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Maekawa M, Yoshii E, Akase Y, Huang H, Yoshikawa S, Matsuda M, Kuruma Y, Sawayama E. Sex-Associated SNP Confirmation of Sex-Reversed Male Farmed Japanese Flounder Paralichthys olivaceus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:718-728. [PMID: 37541964 DOI: 10.1007/s10126-023-10235-2] [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: 04/27/2023] [Accepted: 07/21/2023] [Indexed: 08/06/2023]
Abstract
Female Japanese flounder Paralichthys olivaceus grow more rapidly than the male. The goal of all-female commercial production requires an efficient method of genetic sex identification. We conducted genome-wide association analysis of female and male farmed Japanese flounder (n = 24 per phenotypic sex) and found all regions of chromosome 24 to be significantly associated with phenotypic sex, suggesting it as the sex chromosome. Genetic sex was identified based on single nucleotide polymorphisms (SNP) on chromosome 24 (n = 3568) using multidimensional scaling analysis, and individuals were clearly separated according to sex by the first dimension. The 61 SNPs most highly associated with sex were selected, and an amplicon-based SNP panel was developed. This was used to determine genetic sex of 39 females and 40 males. Eleven phenotypic males were assigned as female with XX genotype, suggesting sex reversal. Genetic sex was also assessed based on the indel of the amh gene promoter, which is the major candidate sex gene of Japanese flounder. We found four SNPs perfectly associated with genotypic sex in the sex-associated SNP panel, one of which was located in exon 2 of the amh gene. Along with the indel of the amh gene promoter, the sex-associated SNP panel will be of value in identifying genetic sex of farmed Japanese flounder. Molecular sexing will facilitate all-female production by breeding sex-reversed males.
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Affiliation(s)
- Mari Maekawa
- Department of Marine Science, College of Bioresource Sciences, Nihon University, Kanagawa, Japan
| | - Emiri Yoshii
- Department of Marine Science, College of Bioresource Sciences, Nihon University, Kanagawa, Japan
| | - Yuri Akase
- R&D Division, Marua Suisan Co., Ltd., Ehime, Japan
| | - He Huang
- Bioengineering Lab. Co., Ltd., Kanagawa, Japan
| | - Sota Yoshikawa
- Nagasaki Prefectural Institute of Fisheries, Nagasaki, Japan
| | | | - Yosuke Kuruma
- Nagasaki Prefectural Institute of Fisheries, Nagasaki, Japan
| | - Eitaro Sawayama
- Department of Marine Science, College of Bioresource Sciences, Nihon University, Kanagawa, Japan.
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Malintha GHT, Jeong JB, Gunathilaka BE, Hasanthi M, Yun KS, Lee KJ. Effects of dietary piperine supplementation on innate immunity, growth performance, feed utilization and intestinal morphology of olive flounder (Paralichthys olivaceus). FISH PHYSIOLOGY AND BIOCHEMISTRY 2023; 49:925-937. [PMID: 37594621 DOI: 10.1007/s10695-023-01229-x] [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: 01/09/2023] [Accepted: 07/30/2023] [Indexed: 08/19/2023]
Abstract
Piperine, the main bioactive component of black pepper (Piper nigrum) or long pepper (Piper longum), has anti-inflammatory, antifungal, and antibacterial properties. This study was carried out to evaluate the supplemental effects of piperine in olive flounder (Paralichthys olivaceus) diets. Six isonitrogenous and isolipidic diets were formulated to contain different levels of piperine at 0.00, 0.25, 0.50, 0.75, 1.00, and 2.00 g/kg (Con, P25, P50, P75, P100, and P200, respectively). Diets were randomly allocated to triplicate groups of fish (initial weight 27.6 ± 0.4 g, 30 fish/tank) and fed three times daily for 8 weeks. Results showed that dietary piperine significantly improved fish growth and feed utilization efficiency. The highest growth, including the highest Igf-1 mRNA expression, was observed in the P50 group, while P50 and P75 groups showed the highest protein efficiency ratio. Compared to the Con group piperine supplemented groups had significantly higher lysozyme activity, immunoglobulin level, and phagocytosis activities. Plasma cholesterol was significantly lower in fish fed P200 diet. Dry matter and protein digestibility were higher in P25, P50, and P75 groups than in Con group. Dietary piperine increased the intestinal villi length and goblet cell counts. In the challenge test against Edwardsiella tarda, all the groups supplemented with piperine showed higher cumulative survival compared to Con group. Therefore, these findings indicate that dietary piperine supplementation can improve growth performance, innate immunity, disease resistance, diet digestibility, and intestinal morphology of olive flounder. The optimum dietary piperine level seems to be approximately 0.5 g/kg for the fish.
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Affiliation(s)
- G H T Malintha
- Department of Marine Life Sciences, Jeju National University, 63243, Jeju, South Korea
| | - Joon Bum Jeong
- Department of Marine Life Sciences, Jeju National University, 63243, Jeju, South Korea
| | - Buddhi E Gunathilaka
- Department of Marine Life Sciences, Jeju National University, 63243, Jeju, South Korea
| | - Mirasha Hasanthi
- Department of Marine Life Sciences, Jeju National University, 63243, Jeju, South Korea
| | - Kwan-Sik Yun
- Synergen Inc., Bucheon-Si, Gyeonggi-Do, South Korea
| | - Kyeong-Jun Lee
- Department of Marine Life Sciences, Jeju National University, 63243, Jeju, South Korea.
- Marine Science Institute, Jeju National University, Jeju, 63333, South Korea.
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Hattori RS, Kumazawa K, Nakamoto M, Nakano Y, Yamaguchi T, Kitano T, Yamamoto E, Fuji K, Sakamoto T. Y-specific amh allele, amhy, is the master sex-determining gene in Japanese flounder Paralichthys olivaceus. Front Genet 2022; 13:1007548. [PMID: 36186422 PMCID: PMC9523440 DOI: 10.3389/fgene.2022.1007548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 08/25/2022] [Indexed: 01/12/2023] Open
Abstract
Japanese flounder (Paralichthys olivaceus) is an important marine fish species of both fisheries and aquaculture in Northeast Asia. The commercial interest for all-female progenies due to several sex-related traits has prompted basic research on the mechanisms of sex determination in this species. By conducting a linkage analysis of the sex-determining locus, we initially identified 12 microsatellite markers linked to sex in 11 scaffolds, whose localization was restricted to a specific region of linkage group 9. Sequence analysis of this region identified 181 genes based on the UniProt database annotations. Among them, the amh gene was considered a potential candidate for sex determination because this gene is known to have taken over the role of sex determination in many teleosts. An in-depth sequence analysis of both the coding and non-coding regions of amh in XX and XY individuals detected nine SNPs linked with maleness. However, because these substitutions were synonymous, the upstream and downstream regions of amh were also investigated and a male-specific variant with deletions in the promoter region was detected. This truncated Y-specific amh variant was named amhy, and the amh shared by both sexes was named amhx. The association analysis using both females and males of the genotypic sex inferred by the presence/absence of amhy found complete association with phenotypic sex and genotype. Gene expression analysis in larvae derived from a single-pair progeny by quantitative real-time PCR detected amhy transcripts in the larval trunks between 20 and 100 days after hatching only in XY larvae. Localization of amhy by in situ hybridization was detected in presumptive Sertoli cells of XY gonads. Expression of amhx was almost undetectable in both XX and XY genotypes. Loss of Amh function by CRISPR-Cas9 induced male-to-female sex reversal, indicating that this gene was necessary for the masculinization of XY individuals. In conclusion, the complete linkage of amhy with males, its early expression in XY gonads before testicular differentiation, and the induction of sex reversal by loss-of-function mutation support the view that amhy is the sex-determining gene in this species.
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Affiliation(s)
- Ricardo Shohei Hattori
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Keiichiro Kumazawa
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Masatoshi Nakamoto
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Yuki Nakano
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Toshiya Yamaguchi
- Nansei Field Station, National Research and Development Agency, Japan Fisheries Research and Education Agency, Mie, Japan
| | - Takeshi Kitano
- Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Eiichi Yamamoto
- Tottori Prefectural Fisheries Experimental Station, Tottori, Japan
| | - Kanako Fuji
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Takashi Sakamoto
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
- *Correspondence: Takashi Sakamoto,
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Liyanage DS, Lee S, Yang H, Lim C, Omeka WKM, Sandamalika WMG, Udayantha HMV, Kim G, Ganeshalingam S, Jeong T, Oh SR, Won SH, Koh HB, Kim MK, Jones DB, Massault C, Jerry DR, Lee J. Genome-wide association study of VHSV-resistance trait in Paralichthys olivaceus. FISH & SHELLFISH IMMUNOLOGY 2022; 124:391-400. [PMID: 35462004 DOI: 10.1016/j.fsi.2022.04.021] [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: 12/20/2021] [Revised: 03/26/2022] [Accepted: 04/17/2022] [Indexed: 06/14/2023]
Abstract
In flounder aquaculture, selective breeding plays a vital role in the development of disease-resistant traits and animals with high growth rates. Moreover, superior animals are required to achieve high profits. Unlike growth-related traits, disease-resistant experiments need to be conducted in a controlled environment, as the improper measurement of traits often leads to low genetic correlation and incorrect estimation of breeding values. In this study, viral hemorrhagic septicemia virus (VHSV) resistance was studied using a genome-wide association study (GWAS), and the genetic parameters were estimated. Genotyping was performed using a high-quality 70 K single nucleotide polymorphism (SNP) Affymetrix® Axiom® myDesign™ Genotyping Array of olive flounder. A heritability of ∼0.18 for resistance to VHSV was estimated using genomic information of the fish. According to the GWAS, significant SNPs were detected in chromosomes 21, 24, and contig AGQT02032065.1. Three SNPs showed significance at the genome-wide level (p < 1 × 10-6), while others showed significance above the suggestive cutoff (p < 1 × 10-4). The 3% phenotypic variation was explained by the highest significant SNP, named AX-419319631. Of the important genes for disease resistance, SNPs were associated with plcg1, epha4, clstn2, pik3cb, hes6, meis3, prx6, cep164, siae, and kirrel3b. Most of the genes associated with these SNPs have been previously reported with respect to viral entry, propagation, and immune mechanisms. Therefore, our study provides helpful information regarding VHSV resistance in olive flounder, which can be used for breeding applications.
