W.); (F.Y.)
| | - Fei Yang
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Yibin 644000, China; (B.Z.); (B.W.); (F.Y.)
| | - Mengdan Hou
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China; (L.L.); (M.H.); (F.L.); (Y.L.); (H.L.); (W.H.)
| | - Fan Liu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China; (L.L.); (M.H.); (F.L.); (Y.L.); (H.L.); (W.H.)
| | - Yu Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China; (L.L.); (M.H.); (F.L.); (Y.L.); (H.L.); (W.H.)
| | - Hui Luo
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China; (L.L.); (M.H.); (F.L.); (Y.L.); (H.L.); (W.H.)
| | - Wenping He
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China; (L.L.); (M.H.); (F.L.); (Y.L.); (H.L.); (W.H.)
| | - Hua Ye
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China; (L.L.); (M.H.); (F.L.); (Y.L.); (H.L.); (W.H.)
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Zhang J, Wang J, Gu Z, Liu X. Transcriptome Analysis of Different Aquaculture Substrates on the Immune Response of Babylonia areolata. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:609-622. [PMID: 38717622 DOI: 10.1007/s10126-024-10324-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 04/29/2024] [Indexed: 06/15/2024]
Abstract
To assess the impact of different substrates in a recirculating water system on the immune response and antioxidant capacity of Babylonia areolata, we conducted a comparative analysis of the transcriptomes and antioxidant performance of the digestive glands in three substrate environments (sand-S group, ceramic granules-C group, and PVC breeding nest-P group). Transcriptome results revealed that the S group and P group exhibited the highest number of differentially expressed genes (DEGs), with a total of 2218 DEGs, including 928 upregulated and 1290 downregulated DEGs. The C group and P group had 1055 DEGs in common, with 316 upregulated and 739 downregulated DEGs. The C group and S group had the fewest DEGs, with 521 in total, including 303 upregulated and 218 downregulated DEGs. GO enrichment analysis showed that in the S vs P group, terms such as catalytic activity, membrane part, and cellular process were enriched with 287, 262, and 180 DEGs, respectively. In the C vs P group, binding, cellular process, and cell part were enriched with 146, 135, and 127 DEGs, respectively. In the C vs S group, catalytic activity, membrane part, and metabolic process were enriched with 90, 83, and 59 DEGs, respectively. Kegg enrichment analysis revealed significant changes in immune-related pathways in the S vs P group, including lysosome, phagosome, and leukocyte transendothelial migration, with 30, 13, and 10 enriched DEGs, respectively. In the C vs P group, phagosome, drug metabolism-other enzymes, and N-Glycan biosynthesis showed significant changes in immune-related pathways, with 9, 6, and 4 enriched DEGs, respectively. In the C vs S group, lysosome, PPAR signaling pathway, and fatty acid degradation exhibited significant changes in immune-related pathways, with 8, 4, and 3 enriched DEGs, respectively. Regarding antioxidant capacity, the S group showed significantly higher total T-AOC than the other experimental groups, while CAT, SOD, POD, and AKP were lower than in the C and P groups. The ACP level in the Sand group was not significantly different from the P group but significantly lower than the C group. In conclusion, substrate environments significantly influence the immune-related genes and key antioxidant enzyme activities in B. areolata.
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Affiliation(s)
- Jiahua Zhang
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200092, China.
- Key Laboratory of Aquaculture Facilities Engineering, Ministry of Agriculture and Rural Affairs, Shanghai, China.
