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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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Vea IM, Wilcox AS, Frankino WA, Shingleton AW. Genetic Variation in Sexual Size Dimorphism Is Associated with Variation in Sex-Specific Plasticity in Drosophila. Am Nat 2023; 202:368-381. [PMID: 37606943 DOI: 10.1086/725420] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
AbstractThe difference in body size between females and males, or sexual size dimorphism (SSD), is ubiquitous, yet we have a poor understanding of the developmental genetic mechanisms that generate it and how these mechanisms may vary within and among species. Such an understanding of the genetic architecture of SSD is important if we are to evaluate alternative models of SSD evolution, but the genetic architecture is difficult to describe because SSD is a characteristic of populations, not individuals. Here, we overcome this challenge by using isogenic lineages of Drosophila to measure SSD for 196 genotypes. We demonstrate extensive genetic variation for SSD, primarily driven by higher levels of genetic variation for body size among females than among males. While we observe a general increase in SSD with sex-averaged body size (pooling for sex) among lineages, most of the variation in SSD is independent of sex-averaged body size and shows a strong genetic correlation with sex-specific plasticity, such that increased female-biased SSD is associated with increased body size plasticity in females. Our data are consistent with the condition dependence hypothesis of sexual dimorphism and suggest that SSD in Drosophila is a consequence of selection on the developmental genetic mechanisms that regulate the plasticity of body size.
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3
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Kayansamruaj P, Dinh-Hung N, Srisapoome P, Na-Nakorn U, Chatchaiphan S. Genomics-driven prophylactic measures to increase streptococcosis resistance in tilapia. JOURNAL OF FISH DISEASES 2023; 46:597-610. [PMID: 36708284 DOI: 10.1111/jfd.13763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 05/07/2023]
Abstract
Streptococcosis caused by Streptococcus agalactiae and S. iniae is a significant problem that affects the success of tilapia aquaculture industries worldwide. In this critical review, we summarize the applicable practical strategies which may effectively enhance the world tilapia aquaculture development. Recently, the effect of vaccination and selective breeding programmes has been recognized as valuable tools to control the target disease and other consequent negative impacts caused by chemical and drug application. Advances in sequencing and molecular technologies are vital helpful factors with which to develop robust vaccines and increase the selective breeding programme's precision against streptococcosis. The genomic selection for streptococcosis-resistant tilapia strains and crucial genomic application for genomics' contribution to the development of novel Streptococcus vaccine, comparative genomics approach identifying vaccine candidates by reverse vaccinology, and next-generation vaccine design were described. Information from our review is encouraging for practical implementation of the development of vaccination and genomic selection in tilapia for streptococcosis resistance, which may be vital factors to sustain the world tilapia aquaculture industry effectively.
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Affiliation(s)
- Pattanapon Kayansamruaj
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
- Center of Excellence in Aquatic Animal Health Management, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Nguyen Dinh-Hung
- Center of Excellence in Fish Infectious Diseases (CE FID), Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Prapansak Srisapoome
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
- Center of Excellence in Aquatic Animal Health Management, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Uthairat Na-Nakorn
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok, Thailand
| | - Satid Chatchaiphan
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
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4
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Liu Z, Zhou T, Gao D. Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture. Front Genet 2022; 13:994471. [PMID: 36406125 PMCID: PMC9666392 DOI: 10.3389/fgene.2022.994471] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/20/2022] [Indexed: 11/25/2022] Open
Abstract
Major progress has been made with genomic and genetic studies in aquaculture in the last decade. However, research on epigenetic regulation of aquaculture traits is still at an early stage. It is apparent that most, if not all, aquaculture traits are regulated at both genetic and epigenetic levels. This paper reviews recent progress in understanding of genetic and epigenetic regulation of important aquaculture traits such as growth, reproduction, disease resistance, and stress responses. Although it is challenging to make generalized statements, DNA methylation is mostly correlated with down-regulation of gene expression, especially when at promoters and enhancers. As such, methylation of growth factors and their receptors is negatively correlated with growth; hypomethylation of genes important for stress tolerance is correlated with increased stress tolerance; hypomethylation of genes important for male or female sex differentiation leads to sex differentiation into males or females, respectively. It is apparent that environmental regulation of aquaculture traits is mediated at the level of epigenetic regulation, and such environment-induced epigenetic changes appeared to be intergenerationally inherited, but evidences for transgenerational inheritance are still limited.
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Affiliation(s)
- Zhanjiang Liu
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, United States,*Correspondence: Zhanjiang Liu,
| | - Tao Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Dongya Gao
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, United States
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5
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Shen Y, Ma K, Zhu Q, Xu X, Li J. Transcriptomic analysis reveals growth-related genes in juvenile grass carp, Ctenopharyngodon idella. AQUACULTURE AND FISHERIES 2022. [DOI: 10.1016/j.aaf.2020.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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6
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Lu Y, Liu Q, Huang Z, Chen X, Yang C, Zhang Y, Zhao Y, Wang F. ATP synthase subunit e is a shrimp growth-associated breeding marker. Genomics 2022; 114:110410. [PMID: 35716822 DOI: 10.1016/j.ygeno.2022.110410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/21/2022] [Accepted: 06/10/2022] [Indexed: 12/11/2022]
Abstract
Penaeus vannamei is one of the most popular aquaculture species in the world. This species is featured with its fast-growing and delicious taste, which drives people develop various strains. During this process identification of trait-associated markers could effectively increase breeding efficiency. Driven by this, we tried to screen fast-growing key regulators via a FACS-based high throughput method, in which 2-NBDG was applied as a fluorescent indicator for direct glucose uptake measurement. Totally six candidate genes were screened out followed by in vitro validation in 293T cells. After that, the correlation between these genes and shrimp growing was further verified in a hybrid lineage. The expression level of two genes including ATP synthase subunit e and inhibitor of apoptosis protein showed some correlation with shrimp growth speed. Furthermore, we tested these two candidate markers in various lineages and confirmed that ATP synthase subunit e could be a shrimp growth-associated breeding marker.
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Affiliation(s)
- Yucheng Lu
- Department of Biology, College of Science, Shantou University, Shantou 515063, China
| | - Qingyun Liu
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Zhiqi Huang
- Department of Biology, College of Science, Shantou University, Shantou 515063, China
| | - Xiuli Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Chunling Yang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Yueling Zhang
- Department of Biology, College of Science, Shantou University, Shantou 515063, China; Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; Shantou University-Universiti Malaysia Terengganu Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China
| | - Yongzhen Zhao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China.
| | - Fan Wang
- Department of Biology, College of Science, Shantou University, Shantou 515063, China; Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; Shantou University-Universiti Malaysia Terengganu Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China.
