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Song H, Dong T, Wang W, Yan X, Geng C, Bai S, Hu H. GWAS Enhances Genomic Prediction Accuracy of Caviar Yield, Caviar Color and Body Weight Traits in Sturgeons Using Whole-Genome Sequencing Data. Int J Mol Sci 2024; 25:9756. [PMID: 39273703 PMCID: PMC11395957 DOI: 10.3390/ijms25179756] [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: 08/03/2024] [Revised: 09/05/2024] [Accepted: 09/07/2024] [Indexed: 09/15/2024] Open
Abstract
Caviar yield, caviar color, and body weight are crucial economic traits in sturgeon breeding. Understanding the molecular mechanisms behind these traits is essential for their genetic improvement. In this study, we performed whole-genome sequencing on 673 Russian sturgeons, renowned for their high-quality caviar. With an average sequencing depth of 13.69×, we obtained approximately 10.41 million high-quality single nucleotide polymorphisms (SNPs). Using a genome-wide association study (GWAS) with a single-marker regression model, we identified SNPs and genes associated with these traits. Our findings revealed several candidate genes for each trait: caviar yield: TFAP2A, RPS6KA3, CRB3, TUBB, H2AFX, morc3, BAG1, RANBP2, PLA2G1B, and NYAP1; caviar color: NFX1, OTULIN, SRFBP1, PLEK, INHBA, and NARS; body weight: ACVR1, HTR4, fmnl2, INSIG2, GPD2, ACVR1C, TANC1, KCNH7, SLC16A13, XKR4, GALR2, RPL39, ACVR2A, ADCY10, and ZEB2. Additionally, using the genomic feature BLUP (GFBLUP) method, which combines linkage disequilibrium (LD) pruning markers with GWAS prior information, we improved genomic prediction accuracy by 2%, 1.9%, and 3.1% for caviar yield, caviar color, and body weight traits, respectively, compared to the GBLUP method. In conclusion, this study enhances our understanding of the genetic mechanisms underlying caviar yield, caviar color, and body weight traits in sturgeons, providing opportunities for genetic improvement of these traits through genomic selection.
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Affiliation(s)
- Hailiang Song
- Fisheries Science Institute, Beijing Academy of Agriculture and Forestry Sciences & Beijing Key Laboratory of Fisheries Biotechnology, Beijing 100068, China
- Key Laboratory of Sturgeon Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hangzhou 311799, China
- National Innovation Center for Digital Seed Industry, Beijing 100097, China
| | - Tian Dong
- Fisheries Science Institute, Beijing Academy of Agriculture and Forestry Sciences & Beijing Key Laboratory of Fisheries Biotechnology, Beijing 100068, China
- Key Laboratory of Sturgeon Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hangzhou 311799, China
| | - Wei Wang
- Fisheries Science Institute, Beijing Academy of Agriculture and Forestry Sciences & Beijing Key Laboratory of Fisheries Biotechnology, Beijing 100068, China
- Key Laboratory of Sturgeon Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hangzhou 311799, China
| | - Xiaoyu Yan
- Fisheries Science Institute, Beijing Academy of Agriculture and Forestry Sciences & Beijing Key Laboratory of Fisheries Biotechnology, Beijing 100068, China
- Key Laboratory of Sturgeon Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hangzhou 311799, China
| | - Chenfan Geng
- Fisheries Science Institute, Beijing Academy of Agriculture and Forestry Sciences & Beijing Key Laboratory of Fisheries Biotechnology, Beijing 100068, China
- Key Laboratory of Sturgeon Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hangzhou 311799, China
| | - Song Bai
- Fisheries Science Institute, Beijing Academy of Agriculture and Forestry Sciences & Beijing Key Laboratory of Fisheries Biotechnology, Beijing 100068, China
- Key Laboratory of Sturgeon Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hangzhou 311799, China
| | - Hongxia Hu
- Fisheries Science Institute, Beijing Academy of Agriculture and Forestry Sciences & Beijing Key Laboratory of Fisheries Biotechnology, Beijing 100068, China
- Key Laboratory of Sturgeon Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hangzhou 311799, China
- National Innovation Center for Digital Seed Industry, Beijing 100097, China
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2