| | - Jie Wang
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200092, China
- Key Laboratory of Aquaculture Facilities Engineering, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Zhaojun Gu
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200092, China
- Key Laboratory of Aquaculture Facilities Engineering, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Xingguo Liu
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200092, China
- Key Laboratory of Aquaculture Facilities Engineering, Ministry of Agriculture and Rural Affairs, Shanghai, China
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Hua J, Zhong C, Chen W, Fu J, Wang J, Wang Q, Zhu G, Li Y, Tao Y, Zhang M, Dong Y, Lu S, Liu W, Qiang J. Single nucleotide polymorphism SNP19140160 A > C is a potential breeding locus for fast-growth largemouth bass (Micropterus salmoides). BMC Genomics 2024; 25:64. [PMID: 38229016 DOI: 10.1186/s12864-024-09962-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/02/2024] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Largemouth bass (Micropterus salmoides) has significant economic value as a high-yielding fish species in China's freshwater aquaculture industry. Determining the major genes related to growth traits and identifying molecular markers associated with these traits serve as the foundation for breeding strategies involving gene pyramiding. In this study, we screened restriction-site associated DNA sequencing (RAD-seq) data to identify single nucleotide polymorphism (SNP) loci potentially associated with extreme growth differences between fast-growth and slow-growth groups in the F1 generation of a largemouth bass population. RESULTS We subsequently identified associations between these loci and specific candidate genes related to four key growth traits (body weight, body length, body height, and body thickness) based on SNP genotyping. In total, 4,196,486 high-quality SNPs were distributed across 23 chromosomes. Using a population-specific genotype frequency threshold of 0.7, we identified 30 potential SNPs associated with growth traits. Among the 30 SNPs, SNP19140160, SNP9639603, SNP9639605, and SNP23355498 showed significant associations; three of them (SNP9639603, SNP9639605, and SNP23355498) were significantly associated with one trait, body length, in the F1 generation, and one (SNP19140160) was significantly linked with four traits (body weight, height, length, and thickness) in the F1 generation. The markers SNP19140160 and SNP23355498 were located near two growth candidate genes, fam174b and ppip5k1b, respectively, and these candidate genes were closely linked with growth, development, and feeding. The average body weight of the group with four dominant genotypes at these SNP loci in the F1 generation population (703.86 g) was 19.63% higher than that of the group without dominant genotypes at these loci (588.36 g). CONCLUSIONS Thus, these four markers could be used to construct a population with dominant genotypes at loci related to fast growth. These findings demonstrate how markers can be used to identify genes related to fast growth, and will be useful for molecular marker-assisted selection in the breeding of high-quality largemouth bass.
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Grants
- No. JBGS [2021] 130 Project of Seed Industry Revitalization in Jiangsu Province, China
- No. JBGS [2021] 130 Project of Seed Industry Revitalization in Jiangsu Province, China
- No. JBGS [2021] 130 Project of Seed Industry Revitalization in Jiangsu Province, China
- No. JBGS [2021] 130 Project of Seed Industry Revitalization in Jiangsu Province, China
- No. JBGS [2021] 130 Project of Seed Industry Revitalization in Jiangsu Province, China
- No. JBGS [2021] 130 Project of Seed Industry Revitalization in Jiangsu Province, China
- No. JBGS [2021] 130 Project of Seed Industry Revitalization in Jiangsu Province, China
- No. JBGS [2021] 130 Project of Seed Industry Revitalization in Jiangsu Province, China
- No. JBGS [2021] 130 Project of Seed Industry Revitalization in Jiangsu Province, China
- No. JBGS [2021] 130 Project of Seed Industry Revitalization in Jiangsu Province, China
- No. JBGS [2021] 130 Project of Seed Industry Revitalization in Jiangsu Province, China