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Affiliation(s)
- D S Liyanage
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - Sukkyoung Lee
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju Self-Governing Province, 63333, Republic of Korea
| | - Hyerim Yang
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - Chaehyeon Lim
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - W K M Omeka
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - W M Gayashani Sandamalika
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - H M V Udayantha
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - Gaeun Kim
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - Subothini Ganeshalingam
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - Taehyug Jeong
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju Self-Governing Province, 63333, Republic of Korea
| | - Seong-Rip Oh
- Ocean and Fisheries Research Institute, Jeju Self-Governing Province, 63629, Republic of Korea
| | - Seung-Hwan Won
- Ocean and Fisheries Research Institute, Jeju Self-Governing Province, 63629, Republic of Korea
| | - Hyoung-Bum Koh
- Ocean and Fisheries Research Institute, Jeju Self-Governing Province, 63629, Republic of Korea
| | - Mun-Kwan Kim
- Ocean and Fisheries Research Institute, Jeju Self-Governing Province, 63629, Republic of Korea
| | - David B Jones
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - Cecile Massault
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - Dean R Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia; Tropical Futures Institute, James Cook University, Singapore.
| | - Jehee Lee
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju Self-Governing Province, 63333, Republic of Korea.
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Guerrero-Cózar I, Gomez-Garrido J, Berbel C, Martinez-Blanch JF, Alioto T, Claros MG, Gagnaire PA, Manchado M. Chromosome anchoring in Senegalese sole (Solea senegalensis) reveals sex-associated markers and genome rearrangements in flatfish. Sci Rep 2021; 11:13460. [PMID: 34188074 PMCID: PMC8242048 DOI: 10.1038/s41598-021-92601-5] [Citation(s) in RCA: 3] [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: 11/21/2020] [Accepted: 06/07/2021] [Indexed: 11/16/2022] Open
Abstract
The integration of physical and high-density genetic maps is a very useful approach to achieve chromosome-level genome assemblies. Here, the genome of a male Senegalese sole (Solea senegalensis) was de novo assembled and the contigs were anchored to a high-quality genetic map for chromosome-level scaffolding. Hybrid assembled genome was 609.3 Mb long and contained 3403 contigs with a N50 of 513 kb. The linkage map was constructed using 16,287 informative SNPs derived from ddRAD sequencing in 327 sole individuals from five families. Markers were assigned to 21 linkage groups with an average number of 21.9 markers per megabase. The anchoring of the physical to the genetic map positioned 1563 contigs into 21 pseudo-chromosomes covering 548.6 Mb. Comparison of genetic and physical distances indicated that the average genome-wide recombination rate was 0.23 cM/Mb and the female-to-male ratio 1.49 (female map length: 2,698.4 cM, male: 2,036.6 cM). Genomic recombination landscapes were different between sexes with crossovers mainly concentrated toward the telomeres in males while they were more uniformly distributed in females. A GWAS analysis using seven families identified 30 significant sex-associated SNP markers located in linkage group 18. The follicle-stimulating hormone receptor appeared as the most promising locus associated with sex within a region with very low recombination rates. An incomplete penetrance of sex markers with males as the heterogametic sex was determined. An interspecific comparison with other Pleuronectiformes genomes identified a high sequence similarity between homologous chromosomes, and several chromosomal rearrangements including a lineage-specific Robertsonian fusion in S. senegalensis.
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Affiliation(s)
- Israel Guerrero-Cózar
- IFAPA Centro El Toruño, Junta de Andalucía, Camino Tiro Pichón s/n, 11500 El Puerto de Santa María, Cádiz, Spain
| | - Jessica Gomez-Garrido
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Concha Berbel
- IFAPA Centro El Toruño, Junta de Andalucía, Camino Tiro Pichón s/n, 11500 El Puerto de Santa María, Cádiz, Spain
| | - Juan F Martinez-Blanch
- Biopolis S.L.-ADM, Parc Cientific Universidad De Valencia, Edif. 2, C/ Catedrático Agustín Escardino Benlloch, 9, 46980, Paterna, Spain
| | - Tyler Alioto
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - M Gonzalo Claros
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, 29071, Málaga, Spain
- CIBER de Enfermedades Raras (CIBERER), 29071, Málaga, Spain
- Institute of Biomedical Research in Málaga (IBIMA), IBIMA-RARE, 29010, Málaga, Spain
- Instituto de Hortofruticultura Subtropical Y Mediterránea (IHSM-UMA-CSIC), 29010, Málaga, Spain
| | | | - Manuel Manchado
- IFAPA Centro El Toruño, Junta de Andalucía, Camino Tiro Pichón s/n, 11500 El Puerto de Santa María, Cádiz, Spain.
- Crecimiento Azul, Centro IFAPA El Toruño, Unidad Asociada al CSIC, El Puerto de Santa María, Spain.
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Abstract
Sex differences in overall recombination rates are well known, but little theoretical or empirical attention has been given to how and why sexes differ in their recombination landscapes: the patterns of recombination along chromosomes. In the first scientific review of this phenomenon, we find that recombination is biased toward telomeres in males and more uniformly distributed in females in most vertebrates and many other eukaryotes. Notable exceptions to this pattern exist, however. Fine-scale recombination patterns also frequently differ between males and females. The molecular mechanisms responsible for sex differences remain unclear, but chromatin landscapes play a role. Why these sex differences evolve also is unclear. Hypotheses suggest that they may result from sexually antagonistic selection acting on coding genes and their regulatory elements, meiotic drive in females, selection during the haploid phase of the life cycle, selection against aneuploidy, or mechanistic constraints. No single hypothesis, however, can adequately explain the evolution of sex differences in all cases. Sex-specific recombination landscapes have important consequences for population differentiation and sex chromosome evolution.
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Affiliation(s)
- Jason M. Sardell
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712
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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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Conte MA, Joshi R, Moore EC, Nandamuri SP, Gammerdinger WJ, Roberts RB, Carleton KL, Lien S, Kocher TD. Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes. Gigascience 2019; 8:giz030. [PMID: 30942871 PMCID: PMC6447674 DOI: 10.1093/gigascience/giz030] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 01/11/2019] [Accepted: 03/07/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND African cichlid fishes are well known for their rapid radiations and are a model system for studying evolutionary processes. Here we compare multiple, high-quality, chromosome-scale genome assemblies to elucidate the genetic mechanisms underlying cichlid diversification and study how genome structure evolves in rapidly radiating lineages. RESULTS We re-anchored our recent assembly of the Nile tilapia (Oreochromis niloticus) genome using a new high-density genetic map. We also developed a new de novo genome assembly of the Lake Malawi cichlid, Metriaclima zebra, using high-coverage Pacific Biosciences sequencing, and anchored contigs to linkage groups (LGs) using 4 different genetic maps. These new anchored assemblies allow the first chromosome-scale comparisons of African cichlid genomes. Large intra-chromosomal structural differences (∼2-28 megabase pairs) among species are common, while inter-chromosomal differences are rare (<10 megabase pairs total). Placement of the centromeres within the chromosome-scale assemblies identifies large structural differences that explain many of the karyotype differences among species. Structural differences are also associated with unique patterns of recombination on sex chromosomes. Structural differences on LG9, LG11, and LG20 are associated with reduced recombination, indicative of inversions between the rock- and sand-dwelling clades of Lake Malawi cichlids. M. zebra has a larger number of recent transposable element insertions compared with O. niloticus, suggesting that several transposable element families have a higher rate of insertion in the haplochromine cichlid lineage. CONCLUSION This study identifies novel structural variation among East African cichlid genomes and provides a new set of genomic resources to support research on the mechanisms driving cichlid adaptation and speciation.
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Affiliation(s)
- Matthew A Conte
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Rajesh Joshi
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, PO Box 5003, Ås, Norway
| | - Emily C Moore
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695, USA
| | | | | | - Reade B Roberts
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Karen L Carleton
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, PO Box 5003, Ås, Norway
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD 20742, USA
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Estimationof genetic parameters for juvenile growth performance traits in oliveflounder (Paralichthys olivaceus). AQUACULTURE AND FISHERIES 2019. [DOI: 10.1016/j.aaf.2018.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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10
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Hoey JA, Pinsky ML. Genomic signatures of environmental selection despite near-panmixia in summer flounder. Evol Appl 2018; 11:1732-1747. [PMID: 30344639 PMCID: PMC6183468 DOI: 10.1111/eva.12676] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 06/13/2018] [Accepted: 06/16/2018] [Indexed: 01/01/2023] Open
Abstract
Rapid environmental change is altering the selective pressures experienced by marine species. While adaptation to local environmental conditions depends on a balance between dispersal and natural selection across the seascape, the spatial scale of adaptation and the relative importance of mechanisms maintaining adaptation in the ocean are not well understood. Here, using population assignment tests, Approximate Bayesian Computation (ABC), and genome scans with double-digest restriction-site associated DNA sequencing data, we evaluated population structure and locus-environment associations in a commercially important species, summer flounder (Paralichthys dentatus), along the U.S. east coast. Based on 1,137 single nucleotide polymorphisms across 232 individuals spanning nearly 1,900 km, we found no indication of population structure across Cape Hatteras, North Carolina (F ST = 0.0014) or of isolation by distance along the coast using individual relatedness. ABC estimated the probability of dispersal across the biogeographic break at Cape Hatteras to be high (95% credible interval: 7%-50% migration). However, we found 15 loci whose allele frequencies were associated with at least one of four environmental variables. Of those, 11 were correlated with bottom temperature. For summer flounder, our results suggest continued fisheries management as a single population and identify likely response mechanisms to climate change. Broadly speaking, our findings suggest that spatial balancing selection can manifest in adaptive divergence on regional scales in marine fish despite high dispersal, and that these conditions likely result in the widespread distribution of adaptive alleles and a high potential for future genetic adaptation in response to changing environmental conditions. In the context of a rapidly changing world, a landscape genomics perspective offers a useful approach for understanding the causes and consequences of genetic differentiation.
