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Hu Q, Liu Y, Liao X, Tian H, Ji X, Zhu J, Xiao H. A high-density genetic map construction and sex-related loci identification in Chinese Giant salamander. BMC Genomics 2021; 22:230. [PMID: 33794798 PMCID: PMC8017863 DOI: 10.1186/s12864-021-07550-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 03/24/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Chinese giant salamander Andrias davidianus is an important amphibian species in China because of its increasing economic value, protection status and special evolutionary position from aquatic to terrestrial animal. Its large genome presents challenges to genetic research. Genetic linkage mapping is an important tool for genome assembly and determination of phenotype-related loci. RESULTS In this study, we constructed a high-density genetic linkage map using ddRAD sequencing technology to obtain SNP genotyping data of members from an full-sib family which sex had been determined. A total of 10,896 markers were grouped and oriented into 30 linkage groups, representing 30 chromosomes of A. davidianus. The genetic length of LGs ranged from 17.61 cM (LG30) to 280.81 cM (LG1), with a mean inter-locus distance ranging from 0.11(LG3) to 0.48 cM (LG26). The total genetic map length was 2643.10 cM with an average inter-locus distance of 0.24 cM. Three sex-related loci and four sex-related markers were found on LG6 and LG23, respectively. CONCLUSION We constructed the first High-density genetic linkage map and identified three sex-related loci in the Chinese giant salamander. Current results are expected to be a useful tool for future genomic studies aiming at the marker-assisted breeding of the species.
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Affiliation(s)
- Qiaomu Hu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, Hubei, China.
| | - Yang Liu
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xiaolin Liao
- Key Laboratory of Ecological Impacts of Hydraulic-Projects and Restoration of Aquatic Ecosystem of Ministry of Water Resources, Institute of Hydroecology, Ministry of Water Resources and Chinese Academy of Sciences, Wuhan, 430079, China
| | - Haifeng Tian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, Hubei, China
| | - Xiangshan Ji
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Jiajie Zhu
- Guangxi Academy of Fishery Sciences, Nanning, 530021, Guangxi Province, China
| | - Hanbing Xiao
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, Hubei, China
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Mastrochirico-Filho VA, Borges CHS, Freitas MV, Ariede RB, Pilarski F, Utsunomia R, Carvalheiro R, Gutierrez AP, Peñaloza C, Yáñez JM, Houston RD, Hashimoto DT. Development of a SNP linkage map and genome-wide association study for resistance to Aeromonas hydrophila in pacu (Piaractus mesopotamicus). BMC Genomics 2020; 21:672. [PMID: 32993504 PMCID: PMC7526211 DOI: 10.1186/s12864-020-07090-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/21/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Pacu (Piaractus mesopotamicus) is one of the most important Neotropical aquaculture species from South America. Disease outbreaks caused by Aeromonas hydrophila infection have been considered significant contributors to the declining levels of pacu production. The current implementation of genomic selection for disease resistance has been adopted as a powerful strategy for improvement in fish species. This study aimed to investigate the genetic architecture of resistance to A. hydrophila in pacu via Genome-Wide Association Study (GWAS), the identification of suggestive Quantitative Trait Loci (QTLs) and putative genes associated with this trait. The genetic data were obtained from 381 juvenile individuals belonging to 14 full-sibling families. An experimental challenge was performed to gain access to the levels of genetic variation for resistance against the bacteria using the following trait definitions: binary test survival (TS) and time of death (TD). RESULTS The analyses of genetic parameters estimated moderate heritability (h2) for both resistance traits: 0.20 (± 0.09) for TS and 0.35 (± 0.15) for TD. A linkage map for pacu was developed to enable the GWAS, resulting in 27 linkage groups (LGs) with 17,453 mapped Single Nucleotide Polymorphisms (SNPs). The length of the LGs varied from 79.95 (LG14) to 137.01 (LG1) cM, with a total map length of 2755.60 cM. GWAS identified 22 putative QTLs associated to A. hydrophila resistance. They were distributed into 17 LGs, and were considered suggestive genomic regions explaining > 1% of the additive genetic variance (AGV) for the trait. Several candidate genes related to immune response were located close to the suggestive QTLs, such as tbk1, trim16, Il12rb2 and lyz2. CONCLUSION This study describes the development of the first medium density linkage map for pacu, which will be used as a framework to study relevant traits to the production of this species. In addition, the resistance to A. hydrophila was found to be moderately heritable but with a polygenic architecture suggesting that genomic selection, instead of marker assisted selection, might be useful for efficiently improving resistance to one of the most problematic diseases that affects the South American aquaculture.
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Affiliation(s)
- Vito A Mastrochirico-Filho
- São Paulo State University (Unesp), Aquaculture Center of Unesp, Via de Acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, SP, 14884-900, Brazil
| | - Carolina H S Borges
- São Paulo State University (Unesp), Aquaculture Center of Unesp, Via de Acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, SP, 14884-900, Brazil
| | - Milena V Freitas
- São Paulo State University (Unesp), Aquaculture Center of Unesp, Via de Acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, SP, 14884-900, Brazil
| | - Raquel B Ariede
- São Paulo State University (Unesp), Aquaculture Center of Unesp, Via de Acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, SP, 14884-900, Brazil
| | - Fabiana Pilarski
- São Paulo State University (Unesp), Aquaculture Center of Unesp, Via de Acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, SP, 14884-900, Brazil
| | - Ricardo Utsunomia
- Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, 23897-000, Brazil
| | - Roberto Carvalheiro
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP, Brazil
- National Council for Scientific and Technological Development (CNPq), Brasília, DF, 71605-001, Brazil
| | - Alejandro P Gutierrez
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Carolina Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, UK
| | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Diogo T Hashimoto
- São Paulo State University (Unesp), Aquaculture Center of Unesp, Via de Acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, SP, 14884-900, Brazil.