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Zhang H, Li P, Zhu Y, Jiang Y, Feng J, Zhao Z, Xu J. Contribution of elovl5a to Docosahexaenoic Acid (DHA) Synthesis at the Transcriptional Regulation Level in Common Carp, Cyprinus carpio. Animals (Basel) 2024; 14:544. [PMID: 38396511 PMCID: PMC10886045 DOI: 10.3390/ani14040544] [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: 12/22/2023] [Revised: 01/29/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Docosahexaenoic acid (DHA) is an essential nutrient for humans and plays a critical role in human development and health. Freshwater fish, such as the common carp (Cyprinus carpio), have a certain degree of DHA biosynthesis ability and could be a supplemental source of human DHA needs. The elongase of very-long-chain fatty acid 5 (Elovl5) is an important enzyme affecting polyunsaturated fatty acid (PUFA) biosynthesis. However, the function and regulatory mechanism of the elovl5 gene related to DHA synthesis in freshwater fish is not clear yet. Previous studies have found that there are two copies of the elovl5 gene, elovl5a and elovl5b, which have different functions. Our research group found significant DHA content differences among individuals in Yellow River carp (Cyprinus carpio var.), and four candidate genes were found to be related to DHA synthesis through screening. In this study, the expression level of elovl5a is decreased in the high-DHA group compared to the low-DHA group, which indicated the down-regulation of elovl5a in the DHA synthesis pathways of Yellow River carp. In addition, using a dual-luciferase reporter gene assay, we found that by targeting the 3'UTR region of elovl5a, miR-26a-5p could regulate DHA synthesis in common carp. After CRISPR/Cas9 disruption of elovl5a, the DHA content in the disrupted group was significantly higher than in the wildtype group; meanwhile, the expression level of elovl5a in the disrupted group was significantly reduced compared with the wildtype group. These results suggest that elovl5a may be down-regulating DHA synthesis in Yellow River carp. This study could provide useful information for future research on the genes and pathways that affect DHA synthesis.
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Affiliation(s)
- Hanyuan Zhang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (P.L.); (Y.Z.); (Y.J.); (Z.Z.)
| | - Peizhen Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (P.L.); (Y.Z.); (Y.J.); (Z.Z.)
| | - Youxiu Zhu
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (P.L.); (Y.Z.); (Y.J.); (Z.Z.)
| | - Yanliang Jiang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (P.L.); (Y.Z.); (Y.J.); (Z.Z.)
| | - Jianxin Feng
- Henan Academy of Fishery Sciences, Zhengzhou 450044, China;
| | - Zixia Zhao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (P.L.); (Y.Z.); (Y.J.); (Z.Z.)
| | - Jian Xu
- Fisheries Engineering Institute, Chinese Academy of Fishery Sciences, Beijing 100141, China
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3
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Li P, Liu W, Lu W, Wang J. Biochemical indices, gene expression, and SNPs associated with salinity adaptation in juvenile chum salmon ( Oncorhynchus keta) as determined by comparative transcriptome analysis. PeerJ 2022; 10:e13585. [PMID: 36117540 PMCID: PMC9477081 DOI: 10.7717/peerj.13585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/23/2022] [Indexed: 01/17/2023] Open
Abstract
Chum salmon (Oncorhynchus keta) migrate from freshwater to saltwater, and incur developmental, physiological and molecular adaptations as the salinity changes. The molecular regulation for salinity adaptation in chum salmon is currently not well defined. In this study, 1-g salmon were cultured under 0 (control group, D0), 8‰ (D8), 16‰ (D16), and 24‰ (D24) salinity conditions for 42 days. Na+/K+-ATPase and Ca2+/Mg2+-ATPase activities in the gill first increased and then decreased in response to higher salinity environments where D8 exhibited the highest Na+/K+ATPase and Ca2+/Mg2+-ATPase activity and D24 exhibited the lowest. Alkaline phosphatase (AKP) activity was elevated in all salinity treatment groups relative to controls, while no significant difference in acid phosphatase (ACP) activity was observed across treatment groups. De novo transcriptome sequencing in the D0 and D24 groups using RNA-Seq analysis identified 187,836 unigenes, of which 2,143 were differentially expressed in response to environmental salinity (71 up-regulated and 2,072 down-regulated). A total of 56,020 putative single nucleotide polymorphisms (SNPs) were also identified. The growth, development, osmoregulation and maturation factors of N-methyl-D-aspartate receptors (nmdas) expressed in memory formation, as well as insulin-like growth factor 1 (igf-1) and igf-binding proteins (igfbps) were further investigated using targeted qRT-PCR. The lowest expression of all these genes occurred in the low salinity environments (D8 or D16), while their highest expression occurred in the high salinity environments (D24). These results provide preliminary insight into salinity adaptation in chum salmon and a foundation for the development of marker-assisted breeding for this species.
