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Bhardwaj S, Thakur K, Sharma AK, Sharma D, Brar B, Mahajan D, Kumar S, Kumar R. Regulation of omega-3 fatty acids production by different genes in freshwater fish species: a review. FISH PHYSIOLOGY AND BIOCHEMISTRY 2023; 49:1005-1016. [PMID: 37684550 DOI: 10.1007/s10695-023-01236-y] [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: 03/10/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023]
Abstract
The present study aims to compare the gene expression of three different fish species (common carp, tilapia, and trout) with varying levels of fatty acids (FA). Based on transcriptome analysis and RNA sequencing, various genes and their associated metabolic pathways are identified. Pathways are categorized based on the genes they encode. Genes that were differentially expressed and their promoter's methylation patterns were revealed by RNA-seq analysis in common carp. Furthermore, fatty acid-enriched pathways, such as ARA4 and adipocytokine signaling, were also identified. Many genes and pathways may influence tilapia's growth and omega-3 content. Using the mTOR pathway, trout with differential expression were discovered to be involved in producing omega-3 fatty acids. This study revealed major pathways in fish species to produce omega-3 fatty acids.
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Affiliation(s)
- Shivani Bhardwaj
- Department of Animal Sciences, School of Life Sciences, Central University of Himachal Pradesh, District Kangra, Himachal Pradesh, 176206, India
| | - Kushal Thakur
- Department of Animal Sciences, School of Life Sciences, Central University of Himachal Pradesh, District Kangra, Himachal Pradesh, 176206, India
| | - Amit Kumar Sharma
- Department of Animal Sciences, School of Life Sciences, Central University of Himachal Pradesh, District Kangra, Himachal Pradesh, 176206, India
| | - Dixit Sharma
- Department of Animal Sciences, School of Life Sciences, Central University of Himachal Pradesh, District Kangra, Himachal Pradesh, 176206, India
| | - Bhavna Brar
- Department of Animal Sciences, School of Life Sciences, Central University of Himachal Pradesh, District Kangra, Himachal Pradesh, 176206, India
| | - Danish Mahajan
- Department of Animal Sciences, School of Life Sciences, Central University of Himachal Pradesh, District Kangra, Himachal Pradesh, 176206, India
| | - Sunil Kumar
- Department of Animal Sciences, School of Life Sciences, Central University of Himachal Pradesh, District Kangra, Himachal Pradesh, 176206, India
| | - Rakesh Kumar
- Department of Animal Sciences, School of Life Sciences, Central University of Himachal Pradesh, District Kangra, Himachal Pradesh, 176206, India.
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2
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Blay C, Haffray P, D'Ambrosio J, Prado E, Dechamp N, Nazabal V, Bugeon J, Enez F, Causeur D, Eklouh-Molinier C, Petit V, Phocas F, Corraze G, Dupont-Nivet M. Genetic architecture and genomic selection of fatty acid composition predicted by Raman spectroscopy in rainbow trout. BMC Genomics 2021; 22:788. [PMID: 34732127 PMCID: PMC8564959 DOI: 10.1186/s12864-021-08062-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 09/29/2021] [Indexed: 01/22/2023] Open
Abstract
Background In response to major challenges regarding the supply and sustainability of marine ingredients in aquafeeds, the aquaculture industry has made a large-scale shift toward plant-based substitutions for fish oil and fish meal. But, this also led to lower levels of healthful n−3 long-chain polyunsaturated fatty acids (PUFAs)—especially eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids—in flesh. One potential solution is to select fish with better abilities to retain or synthesise PUFAs, to increase the efficiency of aquaculture and promote the production of healthier fish products. To this end, we aimed i) to estimate the genetic variability in fatty acid (FA) composition in visceral fat quantified by Raman spectroscopy, with respect to both individual FAs and groups under a feeding regime with limited n-3 PUFAs; ii) to study the genetic and phenotypic correlations between FAs and processing yields- and fat-related traits; iii) to detect QTLs associated with FA composition and identify candidate genes; and iv) to assess the efficiency of genomic selection compared to pedigree-based BLUP selection. Results Proportions of the various FAs in fish