- No. JBGS [2021] 130 Project of Seed Industry Revitalization in Jiangsu Province, China
- No. JBGS [2021] 130 Project of Seed Industry Revitalization in Jiangsu Province, China
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- No. SNG2021009 the Suzhou Science and Technology Program
- No. SNG2021009 the Suzhou Science and Technology Program
- No. SNG2021009 the Suzhou Science and Technology Program
- No. SNG2021009 the Suzhou Science and Technology Program
- No. SNG2021009 the Suzhou Science and Technology Program
- No. SNG2021009 the Suzhou Science and Technology Program
- No. SNG2021009 the Suzhou Science and Technology Program
- No. SNG2021009 the Suzhou Science and Technology Program
- No. SNG2021009 the Suzhou Science and Technology Program
- No. SNG2021009 the Suzhou Science and Technology Program
- No. SNG2021009 the Suzhou Science and Technology Program
- No. SNG2021009 the Suzhou Science and Technology Program
- No. SNG2021009 the Suzhou Science and Technology Program
- No. SNG2021009 the Suzhou Science and Technology Program
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Affiliation(s)
- Jixiang Hua
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Chunyi Zhong
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Wenhua Chen
- Suzhou Aquatic Technology Extension Station, Suzhou, 215004, China
| | - Jianjun Fu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Jian Wang
- Guangxi Xinjian Investment Group Limited Company, Hechi, 530201, China
| | - Qingchun Wang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Geyan Zhu
- Suzhou Aquatic Technology Extension Station, Suzhou, 215004, China
| | - Yan Li
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Yifan Tao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Maoyou Zhang
- Suzhou Aquatic Technology Extension Station, Suzhou, 215004, China
| | - Yalun Dong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Siqi Lu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Wenting Liu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Jun Qiang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China.
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
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Yang J, Lu B, Yu Z, Zhang L, Chen Y, Chen Z, Han C, Shu H. Multiple Tissues Transcriptome of Zig-Zag Eel ( Mastacembelus armatus) with Different Growth Rates. Animals (Basel) 2024; 14:248. [PMID: 38254417 PMCID: PMC10812625 DOI: 10.3390/ani14020248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/06/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
In order to explore the main regulatory genes and related pathways of growth traits, transcriptome sequencing was first performed on the brain, liver, and muscle tissues of 3-month-old M. armatus with different growth rates. By comparative transcriptome analysis of fast-growing and slow-growing groups of M. armatus, a total of 2887 DEGs were screened, of which 59 up-regulated genes and 105 down-regulated genes were detected in the brain, 146 up-regulated genes and 202 down-regulated genes were detected in the liver, and 529 up-regulated genes and 1846 down-regulated genes were detected in muscle, including insulin-like growth factor binding protein 1a (IGFBP1A), insulin-like growth factor binding protein 1b (IGFBP1B), myosin, light chain 1 (MYL1), and myoglobin (MB). Through Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, we identified a total of 288 significantly enriched GO entries and 68 significantly enriched KEGG pathways related to growth, such as skeletal muscle tissue development, insulin-like growth factor binding, and the mitotic cell cycle. These key genes and signaling pathways may play a key role in regulating the growth of M. armatus. Digging into the regulatory mechanisms of these key genes will provide a theoretical basis for further exploration of the molecular mechanisms related to the growth and development of M. armatus, and help to breed new varieties of M. armatus with rapid growth.
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Affiliation(s)
| | | | | | | | | | | | - Chong Han
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China; (J.Y.); (B.L.); (Z.Y.); (L.Z.); (Y.C.); (Z.C.)
| | - Hu Shu
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China; (J.Y.); (B.L.); (Z.Y.); (L.Z.); (Y.C.); (Z.C.)