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Santiago E, Novo I, Pardiñas AF, Saura M, Wang J, Caballero A. Recent Demographic History Inferred by High-Resolution Analysis of Linkage Disequilibrium. Mol Biol Evol 2020; 37:3642-3653. [DOI: 10.1093/molbev/msaa169] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
AbstractInferring changes in effective population size (Ne) in the recent past is of special interest for conservation of endangered species and for human history research. Current methods for estimating the very recent historical Ne are unable to detect complex demographic trajectories involving multiple episodes of bottlenecks, drops, and expansions. We develop a theoretical and computational framework to infer the demographic history of a population within the past 100 generations from the observed spectrum of linkage disequilibrium (LD) of pairs of loci over a wide range of recombination rates in a sample of contemporary individuals. The cumulative contributions of all of the previous generations to the observed LD are included in our model, and a genetic algorithm is used to search for the sequence of historical Ne values that best explains the observed LD spectrum. The method can be applied from large samples to samples of fewer than ten individuals using a variety of genotyping and DNA sequencing data: haploid, diploid with phased or unphased genotypes and pseudohaploid data from low-coverage sequencing. The method was tested by computer simulation for sensitivity to genotyping errors, temporal heterogeneity of samples, population admixture, and structural division into subpopulations, showing high tolerance to deviations from the assumptions of the model. Computer simulations also show that the proposed method outperforms other leading approaches when the inference concerns recent timeframes. Analysis of data from a variety of human and animal populations gave results in agreement with previous estimations by other methods or with records of historical events.
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Affiliation(s)
- Enrique Santiago
- Departamento de Biología Funcional, Facultad de Biología, Universidad de Oviedo, Oviedo, Spain
| | - Irene Novo
- Centro de Investigación Mariña, Departamento de Bioquímica, Genética e Inmunología, Edificio CC Experimentais, Campus de Vigo, Universidade de Vigo, Vigo, Spain
| | - Antonio F Pardiñas
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - María Saura
- Departamento de Mejora Genética Animal, INIA, Madrid, Spain
| | - Jinliang Wang
- Institute of Zoology, Zoological Society of London, London, United Kingdom
| | - Armando Caballero
- Centro de Investigación Mariña, Departamento de Bioquímica, Genética e Inmunología, Edificio CC Experimentais, Campus de Vigo, Universidade de Vigo, Vigo, Spain
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Houston RD, Bean TP, Macqueen DJ, Gundappa MK, Jin YH, Jenkins TL, Selly SLC, Martin SAM, Stevens JR, Santos EM, Davie A, Robledo D. Harnessing genomics to fast-track genetic improvement in aquaculture. Nat Rev Genet 2020; 21:389-409. [PMID: 32300217 DOI: 10.1038/s41576-020-0227-y] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2020] [Indexed: 12/12/2022]
Abstract
Aquaculture is the fastest-growing farmed food sector and will soon become the primary source of fish and shellfish for human diets. In contrast to crop and livestock production, aquaculture production is derived from numerous, exceptionally diverse species that are typically in the early stages of domestication. Genetic improvement of production traits via well-designed, managed breeding programmes has great potential to help meet the rising seafood demand driven by human population growth. Supported by continuous advances in sequencing and bioinformatics, genomics is increasingly being applied across the broad range of aquaculture species and at all stages of the domestication process to optimize selective breeding. In the future, combining genomic selection with biotechnological innovations, such as genome editing and surrogate broodstock technologies, may further expedite genetic improvement in aquaculture.
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Affiliation(s)
- Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK.
| | - Tim P Bean
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Daniel J Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Manu Kumar Gundappa
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Ye Hwa Jin
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Tom L Jenkins
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | | | | | - Jamie R Stevens
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Eduarda M Santos
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Andrew Davie
- Institute of Aquaculture, University of Stirling, Stirling, UK
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
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Yang W, Wang Y, Jiang D, Tian C, Zhu C, Li G, Chen H. ddRADseq-assisted construction of a high-density SNP genetic map and QTL fine mapping for growth-related traits in the spotted scat (Scatophagus argus). BMC Genomics 2020; 21:278. [PMID: 32245399 PMCID: PMC7126399 DOI: 10.1186/s12864-020-6658-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 03/09/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Scatophagus argus is a popular farmed fish in several countries of Southeast Asia, including China. Although S. argus has a highly promising economic value, a significant lag of breeding research severely obstructs the sustainable development of aquaculture industry. As one of the most important economic traits, growth traits are controlled by multiple gene loci called quantitative trait loci (QTLs). It is urgently needed to launch a marker assisted selection (MAS) breeding program to improve growth and other pivotal traits. Thus a high-density genetic linkage map is necessary for the fine mapping of QTLs associated with target traits. RESULTS Using restriction site-associated DNA sequencing, 6196 single nucleotide polymorphism (SNP) markers were developed from a full-sib mapping population for genetic map construction. A total of 6193 SNPs were grouped into 24 linkage groups (LGs), and the total length reached 2191.65 cM with an average marker interval of 0.35 cM. Comparative genome mapping revealed 23 one-to-one and 1 one-to-two syntenic relationships between S. argus LGs and Larimichthys crocea chromosomes. Based on the high-quality linkage map, a total of 44 QTLs associated with growth-related traits were identified on 11 LGs. Of which, 19 significant QTLs for body weight were detected on 9 LGs, explaining 8.8-19.6% of phenotypic variances. Within genomic regions flanking the SNP markers in QTL intervals, we predicted 15 candidate genes showing potential relationships with growth, such as Hbp1, Vgll4 and Pim3, which merit further functional exploration. CONCLUSIONS The first SNP genetic map with a fine resolution of 0.35 cM for S. argus has been developed, which shows a high level of syntenic relationship with L. crocea genomes. This map can provide valuable information for future genetic, genomic and evolutionary studies. The QTLs and SNP markers significantly associated with growth-related traits will act as useful tools in gene mapping, map-based cloning and MAS breeding to speed up the genetic improvement in important traits of S. argus. The interesting candidate genes are promising for further investigations and have the potential to provide deeper insights into growth regulation in the future.