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7
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Nousias O, Oikonomou S, Manousaki T, Papadogiannis V, Angelova N, Tsaparis D, Tsakogiannis A, Duncan N, Estevez A, Tzokas K, Pavlidis M, Chatziplis D, Tsigenopoulos CS. Linkage mapping, comparative genome analysis, and QTL detection for growth in a non-model teleost, the meagre Argyrosomus regius, using ddRAD sequencing. Sci Rep 2022; 12:5301. [PMID: 35351938 PMCID: PMC8964699 DOI: 10.1038/s41598-022-09289-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 03/17/2022] [Indexed: 01/05/2023] Open
Abstract
Meagre (Argyrosomus regius), is a benthopelagic species rapidly emerging in aquaculture, due to its low food to biomass conversion rate, good fillet yield and ease of production. Tracing a species genomic background along with describing the genetic basis of important traits can greatly influence both conservation strategies and production perspectives. In this study, we employed ddRAD sequencing of 266 fish from six F1 meagre families, to construct a high-density genetic map comprising 4529 polymorphic SNP markers. The QTL mapping analysis provided a genomic appreciation for the weight trait identifying a statistically significant QTL on linkage group 15 (LG15). The comparative genomics analysis with six teleost species revealed an evolutionarily conserved karyotype structure. The synteny observed, verified the already well-known fusion events of the three-spine stickleback genome, reinforced the evidence of reduced evolutionary distance of Sciaenids with the Sparidae family, reflected the evolutionary proximity with Dicentrarchus labrax, traced several putative chromosomal rearrangements and a prominent putative fusion event in meagre’s LG17. This study presents novel elements concerning the genome evolutionary history of a non-model teleost species recently adopted in aquaculture, starts to unravel the genetic basis of the species growth-related traits, and provides a high-density genetic map as a tool that can help to further establish meagre as a valuable resource for research and production.
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Affiliation(s)
- O Nousias
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece.,Department of Biology, University of Crete, Heraklion, Greece
| | - S Oikonomou
- Department of Agriculture, International Hellenic University (IHU), Thessaloniki, Greece
| | - T Manousaki
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - V Papadogiannis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - N Angelova
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - D Tsaparis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - A Tsakogiannis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - N Duncan
- IRTA Institute of Agrifood Research and Technology, Barcelona, Spain
| | - A Estevez
- IRTA Institute of Agrifood Research and Technology, Barcelona, Spain
| | - K Tzokas
- Andromeda S.A., Agios Vasilios, Rion, Greece
| | - M Pavlidis
- Department of Biology, University of Crete, Heraklion, Greece
| | - D Chatziplis
- Department of Agriculture, International Hellenic University (IHU), Thessaloniki, Greece
| | - C S Tsigenopoulos
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece.
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8
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Mapping of quantitative trait loci underlying a magic trait in ongoing ecological speciation. BMC Genomics 2021; 22:615. [PMID: 34384356 PMCID: PMC8361645 DOI: 10.1186/s12864-021-07908-4] [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: 02/28/2021] [Accepted: 07/22/2021] [Indexed: 01/09/2023] Open
Abstract
Background Telmatochromis temporalis is a cichlid fish endemic to Lake Tanganyika. The normal and dwarf morphs of this fish are a clear example of ongoing ecological speciation, and body size plays an important role in this speciation event as a magic trait. However, the genetic basis underlying this trait has not been studied. Results Based on double-digested restriction-site associated DNA (ddRAD) sequencing of a hybrid cross between the morphs that includes F0 male, F0 female, and 206 F2 individuals, we obtained a linkage map consisting of 708 ddRAD markers in 22 linkage groups, which corresponded to the previously reported Oreochromis niloticus chromosomes, and identified one significant and five suggestive quantitative trait loci (QTL) for body size. From the body-size distribution pattern, the significant and three of the five suggestive QTL are possibly associated with genes responsible for the difference in body size between the morphs. Conclusions The QTL analysis presented here suggests that multiple genes, rather than a single gene, control morph-specific body size. The present results provide further insights about the genes underlying the morph specific body size and evolution of the magic trait during ecological speciation. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07908-4.
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9
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Function of Circular RNAs in Fish and Their Potential Application as Biomarkers. Int J Mol Sci 2021; 22:ijms22137119. [PMID: 34281172 PMCID: PMC8268770 DOI: 10.3390/ijms22137119] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/25/2021] [Accepted: 06/27/2021] [Indexed: 11/16/2022] Open
Abstract
Circular RNAs (circRNAs) are an emerging class of regulatory RNAs with a covalently closed-loop structure formed during pre-mRNA splicing. Recent advances in high-throughput RNA sequencing and circRNA-specific computational tools have driven the development of novel approaches to their identification and functional characterization. CircRNAs are stable, developmentally regulated, and show tissue- and cell-type-specific expression across different taxonomic groups. They play a crucial role in regulating various biological processes at post-transcriptional and translational levels. However, the involvement of circRNAs in fish immunity has only recently been recognized. There is also broad evidence in mammals that the timely expression of circRNAs in muscle plays an essential role in growth regulation but our understanding of their expression and function in teleosts is still very limited. Here, we discuss the available knowledge about circRNAs and their role in growth and immunity in vertebrates from a comparative perspective, with emphasis on cultured teleost fish. We expect that the interest in teleost circRNAs will increase substantially soon, and we propose that they may be used as biomarkers for selective breeding of farmed fish, thus contributing to the sustainability of the aquaculture sector.
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A first genetic linage map construction and QTL mapping for growth traits in Larimichthys polyactis. Sci Rep 2020; 10:11621. [PMID: 32669609 PMCID: PMC7363912 DOI: 10.1038/s41598-020-68592-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 06/30/2020] [Indexed: 11/08/2022] Open
Abstract
Larimichthys polyactis is a commercially important marine fish species in Eastern Asia, yet very few genetic resources exist. In particular, genetic linkage maps are critical tools for genetic breeding. In this study, we generated a high resolution linkage map from a family of 110 individuals and their parents by resequencing the individuals. 3,802 effective SNPs were mapped to 24 linkage groups (LGs). The map spanned 2,567.39 cm, with an average marker interval of 0.66 cm. We used the map to conduct QTL analysis for growth traits, and found 31 markers were significantly associated with growth-related traits. Specifically, three SNPs were identified for total length, nineteen SNPs for body length, and nine SNPs for body weight. The identified SNPs could explain 15.2-22.6% of the phenotypic variation. SNPs associated with growth traits were distributed on LG6 and LG11, and candidate genes included, kif26b, bat1, gna1, gbgt1, and amfr, which may regulate growth. The linkage map and mapped QTLs would be useful for improving the quality of L. polyactis via marker-assisted selection.