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Yin Y, Zhang Y, Hua Z, Wu A, Pan X, Yang J, Wang X. Muscle transcriptome analysis provides new insights into the growth gap between fast- and slow-growing Sinocyclocheilus grahami. Front Genet 2023; 14:1217952. [PMID: 37538358 PMCID: PMC10394708 DOI: 10.3389/fgene.2023.1217952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 07/06/2023] [Indexed: 08/05/2023] Open
Abstract
Sinocyclocheilus grahami is an economically valuable and famous fish in Yunnan Province, China. However, given its slow growth (40 g/2 years) and large growth differences among individuals, its growth performance needs to be improved for sustainable future use, in which molecular breeding technology can play an important role. In the current study, we conducted muscle transcriptomic analysis to investigate the growth gaps among individuals and the mechanism underlying growth within 14 fast- and 14 slow-growth S. grahami. In total, 1,647 differentially expressed genes (DEGs) were obtained, including 947 up-regulated and 700 down-regulated DEGs in fast-growth group. Most DEGs were significantly enriched in ECM-receptor interaction, starch and sucrose metabolism, glycolysis/gluconeogenesis, pyruvate metabolism, amino acids biosynthesis and metabolism, peroxisome, and PPAR signaling pathway. Some genes related to glycogen degradation, glucose transport, and glycolysis (e.g., adipoq, prkag1, slc2a1, agl, pygm, pgm1, pfkm, gapdh, aldoa, pgk1, pgam2, bpgm, and eno3) were up-regulated, while some genes related to fatty acid degradation and transport (e.g., acox1, acaa1, fabp1b.1, slc27a1, and slc27a2) and amino acid metabolism (e.g., agxt, shmt1, glula, and cth) were down-regulated in the fast-growth group. Weighted gene co-expression network analysis identified col1a1, col1a2, col5a1, col6a2, col10a1, col26a1, bglap, and krt15 as crucial genes for S. grahami growth. Several genes related to bone and muscle growth (e.g., bmp2, bmp3, tgfb1, tgfb2, gdf10, and myog) were also up-regulated in the fast-growth group. These results suggest that fast-growth fish may uptake adequate energy (e.g., glucose, fatty acid, and amino acids) from fodder, with excess energy substances used to synthesize collagen to accelerate bone and muscle growth after normal life activities are maintained. Moreover, energy uptake may be the root cause, while collagen synthesis may be the direct reason for the growth gap between fast- and slow-growth fish. Hence, improving food intake and collagen synthesis may be crucial for accelerating S. grahami growth, and further research is required to fully understand and confirm these associations.
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Affiliation(s)
- Yanhui Yin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yuanwei Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zexiang Hua
- Fishery Technology Extension Station of Yunnan, Kunming, Yunnan, China
| | - Anli Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xiaofu Pan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Junxing Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xiaoai Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
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Guo Z, Zuo J, Feng J, Li J, Zhang S, Ma K. Impact of Titanium Dioxide-Graphene Oxide (TiO 2-GO) Composite Nanoparticle on the Juveniles of the Giant River Prawn, Macrobrachium rosenbergii: Physio-Biochemistry and Transcriptional Response. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:45-56. [PMID: 36527515 DOI: 10.1007/s10126-022-10180-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/31/2022] [Indexed: 06/17/2023]
Abstract
Nanomaterials are used in many fields, resulting in inevitably releasing into the aquatic environment. The presence of nanomaterials, including TiO2-GO in the aquatic environment, can be toxic to aquatic organisms. However, few studies have focused on the effects of TiO2-GO composite nanoparticle on crustaceans. In the present study, the giant river prawn Macrobrachium rosenbergii juveniles were exposed to two concentrations of TiO2-GO composite nanoparticle (0.1 and 0.5 mg/L). The effects of TiO2-GO composite exposure on activities of digestive and antioxidant-related enzymes and expressions of growth and immune-related genes at the transcriptome were studied. The results showed that the survival rate and growth performance were not negatively affected by TiO2-GO composite at the two exposure levels. Nevertheless, exposure to TiO2-GO composite causes an effect on the activities of digestive and antioxidant enzymes in the juvenile prawns. The enzyme activities of CAT, SOD, GSH-Px, AMS, TPS, and LPS in the 0.1 mg/L TiO2-GO composite experimental group were markedly reduced than those in the control group. Additionally, the expression level of genes involved in growth and immunity was significantly affected by TiO2-GO composite. After exposure to the 0.1 mg/L TiO2-GO composite, the mRNA expression level of MSTN was significantly increased, but the level of EcR, Raptor, and CaBP was significantly decreased. However, the mRNA levels of the CTL, TLR, JAK, and STAT were significantly increased after exposure to the 0.5 mg/L concentration of TiO2-GO composite. Furthermore, to understand the molecular mechanism of M. rosenbergii under TiO2-GO composite exposure, RNA-Seq was employed to analyze the changes of the muscle and hepatopancreas transcriptome. Compared with the control group, we identified 5166 and 4784 differentially expressed genes (DEGs) in the muscle and hepatopancreas, respectively (p < 0.05). Based on gene ontology and KEGG analysis, significant differences were observed in the DEGs involved in activity and binding, metabolism, immune response, and environmental information processing. These results showed that exposure to TiO2-GO composite nanoparticle led to the changes of enzyme activity and gene expression, suggesting that TiO2-GO composite existing in aquatic environments would disrupt the physiology of M. rosenbergii. This study will serve as a foundation for subsequent research into the evaluation of nanomaterial toxicity on crustacean species.