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Affiliation(s)
- Wei Yang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
- Food and Environmental Engineering Department, Yangjiang Polytechnic, Yangjiang, 529566, China
| | - Yaorong Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Dongneng Jiang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Changxu Tian
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Chunhua Zhu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Guangli Li
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Huapu Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China.
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An SNP-Based Genetic Map and QTL Mapping for Growth Traits in the Red-Spotted Grouper ( Epinephelus akaara). Genes (Basel) 2019; 10:genes10100793. [PMID: 31614822 PMCID: PMC6826704 DOI: 10.3390/genes10100793] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/04/2019] [Accepted: 10/04/2019] [Indexed: 12/13/2022] Open
Abstract
The red-spotted grouper (Epinephelus akaara) is one of the most commercially important aquatic species in China. However, its seedstock has low larval survival rates, and its stability is confronted with the danger of overexploitation. In this study, a high-density genetic map was constructed using 3435 single nucleotide polymorphisms (SNPs) from 142 first generation (F1) full-sib offspring and two parents of a red-spotted grouper population. The total genetic length of the map was 2300.12 cM with an average intermarker distance of 0.67 cM. Seventeen genome-wide significant quantitative trait loci (QTLs) for growth-related traits were detected on 24 linkage groups, including 5 QTLs for full length, 7 QTLs for body length, and 5 QTLs for body weight. The contribution values of explained phenotypic variance ranged from 10.7% to 12.9%. Moreover, 13 potential candidate genes for growth-related traits were identified. Collectively, these findings will be useful for conducting marker-assisted selection of the red-spotted grouper in future studies.
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High-Density Linkage Map and QTLs for Growth in Snapper ( Chrysophrys auratus). G3-GENES GENOMES GENETICS 2019; 9:1027-1035. [PMID: 30804023 PMCID: PMC6469409 DOI: 10.1534/g3.118.200905] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Characterizing the genetic variation underlying phenotypic traits is a central objective in biological research. This research has been hampered in the past by the limited genomic resources available for most non-model species. However, recent advances in sequencing technologies and related genotyping methods are rapidly changing this. Here we report the use of genome-wide SNP data from the ecologically and commercially important marine fish species Chrysophrys auratus (snapper) to 1) construct the first linkage map for this species, 2) scan for growth QTL, and 3) search for putative candidate genes in the surrounding QTL regions. The newly constructed linkage map contained ∼11K SNP markers and is one of the densest maps to date in the fish family Sparidae. Comparisons with genome scaffolds of the recently assembled snapper genome indicated that marker placement was mostly consistent between the scaffolds and linkage map (R = 0.7), but that at fine scales (< 5 cM) some precision limitations occurred. Of the 24 linkage groups, which likely reflect the 24 chromosomes of this species, three were found to contain QTL with genome-wide significance for growth-related traits. A scan of 13 candidate growth genes located the growth hormone, myogenin, and parvalbumin genes within 5.3, 9.6, and 25.0 cM of these QTL, respectively. The linkage map and QTL found in this study will advance the investigation of genome structure and aquaculture breeding efforts in this and related species.
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Houston RD, Macqueen DJ. Atlantic salmon (Salmo salar L.) genetics in the 21st century: taking leaps forward in aquaculture and biological understanding. Anim Genet 2019; 50:3-14. [PMID: 30426521 PMCID: PMC6492011 DOI: 10.1111/age.12748] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2018] [Indexed: 12/17/2022]
Abstract
Atlantic salmon (Salmo salar L.) is among the most iconic and economically important fish species and was the first member of Salmonidae to have a high-quality reference genome assembly published. Advances in genomics have become increasingly central to the genetic improvement of farmed Atlantic salmon as well as conservation of wild salmon stocks. The salmon genome has also been pivotal in shaping our understanding of the evolutionary and functional consequences arising from an ancestral whole-genome duplication event characterising all Salmonidae members. Here, we provide a review of the current status of Atlantic salmon genetics and genomics, focussed on progress made from genome-wide research aimed at improving aquaculture production and enhancing understanding of salmonid ecology, physiology and evolution. We present our views on the future direction of salmon genomics, including the role of emerging technologies (e.g. genome editing) in elucidating genetic features that underpin functional variation in traits of commercial and evolutionary importance.