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11
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Yassumoto TI, Nakatsukasa M, Nagano AJ, Yasugi M, Yoshimura T, Shinomiya A. Genetic analysis of body weight in wild populations of medaka fish from different latitudes. PLoS One 2020; 15:e0234803. [PMID: 32544202 PMCID: PMC7297337 DOI: 10.1371/journal.pone.0234803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 06/02/2020] [Indexed: 11/19/2022] Open
Abstract
The genetic bases of growth and body weight are of economic and scientific interest, and teleost fish models have proven useful in such investigations. The Oryzias latipes species complex (medaka) is an abundant freshwater fish in Japan and suitable for genetic studies. We compared two wild medaka stocks originating from different latitudes. The Maizuru population from higher latitudes weighed more than the Ginoza population. We investigated the genetic basis of body weight, using quantitative trait locus (QTL) analysis of the F2 offspring of these populations. We detected one statistically significant QTL for body weight on medaka chromosome 4 and identified 12 candidate genes that might be associated with body weight or growth. Nine of these 12 genes had at least one single nucleotide polymorphism that caused amino acid substitutions in protein-coding regions, and we estimated the effects of these substitutions. The present findings might contribute to the marker-assisted selection of economically important aquaculture species.
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Affiliation(s)
- Tamiris I. Yassumoto
- Laboratory of Animal Integrative Physiology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Mana Nakatsukasa
- Laboratory of Animal Integrative Physiology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Division of Seasonal Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | | | - Masaki Yasugi
- Laboratory of Neurophysiology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Takashi Yoshimura
- Laboratory of Animal Integrative Physiology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Division of Seasonal Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
| | - Ai Shinomiya
- Division of Seasonal Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
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Wang J, Li D, Zhao X, Sun T, Jin S, Wang H, Xiao T, Li Y. GH and GHR gene cloning, expression and their associations with growth-related traits of the barbel chub (Squaliobarbus curriculus). Comp Biochem Physiol B Biochem Mol Biol 2020; 243-244:110429. [PMID: 32097715 DOI: 10.1016/j.cbpb.2020.110429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 02/15/2020] [Accepted: 02/20/2020] [Indexed: 01/12/2023]
Abstract
Growth hormone (ScGH) and growth hormone receptor (ScGHR) genes from the barbel chub (Squaliobarbus curriculus), in addition to their cDNAs, were cloned. The associations between their mRNA expression levels and growth-related traits were analysed, and the differences in the levels of expression of growth regulation-related genes between the largest and smallest individuals were compared. The full-length 1182-bp cDNA of ScGH contained a 633-bp open reading frame (ORF), and the length of the gene had 2492 bp. The full-length 2825-bp cDNA of ScGHRa contained a 1818-bp ORF, and the gene had 6970 bp. The full-length 2822-bp cDNA of ScGHRb contained a 1737-bp ORF, and the gene had 8149 bp. Quantitative real-time PCR revealed that ScGH was only expressed in the pituitary. ScGHRa was expressed predominantly in muscle, and the expression level of ScGHRb was the highest in the liver. The ScGHRa mRNA levels in the muscle were significantly negatively correlated with the caudal peduncle length. However, no correlation between growth-related traits and ScGH and ScGHRb expression levels were found. Pituitary ScGH, liver GHRb and liver insulin-like growth factor I (igf-1) expression levels were significantly higher in the largest individuals than those in the smallest S. curriculus individuals. Contrarily, the largest individuals had significantly lower expression levels of muscle igf-1 and liver myog than the smallest individuals. Overall, our results provide novel molecular information for growth-regulation study of S. curriculus.
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Affiliation(s)
- Jing'an Wang
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha 410128, China
| | - Dongfang Li
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha 410128, China
| | - Xin Zhao
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha 410128, China
| | - Tong Sun
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha 410128, China
| | - Shengzhen Jin
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha 410128, China
| | - Hongquan Wang
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha 410128, China
| | - Tiaoyi Xiao
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha 410128, China.
| | - Yaoguo Li
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha 410128, China.
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13
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Wang X, Liu H, Pang M, Fu B, Yu X, He S, Tong J. Construction of a high-density genetic linkage map and mapping of quantitative trait loci for growth-related traits in silver carp (Hypophthalmichthys molitrix). Sci Rep 2019; 9:17506. [PMID: 31767872 PMCID: PMC6877629 DOI: 10.1038/s41598-019-53469-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 10/29/2019] [Indexed: 01/26/2023] Open
Abstract
High-density genetic map and quantitative trait loci (QTL) mapping are powerful tools for identifying genomic regions that may be responsible for such polygenic trait as growth. A high-density genetic linkage map was constructed by sequencing 198 individuals in a F1 family of silver carp (Hypophthalmichthys molitrix) in this study. This genetic map spans a length of 2,721.07 cM with 3,134 SNPs distributed on 24 linkage groups (LGs). Comparative genomic mapping presented a high level of syntenic relationship between silver carp and zebrafish. We detected one major and nineteen suggestive QTL for 4 growth-related traits (body length, body height, head length and body weight) at 6, 12 and 18 months post hatch (mph), explaining 10.2~19.5% of phenotypic variation. All six QTL for growth traits of 12 mph generally overlapped with QTL for 6 mph, while the majority of QTL for 18 mph were identified on two additional LGs, which may reveal a different genetic modulation during early and late muscle growth stages. Four potential candidate genes were identified from the QTL regions by homology searching of marker sequences against zebrafish genome. Hepcidin, a potential candidate gene identified from a QTL interval on LG16, was significantly associated with growth traits in the analyses of both phenotype-SNP association and mRNA expression between small-size and large-size groups of silver carp. These results provide a basis for elucidating the genetic mechanisms for growth and body formation in silver carp, a world aquaculture fish.
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Affiliation(s)
- Xinhua Wang
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, 450046, China.,State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Haiyang Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Meixia Pang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Beide Fu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiaomu Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Shunping He
- Key Laboratory of Aquatic Biodiversity and Conservation of the CAS, Institute of Hydrobiology, the Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jingou Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.
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14
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Wan ZY, Lin G, Yue G. Genes for sexual body size dimorphism in hybrid tilapia (Oreochromis sp. x Oreochromis mossambicus). AQUACULTURE AND FISHERIES 2019. [DOI: 10.1016/j.aaf.2019.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Yu Y, Wang Q, Zhang Q, Luo Z, Wang Y, Zhang X, Huang H, Xiang J, Li F. Genome Scan for Genomic Regions and Genes Associated with Growth Trait in Pacific White Shrimp Litopeneaus vannamei. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:374-383. [PMID: 30887268 DOI: 10.1007/s10126-019-09887-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
The Pacific white shrimp Litopeneaus vannmei (L. vannmei) is a predominant aquaculture shrimp species worldwide, and it is considered as the aquaculture species with the highest single output value. Advances in selective breeding have accelerated the development of L. vannmei aquaculture. Recently, the genome-wide association studies (GWAS) have been applied in aquaculture animals and markers associated with economic traits were identified. In this study, we focused on the growth trait of L. vannamei and performed GWAS to identify SNPs or genes associated with growth. Genomic regions in linkage group 7, 27, 33, and 38 were identified to be associated with body weight and body length of the shrimp. Further, candidate gene association analysis was performed in two independent populations and the result demonstrated that the SNPs in the genes protein kinase C delta type and ras-related protein Rap-2a were significantly associated with the growth trait of L. vannamei. This study showed that GWAS analysis is an efficient approach for screening trait-related markers or genes. The genomic regions and genes identified in this study are essential for further fine mapping of growth-related genes. The identified markers will provide useful information for marker-assisted selection in L. vannamei.