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Affiliation(s)
- Ziqi Guo
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai, People's Republic of China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, People's Republic of China
| | - Jiabao Zuo
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, People's Republic of China
| | - Jianbin Feng
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai, People's Republic of China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, People's Republic of China
| | - Jiale Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai, People's Republic of China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, People's Republic of China
| | - Shupeng Zhang
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, People's Republic of China
| | - Keyi Ma
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai, People's Republic of China.
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, People's Republic of China.
- College of Fisheries and Life Science, Pudong New Area, Shanghai Ocean University, 999 Hucheng Huan Road, Shanghai, 201306, People's Republic of China.
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7
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Li Z, Du X, Wen L, Li Y, Qin J, Chen Z, Huang Y, Wu X, Luo H, Lin Y, Ye H. Transcriptome analysis reveals the involvement of ubiquitin-proteasome pathway in the regulation of muscle growth of rice flower carp. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2021; 41:100948. [PMID: 34942523 DOI: 10.1016/j.cbd.2021.100948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 12/13/2022]
Abstract
Growth mechanism of economically important aquaculture species has aroused widespread interest among scholars. Rice flower carp (Cyprinus carpio), commonly cultured in rice-fish farming systems, shows wide variation in body mass at the same age, which limits the development of commercial aquaculture. In this study, muscle tissues from 20-month-old fish of different sizes were used for transcriptome analysis and muscle histological studies. The muscle histological analysis showed the muscle growth in rice flower carp main depends on the hypertrophic growth of muscle fibers. A total of 30,590 unigenes were generated by muscle trancriptome analysis, including 403 differentially expressed genes (DEGs). Of these, 157 DEGs were upregulated and 246 DEGs were downregulated. Nine unigenes related to the ubiquitin-proteasome pathway were identified using differential expression analysis. This study initially revealed that the differences in growth of rice flower carp could be due to hypertrophic growth of muscle fibers caused by higher protein deposition, and the ubiquitin-proteasome pathway was an important factor affecting the growth rate of rice flower carp. E3 ubiquitin-protein ligase ari7, g2e3, Neurl1 and rnf144ab were upregulated in the slow-growing fish, indicating the binding of ubiquitin to target protein was enhanced. Foxo3 was upregulated in the slow-growing fish, which could promote the muscle loss. Eif4a2 was upregulated in the fast-growing fish, increasing protein translation efficiency. Some genes related to active muscle contraction such as actb, actg, camk2a, and camk2b were upregulated in the fast-growing rice flower carp muscle. In summary, these results provide valuable information about the key genes for use as biomarkers of growth in selective breeding programs for rice flower carp and provide novel insights into the regulatory mechanisms of muscle growth.