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Affiliation(s)
- R. D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghMidlothianEH25 9RGUK
| | - D. J. Macqueen
- School of Biological SciencesUniversity of AberdeenAberdeenAB24 2TZUK
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Leitwein M, Gagnaire PA, Desmarais E, Berrebi P, Guinand B. Genomic consequences of a recent three-way admixture in supplemented wild brown trout populations revealed by local ancestry tracts. Mol Ecol 2018; 27:3466-3483. [PMID: 30054960 DOI: 10.1111/mec.14816] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/11/2018] [Accepted: 07/19/2018] [Indexed: 12/20/2022]
Abstract
Understanding the evolutionary consequences of human-mediated introductions of domesticated strains into the wild and their subsequent admixture with natural populations is of major concern in conservation biology. However, the genomic impacts of stocking from distinct sources (locally derived vs. divergent) on the genetic integrity of wild populations remain poorly understood. We designed an approach based on estimating local ancestry along individual chromosomes to provide a detailed picture of genomic admixture in supplemented populations. We used this approach to document admixture consequences in the brown trout Salmo trutta, for which decades of stocking practices have profoundly impacted the genetic make-up of wild populations. In southern France, small local Mediterranean populations have been subject to successive introductions of domestic strains derived from the Atlantic and Mediterranean lineages. To address the impact of stocking, we evaluate the extent of admixture from both domestic strains within populations, using 75,684 mapped SNPs obtained from double-digested restriction site-associated DNA sequencing. Then, the chromosomal ancestry profiles of admixed individuals reveal a wider diversity of hybrid and introgressed genotypes than estimated using classical methods for inferring ancestry and hybrid pedigrees. In addition, the length distribution of introgressed tracts retained different timings of introgression between the two domestic strains. We finally reveal opposite consequences of admixture on the level of polymorphism of the recipient populations between domestic strains. Our study illustrates the potential of using the information contained in the genomic mosaic of ancestry tracts in combination with classical methods based on allele frequencies for analysing multiple-way admixture with population genomic data.
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Affiliation(s)
- Maeva Leitwein
- ISEM, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | | | - Erick Desmarais
- ISEM, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - Patrick Berrebi
- ISEM, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - Bruno Guinand
- ISEM, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France.,Département Biologie-Ecologie, Université de Montpellier, Montpellier Cedex 5, France
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Maroso F, Hermida M, Millán A, Blanco A, Saura M, Fernández A, Dalla Rovere G, Bargelloni L, Cabaleiro S, Villanueva B, Bouza C, Martínez P. Highly dense linkage maps from 31 full-sibling families of turbot (Scophthalmus maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly. DNA Res 2018; 25:439-450. [PMID: 29897548 PMCID: PMC6105115 DOI: 10.1093/dnares/dsy015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/05/2018] [Indexed: 12/26/2022] Open
Abstract
Highly dense linkage maps enable positioning thousands of landmarks useful for anchoring the whole genome and for analysing genome properties. Turbot is the most important cultured flatfish worldwide and breeding programs in the fifth generation of selection are targeted to improve growth rate, obtain disease resistant broodstock and understand sex determination to control sex ratio. Using a Restriction-site Associated DNA approach, we genotyped 18,214 single nucleotide polymorphism in 1,268 turbot individuals from 31 full-sibling families. Individual linkage maps were combined to obtain a male, female and species consensus maps. The turbot consensus map contained 11,845 markers distributed across 22 linkage groups representing a total normalised length of 3,753.9 cM. The turbot genome was anchored to this map, and scaffolds representing 96% of the assembly were ordered and oriented to obtain the expected 22 megascaffolds according to its karyotype. Recombination rate was lower in males, especially around centromeres, and pairwise comparison of 44 individual maps suggested chromosome polymorphism at specific genomic regions. Genome comparison across flatfish provided new evidence on karyotype reorganisations occurring across the evolution of this fish group.
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Affiliation(s)
| | - M Hermida
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | | | - A Blanco
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - M Saura
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - A Fernández
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - G Dalla Rovere
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padova, Italy
| | - L Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padova, Italy
| | - S Cabaleiro
- Cluster de Acuicultura de Galicia (Punta do Couso), Aguiño-Ribeira, Spain
| | - B Villanueva
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - C Bouza
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - P Martínez
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
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Robledo D, Palaiokostas C, Bargelloni L, Martínez P, Houston R. Applications of genotyping by sequencing in aquaculture breeding and genetics. REVIEWS IN AQUACULTURE 2018; 10:670-682. [PMID: 30220910 PMCID: PMC6128402 DOI: 10.1111/raq.12193] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/27/2016] [Indexed: 05/18/2023]
Abstract
Selective breeding is increasingly recognized as a key component of sustainable production of aquaculture species. The uptake of genomic technology in aquaculture breeding has traditionally lagged behind terrestrial farmed animals. However, the rapid development and application of sequencing technologies has allowed aquaculture to narrow the gap, leading to substantial genomic resources for all major aquaculture species. While high-density single-nucleotide polymorphism (SNP) arrays for some species have been developed recently, direct genotyping by sequencing (GBS) techniques have underpinned many of the advances in aquaculture genetics and breeding to date. In particular, restriction-site associated DNA sequencing (RAD-Seq) and subsequent variations have been extensively applied to generate population-level SNP genotype data. These GBS techniques are not dependent on prior genomic information such as a reference genome assembly for the species of interest. As such, they have been widely utilized by researchers and companies focussing on nonmodel aquaculture species with relatively small research communities. Applications of RAD-Seq techniques have included generation of genetic linkage maps, performing genome-wide association studies, improvements of reference genome assemblies and, more recently, genomic selection for traits of interest to aquaculture like growth, sex determination or disease resistance. In this review, we briefly discuss the history of GBS, the nuances of the various GBS techniques, bioinformatics approaches and application of these techniques to various aquaculture species.