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Affiliation(s)
- Yang Yu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Quanchao Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Qian Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zheng Luo
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yue Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaojun Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hao Huang
- Hainan Grand Suntop Ocean Breeding Co., Ltd, Wenchang, 571300, China
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Fuhua Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
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16
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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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17
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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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18
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Feng X, Yu X, Fu B, Wang X, Liu H, Pang M, Tong J. A high-resolution genetic linkage map and QTL fine mapping for growth-related traits and sex in the Yangtze River common carp (Cyprinus carpio haematopterus). BMC Genomics 2018; 19:230. [PMID: 29609551 PMCID: PMC5879560 DOI: 10.1186/s12864-018-4613-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 03/20/2018] [Indexed: 01/08/2023] Open
Abstract
Background A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection for economic traits in aquaculture species. The Yangtze River common carp (Cyprinus carpio haematopterus) is one of the most important aquacultured strains in China. However, quite limited genetics and genomics resources have been developed for genetic improvement of economic traits in such strain. Results A high-resolution genetic linkage map was constructed by using 7820 2b-RAD (2b-restriction site-associated DNA) and 295 microsatellite markers in a F2 family of the Yangtze River common carp (C. c. haematopterus). The length of the map was 4586.56 cM with an average marker interval of 0.57 cM. Comparative genome mapping revealed that a high proportion (70%) of markers with disagreed chromosome location was observed between C. c. haematopterus and another common carp strain (subspecies) C. c. carpio. A clear 2:1 relationship was observed between C. c. haematopterus linkage groups (LGs) and zebrafish (Danio rerio) chromosomes. Based on the genetic map, 21 QTLs for growth-related traits were detected on 12 LGs, and contributed values of phenotypic variance explained (PVE) ranging from 16.3 to 38.6%, with LOD scores ranging from 4.02 to 11.13. A genome-wide significant QTL (LOD = 10.83) and three chromosome-wide significant QTLs (mean LOD = 4.84) for sex were mapped on LG50 and LG24, respectively. A 1.4 cM confidence interval of QTL for all growth-related traits showed conserved synteny with a 2.06 M segment on chromosome 14 of D. rerio. Five potential candidate genes were identified by blast search in this genomic region, including a well-studied multi-functional growth related gene, Apelin. Conclusions We mapped a set of suggestive and significant QTLs for growth-related traits and sex based on a high-density genetic linkage map using SNP and microsatellite markers for Yangtze River common carp. Several candidate growth genes were also identified from the QTL regions by comparative mapping. This genetic map would provide a basis for genome assembly and comparative genomics studies, and those QTL-derived candidate genes and genetic markers are useful genomic resources for marker-assisted selection (MAS) of growth-related traits in the Yangtze River common carp. Electronic supplementary material The online version of this article (10.1186/s12864-018-4613-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiu Feng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiaomu Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Beide Fu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xinhua Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Haiyang Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Meixia Pang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jingou Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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19
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Kodama M, Hard JJ, Naish KA. Mapping of quantitative trait loci for temporal growth and age at maturity in coho salmon: Evidence for genotype-by-sex interactions. Mar Genomics 2018; 38:33-44. [DOI: 10.1016/j.margen.2017.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 07/01/2017] [Accepted: 07/22/2017] [Indexed: 11/26/2022]
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20
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Yu H, You X, Li J, Zhang X, Zhang S, Jiang S, Lin X, Lin HR, Meng Z, Shi Q. A genome-wide association study on growth traits in orange-spotted grouper (Epinephelus coioides) with RAD-seq genotyping. SCIENCE CHINA-LIFE SCIENCES 2018. [DOI: 10.1007/s11427-017-9161-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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21
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Lin G, Wang L, Ngoh ST, Ji L, Orbán L, Yue GH. Mapping QTL for Omega-3 Content in Hybrid Saline Tilapia. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:10-19. [PMID: 29204906 DOI: 10.1007/s10126-017-9783-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 11/07/2017] [Indexed: 06/07/2023]
Abstract
Tilapia is one of most important foodfish species. The low omega-3 to omega-6 fatty acid ratio in freshwater tilapia meat is disadvantageous for human health. Increasing omega-3 content is an important task in breeding to increase the nutritional value of tilapia. However, conventional breeding to increase omega-3 content is difficult and slow. To accelerate the increase of omega-3 through marker-assisted selection (MAS), we conducted QTL mapping for fatty acid contents and profiles in a F2 family of saline tilapia generated by crossing red tilapia and Mozambique tilapia. The total omega-3 content in F2 hybrid tilapia was 2.5 ± 1.0 mg/g, higher than that (2.00 mg/g) in freshwater tilapia. Genotyping by sequencing (GBS) technology was used to discover and genotype SNP markers, and microsatellites were also genotyped. We constructed a linkage map with 784 markers (151 microsatellites and 633 SNPs). The linkage map was 2076.7 cM long and consisted of 22 linkage groups. Significant and suggestive QTL for total lipid content were mapped on six linkage groups (LG3, -4, -6, -8, -13, and -15) and explained 5.8-8.3% of the phenotypic variance. QTL for omega-3 fatty acids were located on four LGs (LG11, -18, -19, and -20) and explained 5.0 to 7.5% of the phenotypic variance. Our data suggest that the total lipid and omega-3 fatty acid content were determined by multiple genes in tilapia. The markers flanking the QTL for omega-3 fatty acids can be used in MAS to accelerate the genetic improvements of these traits in salt-tolerant tilapia.
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Affiliation(s)
- Grace Lin
- 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
| | - Le Wang
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Si Te Ngoh
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Lianghui Ji
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Laszlo Orbán
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
- Department of Animal Sciences and Animal Husbandry, Georgikon Faculty, University of Pannonia, Keszthely, H-8360, Hungary.