were indirectly estimated using Raman scattering spectroscopy. Fish were genotyped using the 57 K SNP Axiom™ Trout Genotyping Array. Following quality control, the final analysis contained 29,652 SNPs from 1382 fish. Heritability estimates for traits ranged from 0.03 ± 0.03 (n-3 PUFAs) to 0.24 ± 0.05 (n-6 PUFAs), confirming the potential for genomic selection. n-3 PUFAs are positively correlated to a decrease in fat deposition in the fillet and in the viscera but negatively correlated to body weight. This highlights the potential interest to combine selection on FA and against fat deposition to improve nutritional merit of aquaculture products. Several QTLs were identified for FA composition, containing multiple candidate genes with indirect links to FA metabolism. In particular, one region on Omy1 was associated with n-6 PUFAs, monounsaturated FAs, linoleic acid, and EPA, while a region on Omy7 had effects on n-6 PUFAs, EPA, and linoleic acid. When we compared the effectiveness of breeding programmes based on genomic selection (using a reference population of 1000 individuals related to selection candidates) or on pedigree-based selection, we found that the former yielded increases in selection accuracy of 12 to 120% depending on the FA trait. Conclusion This study reveals the polygenic genetic architecture for FA composition in rainbow trout and confirms that genomic selection has potential to improve EPA and DHA proportions in aquaculture species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08062-7.
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Affiliation(s)
- Carole Blay
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | | | - Jonathan D'Ambrosio
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.,SYSAAF, Station LPGP-INRAE, Rennes, France
| | - Enora Prado
- University of Rennes, CNRS, ISCR - UMR 6226, ScanMAT - UMS 2001, Rennes, France
| | - Nicolas Dechamp
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Virginie Nazabal
- University of Rennes, CNRS, ISCR - UMR 6226, ScanMAT - UMS 2001, Rennes, France
| | | | | | - David Causeur
- Laboratoire de Mathématiques Appliquées, IRMAR, Agrocampus Ouest, Rennes, France
| | | | | | - Florence Phocas
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Geneviève Corraze
- INRAE, University of Pau & Pays Adour, E2S UPPA, UMR1419 NuMéA, St Pée sur, Nivelle, France
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3
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Twining CW, Bernhardt JR, Derry AM, Hudson CM, Ishikawa A, Kabeya N, Kainz MJ, Kitano J, Kowarik C, Ladd SN, Leal MC, Scharnweber K, Shipley JR, Matthews B. The evolutionary ecology of fatty-acid variation: Implications for consumer adaptation and diversification. Ecol Lett 2021; 24:1709-1731. [PMID: 34114320 DOI: 10.1111/ele.13771] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/20/2021] [Accepted: 04/09/2021] [Indexed: 12/20/2022]
Abstract
The nutritional diversity of resources can affect the adaptive evolution of consumer metabolism and consumer diversification. The omega-3 long-chain polyunsaturated fatty acids eicosapentaenoic acid (EPA; 20:5n-3) and docosahexaenoic acid (DHA; 22:6n-3) have a high potential to affect consumer fitness, through their widespread effects on reproduction, growth and survival. However, few studies consider the evolution of fatty acid metabolism within an ecological context. In this review, we first document the extensive diversity in both primary producer and consumer fatty acid distributions amongst major ecosystems, between habitats and amongst species within habitats. We highlight some of the key nutritional contrasts that can shape behavioural and/or metabolic adaptation in consumers, discussing how consumers can evolve in response to the spatial, seasonal and community-level variation of resource quality. We propose a hierarchical trait-based approach for studying the evolution of consumers' metabolic networks and review the evolutionary genetic mechanisms underpinning consumer adaptation to EPA and DHA distributions. In doing so, we consider how the metabolic traits of consumers are hierarchically structured, from cell membrane function to maternal investment, and have strongly environment-dependent expression. Finally, we conclude with an outlook on how studying the metabolic adaptation of consumers within the context of nutritional landscapes can open up new opportunities for understanding evolutionary diversification.