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Affiliation(s)
- Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Christos Palaiokostas
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroPadovaItaly
| | - Paulino Martínez
- Department of ZoologyGenetics and Physical AnthropologyFaculty of VeterinaryUniversity of Santiago de CompostelaLugoSpain
| | - Ross Houston
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
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Weigand H, Leese F. Detecting signatures of positive selection in non-model species using genomic data. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly007] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Hannah Weigand
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
| | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße, Essen, Germany
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Whole Genome Sequencing of Greater Amberjack ( Seriola dumerili) for SNP Identification on Aligned Scaffolds and Genome Structural Variation Analysis Using Parallel Resequencing. Int J Genomics 2018; 2018:7984292. [PMID: 29785397 PMCID: PMC5896239 DOI: 10.1155/2018/7984292] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 01/04/2018] [Accepted: 01/14/2018] [Indexed: 01/30/2023] Open
Abstract
Greater amberjack (Seriola dumerili) is distributed in tropical and temperate waters worldwide and is an important aquaculture fish. We carried out de novo sequencing of the greater amberjack genome to construct a reference genome sequence to identify single nucleotide polymorphisms (SNPs) for breeding amberjack by marker-assisted or gene-assisted selection as well as to identify functional genes for biological traits. We obtained 200 times coverage and constructed a high-quality genome assembly using next generation sequencing technology. The assembled sequences were aligned onto a yellowtail (Seriola quinqueradiata) radiation hybrid (RH) physical map by sequence homology. A total of 215 of the longest amberjack sequences, with a total length of 622.8 Mbp (92% of the total length of the genome scaffolds), were lined up on the yellowtail RH map. We resequenced the whole genomes of 20 greater amberjacks and mapped the resulting sequences onto the reference genome sequence. About 186,000 nonredundant SNPs were successfully ordered on the reference genome. Further, we found differences in the genome structural variations between two greater amberjack populations using BreakDancer. We also analyzed the greater amberjack transcriptome and mapped the annotated sequences onto the reference genome sequence.
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Robledo D, Matika O, Hamilton A, Houston RD. Genome-Wide Association and Genomic Selection for Resistance to Amoebic Gill Disease in Atlantic Salmon. G3 (BETHESDA, MD.) 2018; 8:1195-1203. [PMID: 29420190 PMCID: PMC5873910 DOI: 10.1534/g3.118.200075] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 02/01/2018] [Indexed: 11/18/2022]
Abstract
Amoebic gill disease (AGD) is one of the largest threats to salmon aquaculture, causing serious economic and animal welfare burden. Treatments can be expensive and environmentally damaging, hence the need for alternative strategies. Breeding for disease resistance can contribute to prevention and control of AGD, providing long-term cumulative benefits in selected stocks. The use of genomic selection can expedite selection for disease resistance due to improved accuracy compared to pedigree-based approaches. The aim of this work was to quantify and characterize genetic variation in AGD resistance in salmon, the genetic architecture of the trait, and the potential of genomic selection to contribute to disease control. An AGD challenge was performed in ∼1,500 Atlantic salmon, using gill damage and amoebic load as indicator traits for host resistance. Both traits are heritable (h2 ∼0.25-0.30) and show high positive correlation, indicating they may be good measurements of host resistance to AGD. While the genetic architecture of resistance appeared to be largely polygenic in nature, two regions on chromosome 18 showed suggestive association with both AGD resistance traits. Using a cross-validation approach, genomic prediction accuracy was up to 18% higher than that obtained using pedigree, and a reduction in marker density to ∼2,000 SNPs was sufficient to obtain accuracies similar to those obtained using the whole dataset. This study indicates that resistance to AGD is a suitable trait for genomic selection, and the addition of this trait to Atlantic salmon breeding programs can lead to more resistant stocks.
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Affiliation(s)
- Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies and
| | - Oswald Matika
- The Roslin Institute and Royal (Dick) School of Veterinary Studies and
| | - Alastair Hamilton
- Landcatch Natural Selection Ltd., Roslin Innovation Centre, University of Edinburgh, EH25 9RG Midlothian, United Kingdom,and
- Hendrix Genetics Aquaculture BV/ Netherlands, Villa 'de Körver', Spoorstraat 69, 5831 CK Boxmeer, The Netherlands
| | - Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies and
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Laurent B, Palaiokostas C, Spataro C, Moinard M, Zehraoui E, Houston RD, Foulongne‐Oriol M. High-resolution mapping of the recombination landscape of the phytopathogen Fusarium graminearum suggests two-speed genome evolution. MOLECULAR PLANT PATHOLOGY 2018; 19:341-354. [PMID: 27998012 PMCID: PMC6638080 DOI: 10.1111/mpp.12524] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 12/01/2016] [Accepted: 12/03/2016] [Indexed: 05/25/2023]
Abstract
Recombination is a major evolutionary force, increasing genetic diversity and permitting efficient coevolution of fungal pathogen(s) with their host(s). The ascomycete Fusarium graminearum is a devastating pathogen of cereal crops, and can contaminate food and feed with harmful mycotoxins. Previous studies have suggested a high adaptive potential of this pathogen, illustrated by an increase in pathogenicity and resistance to fungicides. In this study, we provide the first detailed picture of the crossover events occurring during meiosis and discuss the role of recombination in pathogen evolution. An experimental recombinant population (n = 88) was created and genotyped using 1306 polymorphic markers obtained from restriction site-associated DNA sequencing (RAD-seq) and aligned to the reference genome. The construction of a high-density linkage map, anchoring 99% of the total length of the reference genome, allowed the identification of 1451 putative crossovers, positioned at a median resolution of 24 kb. The majority of crossovers (87.2%) occurred in a relatively small portion of the genome (30%). All chromosomes demonstrated recombination-active sections, which had a near 15-fold higher crossover rate than non-active recombinant sections. The recombination rate showed a strong positive correlation with nucleotide diversity, and recombination-active regions were enriched for genes with a putative role in host-pathogen interaction, as well as putative diversifying genes. Our results confirm the preliminary analysis observed in other F. graminearum strains and suggest a conserved 'two-speed' recombination landscape. The consequences with regard to the evolutionary potential of this major fungal pathogen are also discussed.