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Affiliation(s)
- Zhe Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), College of Fisheries, Southwest University, Chongqing 402460, China
| | - Xuesong Du
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Science, Nanning 530021, China
| | - Luting Wen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Science, Nanning 530021, China
| | - Yu Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), College of Fisheries, Southwest University, Chongqing 402460, China
| | - Junqi Qin
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Science, Nanning 530021, China
| | - Zhong Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Science, Nanning 530021, China
| | - Yin Huang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Science, Nanning 530021, China
| | - Xia Wu
- College of Life Science, Guangxi Normal University, Guilin 541006, China
| | - Hui Luo
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), College of Fisheries, Southwest University, Chongqing 402460, China.
| | - Yong Lin
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Science, Nanning 530021, China.
| | - Hua Ye
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), College of Fisheries, Southwest University, Chongqing 402460, China.
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Ye W, Duan Y, Zhang W, Cheng Y, Shi M, Xia XQ. Comprehensive analysis of hub mRNA, lncRNA and miRNA, and associated ceRNA networks implicated in grass carp (Ctenopharyngodon idella) growth traits. Genomics 2021; 113:4004-4014. [PMID: 34614437 DOI: 10.1016/j.ygeno.2021.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/03/2021] [Accepted: 10/01/2021] [Indexed: 01/19/2023]
Abstract
Grass carp (Ctenopharyngodon idella) is the most productive freshwater aquaculture fish in worldwide. However, the molecular mechanism of its growth traits has not been fully elucidated. Whole transcriptome analysis of the brain and hepatopancreas of 29 six-month-old grass carp with different growth rates was performed. Weighted gene co-expression network analysis (WGCNA) was used to construct a weighted gene co-expression network of mRNA, miRNA and lncRNA separately. A total of 35 hub mRNAs, 47 hub lncRNAs and 33 hub miRNAs were identified from the brain, 37 hub mRNAs, 110 hub lncRNAs and 36 hub miRNAs were identified from the hepatopancreas. The ceRNA networks in the brain and hepatopancreas were involved in brain development and nutrient metabolism, respectively. Overall, this is the first investigation of the growth-related transcriptomic characteristics in the brain and hepatopancreas of grass carp, thus will help us to further explore the molecular mechanism of grass carp growth rate.
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Affiliation(s)
- Weidong Ye
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - You Duan
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wanting Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingyin Cheng
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Mijuan Shi
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xiao-Qin Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China; The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
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9
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Chen H, Jiang D, Li Z, Wang Y, Yang X, Li S, Li S, Yang W, Li G. Comparative Physiological and Transcriptomic Profiling Offers Insight into the Sexual Dimorphism of Hepatic Metabolism in Size-Dimorphic Spotted Scat ( Scatophagus argus). Life (Basel) 2021; 11:life11060589. [PMID: 34205643 PMCID: PMC8233746 DOI: 10.3390/life11060589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/13/2021] [Accepted: 06/20/2021] [Indexed: 12/13/2022] Open
Abstract
The spotted scat (Scatophagus argus) is an economically important cultured marine fish that exhibits a typical sexual size dimorphism (SSD). SSD has captivated considerable curiosity for farmed fish production; however, up till now the exact underlying mechanism remains largely unclear. As an important digestive and metabolic organ, the liver plays key roles in the regulation of fish growth. It is necessary to elucidate its significance as a downstream component of the hypothalamic-pituitary-liver axis in the formation of SSD. In this study, the liver physiological differences between the sexes were evaluated in S. argus, and the activity of several digestive and metabolic enzymes were affected by sex. Females had higher amylase, protease, and glucose-6-phosphate dehydrogenase activities, while males exhibited markedly higher hepatic lipase and antioxidant enzymes activities. A comparative transcriptomics was then performed to characterize the responsive genes. Illumina sequencing generated 272.6 million clean reads, which were assembled into 79,115 unigenes. A total of 259 differentially expressed genes were identified and a few growth-controlling genes such as igf1 and igfbp1 exhibited female-biased expression. Further analyses showed that several GO terms and pathways associated with metabolic process, particularly lipid and energy metabolisms, were significantly enriched. The male liver showed a more active mitochondrial energy metabolism, implicating an increased energy expenditure associated with reproduction. Collectively, the female-biased growth dimorphism of S. argus may be partially attributed to sexually dimorphic metabolism in the liver. These findings would facilitate further understanding of the nature of SSD in teleost fish.