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Affiliation(s)
- Cornelia W Twining
- Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Limnological Institute, University of Konstanz, Konstanz-Egg, Germany
| | - Joey R Bernhardt
- Department of Biology, McGill University, Montréal, QC, Canada.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Alison M Derry
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada
| | - Cameron M Hudson
- Department of Fish Ecology and Evolution, Eawag, Center of Ecology, Evolution and Biochemistry, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Asano Ishikawa
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Naoki Kabeya
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology (TUMSAT, Tokyo, Japan
| | - Martin J Kainz
- WasserCluster Lunz-Inter-university Center for Aquatic Ecosystems Research, Lunz am See, Austria
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Carmen Kowarik
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Sarah Nemiah Ladd
- Ecosystem Physiology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Miguel C Leal
- ECOMARE and CESAM - Centre for Environmental and Marine Studies and Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Kristin Scharnweber
- Department of Ecology and Genetics; Limnology, Uppsala University, Uppsala, Sweden.,University of Potsdam, Plant Ecology and Nature Conservation, Potsdam-Golm, Germany
| | - Jeremy R Shipley
- Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Department of Fish Ecology and Evolution, Eawag, Center of Ecology, Evolution and Biochemistry, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Blake Matthews
- Department of Fish Ecology and Evolution, Eawag, Center of Ecology, Evolution and Biochemistry, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
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Shi Y, Zhou Z, Liu B, Kong S, Chen B, Bai H, Li L, Pu F, Xu P. Construction of a High-Density Genetic Linkage Map and QTL Mapping for Growth-Related Traits in Takifugu bimaculatus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:130-144. [PMID: 31900733 DOI: 10.1007/s10126-019-09938-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/03/2019] [Indexed: 06/10/2023]
Abstract
Takifugu bimaculatus is a euryhaline species, distributed ranging from the southern Yellow Sea to the South China Sea. Their tolerance to a wide range of salinity and temperature, coupled with a desirable firm texture, makes T. bimaculatus a strong candidate for Takifugu aquaculture in subtropics areas. Due to the increasing demand in markets and emerging of the Takifugu aquaculture industry, close attention has been paid to improvement on the T. bimaculatus production. In aquaculture, the great effort has been put into marker-assisted selective breeding, and efficient improvement was realized. However, few genetic resources on T. bimaculatus are provided so far. Aiming at understanding the genetic basis underlying important economic growth traits, facilitating genetic improvement and enriching the genetic resource in T. bimaculatus, we constructed the first genetic linkage map for T. bimaculatus via double digestion restriction-site association DNA sequencing and conducted quantitative traits locus (QTL) mapping for growth-related traits. The map comprised 1976 single nucleotide polymorphism markers distributed on 22 linkage groups (LG), with a total genetic distance of 2039.74 cM. Based on the linkage map, a chromosome-level assembly was constructed whereby we carried out comparative genomics analysis, verifying the high accuracy on contigs ordering of the linkage map. On the other hand, 18 QTLs associated with growth traits were detected on LG6, LG7, LG8, LG10, LG20, and LG21 with phenotypical variance ranging from 15.1 to 56.4%. Candidate genes participating in cartilage development, fat accumulation, and other growth-related regulation activities were identified from these QTLs, including col11a1, foxa2, and thrap3. The linkage map provided a solid foundation for chromosomes assembly and refinement. QTLs reported here unraveled the genomic architecture of some growth traits, which will advance the investigation of aquaculture breeding efforts in T. bimaculatus.
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Affiliation(s)
- Yue Shi
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Zhixiong Zhou
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Bo Liu
- Fisheries Research Institute of Fujian, Xiamen, China
| | - Shengnan Kong
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Baohua Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Huaqiang Bai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Leibin Li
- Fisheries Research Institute of Fujian, Xiamen, China
| | - Fei Pu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Peng Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, China.