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Affiliation(s)
- Jennifer A. Hoey
- Department of Ecology, Evolution, & Natural ResourcesRutgers UniversityNew BrunswickNew JerseyUSA
| | - Malin L. Pinsky
- Department of Ecology, Evolution, & Natural ResourcesRutgers UniversityNew BrunswickNew JerseyUSA
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Abstract
Recombination often differs markedly between males and females. Here we present the first analysis of sex-specific recombination in Gasterosteus sticklebacks. Using whole-genome sequencing of 15 crosses between G. aculeatus and G. nipponicus, we localized 698 crossovers with a median resolution of 2.3 kb. We also used a bioinformatic approach to infer historical sex-averaged recombination patterns for both species. Recombination is greater in females than males on all chromosomes, and overall map length is 1.64 times longer in females. The locations of crossovers differ strikingly between sexes. Crossovers cluster toward chromosome ends in males, but are distributed more evenly across chromosomes in females. Suppression of recombination near the centromeres in males causes crossovers to cluster at the ends of long arms in acrocentric chromosomes, and greatly reduces crossing over on short arms. The effect of centromeres on recombination is much weaker in females. Genomic differentiation between G. aculeatus and G. nipponicus is strongly correlated with recombination rate, and patterns of differentiation along chromosomes are strongly influenced by male-specific telomere and centromere effects. We found no evidence for fine-scale correlations between recombination and local gene content in either sex. We discuss hypotheses for the origin of sexual dimorphism in recombination and its consequences for sexually antagonistic selection and sex chromosome evolution.
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O'Leary SJ, Hollenbeck CM, Vega RR, Gold JR, Portnoy DS. Genetic mapping and comparative genomics to inform restoration enhancement and culture of southern flounder, Paralichthys lethostigma. BMC Genomics 2018; 19:163. [PMID: 29471804 PMCID: PMC5824557 DOI: 10.1186/s12864-018-4541-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 02/13/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Southern flounder, Paralichthys lethostigma, historically support a substantial fishery along the Atlantic and Gulf coasts of the southern United States. Low year-class strengths over the past few years in the western Gulf of Mexico have raised concern that spawning stocks may be overfished. Current management of the resource includes releasing hatchery-raised juveniles to restock bays and estuaries; additionally, there is a growing interest in the potential for commercial aquaculture of the species. Currently, genomic resources for southern flounder do not exist. Here, we used two hatchery-reared families and double-digest, restriction-site-associated DNA (ddRAD) sequencing to create a reduced-representation genomic library consisting of several thousand single nucleotide polymorphisms (SNPs) located throughout the genome. RESULTS The relative position of each SNP-containing locus was determined to create a high-density genetic map spanning the 24 linkage groups of the southern flounder genome. The consensus map was used to identify regions of shared synteny between southern flounder and seven other fish species for which genome assemblies are available. Finally, syntenic blocks were used to localize genes identified from transcripts in European flounder as potentially being involved in ecotoxicological and osmoregulatory responses, as well as QTLs associated with growth and disease resistance in Japanese flounder, on the southern flounder linkage map. CONCLUSIONS The information provided by the linkage map will enrich restoration efforts by providing a foundation for interpreting spatial genetic variation within the species, ultimately furthering an understanding of the adaptive potential and resilience of southern flounder to future changes in local environmental conditions. Further, the map will facilitate the use of genetic markers to enhance restoration and commercial aquaculture.
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Affiliation(s)
- Shannon J O'Leary
- Department of Life Sciences, Marine Genomics Laboratory, Texas A&M University Corpus Christi, 6300 Ocean Drive, Unit 5869, Corpus Christi, TX, 78412, USA.
| | - Christopher M Hollenbeck
- Scottish Oceans Institute, University of St. Andrews, East Sands, St. Andrews, Fife, KY16 8LB, UK
| | - Robert R Vega
- Texas Parks and Wildlife Department, CCA Marine Development Center, 4300 Waldron Road, Corpus Christi, TX, 78418, USA
| | - John R Gold
- Department of Life Sciences, Marine Genomics Laboratory, Texas A&M University Corpus Christi, 6300 Ocean Drive, Unit 5869, Corpus Christi, TX, 78412, USA
| | - David S Portnoy
- Department of Life Sciences, Marine Genomics Laboratory, Texas A&M University Corpus Christi, 6300 Ocean Drive, Unit 5869, Corpus Christi, TX, 78412, USA
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13
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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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14
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Development of a 690 K SNP array in catfish and its application for genetic mapping and validation of the reference genome sequence. Sci Rep 2017; 7:40347. [PMID: 28079141 PMCID: PMC5228154 DOI: 10.1038/srep40347] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 12/05/2016] [Indexed: 02/02/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) are capable of providing the highest level of genome coverage for genomic and genetic analysis because of their abundance and relatively even distribution in the genome. Such a capacity, however, cannot be achieved without an efficient genotyping platform such as SNP arrays. In this work, we developed a high-density SNP array with 690,662 unique SNPs (herein 690 K array) that were relatively evenly distributed across the entire genome, and covered 98.6% of the reference genome sequence. Here we also report linkage mapping using the 690 K array, which allowed mapping of over 250,000 SNPs on the linkage map, the highest marker density among all the constructed linkage maps. These markers were mapped to 29 linkage groups (LGs) with 30,591 unique marker positions. This linkage map anchored 1,602 scaffolds of the reference genome sequence to LGs, accounting for over 97% of the total genome assembly. A total of 1,007 previously unmapped scaffolds were placed to LGs, allowing validation and in few instances correction of the reference genome sequence assembly. This linkage map should serve as a valuable resource for various genetic and genomic analyses, especially for GWAS and QTL mapping for genes associated with economically important traits.
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15
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Robledo D, Hermida M, Rubiolo JA, Fernández C, Blanco A, Bouza C, Martínez P. Integrating genomic resources of flatfish (Pleuronectiformes) to boost aquaculture production. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2016; 21:41-55. [PMID: 28063346 DOI: 10.1016/j.cbd.2016.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 12/09/2016] [Accepted: 12/13/2016] [Indexed: 12/15/2022]
Abstract
Flatfish have a high market acceptance thus representing a profitable aquaculture production. The main farmed species is the turbot (Scophthalmus maximus) followed by Japanese flounder (Paralichthys olivaceous) and tongue sole (Cynoglossus semilaevis), but other species like Atlantic halibut (Hippoglossus hippoglossus), Senegalese sole (Solea senegalensis) and common sole (Solea solea) also register an important production and are very promising for farming. Important genomic resources are available for most of these species including whole genome sequencing projects, genetic maps and transcriptomes. In this work, we integrate all available genomic information of these species within a common framework, taking as reference the whole assembled genomes of turbot and tongue sole (>210× coverage). New insights related to the genetic basis of productive traits and new data useful to understand the evolutionary origin and diversification of this group were obtained. Despite a general 1:1 chromosome syntenic relationship between species, the comparison of turbot and tongue sole genomes showed huge intrachromosomic reorganizations. The integration of available mapping information supported specific chromosome fusions along flatfish evolution and facilitated the comparison between species of previously reported genetic associations for productive traits. When comparing transcriptomic resources of the six species, a common set of ~2500 othologues and ~150 common miRNAs were identified, and specific sets of putative missing genes were detected in flatfish transcriptomes, likely reflecting their evolutionary diversification.
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Affiliation(s)
- Diego Robledo
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Biology (CIBUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Miguel Hermida
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Juan A Rubiolo
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Carlos Fernández
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Andrés Blanco
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Carmen Bouza
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Paulino Martínez
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain.
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16
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CHEN MENG, GAO LINLIN, ZHANG WEIJIE, YOU HONGZHENG, SUN QIAN, CHANG YAQING. Identification of forty-five gene-derived polymorphic microsatellite loci for the sea cucumber, Apostichopus japonicus. J Genet 2016. [DOI: 10.1007/s12041-013-0234-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Hou J, Wang G, Zhang X, Wang Y, Sun Z, Si F, Jiang X, Liu H. Production and verification of a 2 nd generation clonal group of Japanese flounder, Paralichthys olivaceus. Sci Rep 2016; 6:35776. [PMID: 27767055 PMCID: PMC5073307 DOI: 10.1038/srep35776] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 10/05/2016] [Indexed: 12/02/2022] Open
Abstract
Clonal fishes are useful tools in biology and aquaculture studies due to their isogenicity. In Japanese flounder (Paralichthys olivaceus), a group of homozygous clones was created by inducing meiogynogenesis in eggs from a mitogynogenetic homozygous diploid. As the clones reached sexual maturity, meiogynogenesis was again induced in order to produce a 2nd generation clonal group of Japanese flounder. After 3 months, there were 611 healthy, surviving individuals. Twenty-four microsatellite markers, that covered all the linkage groups of Japanese flounder, were used to identify the homozygosity of the 2nd generation clones; no heterozygous locus was detected. This indicates that the production of a 2nd generation clonal group of Japanese flounder was successful. Restriction-site DNA associated sequencing at the genomic level also confirmed the homozygosity and clonality of the 2nd generation clonal group. Furthermore, these 2nd generation clones had a small coefficient of variation for body shape indices at 210 days of age and showed a high degree of similarity in body characteristics among individuals. The successful production of 2nd generation clones has laid the foundation for the large-scale production of clonal Japanese flounder.
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Affiliation(s)
- Jilun Hou
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
| | - Guixing Wang
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
| | - Xiaoyan Zhang
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
| | - Yufen Wang
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
| | - Zhaohui Sun
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
| | - Fei Si
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
| | - Xiufeng Jiang
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
| | - Haijin Liu
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
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18
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Kessuwan K, Kubota S, Liu Q, Sano M, Okamoto N, Sakamoto T, Yamashita H, Nakamura Y, Ozaki A. Detection of Growth-Related Quantitative Trait Loci and High-Resolution Genetic Linkage Maps Using Simple Sequence Repeat Markers in the Kelp Grouper (Epinephelus bruneus). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:57-84. [PMID: 26511529 PMCID: PMC4705122 DOI: 10.1007/s10126-015-9673-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 09/14/2015] [Indexed: 06/05/2023]
Abstract
To initiate breeding programs for kelp grouper (Epinephelus bruneus), the establishment of genetic linkage maps becomes essential accompanied by the search for quantitative trait loci that may be utilized in selection programs. We constructed a high-resolution genetic linkage map using 1055 simple sequence repeat (SSR) markers in an F1 family. Genome-wide and chromosome-wide significances of growth-related quantitative trait loci (QTLs) (body weight (BW) and total length (TL)) were detected using non-parametric mapping, Kruskal-Wallis (K-W) analysis, simple interval mapping (IM) and a permutation test (PT). Two stages and two families of fish were used to confirm the QTL regions. Ultimately, 714 SSR markers were matched that evenly covered the 24 linkage groups. In total, 509 and 512 markers were localized to the female and male maps, respectively. The genome lengths were approximately 1475.95 and 1370.39 cM and covered 84.68 and 83.21% of the genome, with an average interval of 4.1 and 4.0 cM, in females and males, respectively. One major QTL affecting BW and TL was found on linkage group EBR 17F that identified for 1% of the genome-wide significance and accounted for 14.6-18.9 and 14.7-18.5% of the phenotypic variance, and several putative QTL with 5% chromosome-wide significance were detected on eight linkage groups. Furthermore, the confirmed results of the regions harboring the major and putative QTLs showed consistent significant experiment-wide values of 1 and 5% as well as a chromosome-wide value of 5%. We identified growth-related QTLs that could be applied to find candidate genes for growth traits in further studies, and potentially useful in MAS breeding.