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Affiliation(s)
- Peilun Li
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China,Key Open Laboratory of Cold Water Fish Germplasm Resources and Breeding of Heilongjiang Province, Heilongjiang River Fisheries Research Institute, Harbin, China
| | - Wei Liu
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China,Key Open Laboratory of Cold Water Fish Germplasm Resources and Breeding of Heilongjiang Province, Heilongjiang River Fisheries Research Institute, Harbin, China
| | - Wanqiao Lu
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China,Key Open Laboratory of Cold Water Fish Germplasm Resources and Breeding of Heilongjiang Province, Heilongjiang River Fisheries Research Institute, Harbin, China
| | - Jilong Wang
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China,Key Open Laboratory of Cold Water Fish Germplasm Resources and Breeding of Heilongjiang Province, Heilongjiang River Fisheries Research Institute, Harbin, China
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4
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Yuan D, Chen X, Gu H, Zou M, Zou Y, Fang J, Tao W, Dai X, Xiao S, Wang Z. Chromosomal genome of Triplophysa bleekeri provides insights into its evolution and environmental adaptation. Gigascience 2020; 9:giaa132. [PMID: 33231676 PMCID: PMC7684707 DOI: 10.1093/gigascience/giaa132] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 09/18/2020] [Accepted: 10/30/2020] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Intense stresses caused by high-altitude environments may result in noticeable genetic adaptions in native species. Studies of genetic adaptations to high elevations have been largely limited to terrestrial animals. How fish adapt to high-elevation environments is largely unknown. Triplophysa bleekeri, an endemic fish inhabiting high-altitude regions, is an excellent model to investigate the genetic mechanisms of adaptation to the local environment. Here, we assembled a chromosomal genome sequence of T. bleekeri, with a size of ∼628 Mb (contig and scaffold N50 of 3.1 and 22.9 Mb, respectively). We investigated the origin and environmental adaptation of T. bleekeri based on 21,198 protein-coding genes in the genome. RESULTS Compared with fish species living at low altitudes, gene families associated with lipid metabolism and immune response were significantly expanded in the T. bleekeri genome. Genes involved in DNA repair exhibit positive selection for T. bleekeri, Triplophysa siluroides, and Triplophysa tibetana, indicating that adaptive convergence in Triplophysa species occurred at the positively selected genes. We also analyzed whole-genome variants among samples from 3 populations. The results showed that populations separated by geological and artificial barriers exhibited obvious differences in genetic structures, indicating that gene flow is restricted between populations. CONCLUSIONS These results will help us expand our understanding of environmental adaptation and genetic diversity of T. bleekeri and provide valuable genetic resources for future studies on the evolution and conservation of high-altitude fish species such as T. bleekeri.