- Shenzhen Research Institute of Xiamen University, Shenzhen, China.
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5
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Wang L, Chua E, Sun F, Wan ZY, Ye B, Pang H, Wen Y, Yue GH. Mapping and Validating QTL for Fatty Acid Compositions and Growth Traits in Asian Seabass. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:643-654. [PMID: 31273567 DOI: 10.1007/s10126-019-09909-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 06/17/2019] [Indexed: 06/09/2023]
Abstract
Asian seabass is an important food fish species. While improving growth, increasing the nutritional value is important, omega-3 fatty acids are indispensable to human health. Identifying and validating DNA markers associated with traits is the first step towards marker-assisted selection (MAS). We quantified 13 different fatty acids and three growth traits in 213 F2 Asian seabass from a family at the age 270 days post hatch, and screened QTL for these traits. The content of total fatty acids in 100 g flesh was 2.57 ± 0.80 g, while the proportions of docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) were 16.96 ± 2.20% and 5.42 ± 0.90%, respectively. A linkage map with 2424 SNPs was constructed and used for QTL mapping. For fatty acid compositions, 14 significant QTL were identified on three linkage groups (LG5, LG11 and LG14), with phenotypic variance explained (PVE) from 12.8 to 24.6%. Thirty-nine suggestive QTL were detected on 16 LGs. Two significant QTL for EPA were identified on LG5 and LG14, with PVE of 15.2% and 15.1%, respectively. No significant QTL was identified for DHA. For growth traits, six significant and 13 suggestive QTL were identified on two and seven LGs, respectively. Only a few significant QTL for fatty acids overlapped with previously mapped QTL for these traits, suggesting that most QTL detected in a family are family-specific and could only be used in MAS in the family per se. To facilitate population-wide molecular breeding, more powerful methods (e.g. GWAS) should be used to identify SNPs for genomic selection.
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Affiliation(s)
- Le Wang
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Elaine Chua
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Fei Sun
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Zi Yi Wan
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Baoqing Ye
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Hongyan Pang
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Yanfei Wen
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Gen Hua Yue
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.
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6
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Li BJ, Zhu ZX, Gu XH, Lin HR, Xia JH. QTL Mapping for Red Blotches in Malaysia Red Tilapia (Oreochromis spp.). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:384-395. [PMID: 30863905 DOI: 10.1007/s10126-019-09888-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 02/21/2019] [Indexed: 06/09/2023]
Abstract
Body color is an interesting economic trait in fish. Red tilapia with red blotches may decrease its commercial values. Conventional selection of pure red color lines is a time-consuming and labor-intensive process. To accelerate selection of pure lines through marker-assisted selection, in this study, double-digest restriction site-associated DNA sequencing (ddRAD-seq) technology was applied to genotype a full-sib mapping family of Malaysia red tilapia (Oreochromis spp.) (N = 192). Genome-wide significant quantitative trait locus (QTL)-controlling red blotches were mapped onto two chromosomes (chrLG5 and chrLG15) explaining 9.7% and 8.2% of phenotypic variances by a genome-wide association study (GWAS) and linkage-based QTL mapping. Six SNPs from the chromosome chrLG5 (four), chrLG15 (one), and unplaced supercontig GL831288-1 (one) were significantly associated to the red blotch trait in GWAS analysis. We developed nine microsatellite markers and validated significant correlations between genotypes and blotch data (p < 0.05). Our study laid a foundation for exploring a genetic mechanism of body colors and carrying out genetic improvement for color quality in tilapia.
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Affiliation(s)
- Bi Jun Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Zong Xian Zhu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Xiao Hui Gu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Hao Ran Lin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Jun Hong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China.