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Affiliation(s)
- Benoit Laurent
- MycSA, INRA, Université de Bordeaux33882Villenave d'OrnonFrance
| | | | - Cathy Spataro
- MycSA, INRA, Université de Bordeaux33882Villenave d'OrnonFrance
| | - Magalie Moinard
- MycSA, INRA, Université de Bordeaux33882Villenave d'OrnonFrance
| | - Enric Zehraoui
- MycSA, INRA, Université de Bordeaux33882Villenave d'OrnonFrance
| | - Ross D. Houston
- The Roslin Institute, University of EdinburghMidlothianEH25 9RGUK
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Pedersen S, Liu L, Glebe B, Leadbeater S, Lien S, Boulding EG. Mapping of quantitative trait loci associated with size, shape, and parr mark traits using first- and second-generation backcrosses between European and North American Atlantic salmon (Salmo salar). Genome 2018; 61:33-42. [DOI: 10.1139/gen-2017-0026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Little is known about the genetic architecture of traits important for salmonid restoration ecology. We mapped quantitative trait loci (QTL) using single nucleotide polymorphisms (SNPs) for juvenile body length, weight, shape, and vertical skin pigmentation patterns (parr marks) within three hybrid backcross families between European and North American subspecies of Atlantic salmon. Amounts of variation in skin colour and pattern quantified in the two second-generation transAtlantic families exceeded the ranges seen in purebred populations. GridQTL analyses using low-density female-specific linkage maps detected QTL showing experiment-wide significance on Ssa02, Ssa03, Ssa09, Ssa11, Ssa19, and Ssa26/28 for both length and weight; on Ssa04 and Ssa23 for parr mark number; on Ssa09 and Ssa13 for parr mark contrast; and on Ssa05, Ssa07, Ssa10, Ssa11, Ssa18, Ssa23, and Ssa26/28 for geometric morphometric shape coordinates. Pleiotrophic QTL on Ssa11 affected length, weight, and shape. No QTL was found that explained more than 10% of the phenotypic variance in pigmentation or shape traits. Each QTL was approximately positioned on the physical map of the Atlantic salmon genome. Some QTL locations confirmed previous studies but many were new. Studies like ours may increase the success of salmon restoration projects by enabling better phenotypic and genetic matching between introduced and extirpated strains.
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Affiliation(s)
- Stephanie Pedersen
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Lei Liu
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Brian Glebe
- Department of Fisheries and Oceans Canada, St. Andrews Biological Station, St. Andrews, NB E5B 2L9, Canada
| | - Steven Leadbeater
- Department of Fisheries and Oceans Canada, St. Andrews Biological Station, St. Andrews, NB E5B 2L9, Canada
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Ås, Norway
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Zhao J, Han D, Shi K, Wang L, Gao J, Yang R. Influence of epistatic segregation distortion loci on genetic marker linkages in Japanese flounder. Genomics 2017; 110:59-66. [PMID: 28830780 DOI: 10.1016/j.ygeno.2017.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 08/11/2017] [Accepted: 08/18/2017] [Indexed: 11/28/2022]
Abstract
For genetic linkage analysis of Japanese flounder, 160 doubled haploids (DH) were artificially produced using mitotic gynogenesis and were genotyped for 458 simple sequence repeat (SSR) markers, 101 of which show distortional segregation. The genetic linkage map was constructed by modifying recombination fractions between the distorted markers. Between the corrected and uncorrected genetic maps, there were considerable differences in genetic distance, but not in relative locations among markers. Using a liability model, a segregation distortion locus (SDL), with an additive genetic effect of 1.772, was mapped between markers BDHYP387 and Poli56TUF of chromosome 24 in the corrected genetic map. Additionally, six pairs of epistatic SDLs were identified on chromosomes 1, 5, 8, 9, 23, and 24. Changes in genetic distances between markers did not occur on chromosome regions with main effect SDLs. However, most chromosome regions where genetic distances changed covered the detected epistatic SDLs. This study concluded that epistatic SDLs decrease linkages between markers and lengthen genetic distances in Japanese flounder. This finding has been partially validated in other DH populations derived from three female Japanese flounders.
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Affiliation(s)
- Jingli Zhao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, Research Centre for Aquatic Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China
| | - Dandan Han
- Department of Biological Science and Technology, Heilongjiang Vocational College for Nationalities, Harbin 150066, China
| | - Kuntao Shi
- Division of Comprehensive Aquaculture, Shandong Weihai Institute of Ocean and Aquaculture, Weihai 264200, China
| | - Li Wang
- Division of Comprehensive Aquaculture, Shandong Weihai Institute of Ocean and Aquaculture, Weihai 264200, China
| | - Jin Gao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, Research Centre for Aquatic Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China
| | - Runqing Yang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, Research Centre for Aquatic Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China.