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Affiliation(s)
- Huapu Chen
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; (H.C.); (D.J.); (Z.L.); (Y.W.)
| | - Dongneng Jiang
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; (H.C.); (D.J.); (Z.L.); (Y.W.)
| | - Zhiyuan Li
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; (H.C.); (D.J.); (Z.L.); (Y.W.)
| | - Yaorong Wang
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; (H.C.); (D.J.); (Z.L.); (Y.W.)
| | - Xuewei Yang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518052, China; (X.Y.); (S.L.)
| | - Shuangfei Li
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518052, China; (X.Y.); (S.L.)
| | - Shuisheng Li
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China;
- Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou 510275, China
| | - Wei Yang
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; (H.C.); (D.J.); (Z.L.); (Y.W.)
- Food and Environmental Engineering Department, Yangjiang Polytechnic, Yangjiang 529566, China
- Correspondence: (W.Y.); (G.L.); Tel.: +86-662-3362800 (W.Y.); +86-759-2383124 (G.L.); Fax: +86-662-3316729 (W.Y.); +86-759-2382459 (G.L.)
| | - Guangli Li
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; (H.C.); (D.J.); (Z.L.); (Y.W.)
- Correspondence: (W.Y.); (G.L.); Tel.: +86-662-3362800 (W.Y.); +86-759-2383124 (G.L.); Fax: +86-662-3316729 (W.Y.); +86-759-2382459 (G.L.)
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Dai YF, Shen YB, Wang ST, Zhang JH, Su YH, Bao SC, Xu XY, Li JL. RNA-Seq Transcriptome Analysis of the Liver and Brain of the Black Carp (Mylopharyngodon piceus) During Fasting. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2021; 23:389-401. [PMID: 33864541 DOI: 10.1007/s10126-021-10032-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
The black carp (Mylopharyngodon piceus) is an important carnivorous freshwater-cultured species. To understand the molecular basis underlying the response of black carp to fasting, we used RNA-Seq to analyze the liver and brain transcriptome of fasting fish. Annotation to the NCBI database identified 66,609 unigenes, of which 22,841 were classified into the Gene Ontology database and 15,925 were identified in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Comparative analysis of the expression profile between fasting and normal feeding fish revealed 13,737 differentially expressed genes (P < 0.05), of which 12,480 were found in liver tissue and 1257 were found in brain tissue. The KEGG pathway analysis showed significant differences in expression of genes involved in metabolic and immune pathways, such as the insulin signaling pathway, PI3K-Akt signaling pathway, cAMP signaling pathway, FoxO signaling pathway, AMPK signaling pathway, endocytosis, and apoptosis. Quantitative real-time PCR analysis confirmed that expression of the genes encoding the factors involved in those pathways differed between fasting and feeding fish. These results provide valuable information about the molecular response mechanism of black carp under fasting conditions.
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Affiliation(s)
- Ya-Fan Dai
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China
| | - Yu-Bang Shen
- College of Aquaculture and Life Science, Shanghai Ocean University, Shanghai, 201306, China.
| | - Shen-Tong Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China
| | - Jia-Hua Zhang
- Shanghai Engineering Research Centre of Aquaculture, Shanghai Ocean University, Shanghai, 201306, China
| | - Yu-Hong Su
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China
| | - Sheng-Chen Bao
- Shanghai Engineering Research Centre of Aquaculture, Shanghai Ocean University, Shanghai, 201306, China
| | - Xiao-Yan Xu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China
| | - Jia-Le Li
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, P. R. China.
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11
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Cloning, prokaryotic expression, purification, and functional verification of the insulin gene in black carp (Mylopharyngodon piceus). AQUACULTURE AND FISHERIES 2021. [DOI: 10.1016/j.aaf.2021.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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