- Centre for Comparative Genomics, Murdoch University, Murdoch, WA 6150, Australia.
| | - Gen Hua Yue
- 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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22
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Li N, Zhou T, Geng X, Jin Y, Wang X, Liu S, Xu X, Gao D, Li Q, Liu Z. Identification of novel genes significantly affecting growth in catfish through GWAS analysis. Mol Genet Genomics 2017; 293:587-599. [PMID: 29230585 DOI: 10.1007/s00438-017-1406-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 12/07/2017] [Indexed: 12/01/2022]
Abstract
Growth is the most important economic trait in aquaculture. Improvements in growth-related traits can enhance production, reduce costs and time to produce market-size fish. Catfish is the major aquaculture species in the United States, accounting for 65% of the US finfish production. However, the genes underlying growth traits in catfish were not well studied. Currently, the majority of the US catfish industry uses hybrid catfish derived from channel catfish female mated with blue catfish male. Interestingly, channel catfish and blue catfish exhibit differences in growth-related traits, and therefore the backcross progenies provide an efficient system for QTL analysis. In this study, we conducted a genome-wide association study for catfish body weight using the 250 K SNP array with 556 backcross progenies generated from backcross of male F1 hybrid (female channel catfish × male blue catfish) with female channel catfish. A genomic region of approximately 1 Mb on linkage group 5 was found to be significantly associated with body weight. In addition, four suggestively associated QTL regions were identified on linkage groups 1, 2, 23 and 24. Most candidate genes in the associated regions are known to be involved in muscle growth and bone development, some of which were reported to be associated with obesity in humans and pigs, suggesting that the functions of these genes may be evolutionarily conserved in controlling growth. Additional fine mapping or functional studies should allow identification of the causal genes for fast growth in catfish, and elucidation of molecular mechanisms of regulation of growth in fish.
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Affiliation(s)
- Ning Li
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Tao Zhou
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Xin Geng
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yulin Jin
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Xiaozhu Wang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Xiaoyan Xu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, 201306, China
| | - Dongya Gao
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Qi Li
- The Shellfish Genetics and Breeding Laboratory, Fisheries College, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Zhanjiang Liu
- Department of Biology, Syracuse University, Syracuse, NY, 13244, USA.
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23
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Robledo D, Rubiolo JA, Cabaleiro S, Martínez P, Bouza C. Differential gene expression and SNP association between fast- and slow-growing turbot (Scophthalmus maximus). Sci Rep 2017; 7:12105. [PMID: 28935875 PMCID: PMC5608734 DOI: 10.1038/s41598-017-12459-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/08/2017] [Indexed: 12/20/2022] Open
Abstract
Growth is among the most important traits for animal breeding. Understanding the mechanisms underlying growth differences between individuals can contribute to improving growth rates through more efficient breeding schemes. Here, we report a transcriptomic study in muscle and brain of fast- and slow-growing turbot (Scophthalmus maximus), a relevant flatfish in European and Asian aquaculture. Gene expression and allelic association between the two groups were explored. Up-regulation of the anaerobic glycolytic pathway in the muscle of fast-growing fish was observed, indicating a higher metabolic rate of white muscle. Brain expression differences were smaller and not associated with major growth-related genes, but with regulation of feeding-related sensory pathways. Further, SNP variants showing frequency differences between fast- and slow-growing fish pointed to genomic regions likely involved in growth regulation, and three of them were individually validated through SNP typing. Although different mechanisms appear to explain growth differences among families, general mechanisms seem also to be involved, and thus, results provide a set of useful candidate genes and markers to be evaluated for more efficient growth breeding programs and to perform comparative genomic studies of growth in fish and vertebrates.
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Affiliation(s)
- Diego Robledo
- Departamento de Zooloxía, Xenética e Antropoloxía Física, Facultade de Veterinaria, Universidade de Santiago de Compostela, 27002, Lugo, Spain.,The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, United Kingdom
| | - Juan A Rubiolo
- Departamento de Zooloxía, Xenética e Antropoloxía Física, Facultade de Veterinaria, Universidade de Santiago de Compostela, 27002, Lugo, Spain
| | - Santiago Cabaleiro
- Cluster de Acuicultura de Galicia (Punta do Couso), Aguiño-Ribeira, 15695, Spain
| | - Paulino Martínez
- Departamento de Zooloxía, Xenética e Antropoloxía Física, Facultade de Veterinaria, Universidade de Santiago de Compostela, 27002, Lugo, Spain
| | - Carmen Bouza
- Departamento de Zooloxía, Xenética e Antropoloxía Física, Facultade de Veterinaria, Universidade de Santiago de Compostela, 27002, Lugo, Spain.
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24
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Abdelrahman H, ElHady M, Alcivar-Warren A, Allen S, Al-Tobasei R, Bao L, Beck B, Blackburn H, Bosworth B, Buchanan J, Chappell J, Daniels W, Dong S, Dunham R, Durland E, Elaswad A, Gomez-Chiarri M, Gosh K, Guo X, Hackett P, Hanson T, Hedgecock D, Howard T, Holland L, Jackson M, Jin Y, Khalil K, Kocher T, Leeds T, Li N, Lindsey L, Liu S, Liu Z, Martin K, Novriadi R, Odin R, Palti Y, Peatman E, Proestou D, Qin G, Reading B, Rexroad C, Roberts S, Salem M, Severin A, Shi H, Shoemaker C, Stiles S, Tan S, Tang KFJ, Thongda W, Tiersch T, Tomasso J, Prabowo WT, Vallejo R, van der Steen H, Vo K, Waldbieser G, Wang H, Wang X, Xiang J, Yang Y, Yant R, Yuan Z, Zeng Q, Zhou T. Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research. BMC Genomics 2017; 18:191. [PMID: 28219347 PMCID: PMC5319170 DOI: 10.1186/s12864-017-3557-1] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 02/06/2017] [Indexed: 12/31/2022] Open
Abstract
Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships. In addition, it is also important to understand the mechanisms of regulation and evolutionary conservation at the levels of genome, transcriptome, proteome, epigenome, and systems biology. With genomic information and information between the genomes and phenomes, technologies for marker/causal mutation-assisted selection, genome selection, and genome editing can be developed for applications in aquaculture. A set of genomic tools and resources must be made available including reference genome sequences and their annotations (including coding and non-coding regulatory elements), genome-wide polymorphic markers, efficient genotyping platforms, high-density and high-resolution linkage maps, and transcriptome resources including non-coding transcripts. Genomic and genetic control of important performance and production traits, such as disease resistance, feed conversion efficiency, growth rate, processing yield, behaviour, reproductive characteristics, and tolerance to environmental stressors like low dissolved oxygen, high or low water temperature and salinity, must be understood. QTL need to be identified, validated across strains, lines and populations, and their mechanisms of control understood. Causal gene(s) need to be identified. Genetic and epigenetic regulation of important aquaculture traits need to be determined, and technologies for marker-assisted selection, causal gene/mutation-assisted selection, genome selection, and genome editing using CRISPR and other technologies must be developed, demonstrated with applicability, and application to aquaculture industries.Major progress has been made in aquaculture genomics for dozens of fish and shellfish species including the development of genetic linkage maps, physical maps, microarrays, single nucleotide polymorphism (SNP) arrays, transcriptome databases and various stages of genome reference sequences. This paper provides a general review of the current status, challenges and future research needs of aquaculture genomics, genetics, and breeding, with a focus on major aquaculture species in the United States: catfish, rainbow trout, Atlantic salmon, tilapia, striped bass, oysters, and shrimp. While the overall research priorities and the practical goals are similar across various aquaculture species, the current status in each species should dictate the next priority areas within the species. This paper is an output of the USDA Workshop for Aquaculture Genomics, Genetics, and Breeding held in late March 2016 in Auburn, Alabama, with participants from all parts of the United States.