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A High-Density Genetic Linkage Map and QTL Fine Mapping for Body Weight in Crucian Carp ( Carassius auratus) Using 2b-RAD Sequencing. G3-GENES GENOMES GENETICS 2017; 7:2473-2487. [PMID: 28600439 PMCID: PMC5555455 DOI: 10.1534/g3.117.041376] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A high-resolution genetic linkage map is essential for a wide range of genetics and genomics studies such as comparative genomics analysis and QTL fine mapping. Crucian carp (Carassius auratus) is widely distributed in Eurasia, and is an important aquaculture fish worldwide. In this study, a high-density genetic linkage map was constructed for crucian carp using 2b-RAD technology. The consensus map contains 8487 SNP markers, assigning to 50 linkage groups (LGs) and spanning 3762.88 cM, with an average marker interval of 0.44 cM and genome coverage of 98.8%. The female map had 4410 SNPs, and spanned 3500.42 cM (0.79 cM/marker), while the male map had 4625 SNPs and spanned 3346.33 cM (0.72 cM/marker). The average recombination ratio of female to male was 2.13:1, and significant male-biased recombination suppressions were observed in LG47 and LG49. Comparative genomics analysis revealed a clear 2:1 syntenic relationship between crucian carp LGs and chromosomes of zebrafish and grass carp, and a 1:1 correspondence, but extensive chromosomal rearrangement, between crucian carp and common carp, providing evidence that crucian carp has experienced a fourth round of whole genome duplication (4R-WGD). Eight chromosome-wide QTL for body weight at 2 months after hatch were detected on five LGs, explaining 10.1-13.2% of the phenotypic variations. Potential candidate growth-related genes, such as an EGF-like domain and TGF-β, were identified within the QTL intervals. This high-density genetic map and QTL analysis supplies a basis for genome evolutionary studies in cyprinid fishes, genome assembly, and QTL fine mapping for complex traits in crucian carp.
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Building Ultra-High-Density Linkage Maps Based on Efficient Filtering of Trustable Markers. Genetics 2017; 206:1285-1295. [PMID: 28512186 DOI: 10.1534/genetics.116.197491] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 05/09/2017] [Indexed: 12/18/2022] Open
Abstract
The study is focused on addressing the problem of building genetic maps in the presence of ∼103-104 of markers per chromosome. We consider a spectrum of situations with intrachromosomal heterogeneity of recombination rate, different level of genotyping errors, and missing data. In the ideal scenario of the absence of errors and missing data, the majority of markers should appear as groups of cosegregating markers ("twins") representing no challenge for map construction. The central aspect of the proposed approach is to take into account the structure of the marker space, where each twin group (TG) and singleton markers are represented as points of this space. The confounding effect of genotyping errors and missing data leads to reduction of TG size, but upon a low level of these effects surviving TGs can still be used as a source of reliable skeletal markers. Increase in the level of confounding effects results in a considerable decrease in the number or even disappearance of usable TGs and, correspondingly, of skeletal markers. Here, we show that the paucity of informative markers can be compensated by detecting kernels of markers in the marker space using a clustering procedure, and demonstrate the utility of this approach for high-density genetic map construction on simulated and experimentally obtained genotyping datasets.
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A Dense Brown Trout ( Salmo trutta) Linkage Map Reveals Recent Chromosomal Rearrangements in the Salmo Genus and the Impact of Selection on Linked Neutral Diversity. G3-GENES GENOMES GENETICS 2017; 7:1365-1376. [PMID: 28235829 PMCID: PMC5386884 DOI: 10.1534/g3.116.038497] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
High-density linkage maps are valuable tools for conservation and eco-evolutionary issues. In salmonids, a complex rediploidization process consecutive to an ancient whole genome duplication event makes linkage maps of prime importance for investigating the evolutionary history of chromosome rearrangements. Here, we developed a high-density consensus linkage map for the brown trout (Salmo trutta), a socioeconomically important species heavily impacted by human activities. A total of 3977 ddRAD markers were mapped and ordered in 40 linkage groups using sex- and lineage-averaged recombination distances obtained from two family crosses. Performing map comparison between S. trutta and its sister species, S. salar, revealed extensive chromosomal rearrangements. Strikingly, all of the fusion and fission events that occurred after the S. salar/S. trutta speciation happened in the Atlantic salmon branch, whereas the brown trout remained closer to the ancestral chromosome structure. Using the strongly conserved synteny within chromosome arms, we aligned the brown trout linkage map to the Atlantic salmon genome sequence to estimate the local recombination rate in S. trutta at 3721 loci. A significant positive correlation between recombination rate and within-population nucleotide diversity (π) was found, indicating that selection constrains variation at linked neutral sites in brown trout. This new high-density linkage map provides a useful genomic resource for future aquaculture, conservation, and eco-evolutionary studies in brown trout.