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Affiliation(s)
- Kanonkporn Kessuwan
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
- Department of Fisheries, Coastal Fisheries Research and Development Bureau, 50 Kaset Klang Jatujak, Bangkok, 10900, Thailand
| | - Satoshi Kubota
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
| | - Qi Liu
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
- Center for Marine Ranching Engineering Science Research of Liaoning, Dalian Ocean University, 52 Heishijiao Street, Dalian, 116023, China
| | - Motohiko Sano
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
- National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Nobuaki Okamoto
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
| | - Takashi Sakamoto
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
| | - Hirofumi Yamashita
- Ehime Research Institute of Agriculture, Forestry and Fisheries, Fisheries Research Center, 5516 Shitaba, Uwajima-shi, Ehime, 798-0104, Japan
| | - Yoji Nakamura
- National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Akiyuki Ozaki
- National Research Institute of Aquaculture, Fisheries Research Agency, 422-1 Nakatsuhamaura, Minamiise-cho, Watarai-gun, Mie, 516-0193, Japan.
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19
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Kessuwan K, Kubota S, Liu Q, Sano M, Okamoto N, Sakamoto T, Yamashita H, Nakamura Y, Ozaki A. Detection of Growth-Related Quantitative Trait Loci and High-Resolution Genetic Linkage Maps Using Simple Sequence Repeat Markers in the Kelp Grouper (Epinephelus bruneus). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016:10.1007/s10126-015-9679-z. [PMID: 26743358 DOI: 10.1007/s10126-015-9679-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 09/14/2015] [Indexed: 10/22/2022]
Abstract
To initiate breeding programs for kelp grouper (Epinephelus bruneus), the establishment of genetic linkage maps becomes essential accompanied by the search for quantitative trait loci (QTLs) that may be utilized in selection programs. We constructed a high-resolution genetic linkage map using 1055 simple sequence repeat (SSR) markers in an F1 family. Genome-wide and chromosome-wide significances of growth-related QTLs (body weight: BW and total length: TL) were detected using non-parametric mapping, Kruskal-Wallis analysis, simple interval mapping (IM), and a permutation test (PT). Two stages and two families of fish were used to confirm the QTL regions. Ultimately, 714 SSR markers were matched that evenly covered the 24 linkage groups. In total, 509 and 512 markers were localized to the female and male maps, respectively. The genome lengths were approximately 1475.95 and 1370.39 cM and covered 84.68 and 83.21 % of the genome, with an average interval of 4.1 and 4.0 cM, in females and males, respectively. One major QTL affecting BW and TL was found on linkage group EBR 17 F that identified for 1 % of the genome-wide significance and accounted for 14.6-18.9 % and 14.7-18.5 % of the phenotypic variance, and several putative QTL with 5 % chromosome-wide significance were detected on eight linkage groups. Furthermore, the confirmed results of the regions harboring the major and putative QTLs showed consistent significant experiment-wide values of 1 and 5 % as well as a chromosome-wide value of 5 %. We identified growth-related QTLs that could be applied to find candidate genes for growth traits in further studies and potentially useful in marker assisted selection (MAS) breeding.
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Affiliation(s)
- Kanonkporn Kessuwan
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
- Department of Fisheries, Coastal Fisheries Research and Development Bureau, 50 Kaset Klang Jatujak, Bangkok, 10900, Thailand
| | - Satoshi Kubota
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
| | - Qi Liu
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
- Center for Marine Ranching Engineering Science Research of Liaoning, Dalian Ocean University, 52 Heishijiao Street, Dalian, 116023, China
| | - Motohiko Sano
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
- National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Nobuaki Okamoto
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
| | - Takashi Sakamoto
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
| | - Hirofumi Yamashita
- Ehime Research Institute of Agriculture, Forestry and Fisheries, Fisheries Research Center, 5516 Shitaba, Uwajima-shi, Ehime, 798-0104, Japan
| | - Yoji Nakamura
- National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Akiyuki Ozaki
- National Research Institute of Aquaculture, Fisheries Research Agency, 422-1 Nakatsuhamaura, Minamiise-cho, Watarai-gun, Mie, 516-0193, Japan.
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Uchino T, Nakamura Y, Sekino M, Kai W, Fujiwara A, Yasuike M, Sugaya T, Fukuda H, Sano M, Sakamoto T. Constructing Genetic Linkage Maps Using the Whole Genome Sequence of Pacific Bluefin Tuna (<i>Thunnus orientalis</i>) and a Comparison of Chromosome Structure among Teleost Species. ACTA ACUST UNITED AC 2016. [DOI: 10.4236/abb.2016.72010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Cui Y, Wang H, Qiu X, Liu H, Yang R. Bayesian Analysis for Genetic Architectures of Body Weights and Morphological Traits Using Distorted Markers in Japanese Flounder Paralichthys olivaceus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2015; 17:693-702. [PMID: 26290270 DOI: 10.1007/s10126-015-9646-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 05/12/2015] [Indexed: 06/04/2023]
Abstract
A doubled haploids (DH) population of 160 individuals is constructed by using mitotic gynogenetics for the study of genetic architectures of the body weight and morphological traits in Japanese flounder. Each DH individual is genotyped for 458 SSR markers, 222 of which segregate distortionally. By modifying conditional probabilities of quantitative trait locus (QTL) genotypes on the distorted flanking markers, Bayesian model selection is used to dissect genetic architectures for the traits. As a result, we identify 42 main-effect QTLs on chromosomes 5, 6, 7, 8, 9, 10, 15, 20, 21, 22, and 59 pairs of interacting QTLs. Among these detected QTLs, the largest interacting QTL is between chromosome 6 and chromosome 9 and accounts for 25.196 % of phenotypic variance for body weights and in a similar trend. Also, many QTLs show pleiotropic effects. The QTL on chromosome 9 simultaneously governs seven traits, BL, BH, FL, HL, PFL, HW, and CW. As compared to method using the uncorrected conditional probabilities of QTL genotypes, our method using corrected conditional probabilities can detect more interacting QTLs for the traits.
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Affiliation(s)
- Yan Cui
- Research Centre for Aquatic Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China
- School of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
| | - Hongwei Wang
- Research Centre for Aquatic Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China
| | - Xuemei Qiu
- School of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
| | - Haijin Liu
- Research Centre for Aquatic Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China
| | - Runqing Yang
- Research Centre for Aquatic Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
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22
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Wang L, Wan ZY, Bai B, Huang SQ, Chua E, Lee M, Pang HY, Wen YF, Liu P, Liu F, Sun F, Lin G, Ye BQ, Yue GH. Construction of a high-density linkage map and fine mapping of QTL for growth in Asian seabass. Sci Rep 2015; 5:16358. [PMID: 26553309 PMCID: PMC4639833 DOI: 10.1038/srep16358] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 10/01/2015] [Indexed: 01/06/2023] Open
Abstract
A high-density genetic map is essential for comparative genomic studies and fine mapping of QTL, and can also facilitate genome sequence assembly. Here, a high density genetic map of Asian seabass was constructed with 3321 SNPs generated by sequencing 144 individuals in a F2 family. The length of the map was 1577.67 cM with an average marker interval of 0.52 cM. A high level of genomic synteny among Asian seabass, European seabass, Nile tilapia and stickleback was detected. Using this map, one genome-wide significant and five suggestive QTL for growth traits were detected in six linkage groups (i.e. LG4, LG5, LG11, LG13, LG14 and LG15). These QTL explained 10.5–16.0% of phenotypic variance. A candidate gene, ACOX1 within the significant QTL on LG5 was identified. The gene was differentially expressed between fast- and slow-growing Asian seabass. The high-density SNP-based map provides an important tool for fine mapping QTL in molecular breeding and comparative genome analysis.
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Affiliation(s)
- Le Wang
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Zi Yi Wan
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Bin Bai
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Shu Qing Huang
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Elaine Chua
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - May Lee
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Hong Yan Pang
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Yan Fei Wen
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Peng Liu
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Feng Liu
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Fei Sun
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Grace Lin
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Bao Qing Ye
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Gen Hua Yue
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604.,Department of Biological Sciences, National University of Singapore, 14 Science Drive, Singapore 117543.,School of Biological Sciences, Nanyang Technological University, 6 Nanyang Drive, Singapore 637551
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Ulloa PE, Rincón G, Islas-Trejo A, Araneda C, Iturra P, Neira R, Medrano JF. RNA sequencing to study gene expression and SNP variations associated with growth in zebrafish fed a plant protein-based diet. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2015; 17:353-63. [PMID: 25702041 DOI: 10.1007/s10126-015-9624-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 01/16/2015] [Indexed: 05/16/2023]
Abstract
The objectives of this study were to measure gene expression in zebrafish and then identify SNP to be used as potential markers in a growth association study. We developed an approach where muscle samples collected from low- and high-growth fish were analyzed using RNA-Sequencing (RNA-seq), and SNP were chosen from the genes that were differentially expressed between the low and high groups. A population of 24 families was fed a plant protein-based diet from the larval to adult stages. From a total of 440 males, 5 % of the fish from both tails of the weight gain distribution were selected. Total RNA was extracted from individual muscle of 8 low-growth and 8 high-growth fish. Two pooled RNA-Seq libraries were prepared for each phenotype using 4 fish per library. Libraries were sequenced using the Illumina GAII Sequencer and analyzed using the CLCBio genomic workbench software. One hundred and twenty-four genes were differentially expressed between phenotypes (p value < 0.05 and FDR < 0.2). From these genes, 164 SNP were selected and genotyped in 240 fish samples. Marker-trait analysis revealed 5 SNP associated with growth in key genes (Nars, Lmod2b, Cuzd1, Acta1b, and Plac8l1). These genes are good candidates for further growth studies in fish and to consider for identification of potential SNPs associated with different growth rates in response to a plant protein-based diet.