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Affiliation(s)
- Hisham Abdelrahman
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Mohamed ElHady
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | | | - Standish Allen
- Aquaculture Genetics & Breeding Technology Center, Virginia Institute of Marine Science, Gloucester Point, VA, 23062, USA
| | - Rafet Al-Tobasei
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Lisui Bao
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ben Beck
- Aquatic Animal Health Research Unit, USDA-ARS, 990 Wire Road, Auburn, AL, 36832, USA
| | - Harvey Blackburn
- USDA-ARS-NL Wheat & Corn Collections at a Glance GRP, National Animal Germplasm Program, 1111 S. Mason St., Fort Collins, CO, 80521-4500, USA
| | - Brian Bosworth
- USDA-ARS/CGRU, 141 Experimental Station Road, Stoneville, MS, 38701, USA
| | - John Buchanan
- Center for Aquaculture Technologies, 8395 Camino Santa Fe, Suite E, San Diego, CA, 92121, USA
| | - Jesse Chappell
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - William Daniels
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Sheng Dong
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Rex Dunham
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Evan Durland
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, 97331, USA
| | - Ahmed Elaswad
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Marta Gomez-Chiarri
- Department of Fisheries, Animal & Veterinary Science, 134 Woodward Hall, 9 East Alumni Avenue, Kingston, RI, 02881, USA
| | - Kamal Gosh
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA
| | - Perry Hackett
- Department of Genetics, Cell Biology and Development, 5-108 MCB, 420 Washington Avenue SE, Minneapolis, MN, 55455, USA
| | - Terry Hanson
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Dennis Hedgecock
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-0371, USA
| | - Tiffany Howard
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Leigh Holland
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Molly Jackson
- Taylor Shellfish Farms, 130 SE Lynch RD, Shelton, WA, 98584, USA
| | - Yulin Jin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Karim Khalil
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Thomas Kocher
- Department of Biology, University of Maryland, 2132 Biosciences Research Building, College Park, MD, 20742, USA
| | - Tim Leeds
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, 25430, USA
| | - Ning Li
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Lauren Lindsey
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Shikai Liu
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Zhanjiang Liu
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA.
| | - Kyle Martin
- Troutlodge, 27090 Us Highway 12, Naches, WA, 98937, USA
| | - Romi Novriadi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ramjie Odin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yniv Palti
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, 25430, USA
| | - Eric Peatman
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Dina Proestou
- USDA ARS NEA NCWMAC Shellfish Genetics at the University Rhode Island, 469 CBLS, 120 Flagg Road, Kingston, RI, 02881, USA
| | - Guyu Qin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Benjamin Reading
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, 27695-7617, USA
| | - Caird Rexroad
- USDA ARS Office of National Programs, George Washington Carver Center Room 4-2106, 5601 Sunnyside Avenue, Beltsville, MD, 20705, USA
| | - Steven Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98105, USA
| | - Mohamed Salem
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Andrew Severin
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA, 50011, USA
| | - Huitong Shi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Craig Shoemaker
- Aquatic Animal Health Research Unit, USDA-ARS, 990 Wire Road, Auburn, AL, 36832, USA
| | - Sheila Stiles
- USDOC/NOAA, National Marine Fisheries Service, NEFSC, Milford Laboratory, Milford, Connectcut, 06460, USA
| | - Suxu Tan
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Kathy F J Tang
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Wilawan Thongda
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Terrence Tiersch
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, LA, 70820, USA
| | - Joseph Tomasso
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Wendy Tri Prabowo
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Roger Vallejo
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, 25430, USA
| | | | - Khoi Vo
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Geoff Waldbieser
- USDA-ARS/CGRU, 141 Experimental Station Road, Stoneville, MS, 38701, USA
| | - Hanping Wang
- Aquaculture Genetics and Breeding Laboratory, The Ohio State University South Centers, Piketon, OH, 45661, USA
| | - Xiaozhu Wang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yujia Yang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Roger Yant
- Hybrid Catfish Company, 1233 Montgomery Drive, Inverness, MS, 38753, USA
| | - Zihao Yuan
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Qifan Zeng
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Tao Zhou
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
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Li BJ, Li HL, Meng Z, Zhang Y, Lin H, Yue GH, Xia JH. Copy Number Variations in Tilapia Genomes. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:11-21. [PMID: 28168542 DOI: 10.1007/s10126-017-9733-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/23/2016] [Indexed: 06/06/2023]
Abstract
Discovering the nature and pattern of genome variation is fundamental in understanding phenotypic diversity among populations. Although several millions of single nucleotide polymorphisms (SNPs) have been discovered in tilapia, the genome-wide characterization of larger structural variants, such as copy number variation (CNV) regions has not been carried out yet. We conducted a genome-wide scan for CNVs in 47 individuals from three tilapia populations. Based on 254 Gb of high-quality paired-end sequencing reads, we identified 4642 distinct high-confidence CNVs. These CNVs account for 1.9% (12.411 Mb) of the used Nile tilapia reference genome. A total of 1100 predicted CNVs were found overlapping with exon regions of protein genes. Further association analysis based on linear model regression found 85 CNVs ranging between 300 and 27,000 base pairs significantly associated to population types (R 2 > 0.9 and P > 0.001). Our study sheds first insights on genome-wide CNVs in tilapia. These CNVs among and within tilapia populations may have functional effects on phenotypes and specific adaptation to particular environments.