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Genotype Imputation To Improve the Cost-Efficiency of Genomic Selection in Farmed Atlantic Salmon. G3-GENES GENOMES GENETICS 2017; 7:1377-1383. [PMID: 28250015 PMCID: PMC5386885 DOI: 10.1534/g3.117.040717] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Genomic selection uses genome-wide marker information to predict breeding values for traits of economic interest, and is more accurate than pedigree-based methods. The development of high density SNP arrays for Atlantic salmon has enabled genomic selection in selective breeding programs, alongside high-resolution association mapping of the genetic basis of complex traits. However, in sibling testing schemes typical of salmon breeding programs, trait records are available on many thousands of fish with close relationships to the selection candidates. Therefore, routine high density SNP genotyping may be prohibitively expensive. One means to reducing genotyping cost is the use of genotype imputation, where selected key animals (e.g., breeding program parents) are genotyped at high density, and the majority of individuals (e.g., performance tested fish and selection candidates) are genotyped at much lower density, followed by imputation to high density. The main objectives of the current study were to assess the feasibility and accuracy of genotype imputation in the context of a salmon breeding program. The specific aims were: (i) to measure the accuracy of genotype imputation using medium (25 K) and high (78 K) density mapped SNP panels, by masking varying proportions of the genotypes and assessing the correlation between the imputed genotypes and the true genotypes; and (ii) to assess the efficacy of imputed genotype data in genomic prediction of key performance traits (sea lice resistance and body weight). Imputation accuracies of up to 0.90 were observed using the simple two-generation pedigree dataset, and moderately high accuracy (0.83) was possible even with very low density SNP data (∼250 SNPs). The performance of genomic prediction using imputed genotype data was comparable to using true genotype data, and both were superior to pedigree-based prediction. These results demonstrate that the genotype imputation approach used in this study can provide a cost-effective method for generating robust genome-wide SNP data for genomic prediction in Atlantic salmon. Genotype imputation approaches are likely to form a critical component of cost-efficient genomic selection programs to improve economically important traits in aquaculture.
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A SNP Based Linkage Map of the Arctic Charr ( Salvelinus alpinus) Genome Provides Insights into the Diploidization Process After Whole Genome Duplication. G3-GENES GENOMES GENETICS 2017; 7:543-556. [PMID: 27986793 PMCID: PMC5295600 DOI: 10.1534/g3.116.038026] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Diploidization, which follows whole genome duplication events, does not occur evenly across the genome. In salmonid fishes, certain pairs of homeologous chromosomes preserve tetraploid loci in higher frequencies toward the telomeres due to residual tetrasomic inheritance. Research suggests this occurs only in homeologous pairs where one chromosome arm has undergone a fusion event. We present a linkage map for Arctic charr (Salvelinus alpinus), a salmonid species with relatively fewer chromosome fusions. Genotype by sequencing identified 19,418 SNPs, and a linkage map consisting of 4508 markers was constructed from a subset of high quality SNPs and microsatellite markers that were used to anchor the new map to previous versions. Both male- and female-specific linkage maps contained the expected number of 39 linkage groups. The chromosome type associated with each linkage group was determined, and 10 stable metacentric chromosomes were identified, along with a chromosome polymorphism involving the sex chromosome AC04. Two instances of a weak form of pseudolinkage were detected in the telomeric regions of homeologous chromosome arms in both female and male linkage maps. Chromosome arm homologies within the Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) genomes were determined. Paralogous sequence variants (PSVs) were identified, and their comparative BLASTn hit locations showed that duplicate markers exist in higher numbers on seven pairs of homeologous arms, previously identified as preserving tetrasomy in salmonid species. Homeologous arm pairs where neither arm has been part of a fusion event in Arctic charr had fewer PSVs, suggesting faster diploidization rates in these regions.
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Wang L, Bai B, Liu P, Huang SQ, Wan ZY, Chua E, Ye B, Yue GH. Construction of high-resolution recombination maps in Asian seabass. BMC Genomics 2017; 18:63. [PMID: 28068919 PMCID: PMC5223582 DOI: 10.1186/s12864-016-3462-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 12/22/2016] [Indexed: 11/17/2022] Open
Abstract
Background A high-density genetic map is essential for de novo genome assembly, fine mapping QTL for important complex traits, comparative genomic studies and understanding the mechanisms of genome evolution. Although a number of genomic resources are available in Asian seabass (Lates calcarifer), a high-density linkage map is still lacking. To facilitate QTL mapping for marker-assisted selection and genome assembly, and to understand the genome-wide recombination rates, we constructed high density linkage maps using three families and genotyping by sequencing. Results A high-density consensus linkage map consisting of 8, 274 markers was constructed based on sex-averaged genetic maps. The genetic maps were then aligned and integrated with the current genome assembly of Asian seabass. More than 90% of the genome contig sequences were anchored onto the consensus genetic map. Evidence of assembly errors in the current genome assembly was identified. A fragment of up to 2.5 Mb belonging to LG14 was assembled into Chr15. The length of family-specific sex-averaged maps ranged from 1348.96 to 1624.65 cM. Female maps were slightly longer than male maps using common markers. Female-to-male ratios were highly variable both across chromosomes within each family and throughout three families for each chromosome. However, the distribution patterns of recombination along chromosomes were similar between sexes across the whole genome. The overall recombination rates were significantly correlated with genome-wide GC content and the correlations were revealed to be stronger in females than in males. Conclusions These high-density genetic maps provide not only essential tools for facilitating de novo genome assembly and comparative genomic studies in teleosts, but also critical resources for fine mapping QTL and genome-wide association mapping for economically important traits in Asian seabass. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3462-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Le Wang
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Bin Bai
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Peng Liu
- 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, 14 Science Drive 4, Singapore, 117543, Singapore
| | - Shu Qing Huang
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Zi Yi Wan
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Elaine Chua
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Baoqing Ye
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Gen Hua Yue
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore. .,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore. .,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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