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7
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Wang W, Tan S, Luo J, Shi H, Zhou T, Yang Y, Jin Y, Wang X, Niu D, Yuan Z, Gao D, Dunham R, Liu Z. GWAS Analysis Indicated Importance of NF-κB Signaling Pathway in Host Resistance Against Motile Aeromonas Septicemia Disease in Catfish. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:335-347. [PMID: 30895402 DOI: 10.1007/s10126-019-09883-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
Motile Aeromonas septicemia (MAS) disease caused by a bacterial pathogen, Aeromonas hydrophila, is an emerging but severe disease of catfish. Genetic enhancement of disease resistance is considered to be effective to control the disease. To provide an insight into the genomic basis of MAS disease resistance, in this study, we conducted a genome-wide association study (GWAS) to identify quantitative trait loci (QTL). A total of 1820 interspecific backcross catfish of 7 families were challenged with A. hydrophila, and 382 phenotypic extremes were selected for genotyping with the catfish 690 K SNP arrays. Three QTL on linkage group (LG) 2, 26 and 29 were identified to be significantly associated with MAS resistance. Within these regions, a total of 24 genes had known functions in immunity, 10 of which were involved in NF-κB signaling pathway, suggesting the importance of NF-κB signaling pathway in MAS resistance. In addition, three suggestively significant QTL were identified on LG 11, 17, and 20. The limited numbers of QTL involved in MAS resistance suggests that marker-assisted selection may be a viable approach for catfish breeding.
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Affiliation(s)
- Wenwen Wang
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Suxu Tan
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Jian Luo
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Huitong Shi
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Tao Zhou
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yujia Yang
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yulin Jin
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Xiaozhu Wang
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Donghong Niu
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Zihao Yuan
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Dongya Gao
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Rex Dunham
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Zhanjiang Liu
- Department of Biology, College of Art and Sciences, Syracuse University, Syracuse, NY, 13244, USA.
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8
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Jiang DL, Gu XH, Li BJ, Zhu ZX, Qin H, Meng ZN, Lin HR, Xia JH. Identifying a Long QTL Cluster Across chrLG18 Associated with Salt Tolerance in Tilapia Using GWAS and QTL-seq. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:250-261. [PMID: 30737627 DOI: 10.1007/s10126-019-09877-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 01/14/2019] [Indexed: 06/09/2023]
Abstract
Understanding the genetic mechanism of osmoregulation is important for the improvement of salt tolerance in tilapia. In our previous study, we have identified a major quantitative trait locus (QTL) region located at 23.0 Mb of chrLG18 in a Nile tilapia line by QTL-seq. However, the conservation of these QTLs in other tilapia populations or species is not clear. In this study, we successfully investigated the QTLs associated with salt tolerance in a mass cross population from the GIFT line of Nile tilapia (Oreochromis niloticus) using a ddRAD-seq-based genome-wide association study (GWAS) and in a full-sib family from the Malaysia red tilapia strain (Oreochromis spp) using QTL-seq. Our study confirmed the major QTL interval that is located at nearly 23.0 Mb of chrLG18 in Nile tilapia and revealed a long QTL cluster across chrLG18 controlling for the salt-tolerant trait in both red tilapia and Nile tilapia. This is the first GWAS analysis on salt tolerance in tilapia. Our finding provides important insights into the genetic architecture of salinity tolerance in tilapia and supplies a basis for fine mapping QTLs, marker-assisted selection, and further detailed functional analysis of the underlying genes for salt tolerance in tilapia.