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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
| | - Hong Lian 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
| | - Zining 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
| | - Yong Zhang
- 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
| | - Haoran 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
| | - Gen Hua Yue
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| | - 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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Lin G, Chua E, Orban L, Yue GH. Mapping QTL for Sex and Growth Traits in Salt-Tolerant Tilapia (Oreochromis spp. X O. mossambicus). PLoS One 2016; 11:e0166723. [PMID: 27870905 PMCID: PMC5117716 DOI: 10.1371/journal.pone.0166723] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 11/02/2016] [Indexed: 11/18/2022] Open
Abstract
In aquaculture, growth and sex are economically important traits. To accelerate genetic improvement in increasing growth in salt-tolerant tilapia, we conducted QTL mapping for growth traits and sex with an F2 family, including 522 offspring and two parents. We used 144 polymorphic microsatellites evenly covering the genome of tilapia to genotype the family. QTL analyses were carried out using interval mapping for all individuals, males and females in the family, respectively. Using all individuals, three suggestive QTL for body weight, body length and body thickness respectively were detected in LG20, LG22 and LG12 and explained 2.4% to 3.1% of phenotypic variance (PV). When considering only males, five QTL for body weight were detected on five LGs, and explained 4.1 to 6.3% of PV. Using only females from the F2 family, three QTL for body weight were detected on LG1, LG6 and LG8, and explained 7.9-14.3% of PV. The QTL for body weight in males and females were located in different LGs, suggesting that in salt-tolerant tilapia, different set of genes 'switches' control the growth in males and females. QTL for sex were mapped on LG1 and LG22, indicating multigene sex determination in the salt-tolerant tilapia. This study provides new insights on the locations and effects of QTL for growth traits and sex, and sets the foundation for fine mapping for future marker-assisted selection for growth and sex in salt-tolerant tilapia aquaculture.
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Affiliation(s)
- Grace Lin
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Elaine Chua
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Laszlo Orban
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
- Department of Animal Sciences and Breeding, Georgikon Faculty, University of Pannonia, Deák Ferenc utca 16, H-8230 Keszthely, Hungary
- Centre for Comparative Genomics, Murdoch University, Murdoch, 6150 Australia
| | - Gen Hua Yue
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
- * E-mail:
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27
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An ultra-high density linkage map and QTL mapping for sex and growth-related traits of common carp (Cyprinus carpio). Sci Rep 2016; 6:26693. [PMID: 27225429 PMCID: PMC4880943 DOI: 10.1038/srep26693] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/06/2016] [Indexed: 11/13/2022] Open
Abstract
High density genetic linkage maps are essential for QTL fine mapping, comparative genomics and high quality genome sequence assembly. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,194 SNP markers on 14,146 distinct loci for common carp based on high-throughput genotyping with the carp 250 K single nucleotide polymorphism (SNP) array in a mapping family. The genetic length of the consensus map was 10,595.94 cM with an average locus interval of 0.75 cM and an average marker interval of 0.38 cM. Comparative genomic analysis revealed high level of conserved syntenies between common carp and the closely related model species zebrafish and medaka. The genome scaffolds were anchored to the high-density linkage map, spanning 1,357 Mb of common carp reference genome. QTL mapping and association analysis identified 22 QTLs for growth-related traits and 7 QTLs for sex dimorphism. Candidate genes underlying growth-related traits were identified, including important regulators such as KISS2, IGF1, SMTLB, NPFFR1 and CPE. Candidate genes associated with sex dimorphism were also identified including 3KSR and DMRT2b. The high-density and high-resolution genetic linkage map provides an important tool for QTL fine mapping and positional cloning of economically important traits, and improving common carp genome assembly.
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28
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Lv W, Zheng X, Kuang Y, Cao D, Yan Y, Sun X. QTL variations for growth-related traits in eight distinct families of common carp (Cyprinus carpio). BMC Genet 2016; 17:65. [PMID: 27150452 PMCID: PMC4858896 DOI: 10.1186/s12863-016-0370-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 04/15/2016] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Comparing QTL analyses of multiple pair-mating families can provide a better understanding of important allelic variations and distributions. However, most QTL mapping studies in common carp have been based on analyses of individual families. In order to improve our understanding of heredity and variation of QTLs in different families and identify important QTLs, we performed QTL analysis of growth-related traits in multiple segregating families. RESULTS We completed a genome scan for QTLs that affect body weight (BW), total length (TL), and body thickness (BT) of 522 individuals from eight full-sib families using 250 microsatellites evenly distributed across 50 chromosomes. Sib-pair and half-sib model mapping identified 165 QTLs on 30 linkage groups. Among them, 10 (genome-wide P <0.01 or P < 0.05) and 28 (chromosome-wide P < 0.01) QTLs exhibited significant evidence of linkage, while the remaining 127 exhibited a suggestive effect on the above three traits at a chromosome-wide (P < 0.05) level. Multiple QTLs obtained from different families affect BW, TL, and BT and locate at close or identical positions. It suggests that same genetic factors may control variability in these traits. Furthermore, the results of the comparative QTL analysis of multiple families showed that one QTL was common in four of the eight families, nine QTLs were detected in three of the eight families, and 26 QTLs were found common to two of the eight families. These common QTLs are valuable candidates in marker-assisted selection. CONCLUSION A large number of QTLs were detected in the common carp genome and associated with growth-related traits. Some of the QTLs of different growth-related traits were identified at similar chromosomal regions, suggesting a role for pleiotropy and/or tight linkage and demonstrating a common genetic basis of growth trait variations. The results have set up an example for comparing QTLs in common carp and provided insights into variations in the identified QTLs affecting body growth. Discovery of these common QTLs between families and growth-related traits represents an important step towards understanding of quantitative genetic variation in common carp.
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Affiliation(s)
- Weihua Lv
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China
| | - Xianhu Zheng
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China
| | - Youyi Kuang
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China
| | - Dingchen Cao
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China
| | - Yunqin Yan
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China.
| | - Xiaowen Sun
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China.
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Ma K, Liao M, Liu F, Ye B, Sun F, Yue GH. Charactering the ZFAND3 gene mapped in the sex-determining locus in hybrid tilapia (Oreochromis spp.). Sci Rep 2016; 6:25471. [PMID: 27137111 PMCID: PMC4853787 DOI: 10.1038/srep25471] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/18/2016] [Indexed: 01/01/2023] Open
Abstract
Zinc finger AN1-type domain 3 (ZFAND3) is essential for spermatogenesis in mice. However, its function in teleosts remains unclear. In this study, we characterized the ZFAND3 gene (termed as OsZFAND3) in an important food fish, tilapia. The OsZFAND3 cDNA sequence is 1,050 bp in length, containing an ORF of 615 bp, which encodes a putative peptide of 204 amino acid residues. Quantitative real-time PCR revealed that the OsZFAND3 transcripts were exclusively expressed in the testis and ovary. In situ hybridization showed that the high expression of OsZFAND3 transcripts was predominantly localized in the spermatocyte and spermatid. These results suggest that OsZFAND3 is involved in male germ cell maturation. Three single nucleotide polymorphisms (SNPs) were detected in the introns of OsZFAND3. The OsZFAND3 gene was mapped in the sex-determining locus on linkage group 1 (LG1). The three SNPs in the OsZFAND3 gene were strictly associated with sex phenotype, suggesting that the OsZFAND3 gene is tightly linked to the sex-determining locus. Our study provides new insights into the functions of the OsZFAND3 gene in tilapia and a foundation for further detailed analysis of the OsZFAND3 gene in sex determination and differentiation.