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Affiliation(s)
- Dengyue Yuan
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xuehui Chen
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Haoran Gu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Ming Zou
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei 430000, China
| | - Yu Zou
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei 430000, China
| | - Jian Fang
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei 430000, China
| | - Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xiangyan Dai
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Shijun Xiao
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei 430000, China
- College of Plant Protection, Jilin Agriculture University, Changchun, Jilin 130118, China
| | - Zhijian Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
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5
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Zhou T, Chen B, Ke Q, Zhao J, Pu F, Wu Y, Chen L, Zhou Z, Bai Y, Pan Y, Gong J, Zheng W, Xu P. Development and Evaluation of a High-Throughput Single-Nucleotide Polymorphism Array for Large Yellow Croaker ( Larimichthys crocea). Front Genet 2020; 11:571751. [PMID: 33193675 PMCID: PMC7645154 DOI: 10.3389/fgene.2020.571751] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/29/2020] [Indexed: 11/16/2022] Open
Abstract
High-density single-nucleotide polymorphism (SNP) genotyping array is an essential tool for genetic analyses of animals and plants. Large yellow croaker (Larimichthys crocea) is one of the most commercially important marine fish species in China. Although plenty of SNPs have been identified in large yellow croaker, no high-throughput genotyping array is available. In this study, a high-throughput SNP array named NingXin-I with 600K SNPs was developed and evaluated. A set of 82 large yellow croakers were collected from different locations of China and re-sequenced. A total of 9.34M SNPs were identified by mapping sequence reads to the large yellow croaker reference genome. About 1.98M candidate SNPs were selected for further analyses by using criteria such as SNP quality score and conversion performance in the final array. Finally, 579.5K SNPs evenly distributed across the large yellow croaker genome with an average spacing of 1.19 kb were proceeded to array production. The performance of NingXin-I array was evaluated in 96 large yellow croaker individuals from five populations, and 83.38% SNPs on the array were polymorphic sites. A further test of the NingXin-I array in five closely related species in Sciaenidae identified 26.68–56.23% polymorphic SNP rate across species. A phylogenetic tree inferred by using the genotype data generated by NingXin-I confirmed the phylogenetic distance of the species in Sciaenidae. The performance of NingXin-I in large yellow croaker and the other species in Sciaenidae suggested high accuracy and broad application. The NingXin-I array should be valuable for quantitative genetic studies, such as genome-wide association studies (GWASs), high-density linkage map construction, haplotype analysis, and genome-based selection.
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Affiliation(s)
- Tao Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Baohua Chen
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Qiaozhen Ke
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, China
| | - Ji Zhao
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Fei Pu
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yidi Wu
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Lin Chen
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Zhixiong Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yulin Bai
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Ying Pan
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, China
| | - Jie Gong
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Weiqiang Zheng
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, China
| | - Peng Xu
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, China
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6
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Cai M, Zou Y, Xiao S, Li W, Han Z, Han F, Xiao J, Liu F, Wang Z. Chromosome assembly of Collichthys lucidus, a fish of Sciaenidae with a multiple sex chromosome system. Sci Data 2019; 6:132. [PMID: 31341172 PMCID: PMC6656731 DOI: 10.1038/s41597-019-0139-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 06/19/2019] [Indexed: 12/15/2022] Open
Abstract
Collichthys lucidus (C. lucidus) is a commercially important marine fish species distributed in coastal regions of East Asia with the X1X1X2X2/X1X2Y multiple sex chromosome system. The karyotype for female C. lucidus is 2n = 48, while 2n = 47 for male ones. Therefore, C. lucidus is also an excellent model to investigate teleost sex-determination and sex chromosome evolution. We reported the first chromosome genome assembly of C. lucidus using Illumina short-read, PacBio long-read sequencing and Hi-C technology. An 877 Mb genome was obtained with a contig and scaffold N50 of 1.1 Mb and 35.9 Mb, respectively. More than 97% BUSCOs genes were identified in the C. lucidus genome and 28,602 genes were annotated. We identified potential sex-determination genes along chromosomes and found that the chromosome 1 might be involved in the formation of Y specific metacentric chromosome. The first C. lucidus chromosome-level reference genome lays a solid foundation for the following population genetics study, functional gene mapping of important economic traits, sex-determination and sex chromosome evolution studies for Sciaenidae and teleosts. Design Type(s) | sequence assembly objective • sequence annotation objective • transcription profiling design | Measurement Type(s) | whole genome sequencing assay • transcript expression assay | Technology Type(s) | DNA sequencing • RNA sequencing | Factor Type(s) | organism part | Sample Characteristic(s) | Collichthys lucidus |
Machine-accessible metadata file describing the reported data (ISA-Tab format)
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Affiliation(s)
- Mingyi Cai
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs; Fisheries College Jimei University, Xiamen, Fujian, China.