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Affiliation(s)
- Pilar E Ulloa
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Casilla 54-D, Temuco, Chile,
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Shao C, Niu Y, Rastas P, Liu Y, Xie Z, Li H, Wang L, Jiang Y, Tai S, Tian Y, Sakamoto T, Chen S. Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis. DNA Res 2015; 22:161-70. [PMID: 25762582 PMCID: PMC4401326 DOI: 10.1093/dnares/dsv001] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 02/01/2015] [Indexed: 12/18/2022] Open
Abstract
High-resolution genetic maps are essential for fine mapping of complex traits, genome assembly, and comparative genomic analysis. Single-nucleotide polymorphisms (SNPs) are the primary molecular markers used for genetic map construction. In this study, we identified 13,362 SNPs evenly distributed across the Japanese flounder (Paralichthys olivaceus) genome. Of these SNPs, 12,712 high-confidence SNPs were subjected to high-throughput genotyping and assigned to 24 consensus linkage groups (LGs). The total length of the genetic linkage map was 3,497.29 cM with an average distance of 0.47 cM between loci, thereby representing the densest genetic map currently reported for Japanese flounder. Nine positive quantitative trait loci (QTLs) forming two main clusters for Vibrio anguillarum disease resistance were detected. All QTLs could explain 5.1-8.38% of the total phenotypic variation. Synteny analysis of the QTL regions on the genome assembly revealed 12 immune-related genes, among them 4 genes strongly associated with V. anguillarum disease resistance. In addition, 246 genome assembly scaffolds with an average size of 21.79 Mb were anchored onto the LGs; these scaffolds, comprising 522.99 Mb, represented 95.78% of assembled genomic sequences. The mapped assembly scaffolds in Japanese flounder were used for genome synteny analyses against zebrafish (Danio rerio) and medaka (Oryzias latipes). Flounder and medaka were found to possess almost one-to-one synteny, whereas flounder and zebrafish exhibited a multi-syntenic correspondence. The newly developed high-resolution genetic map, which will facilitate QTL mapping, scaffold assembly, and genome synteny analysis of Japanese flounder, marks a milestone in the ongoing genome project for this species.
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Affiliation(s)
- Changwei Shao
- Ministry of Agriculture, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao 266071, China Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao 266071, China Faculty of Marine Science, Tokyo University of Marine Science and Technology, Minato, Tokyo 108-8477, Japan
| | | | - Pasi Rastas
- Department of Biosciences, Metapopulation Research Group, University of Helsinki, Helsinki FI-00014, Finland
| | - Yang Liu
- Ministry of Agriculture, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao 266071, China Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao 266071, China
| | | | - Hengde Li
- Chinese Academy of Fisheries Science, Beijing 100039, China
| | - Lei Wang
- Ministry of Agriculture, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao 266071, China Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao 266071, China
| | - Yong Jiang
- National Oceanographic Center, Qingdao 266071, China
| | | | - Yongsheng Tian
- Ministry of Agriculture, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao 266071, China Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao 266071, China
| | - Takashi Sakamoto
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, Minato, Tokyo 108-8477, Japan
| | - Songlin Chen
- Ministry of Agriculture, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao 266071, China Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao 266071, China
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Su J, Su J, Shang X, Wan Q, Chen X, Rao Y. SNP detection of TLR8 gene, association study with susceptibility/resistance to GCRV and regulation on mRNA expression in grass carp, Ctenopharyngodon idella. FISH & SHELLFISH IMMUNOLOGY 2015; 43:1-12. [PMID: 25514376 DOI: 10.1016/j.fsi.2014.12.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 11/17/2014] [Accepted: 12/06/2014] [Indexed: 05/10/2023]
Abstract
Toll-like receptor 8 (TLR8), a prototypical intracellular member of TLR family, is generally linked closely to antiviral innate immune through recognizing viral nucleic acid. In this study, 5'-flanking region of Ctenopharyngodon idella TLR8 (CiTLR8), 671bp in length, was amplified and eight SNPs containing one SNP in the intron, three SNPs in the coding region (CDS) and four SNPs in the 3'-untranslated region (UTR) were identified and characterized. Of which 4062 A/T was significantly associated with the susceptibility/resistance to GCRV both in genotype and allele (P < 0.05), while 4168 C/T was extremely significantly associated with that (P < 0.01) according to the case (susceptibility)-control (resistance) analysis. Following the verification experiment, further analyses of mRNA expression, linkage disequilibrium (LD), haplotype and microRNA (miRNA) target site indicated that 4062 A/T and 4168 C/T in 3'-UTR might affect the miRNA regulation, while the exertion of antiviral effects of 4062 A/T might rely on its interaction with other SNPs. Additionally, the high-density of SNPs in 3'-UTR might reflect the specific biological functions of 3'-UTR. And also, the mutation of 747 A/G in intron changing the potential transcriptional factor-binding sites (TFBS) nearby might affect the expression of CiTLR8 transcriptionally or post-transcriptionally. Moreover, as predicted, the A/G transition of the only non-synonymous SNP (3846 A/G) in CDS causing threonine/alanine variation, could shorten the length of the α-helix and ultimately affect the integrity of the Toll-IL-1 receptor (TIR) domain. The functional mechanism of 3846 A/G might also involve a threonine phosphorylation signaling. This study may broaden the knowledge of TLR polymorphisms, lay the foundation for further functional research of CiTLR8 and provide potential markers as well as theoretical basis for resistance molecular breeding of grass carp against GCRV.
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Affiliation(s)
- Juanjuan Su
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jianguo Su
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| | - Xueying Shang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Quanyuan Wan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiaohui Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Youliang Rao
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
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Molina-Luzón MJ, Hermida M, Navajas-Pérez R, Robles F, Navas JI, Ruiz-Rejón C, Bouza C, Martínez P, de la Herrán R. First haploid genetic map based on microsatellite markers in Senegalese sole (Solea senegalensis, Kaup 1858). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2015; 17:8-22. [PMID: 25107689 DOI: 10.1007/s10126-014-9589-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 07/12/2014] [Indexed: 06/03/2023]
Abstract
The Senegalese sole (Solea senegalensis, Kaup 1858) is a flatfish species of great value for aquaculture. In this study, we develop the first linkage map in this species based on microsatellite markers characterized from genomic DNA libraries and EST databases of Senegalese sole and from other flatfish species. Three reference gynogenetic families were obtained by chromosome-manipulation techniques: two haploid gynogenetics, used to assign and order microsatellites to linkage groups and another diploid gynogenetic family, used for estimating marker-centromere distances. The consensus map consists of 129 microsatellites distributed in 27 linkage groups (LG), with an average density of 4.7 markers per LG and comprising 1,004 centimorgans (cM). Additionally, 15 markers remained unlinked. Through half-tetrad analysis, we were able to estimate the centromere distance for 81 markers belonging to 24 LG, representing an average of 3 markers per LG. Comparative mapping was performed between flatfish species LG and model fish species chromosomes (stickleback, Tetraodon, medaka, fugu and zebrafish). The usefulness of microsatellite markers and the genetic map as tools for comparative mapping and evolution studies is discussed.
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Affiliation(s)
- Ma Jesús Molina-Luzón
- Facultad de Ciencias, Departamento de Genética, Universidad de Granada, 18071, Granada, Spain
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Diopere E, Maes GE, Komen H, Volckaert FAM, Groenen MAM. A genetic linkage map of sole (Solea solea): a tool for evolutionary and comparative analyses of exploited (flat)fishes. PLoS One 2014; 9:e115040. [PMID: 25541971 PMCID: PMC4277273 DOI: 10.1371/journal.pone.0115040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 09/12/2014] [Indexed: 11/19/2022] Open
Abstract
Linkage maps based on markers derived from genes are essential evolutionary tools for commercial marine fish to help identify genomic regions associated with complex traits and subject to selective forces at play during exploitation or selective breeding. Additionally, they allow the use of genomic information from other related species for which more detailed information is available. Sole (solea solea L.) is a commercially important flatfish species in the North Sea, subject to overexploitation and showing evidence of fisheries-induced evolutionary changes in growth- and maturation-related traits. Sole would definitely benefit from a linkage map to better understand how evolution has shaped its genome structure. This study presents a linkage map of sole based on 423 single nucleotide polymorphisms derived from expressed sequence tags and 8 neutral microsatellite markers. The total map length is 1233.8 cM and consists of 38 linkage groups with a size varying between 0 to 92.1 cM. Being derived from expressed sequence tags allowed us to align the map with the genome of four model fish species, namely medaka (Oryzias latipes), Nile tilapia (Oreochromis niloticus), three-spined stickleback (Gasterosteus aculeatus) and green spotted pufferfish (Tetraodon nigroviridis). This comparison revealed multiple conserved syntenic regions with all four species, and suggested that the linkage groups represent 21 putative sole chromosomes. The map was also compared to the linkage map of turbot (Scophthalmus maximus), another commercially important flatfish species and closely related to sole. For all putative sole chromosomes (except one) a turbot homolog was detected, confirming the even higher degree of synteny between these two flatfish species.
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Affiliation(s)
- Eveline Diopere
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. Deberiotstraat 32, B-3000 Leuven, Belgium
- * E-mail:
| | - Gregory E. Maes
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. Deberiotstraat 32, B-3000 Leuven, Belgium
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, 4811 QLD Townsville, Australia
| | - Hans Komen
- Animal Breeding and Genomics Centre, Wageningen University, Marijkeweg 40, NL-6700 AH Wageningen, the Netherlands
| | - Filip A. M. Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. Deberiotstraat 32, B-3000 Leuven, Belgium
| | - Martien A. M. Groenen
- Animal Breeding and Genomics Centre, Wageningen University, Marijkeweg 40, NL-6700 AH Wageningen, the Netherlands
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Ye H, Liu Y, Liu X, Wang X, Wang Z. Genetic mapping and QTL analysis of growth traits in the large yellow croaker Larimichthys crocea. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2014; 16:729-738. [PMID: 25070688 DOI: 10.1007/s10126-014-9590-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Accepted: 07/06/2014] [Indexed: 06/03/2023]
Abstract
Large yellow croaker (Larimichthys crocea) is an important maricultured species in China. A genetic linkage map of the large yellow croaker was constructed using type II microsatellites and expressed sequence tag (EST)-derived microsatellites in two half-sib families (two females and one male). A total of 289 microsatellite markers (contained 93 EST-SSRs) were integrated into 24 linkage groups, which agreed with the haploid chromosome number. The map spanned a length of 1,430.8 cm with an average interval of 5.4 cm, covering 83.9 % of the estimated genome size (1,704.8 cm). A total of seven quantitative trait locis (QTLs) were detected for growth traits on five linkage groups, including two 1 % and five 5 % chromosome-wide significant QTLs, and explained from 2.33 to 5.31 % of the trait variation. The identified QTLs can be applied in marker-assisted selection programs to improve the growth traits.