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Affiliation(s)
- Keyi Ma
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Minghui Liao
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Feng Liu
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Baoqing Ye
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Fei Sun
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Gen Hua Yue
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Republic of Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
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30
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Robledo D, Fernández C, Hermida M, Sciara A, Álvarez-Dios JA, Cabaleiro S, Caamaño R, Martínez P, Bouza C. Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot. Int J Mol Sci 2016; 17:243. [PMID: 26901189 PMCID: PMC4783974 DOI: 10.3390/ijms17020243] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 02/02/2016] [Accepted: 02/04/2016] [Indexed: 12/30/2022] Open
Abstract
Growth traits represent a main goal in aquaculture breeding programs and may be related to adaptive variation in wild fisheries. Integrating quantitative trait loci (QTL) mapping and next generation sequencing can greatly help to identify variation in candidate genes, which can result in marker-assisted selection and better genetic structure information. Turbot is a commercially important flatfish in Europe and China, with available genomic information on QTLs and genome mapping. Muscle and liver RNA-seq from 18 individuals was carried out to obtain gene sequences and markers functionally related to growth, resulting in a total of 20,447 genes and 85,344 single nucleotide polymorphisms (SNPs). Many growth-related genes and SNPs were identified and placed in the turbot genome and genetic map to explore their co-localization with growth-QTL markers. Forty-five SNPs on growth-related genes were selected based on QTL co-localization and relevant function for growth traits. Forty-three SNPs were technically feasible and validated in a wild Atlantic population, where 91% were polymorphic. The integration of functional and structural genomic resources in turbot provides a practical approach for QTL mining in this species. Validated SNPs represent a useful set of growth-related gene markers for future association, functional and population studies in this flatfish species.
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Affiliation(s)
- Diego Robledo
- Departamento de Xenética, Facultade de Bioloxía (CIBUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain.
| | - Carlos Fernández
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain.
| | - Miguel Hermida
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain.
| | - Andrés Sciara
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Rosario S2002LRK, Argentina.
| | - José Antonio Álvarez-Dios
- Departamento de Matemática Aplicada, Facultade de Matemáticas, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain.
| | - Santiago Cabaleiro
- Cluster de Acuicultura de Galicia (Punta do Couso), Aguiño-Ribeira 15695, Spain.
| | - Rubén Caamaño
- Cluster de Acuicultura de Galicia (Punta do Couso), Aguiño-Ribeira 15695, Spain.
| | - Paulino Martínez
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain.
| | - Carmen Bouza
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain.
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31
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Signatures of selection in tilapia revealed by whole genome resequencing. Sci Rep 2015; 5:14168. [PMID: 26373374 PMCID: PMC4570987 DOI: 10.1038/srep14168] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 08/18/2015] [Indexed: 02/06/2023] Open
Abstract
Natural selection and selective breeding for genetic improvement have left detectable signatures within the genome of a species. Identification of selection signatures is important in evolutionary biology and for detecting genes that facilitate to accelerate genetic improvement. However, selection signatures, including artificial selection and natural selection, have only been identified at the whole genome level in several genetically improved fish species. Tilapia is one of the most important genetically improved fish species in the world. Using next-generation sequencing, we sequenced the genomes of 47 tilapia individuals. We identified a total of 1.43 million high-quality SNPs and found that the LD block sizes ranged from 10–100 kb in tilapia. We detected over a hundred putative selective sweep regions in each line of tilapia. Most selection signatures were located in non-coding regions of the tilapia genome. The Wnt signaling, gonadotropin-releasing hormone receptor and integrin signaling pathways were under positive selection in all improved tilapia lines. Our study provides a genome-wide map of genetic variation and selection footprints in tilapia, which could be important for genetic studies and accelerating genetic improvement of tilapia.
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Xiao S, Han Z, Wang P, Han F, Liu Y, Li J, Wang ZY. Functional marker detection and analysis on a comprehensive transcriptome of large yellow croaker by next generation sequencing. PLoS One 2015; 10:e0124432. [PMID: 25909910 PMCID: PMC4409302 DOI: 10.1371/journal.pone.0124432] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/15/2015] [Indexed: 01/08/2023] Open
Abstract
Large yellow croaker (Larimichthys crocea) is an important economic fish in China and Eastern Asia. Because of the exhaustive fishing and overdense aquaculture, the wild population and the mariculture of the species are facing serious challenges on germplasm degeneration and susceptibility to infectious disease agents. However, a comprehensive transcriptome from multi-tissues of the species has not been reported and functional molecular markers have not yet been detected and analyzed. In this work, we applied RNA-seq with the Illumina Hiseq2000 platform for a multi-tissue sample of large yellow croaker and assembled the transcriptome into 88,103 transcripts. Of them, 52,782 transcripts have been successfully annotated by nt/nr, InterPro, GO and KEGG database. Comparing with public fish proteins, we have found that 34,576 protein coding transcripts are shared in large yellow croaker with zebrafish, medaka, pufferfish, and stickleback. For functional markers, we have discovered 1,276 polymorphic SSRs and 261, 000 SNPs. The functional impact analysis of SNPs showed that the majority (~75%) of small variants cause synonymous mutations in proteins, followed by variations in 3' UTR region. The functional enrichment analysis illuminated that transcripts involved in DNA bindings, enzyme activities, and signal pathways prominently exhibit less single-nucleotide variants but genes for the constituent of the muscular tissue, the cytoskeleton, and the immunity system contain more frequent SNP mutations, which may reflect the structural and functional selections of the translated proteins. This is the first work for the high-throughput detection and analysis of functional polymorphic SSR and SNP markers in a comprehensive transcriptome of large yellow croaker. Our study provides valuable transcript sequence and functional marker resources for the quantitative trait locus (QTL) identification and molecular selection of the species in the research community.
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Affiliation(s)
- Shijun Xiao
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture; Fisheries College, Jimei University, Xiamen, Fujian, China
| | - Zhaofang Han
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture; Fisheries College, Jimei University, Xiamen, Fujian, China
| | - Panpan Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture; Fisheries College, Jimei University, Xiamen, Fujian, China
| | - Fang Han
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture; Fisheries College, Jimei University, Xiamen, Fujian, China
| | - Yang Liu
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture; Fisheries College, Jimei University, Xiamen, Fujian, China
| | - Jiongtang Li
- Chinese Academy of Fishery Sciences, Beijing, China
| | - Zhi Yong Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture; Fisheries College, Jimei University, Xiamen, Fujian, China
- * E-mail:
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