| | - Yu Zou
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs; Fisheries College Jimei University, Xiamen, Fujian, China
| | - Shijun Xiao
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei, China.,Wuhan Frasergen Bioinformatics, East Lake High-Tech Zone, Wuhan, China
| | - Wanbo Li
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs; Fisheries College Jimei University, Xiamen, Fujian, China
| | - Zhaofang Han
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs; Fisheries College Jimei University, Xiamen, Fujian, China
| | - Fang Han
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs; Fisheries College Jimei University, Xiamen, Fujian, China
| | - Junzhu Xiao
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs; Fisheries College Jimei University, Xiamen, Fujian, China
| | - Fujiang Liu
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs; Fisheries College Jimei University, Xiamen, Fujian, China
| | - Zhiyong Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs; Fisheries College Jimei University, Xiamen, Fujian, China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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7
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Waiho K, Shi X, Fazhan H, Li S, Zhang Y, Zheng H, Liu W, Fang S, Ikhwanuddin M, Ma H. High-Density Genetic Linkage Maps Provide Novel Insights Into ZW/ZZ Sex Determination System and Growth Performance in Mud Crab ( Scylla paramamosain). Front Genet 2019; 10:298. [PMID: 31024620 PMCID: PMC6459939 DOI: 10.3389/fgene.2019.00298] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 03/19/2019] [Indexed: 02/06/2023] Open
Abstract
Mud crab, Scylla paramamosain is one of the most important crustacean species in global aquaculture. To determine the genetic basis of sex and growth-related traits in S. paramamosain, a high-density genetic linkage map with 16,701 single nucleotide polymorphisms (SNPs) was constructed using SLAF-seq and a full-sib family. The consensus map has 49 linkage groups, spanning 5,996.66 cM with an average marker-interval of 0.81 cM. A total of 516 SNP markers, including 8 female-specific SNPs segregated in two quantitative trait loci (QTLs) for phenotypic sex were located on LG32. The presence of female-specific SNP markers only on female linkage map, their segregation patterns and lower female: male recombination rate strongly suggest the conformation of a ZW/ZZ sex determination system in S. paramamosain. The QTLs of most (90%) growth-related traits were found within a small interval (25.18–33.74 cM) on LG46, highlighting the potential involvement of LG46 in growth. Four markers on LG46 were significantly associated with 10–16 growth-related traits. BW was only associated with marker 3846. Based on the annotation of transcriptome data, 11 and 2 candidate genes were identified within the QTL regions of sex and growth-related traits, respectively. The newly constructed high-density genetic linkage map with sex-specific SNPs, and the identified QTLs of sex- and growth-related traits serve as a valuable genetic resource and solid foundation for marker-assisted selection and genetic improvement of crustaceans.
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Affiliation(s)
- Khor Waiho
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Xi Shi
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Hanafiah Fazhan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Yueling Zhang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Huaiping Zheng
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Wenhua Liu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Shaobin Fang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Mhd Ikhwanuddin
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China.,Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Hongyu Ma
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
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8
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Zhang H, Xu P, Jiang Y, Zhao Z, Feng J, Tai R, Dong C, Xu J. Genomic, Transcriptomic, and Epigenomic Features Differentiate Genes That Are Relevant for Muscular Polyunsaturated Fatty Acids in the Common Carp. Front Genet 2019; 10:217. [PMID: 30930941 PMCID: PMC6428711 DOI: 10.3389/fgene.2019.00217] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 02/27/2019] [Indexed: 12/15/2022] Open
Abstract
Polyunsaturated fatty acids (PUFAs) are a set of important nutrients that mainly include arachidonic acid (ARA4), docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), and α-linolenic acid (ALA). Recently, fish-derived PUFAs have been associated with cardiovascular health, fetal development, and improvement of brain functions. Studies have shown that fish muscular tissues are rich in PUFAs, which are influenced by various factors, including genetic variations, regulatory profiles, and methylation status of desaturase genes during fatty acid desaturation and elongation processes. However, the genetic mechanism and the pathways involved in fatty acid metabolism in fishes remain unclear. The overall aim of this study was to assess differences in gene expression responses among fishes with different fatty acid levels. To achieve this goal, we conducted genome-wide association analysis (GWAS) using a 250K SNP array in a population of 203 samples of common carp (Cyprinus carpio) and identified nine SNPs and 15 genes associated with muscular PUFA content. Then, RNA-Seq and whole genome bisulfite sequencing (WGBS) of different groups with high and low EPA, DHA, ARA4, and ALA contents in muscle, liver and brain tissues were conducted, resulting in 6,750 differentially expressed genes and 5,631 genes with differentially methylated promoters. Gene ontology and KEGG pathway enrichment analyses of RNA-Seq and WGBS results identified enriched pathways for fatty acid metabolism, which included the adipocytokine signaling pathway, ARA4 and linoleic acid metabolism pathway, and insulin signaling pathway. Integrated analysis indicated significant correlations between gene expression and methylation status among groups with high and low PUFA contents in muscular tissues. Taken together, these multi-level results uncovered candidate genes and pathways that are associated with fatty acid metabolism and paved the way for further genomic selection and carp breeding for PUFA traits.