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Affiliation(s)
- Hua Ye
- Key Laboratory of Healthy Mariculture for East China Sea, Ministry of Agriculture of the People's Republic of China, Jimei University, Xiamen, 361021, China
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Wang L, Fan C, Liu Y, Zhang Y, Liu S, Sun D, Deng H, Xu Y, Tian Y, Liao X, Xie M, Li W, Chen S. A genome scan for quantitative trait loci associated with Vibrio anguillarum infection resistance in Japanese flounder (Paralichthys olivaceus) by bulked segregant analysis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2014; 16:513-521. [PMID: 24562474 DOI: 10.1007/s10126-014-9569-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 01/28/2014] [Indexed: 06/03/2023]
Abstract
A recent genetic linkage map was employed to detect quantitative trait loci (QTLs) associated with Vibrio anguillarum resistance in Japanese flounder. An F1 family established and challenged with V. anguillarum in 2009 was used for QTL mapping. Of the 221 simple sequence repeat (SSR) markers used to detect polymorphisms in the parents of F1, 170 were confirmed to be polymorphic. The average distance between the markers was 10.6 cM. Equal amounts of genomic DNA from 15 fry that died early and from 15 survivors were pooled separately to constitute susceptible bulk and resistance bulk DNA. Bulked segregant analysis and QTL mapping were combined to detect candidate SSR markers and regions associated with the disease. A genome scan identified four polymorphic SSR markers, two of which were significantly different between susceptible and resistance bulk (P=0.008). These two markers were located in linkage group (LG) 7; therefore, all the SSR markers in LG7 were genotyped in all the challenged fry by single marker analysis. Using two different models, 11-17 SSR markers were detected with different levels of significance. To confirm the associations of these markers with the disease, composite interval mapping was employed to genotype all the challenged individuals. One and three QTLs, which explained more than 60 % of the phenotypic variance, were detected by the two models. Two of the QTLs were located at 48.6 cM. The common QTL may therefore be a major candidate region for disease resistance against V. anguillarum infection.
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Affiliation(s)
- Lei Wang
- College of Marine Life Science, Ocean University of China, 266003, Qingdao, The People's Republic of China
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Shin CH, Cha JH, Rahimnejad S, Jeong JB, Yoo BW, Lee BK, Ahn HJ, Choi SI, Choi YJ, Park YH, Kim JD, Lee KJ. Effects of Dietary Supplementation of Barodon, an Anionic Alkali Mineral Complex, on Growth Performance, Feed Utilization, Innate Immunity, Goblet Cell and Digestibility in Olive Flounder (Paralichthys olivaceus). ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 27:383-90. [PMID: 25049965 PMCID: PMC4093262 DOI: 10.5713/ajas.2013.13485] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 12/02/2013] [Accepted: 10/20/2013] [Indexed: 11/27/2022]
Abstract
A 15-wk feeding trial was conducted to examine the supplemental effects of Barodon on growth performance, gastrointestinal histology, feed digestibility and innate immunity in olive founder. A basal commercial diet was used as a control and two other diets were prepared by spraying 0.1% or 0.2% of Barodon. Triplicate groups of fish (BW, 145 g) were fed one of the test diets to apparent satiation twice daily. At the end of the feeding trial, fish growth performance was not significantly affected by dietary treatments; however, feed utilization was significantly improved (linear and quadratic, p<0.05) by Barodon supplementation. Significantly higher (p<0.05) survival rates were obtained in fish fed Barodon containing diets. Hepatosomatic index increased significantly in Barodon treated groups. Also, the use of Barodon resulted in significant increase (linear and quadratic, p<0.05) of intestine length and number of goblet cells. Significantly higher (Quadratic, p<0.05) apparent digestibility coefficient of DM was obtained by supplementation of Barodon. Lysozyme and myeloperoxidase activities increased quadratically and linearly, respectively, in Barodon treated fish. Also, significantly higher (linear and quadratic, p<0.05) superoxide dismutase activity was found in Barodon fed fish. The findings in this study show that inclusion of Barodon in diets for olive flounder improves feed utilization and digestibility, and positively affects digestive tract histology and innate immunity.
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Affiliation(s)
- Chang-Hoon Shin
- Department of Animal Life system, Kangwon National University, Chuncheon 200-701, Korea
| | - Ji-Hoon Cha
- Department of Marine Life Sciences, Jeju National University, Jeju 690-756, Korea
| | - Samad Rahimnejad
- Department of Marine Life Sciences, Jeju National University, Jeju 690-756, Korea
| | - Joon-Bum Jeong
- Department of Aquatic Biomedical Science, Jeju National University, Jeju 690-756, Korea
| | | | - Bo-Kyeun Lee
- Cargill Agri Purina Inc, Seongnam, Gyeonggi, Korea
| | | | - Soo-Il Choi
- Barodon - S.F. Corp, Ansung, Gyeonggi, Korea
| | | | - Yong-Ho Park
- College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Jeong-Dae Kim
- Department of Animal Life system, Kangwon National University, Chuncheon 200-701, Korea
| | - Kyeong-Jun Lee
- Department of Marine Life Sciences, Jeju National University, Jeju 690-756, Korea . ; Marine & Environmental Research Institute, Jeju National University, Jeju 695-814, Korea
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Larson WA, Seeb LW, Everett MV, Waples RK, Templin WD, Seeb JE. Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha). Evol Appl 2014; 7:355-69. [PMID: 24665338 PMCID: PMC3962296 DOI: 10.1111/eva.12128] [Citation(s) in RCA: 162] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 10/02/2013] [Indexed: 12/14/2022] Open
Abstract
Recent advances in population genomics have made it possible to detect previously unidentified structure, obtain more accurate estimates of demographic parameters, and explore adaptive divergence, potentially revolutionizing the way genetic data are used to manage wild populations. Here, we identified 10 944 single-nucleotide polymorphisms using restriction-site-associated DNA (RAD) sequencing to explore population structure, demography, and adaptive divergence in five populations of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska. Patterns of population structure were similar to those of past studies, but our ability to assign individuals back to their region of origin was greatly improved (>90% accuracy for all populations). We also calculated effective size with and without removing physically linked loci identified from a linkage map, a novel method for nonmodel organisms. Estimates of effective size were generally above 1000 and were biased downward when physically linked loci were not removed. Outlier tests based on genetic differentiation identified 733 loci and three genomic regions under putative selection. These markers and genomic regions are excellent candidates for future research and can be used to create high-resolution panels for genetic monitoring and population assignment. This work demonstrates the utility of genomic data to inform conservation in highly exploited species with shallow population structure.
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Affiliation(s)
- Wesley A Larson
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - Lisa W Seeb
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - Meredith V Everett
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - Ryan K Waples
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - William D Templin
- Gene Conservation Laboratory, Alaska Department of Fish and Game Anchorage, AK, USA
| | - James E Seeb
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
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You X, Shu L, Li S, Chen J, Luo J, Lu J, Mu Q, Bai J, Xia Q, Chen Q, Cai Y, Zhang H, Chen G, Lin H, Zhang Y, Shi Q. Construction of high-density genetic linkage maps for orange-spotted grouper Epinephelus coioides using multiplexed shotgun genotyping. BMC Genet 2013; 14:113. [PMID: 24289265 PMCID: PMC3890575 DOI: 10.1186/1471-2156-14-113] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Accepted: 11/25/2013] [Indexed: 12/16/2022] Open
Abstract
Background Orange-spotted grouper, Epinephelus coioides, is one of the most valuable fish species in China. Commercial production of orange-spotted grouper could be increased by developing higher growth rates and improving commercially important traits. Information on genetic markers associated with quantitative trait loci (QTL) can be used in breeding programs to identify and select individuals carrying desired traits. A high-density genetic linkage map is the basis for QTL study, and multiplexed shotgun genotyping (MSG) facilitates the development of single nucleotide polymorphisms (SNPs) and genotyping. In this study, the first high-density genetic linkage maps for groupers were generated on the basis of the MSG method. Results The sex-averaged map contained a total of 4,608 SNPs, which spanned 1581.7 cM, with a mean distance between SNPs of 0.34 cM. The 4,608 SNPs were located in 2,849 unique locations on the linkage map, with an average inter-location space at 0.56 cM. There were 2,516 SNPs on the female map, and the number of unique locus was 1,902. However, the male map contained more numbers of SNP (2,939) and unique locations (2,005). The total length of the female and male maps was 1,370.9 and 1,335.5 cM, respectively. Conclusions The high-resolution genetic linkage maps will be very useful for QTL analyses and marker-assisted selection (MAS) for economically important traits in molecular breeding of the orange-spotted grouper.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Yong Zhang
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
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Constructing a genetic linkage map and mapping quantitative trait loci for skeletal traits in Japanese flounder. Biologia (Bratisl) 2013. [DOI: 10.2478/s11756-013-0265-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Wan Q, Su J, Chen X, Yang C, Chen L, Yan N, Zhang Y. Genomic sequence comparison, promoter activity, SNP detection of RIG-I gene and association with resistance/susceptibility to grass carp reovirus in grass carp (Ctenopharyngodon idella). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2013; 39:333-342. [PMID: 23276879 DOI: 10.1016/j.dci.2012.12.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 12/05/2012] [Accepted: 12/05/2012] [Indexed: 06/01/2023]
Abstract
As an intracellular pattern recognition receptor (PRR), retinoic acid-inducible gene-I (RIG-I) is responsible for detection of nucleic acids from pathogens in infected cells and activation of type I interferon (IFN). In the present study, the 5'-flanking region, introns and single nucleotide polymorphisms (SNPs) of CiRIG-I (Ctenopharyngodon idella RIG-I) were identified and characterized. The genomic CiRIG-I was 12810 bp in length, consisted of an 1864 bp 5'-flank region whose promoter activity was confirmed, 15 exons and 14 introns. By pooled DNA sequencing, two SNPs were detected in the 5'-flanking region; 10 SNPs were discovered in introns; and one SNP was found in exons. After a challenge experiment, these SNPs were selected to analyze their association with the resistance/susceptibility of C. idella to grass carp reovirus (GCRV), using case-control study. Chi-square test was employed to assess the association. The result showed that -780 C/T, 4731 C/T, 4945 A/G, 8461 C/T, and haplotype 3428A-3432G were significantly associated with the phenotype (P<0.05). To confirm the correlation, another independent challenge experiment was performed, in which the cumulative mortality of -780 genotype CC, 4731 genotype CC and 4945 genotype AA were significantly lower than that of -780 genotype TT, 4731 genotype TT and 4945 genotype GG, respectively (P<0.05). In addition, the SNP-SNP interaction analysis revealed that there was no significant interaction among those SNPs (P>0.05). These significant SNPs and the haplotype might be potential genetic markers for the molecular selection of C. idella strains that are resistant to GCRV.