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Affiliation(s)
- Dan Li Jiang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Xiao Hui Gu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Bi Jun Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zong Xian Zhu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Hui Qin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zi Ning Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Hao Ran Lin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jun Hong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
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Kong S, Ke Q, Chen L, Zhou Z, Pu F, Zhao J, Bai H, Peng W, Xu P. Constructing a High-Density Genetic Linkage Map for Large Yellow Croaker (Larimichthys crocea) and Mapping Resistance Trait Against Ciliate Parasite Cryptocaryon irritans. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:262-275. [PMID: 30783862 DOI: 10.1007/s10126-019-09878-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 01/18/2019] [Indexed: 06/09/2023]
Abstract
The large yellow croaker (Larimichthys crocea) is the most economically important marine cage-farming fish in China in the past decade. However, the sustainable development of large yellow croaker aquaculture has been severely hampered by several diseases, of which, the white spot disease caused by ciliate protozoan parasite Cryptocaryon irritans ranks the most damaging disease in large yellow croaker cage farms. To better understand the genetic basis of parasite infection and disease resistance to C. irritans, it is vital to map the traits and localize the underlying candidate genes in L. crocea genome. Here, we constructed a high-density genetic linkage map using double-digest restriction-site associated DNA (ddRAD)-based high-throughput SNP genotyping data of a F1 mapping family, which had been challenged with C. irritans for resistant trait measure. A total of 5261 SNPs was grouped and oriented into 24 linkage groups (LGs), representing 24 chromosomes of L. crocea. The total genetic map length was 1885.67 cM with an average inter-locus distance of 0.36 cM. Quantitative trait loci (QTL) mapping identified seven significant QTLs in four LGs linked to C. irritans disease resistance. Candidate genes underlying disease resistance were identified from the reference genome, including ifnar1, ifngr2, ikbke, and CD112. Comparative genomic analysis between large yellow croaker and the four closely related species revealed high evolutionary conservation of chromosomes, though inter-chromosomal rearrangements do exist. Especially, the croaker genome structure was closer to the medaka genome than stickleback, indicating that the croaker genome might retain the teleost ancestral genome structure. The high-density genetic linkage map provides an important tool and resource for fine mapping, comparative genome analysis, and molecular selective breeding of large yellow croaker.
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Affiliation(s)
- Shengnan Kong
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Qiaozhen Ke
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Lin Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Zhixiong Zhou
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Fei Pu
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China
| | - Ji Zhao
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China
| | - Huaqiang Bai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Wenzhu Peng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Peng Xu
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China.
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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10
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Lin G, Thevasagayam NM, Wan ZY, Ye BQ, Yue GH. Transcriptome Analysis Identified Genes for Growth and Omega-3/-6 Ratio in Saline Tilapia. Front Genet 2019; 10:244. [PMID: 30949199 PMCID: PMC6435965 DOI: 10.3389/fgene.2019.00244] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 03/05/2019] [Indexed: 12/30/2022] Open
Abstract
Growth and omega-3/-6 ratio are important traits in aquaculture. The mechanisms underlying quick growth and high omega-3/-6 ratio in fish are not fully understood. The consumption of the meat of tilapia suffers a bad reputation due to its low omega-3/-6 ratio. To facilitate the improvement of these traits and to understand more about the mechanisms underlying quick growth and high omega-3/-6 ratio, we conducted transcriptome analysis in the muscle and liver of fast- and slow-growing hybrid saline tilapia generated by crossing Mozambique tilapia and red tilapia. A transcriptome with an average length of 963 bp was generated by using 486.65 million clean 100 bp paired-end reads. A total of 42,699 annotated unique sequences with an average length of 3.4 kb were obtained. Differentially expressed genes (DEGs) in the muscle and liver were identified between fast- and slow-growing tilapia. Pathway analysis classified these genes into many pathways. Ten genes, including foxK1, sparc, smad3, usp38, crot, fadps, sqlea, cyp7b1, impa1, and gss, from the DEGs were located within QTL for growth and omega-3, which were previously detected content in tilapia, suggesting that these ten genes could be important candidate genes for growth and omega-3 fatty acid content. Analysis of SNPs in introns 1 and 2 of foxK1 revealed that the SNPs were significantly associated with growth and omega-3/-6 ratio. This study lays the groundwork for further investigation of the molecular mechanisms underlying the phenotypic variation of these two traits and provides SNPs for selecting these traits at fingerling stage.