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Affiliation(s)
- Hanyuan Zhang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Peng Xu
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, China
| | - Yanliang Jiang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Zixia Zhao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Jianxin Feng
- Henan Academy of Fishery Science, Zhengzhou, China
| | - Ruyu Tai
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Chuanju Dong
- College of Fishery, Henan Normal University, Xinxiang, China
| | - Jian Xu
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
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9
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Dong L, Han Z, Fang M, Xiao S, Wang Z. Genome-wide association study identifies loci for body shape in the large yellow croaker (Larimichthys crocea). AQUACULTURE AND FISHERIES 2019. [DOI: 10.1016/j.aaf.2018.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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10
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Gong G, Dan C, Xiao S, Guo W, Huang P, Xiong Y, Wu J, He Y, Zhang J, Li X, Chen N, Gui JF, Mei J. Chromosomal-level assembly of yellow catfish genome using third-generation DNA sequencing and Hi-C analysis. Gigascience 2018; 7:5106933. [PMID: 30256939 PMCID: PMC6228179 DOI: 10.1093/gigascience/giy120] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/25/2018] [Accepted: 09/18/2018] [Indexed: 01/12/2023] Open
Abstract
Background The yellow catfish, Pelteobagrus fulvidraco, belonging to the Siluriformes order, is an economically important freshwater aquaculture fish species in Asia, especially in Southern China. The aquaculture industry has recently been facing tremendous challenges in germplasm degeneration and poor disease resistance. As the yellow catfish exhibits notable sex dimorphism in growth, with adult males about two- to three-fold bigger than females, the way in which the aquaculture industry takes advantage of such sex dimorphism is another challenge. To address these issues, a high-quality reference genome of the yellow catfish would be a very useful resource. Findings To construct a high-quality reference genome for the yellow catfish, we generated 51.2 Gb short reads and 38.9 Gb long reads using Illumina and Pacific Biosciences (PacBio) sequencing platforms, respectively. The sequencing data were assembled into a 732.8 Mb genome assembly with a contig N50 length of 1.1 Mb. Additionally, we applied Hi-C technology to identify contacts among contigs, which were then used to assemble contigs into scaffolds, resulting in a genome assembly with 26 chromosomes and a scaffold N50 length of 25.8 Mb. Using 24,552 protein-coding genes annotated in the yellow catfish genome, the phylogenetic relationships of the yellow catfish with other teleosts showed that yellow catfish separated from the common ancestor of channel catfish ∼81.9 million years ago. We identified 1,717 gene families to be expanded in the yellow catfish, and those gene families are mainly enriched in the immune system, signal transduction, glycosphingolipid biosynthesis, and fatty acid biosynthesis. Conclusions Taking advantage of Illumina, PacBio, and Hi-C technologies, we constructed the first high-quality chromosome-level genome assembly for the yellow catfish P. fulvidraco. The genomic resources generated in this work not only offer a valuable reference genome for functional genomics studies of yellow catfish to decipher the economic traits and sex determination but also provide important chromosome information for genome comparisons in the wider evolutionary research community.