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Affiliation(s)
- Quanyuan Wan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
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Jiang L, Chu G, Zhang Q, Wang Z, Wang X, Zhai J, Yu H. A microsatellite genetic linkage map of half smooth tongue sole (Cynoglossus semilaevis). Mar Genomics 2013; 9:17-23. [DOI: 10.1016/j.margen.2012.07.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 07/25/2012] [Accepted: 07/26/2012] [Indexed: 10/28/2022]
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Liu YX, Han HZ, Wang QL, Jiang L, Wang SL, Zhang XY, Liu Y, Wang YF, Liu YJ, Liu HJ. Choice of microsatellite markers for identifying homozygosity of mitotic gynogenetic diploids in Japanese flounder Paralichthys olivaceus. JOURNAL OF FISH BIOLOGY 2013; 82:588-599. [PMID: 23398070 DOI: 10.1111/jfb.12014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 11/03/2012] [Indexed: 06/01/2023]
Abstract
A set of 72 microsatellite markers distributed evenly among 24 linkage groups were selected from the published genetic linkage maps of Japanese flounder Paralichthys olivaceus. In two normal diploid full-sib families, the test for Mendelian inheritance showed that genotypic segregation deviations were not significant at all analysed loci. To estimate microsatellite-centromere map distances, four meiotic gynogenetic diploid lines were produced by the activation of eggs using UV irradiated sperm of red seabream Pagrus major and cold-shock treatment to block the extrusion of the second polar body. Under the assumption of complete interference, 21 markers were located in the centromeric region, 39 in the telomeric region and the rest in the intermediate region of linkage groups. A total of 192 mitotic gynogenetic diploids from one spawn were identified by these markers. Genotype analysis showed that the number of homozygous individuals decreased as microsatellite-centromere map distance increased on each linkage group.
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Affiliation(s)
- Y X Liu
- Chinese Academy of Fishery Sciences, CAFS, Beijing, China
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Song W, Li Y, Zhao Y, Liu Y, Niu Y, Pang R, Miao G, Liao X, Shao C, Gao F, Chen S. Construction of a high-density microsatellite genetic linkage map and mapping of sexual and growth-related traits in half-smooth tongue sole (Cynoglossus semilaevis). PLoS One 2012; 7:e52097. [PMID: 23284884 PMCID: PMC3527371 DOI: 10.1371/journal.pone.0052097] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Accepted: 11/08/2012] [Indexed: 11/19/2022] Open
Abstract
High-density genetic linkage maps of half-smooth tongue sole were developed with 1007 microsatellite markers, two SCAR markers and an F1 family containing 94. The female map was composed of 828 markers in 21 linkage groups, covering a total of 1447.3 cM, with an average interval 1.83 cM between markers. The male map consisted of 794 markers in 21 linkage groups, spanning 1497.5 cM, with an average interval of 1.96 cM. The female and male maps had 812 and 785 unique positions, respectively. The genome length of half-smooth tongue sole was estimated to be 1527.7 cM for the females and 1582.1 cM for the males. Based on estimations of the map lengths, the female and male maps covered 94.74 and 94.65% of the genome, respectively. The consensus map was composed of 1007 microsatellite markers and two SCAR markers in 21 linkage groups, covering a total of 1624 cM with an average interval of 1.67 cM. Furthermore, 159 sex-linked SSR markers were identified. Five sex-linked microsatellite markers were confirmed in their association with sex in a large number of individuals selected from different families. These sex-linked markers were mapped on the female map LG1f with zero recombination. Two QTLs that were identified for body weight, designated as We-1 and We-2, accounted for 26.39% and 10.60% of the phenotypic variation. Two QTLs for body width, designated Wi-1 and Wi-2, were mapped in LG4f and accounted for 14.33% and 12.83% of the phenotypic variation, respectively. Seven sex-related loci were mapped in LG1f, LG14f and LG1m by CIM, accounting for 12.5–25.2% of the trait variation. The results should prove to be very useful for improving growth traits using molecular MAS.
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Affiliation(s)
- Wentao Song
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Weihai Vocational College, Department of Biological and Chemical Engineering, Weihai, China
| | - Yangzhen Li
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Yongwei Zhao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Yang Liu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Yuze Niu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Renyi Pang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Guidong Miao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xiaolin Liao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Changwei Shao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Fengtao Gao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Songlin Chen
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- * E-mail:
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Song W, Pang R, Niu Y, Gao F, Zhao Y, Zhang J, Sun J, Shao C, Liao X, Wang L, Tian Y, Chen S. Construction of high-density genetic linkage maps and mapping of growth-related quantitative trail loci in the Japanese flounder (Paralichthys olivaceus). PLoS One 2012; 7:e50404. [PMID: 23209734 PMCID: PMC3510152 DOI: 10.1371/journal.pone.0050404] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 10/19/2012] [Indexed: 11/19/2022] Open
Abstract
High-density genetic linkage maps were constructed for the Japanese flounder (Paralichthys olivaceus). A total of 1624 microsatellite markers were polymorphic in the reference family. Linkage analysis using JoinMap 4.0 resulted in the mapping of 1487 markers to 24 linkage groups, a result which was consistent with the 24 chromosomes seen in chromosome spreads. The female map was composed of 1257 markers, covering a total of 1663.8 cM with an average interval 1.35 cM between markers. The male map consisted of 1224 markers, spanning 1726.5 cM, with an average interval of 1.44 cM. The genome length in the Japanese flounder was estimated to be 1730.3 cM for the females and 1798.0 cM for the males, a coverage of 96.2% for the female and 96.0% for the male map. The mean recombination at common intervals throughout the genome revealed a slight difference between sexes, i.e. 1.07 times higher in the male than female. High-density genetic linkage maps are very useful for marker-assisted selection (MAS) programs for economically valuable traits in this species and for further evolutionary studies in flatfish and vertebrate species. Furthermore, four quantiative trait loci (QTL) associated with growth traits were mapped on the genetic map. One QTL was identified for body weight on LG 14 f, which explained 14.85% of the total variation of the body weight. Three QTL were identified for body width on LG14f and LG14m, accounting for 16.75%, 13.62% and 13.65% of the total variation in body width, respectively. The additive effects were evident as negative values. There were four QTL for growth traits clustered on LG14, which should prove to be very useful for improving growth traits using molecular MAS.
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Affiliation(s)
- Wentao Song
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Weihai Vocational College, Department of Biological and Chemical Engineering, Weihai, China
| | - Renyi Pang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Yuze Niu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Fengtao Gao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Yongwei Zhao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Jing Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Jian Sun
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Changwei Shao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xiaolin Liao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Lei Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Yongsheng Tian
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Songlin Chen
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
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Li H, Liu X, Zhang G. A consensus microsatellite-based linkage map for the hermaphroditic bay scallop (Argopecten irradians) and its application in size-related QTL analysis. PLoS One 2012; 7:e46926. [PMID: 23077533 PMCID: PMC3473060 DOI: 10.1371/journal.pone.0046926] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 09/06/2012] [Indexed: 01/04/2023] Open
Abstract
Bay scallop (Argopecten irradians) is one of the most economically important aquaculture species in China. In this study, we constructed a consensus microsatellite-based genetic linkage map with a mapping panel containing two hybrid backcross-like families involving two subspecies of bay scallop, A. i. irradians and A. i. concentricus. One hundred sixty-one microsatellite and one phenotypic (shell color) markers were mapped to 16 linkage groups (LGs), which corresponds to the haploid chromosome number of bay scallop. The sex-specific map was 779.2 cM and 781.6 cM long in female and male, respectively, whereas the sex-averaged map spanned 849.3 cM. The average resolution of integrated map was 5.9 cM/locus and the estimated coverage was 81.3%. The proportion of distorted markers occurred more in the hybrid parents, suggesting that the segregation distortion was possibly resulted from heterospecific interaction between genomes of two subspecies of bay scallop. The overall female-to-male recombination rate was 1.13:1 across all linked markers in common to both parents, and considerable differences in recombination also existed among different parents in both families. Four size-related traits, including shell length (SL), shell height (SH), shell width (SW) and total weight (TW) were measured for quantitative trait loci (QTL) analysis. Three significant and six suggestive QTL were detected on five LGs. Among the three significant QTL, two (qSW-10 and qTW-10, controlling SW and TW, respectively) were mapped on the same region near marker AiAD121 on LG10 and explained 20.5% and 27.7% of the phenotypic variance, while the third (qSH-7, controlling SH) was located on LG7 and accounted for 15.8% of the phenotypic variance. Six suggestive QTL were detected on four different LGs. The linkage map and size-related QTL obtained in this study may facilitate marker-assisted selection (MAS) in bay scallop.
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Affiliation(s)
- Hongjun Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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40
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Advances in genomics for flatfish aquaculture. GENES AND NUTRITION 2012; 8:5-17. [PMID: 22903900 DOI: 10.1007/s12263-012-0312-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 08/02/2012] [Indexed: 10/28/2022]
Abstract
Fish aquaculture is considered to be one of the most sustainable sources of protein for humans. Many different species are cultured worldwide, but among them, marine flatfishes comprise a group of teleosts of high commercial interest because of their highly prized white flesh. However, the aquaculture of these fishes is seriously hampered by the scarce knowledge on their biology. In recent years, various experimental 'omics' approaches have been applied to farmed flatfishes to increment the genomic resources available. These tools are beginning to identify genetic markers associated with traits of commercial interest, and to unravel the molecular basis of different physiological processes. This article summarizes recent advances in flatfish genomics research in Europe. We focus on the new generation sequencing technologies, which can produce a massive amount of DNA sequencing data, and discuss their potentials and applications for de novo genome sequencing and transcriptome analysis. The relevance of these methods in nutrigenomics and foodomics approaches for the production of healthy animals, as well as high quality and safety products for the consumer, is also briefly discussed.