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Affiliation(s)
- Grace Lin
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | | | - Z. Y. Wan
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - B. Q. Ye
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Gen Hua Yue
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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11
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Wang Y, Sun G, Zeng Q, Chen Z, Hu X, Li H, Wang S, Bao Z. Predicting Growth Traits with Genomic Selection Methods in Zhikong Scallop (Chlamys farreri). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:769-779. [PMID: 30116982 DOI: 10.1007/s10126-018-9847-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 07/29/2018] [Indexed: 06/08/2023]
Abstract
Selective breeding is a common and effective approach for genetic improvement of aquaculture stocks with parental selection as the key factor. Genomic selection (GS) has been proposed as a promising tool to facilitate selective breeding. Here, we evaluated the predictability of four GS methods in Zhikong scallop (Chlamys farreri) through real dataset analyses of four economical traits (e.g., shell length, shell height, shell width, and whole weight). Our analysis revealed that different GS models exhibited variable performance in prediction accuracy depending on genetic and statistical factors, but non-parametric method, including reproducing kernel Hilbert spaces regression (RKHS) and sparse neural networks (SNN), generally outperformed parametric linear method, such as genomic best linear unbiased prediction (GBLUP) and BayesB. Furthermore, we demonstrated that the predictability relied mainly on the heritability regardless of GS methods. The size of training population and marker density also had considerable effects on the predictive performance. In practice, increasing the training population size could better improve the genomic prediction than raising the marker density. This study is the first to apply non-linear model and neural networks for GS in scallop and should be valuable to help develop strategies for aquaculture breeding programs.
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Affiliation(s)
- Yangfan Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Science, Ocean University of China, Qingdao, 266003, China
| | - Guidong Sun
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Science, Ocean University of China, Qingdao, 266003, China
| | - Qifan Zeng
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Science, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Zhihui Chen
- Division of Cell and Developmental Biology, College of Life Science, University of Dundee, Dundee, DD1 4HN, UK
| | - Xiaoli Hu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Science, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Hengde Li
- Ministry of Agriculture Key Laboratory of Aquatic Genomics, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Center for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China
| | - Shi Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Science, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Zhenmin Bao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Science, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
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12
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Sun F, Tu R, Xia JH, Liu XJ, Yue GH. The FTO Gene Is Associated with Growth and Omega-3/-6 Ratio in Asian Seabass. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:603-610. [PMID: 29766417 DOI: 10.1007/s10126-018-9831-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 04/29/2018] [Indexed: 06/08/2023]
Abstract
Polymorphisms in the FTO gene are associated with obesity and body mass index in humans and livestock. Little information of whether FTO plays an important role in aquaculture fish species is available. We cloned and characterized the FTO gene in an economically important food fish species: Asian seabass (Lates calcarifer). The full-length cDNA of the gene is 3679 bp, containing an ORF of 1935 bp encoding 644 amino acids, a 216 bp 5' UTR and a 1538 bp 3' UTR. The gene consisted of nine exons and eight introns and was 117,679 bp in length. Phylogenetic analysis revealed that the gene in Asian seabass was closely related to those of Japanese flounder and Nile tilapia. Analysis of its expressions using qRT-PCR showed that it was expressed ubiquitously, but was higher in the liver, stomach and intestine. Comparative analysis of the genomic sequences of part of intron 1 of the gene among 10 unrelated individuals identified two SNPs. Analysis of associations between SNPs and traits (i.e. growth, oil content, omega-3 and -6 contents) in an F2 family demonstrated that the two SNPs were significantly associated with growth, oil content, omega-3 content and omega-3/-6 ratio. Altogether, our data suggest that the gene or/and its linked genes play an important role in growth and fatty acid synthesis, and that the SNPs associated with traits may be used as markers for selecting quicker growth and higher omega-3/-6 ratio at the fingerling stage.
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Affiliation(s)
- Fei Sun
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
| | - Rongjian Tu
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Jun Hong Xia
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Xiao Jun Liu
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Gen Hua Yue
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore.
- Department of Biological Sciences, National University of Singapore, 14 Science Drive, Singapore, 117543, Singapore.
- School of Biological Sciences, Nanyang Technological University, 6 Nanyang Drive, Singapore, 637551, Singapore.
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