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Affiliation(s)
- Gaorui Gong
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Cheng Dan
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Shijun Xiao
- Wuhan Frasergen Bioinformatics, East Lake High-Tech Zone, Wuhan, Hubei, 430075, China
| | - Wenjie Guo
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Peipei Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academyof Sciences, University of the Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - Yang Xiong
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Junjie Wu
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yan He
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jicheng Zhang
- Wuhan Frasergen Bioinformatics, East Lake High-Tech Zone, Wuhan, Hubei, 430075, China
| | - Xiaohui Li
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Nansheng Chen
- Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, 266071, China
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Jian-Fang Gui
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jie Mei
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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Wan L, Dong L, Xiao S, Han Z, Wang X, Wang Z. Genomewide association study for economic traits in the large yellow croaker with different numbers of extreme phenotypes. J Genet 2018; 97:887-895. [PMID: 30262700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A traditional genomewide association study (GWAS) detects genotype-phenotype associations by the vast number of genotyped individuals. This method requires large-scale samples and considerable sequencing costs. Extreme phenotypic sampling proposes make GWAS more cost-efficient and are applied more widely. With extreme phenotypic sampling, we performed a GWAS for n-3 highly unsaturated fatty acids (HUFA) and eviscerated weight (EW) traits in the large yellowcroaker population. Of the 32,249 and 29,748 detected SNPs for the two traits, three candidate regions were found in each trait. Three candidate regions associated with HUFA were known near genes on chromosomes 4 and 11, and three candidate regions were on chromosome 6, and 15 for the EW trait. By combing through our GWAS results and the biological functional analysis of the genes, we suggest that the FABP, DGAT, ATP8B1, FAF2 and CERS2 genes, as well as the IGF2, BORA, CYP1A1, GRTP1 and HOX genes are promising candidate genes for n-3 HUFA and EW, respectively, in the large yellow croaker.Moreover, compared with the different numbers of the extreme phenotypic sampling, we conclude that 60% of the extreme phenotypic subsample can obtain a similar result as GWAS with whole phenotypes. Thus, extreme phenotypic sampling could save 40% of the cost for genotyping and DNA extraction without loss of the candidate regions and functional genes. Our study may provide a basis for further genomic breeding and a reference for others who want to perform GWAS with extreme phenotypes.
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Affiliation(s)
- Liang Wan
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, People's Republic of China.
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Wan L, Dong L, Xiao S, Han Z, Wang X, Wang Z. Genomewide association study for economic traits in the large yellow croaker with different numbers of extreme phenotypes. J Genet 2018. [DOI: 10.1007/s12041-018-0973-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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13
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Genomic prediction using an iterative conditional expectation algorithm for a fast BayesC-like model. Genetica 2018; 146:361-368. [PMID: 29948517 DOI: 10.1007/s10709-018-0027-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 05/24/2018] [Indexed: 10/14/2022]
Abstract
Genomic prediction is feasible for estimating genomic breeding values because of dense genome-wide markers and credible statistical methods, such as Genomic Best Linear Unbiased Prediction (GBLUP) and various Bayesian methods. Compared with GBLUP, Bayesian methods propose more flexible assumptions for the distributions of SNP effects. However, most Bayesian methods are performed based on Markov chain Monte Carlo (MCMC) algorithms, leading to computational efficiency challenges. Hence, some fast Bayesian approaches, such as fast BayesB (fBayesB), were proposed to speed up the calculation. This study proposed another fast Bayesian method termed fast BayesC (fBayesC). The prior distribution of fBayesC assumes that a SNP with probability γ has a non-zero effect which comes from a normal density with a common variance. The simulated data from QTLMAS XII workshop and actual data on large yellow croaker were used to compare the predictive results of fBayesB, fBayesC and (MCMC-based) BayesC. The results showed that when γ was set as a small value, such as 0.01 in the simulated data or 0.001 in the actual data, fBayesB and fBayesC yielded lower prediction accuracies (abilities) than BayesC. In the actual data, fBayesC could yield very similar predictive abilities as BayesC when γ ≥ 0.01. When γ = 0.01, fBayesB could also yield similar results as fBayesC and BayesC. However, fBayesB could not yield an explicit result when γ ≥ 0.1, but a similar situation was not observed for fBayesC. Moreover, the computational speed of fBayesC was significantly faster than that of BayesC, making fBayesC a promising method for genomic prediction.
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