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Bouza C, Hermida M, Pardo BG, Vera M, Fernández C, de la Herrán R, Navajas-Pérez R, Álvarez-Dios JA, Gómez-Tato A, Martínez P. An Expressed Sequence Tag (EST)-enriched genetic map of turbot (Scophthalmus maximus): a useful framework for comparative genomics across model and farmed teleosts. BMC Genet 2012; 13:54. [PMID: 22747677 PMCID: PMC3464660 DOI: 10.1186/1471-2156-13-54] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 07/02/2012] [Indexed: 12/18/2022] Open
Abstract
Background The turbot (Scophthalmus maximus) is a relevant species in European aquaculture. The small turbot genome provides a source for genomics strategies to use in order to understand the genetic basis of productive traits, particularly those related to sex, growth and pathogen resistance. Genetic maps represent essential genomic screening tools allowing to localize quantitative trait loci (QTL) and to identify candidate genes through comparative mapping. This information is the backbone to develop marker-assisted selection (MAS) programs in aquaculture. Expressed sequenced tag (EST) resources have largely increased in turbot, thus supplying numerous type I markers suitable for extending the previous linkage map, which was mostly based on anonymous loci. The aim of this study was to construct a higher-resolution turbot genetic map using EST-linked markers, which will turn out to be useful for comparative mapping studies. Results A consensus gene-enriched genetic map of the turbot was constructed using 463 SNP and microsatellite markers in nine reference families. This map contains 438 markers, 180 EST-linked, clustered at 24 linkage groups. Linkage and comparative genomics evidences suggested additional linkage group fusions toward the consolidation of turbot map according to karyotype information. The linkage map showed a total length of 1402.7 cM with low average intermarker distance (3.7 cM; ~2 Mb). A global 1.6:1 female-to-male recombination frequency (RF) ratio was observed, although largely variable among linkage groups and chromosome regions. Comparative sequence analysis revealed large macrosyntenic patterns against model teleost genomes, significant hits decreasing from stickleback (54%) to zebrafish (20%). Comparative mapping supported particular chromosome rearrangements within Acanthopterygii and aided to assign unallocated markers to specific turbot linkage groups. Conclusions The new gene-enriched high-resolution turbot map represents a useful genomic tool for QTL identification, positional cloning strategies, and future genome assembling. This map showed large synteny conservation against model teleost genomes. Comparative genomics and data mining from landmarks will provide straightforward access to candidate genes, which will be the basis for genetic breeding programs and evolutionary studies in this species.
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Affiliation(s)
- Carmen Bouza
- Departamento de Genética, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Campus de Lugo, 27002, Lugo, Spain
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Liu S, Rexroad CE, Couch CR, Cordes JF, Reece KS, Sullivan CV. A microsatellite linkage map of striped bass (Morone saxatilis) reveals conserved synteny with the three-spined stickleback (Gasterosteus aculeatus). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2012; 14:237-244. [PMID: 21968826 DOI: 10.1007/s10126-011-9407-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Accepted: 09/02/2011] [Indexed: 05/31/2023]
Abstract
The striped bass (Morone saxatilis) and its relatives (genus Morone) are of great importance to fisheries and aquaculture in North America. As part of a collaborative effort to employ molecular genetics technologies in striped bass breeding programs, we previously developed nearly 500 microsatellite markers. The objectives of this study were to construct a microsatellite linkage map of striped bass and to examine conserved synteny between striped bass and three-spined stickleback (Gasterosteus aculeatus). Of 480 microsatellite markers screened for polymorphism, 289 informative markers were identified and used to genotype two half-sib mapping families. Twenty-six linkage groups were assembled, and only two markers remain unlinked. The sex-averaged map spans 1,623.8 cM with an average marker density of 5.78 cM per marker. Among 287 striped bass microsatellite markers assigned to linkage groups, 169 (58.9%) showed homology to sequences on stickleback chromosomes or scaffolds. Comparison between the stickleback genome and the striped bass linkage map revealed conserved synteny between these two species. This is the first linkage map for any of the Morone species. This map will be useful for molecular mapping and marker-assisted selection of genes of interest in striped bass breeding programs. The conserved synteny between striped bass and stickleback will facilitate fine mapping of genome regions of interest and will serve as a new resource for comparative mapping with other Perciform fishes such as European sea bass (Dicentrarchus labrax), gilthead sea bream (Sparus aurata), and tilapia (Oreochromis ssp.).
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Affiliation(s)
- Sixin Liu
- USDA/ARS National Center of Cool and Cold Water Aquaculture, Kearneysville, WV 25430, USA.
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Lidder P, Sonnino A. Biotechnologies for the management of genetic resources for food and agriculture. ADVANCES IN GENETICS 2012; 78:1-167. [PMID: 22980921 DOI: 10.1016/b978-0-12-394394-1.00001-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In recent years, the land area under agriculture has declined as also has the rate of growth in agricultural productivity while the demand for food continues to escalate. The world population now stands at 7 billion and is expected to reach 9 billion in 2045. A broad range of agricultural genetic diversity needs to be available and utilized in order to feed this growing population. Climate change is an added threat to biodiversity that will significantly impact genetic resources for food and agriculture (GRFA) and food production. There is no simple, all-encompassing solution to the challenges of increasing productivity while conserving genetic diversity. Sustainable management of GRFA requires a multipronged approach, and as outlined in the paper, biotechnologies can provide powerful tools for the management of GRFA. These tools vary in complexity from those that are relatively simple to those that are more sophisticated. Further, advances in biotechnologies are occurring at a rapid pace and provide novel opportunities for more effective and efficient management of GRFA. Biotechnology applications must be integrated with ongoing conventional breeding and development programs in order to succeed. Additionally, the generation, adaptation, and adoption of biotechnologies require a consistent level of financial and human resources and appropriate policies need to be in place. These issues were also recognized by Member States at the FAO international technical conference on Agricultural Biotechnologies for Developing Countries (ABDC-10), which took place in March 2010 in Mexico. At the end of the conference, the Member States reached a number of key conclusions, agreeing, inter alia, that developing countries should significantly increase sustained investments in capacity building and the development and use of biotechnologies to maintain the natural resource base; that effective and enabling national biotechnology policies and science-based regulatory frameworks can facilitate the development and appropriate use of biotechnologies in developing countries; and that FAO and other relevant international organizations and donors should significantly increase their efforts to support the strengthening of national capacities in the development and appropriate use of pro-poor agricultural biotechnologies.
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Affiliation(s)
- Preetmoninder Lidder
- Office of Knowledge Exchange, Research and Extension, Research and Extension Branch, Food and Agriculture Organization of the UN (FAO), Viale delle Terme di Caracalla, Rome, Italy
| | - Andrea Sonnino
- Office of Knowledge Exchange, Research and Extension, Research and Extension Branch, Food and Agriculture Organization of the UN (FAO), Viale delle Terme di Caracalla, Rome, Italy
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Hwang SD, Fuji K, Takano T, Sakamoto T, Kondo H, Hirono I, Aoki T. Linkage mapping of toll-like receptors (TLRs) in Japanese flounder, Paralichthys olivaceus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2011; 13:1086-1091. [PMID: 21494881 DOI: 10.1007/s10126-011-9371-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 03/23/2011] [Indexed: 05/30/2023]
Abstract
Toll-like receptors (TLRs) are responsible for the recognition of specific pathogen-associated molecular patterns and consequently activate signal pathways leading to inflammatory and interferon responses. The region surrounding several TLRs was previously found to be associated with resistance to specific disease. Hence, we determined the location of 11 TLRs in Japanese flounder (Paralichthys olivaceus) using polymorphic microsatellite markers. TLR1 and TLR3 were located on linkage group (LG) 21 and 7, respectively. Membrane TLR5 and soluble TLR5 were mapped to LG22. TLR7 and TLR8 were mapped to LG3. TLR9 was found on LG1 and TLR14 and TLR21 were located on the same linkage group, LG10. TLR22 was found on LG8. Interestingly, TLR2 was mapped with the previously reported Poli9-8TUF microsatellite marker which is tightly associated with lymphocystis virus disease resistance. Therefore, TLR2 is a candidate gene for resistance to lymphocystis disease. These results imply that the location of a TLR associated with a particular disease may be valuable for the research on the relationship between host immune response and disease resistance.
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Affiliation(s)
- Seong Don Hwang
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo 108-8477, Japan
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Zheng X, Kuang Y, Zhang X, Lu C, Cao D, Li C, Sun X. A genetic linkage map and comparative genome analysis of common carp (Cyprinus carpio L.) using microsatellites and SNPs. Mol Genet Genomics 2011; 286:261-77. [PMID: 21870156 DOI: 10.1007/s00438-011-0644-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 08/10/2011] [Indexed: 01/03/2023]
Abstract
A genetic linkage map is a powerful research tool for mapping traits of interest and is essential to understanding genome evolution. The aim of this study is to provide an expanded genetic linkage map of common carp to effectively carry out quantitative trait loci analysis and conduct comparative mapping analysis between lineages. Here, we constructed a genetic linkage map of common carp (Cyprinus carpio L.) using microsatellite and single-nucleotide polymorphism (SNP) markers in a 159 sibling family. A total of 246 microsatellites and 306 SNP polymorphic markers were genotyped in this family. Linkage analysis using JoinMap 4.0 organized 427 markers (186 microsatellites and 241 SNPs) to 50 linkage groups, ranging in size from 1.4 to 130.1 cM. Each group contained 2-30 markers. The linkage map covered a genetic distance of 2,039.2 cM and the average interval for markers within the linkage groups was approximately 6.4 cM. In addition, comparative genome analysis within five model teleost fish revealed a high percentage (74.7%) of conserved loci corresponding to zebrafish chromosomes. In most cases, each zebrafish chromosome comprised two common carp linkage groups. The comparative analysis also revealed independent chromosome rearrangements in common carp and zebrafish. The linkage map will be of great assistance in mapping genes of interest and serve as a reference to approach comparative mapping and enable further insights into the comprehensive investigations of genome evolution of common carp.
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Affiliation(s)
- Xianhu Zheng
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, No 43 Songfa Road, Daoli District, Harbin 150070, Heilongjiang, China
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Wang Y, Osatomi K, Nagatomo Y, Yoshida A, Hara K. Purification, molecular cloning, and some properties of a manganese-containing superoxide dismutase from Japanese flounder (Paralichthys olivaceus). Comp Biochem Physiol B Biochem Mol Biol 2011; 158:289-96. [DOI: 10.1016/j.cbpb.2010.12.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 12/28/2010] [Accepted: 12/29/2010] [Indexed: 11/30/2022]
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