1
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Kitanishi S, Kondou T, Takahashi H, Takeshita N, Nagata S, Edo K. Recent reduction of genetic diversity in markless form of the red-spotted masu salmon Oncorhynchus masou ishikawae in the Ono River, Kyushu, Japan. CONSERV GENET 2023. [DOI: 10.1007/s10592-023-01515-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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2
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Ocalewicz K, Gurgul A, Polonis M, Dobosz S. Preliminary Identification of Candidate Genes Related to Survival of Gynogenetic Rainbow Trout ( Oncorhynchus mykiss) Based on Comparative Transcriptome Analysis. Animals (Basel) 2020; 10:ani10081326. [PMID: 32751994 PMCID: PMC7459965 DOI: 10.3390/ani10081326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 11/16/2022] Open
Abstract
In the present research, the eggs from four rainbow trout females were used to provide four groups of gynogenetic doubled haploids (DHs). The quality of the eggs from different clutches was comparable, however, interclutch differences were observed in the gynogenetic variants of the experiment and the survival of DH specimens from different groups varied from 3% to 57% during embryogenesis. Transcriptome analysis of the eggs from different females exhibited inter-individual differences in the maternal genes' expression. Eggs originating from females whose gynogenetic offspring had the highest survival showed an increased expression of 46 genes when compared to the eggs from three other females. Eggs with the highest survival of gynogenetic embryos showed an up-regulation of genes that are associated with cell survival, migration and differentiation (tyrosine-protein kinase receptor TYRO3-like gene), triglyceride metabolism (carnitine O-palmitoyltransferase 1 gene), biosynthesis of polyunsaturated fat (3-oxoacyl-acyl-carrier-protein reductase gene), early embryogenic development (protein argonaute-3 gene, leucine-rich repeat-containing protein 3-like gene), 5S RNA binding (ribosome biogenesis regulatory protein homolog) as well as senescence and aging (telomerase reverse transcriptase, TERT gene), among others. Positive correlation between the genotypic efficiency and egg transcriptome profiles indicated that at least some of the differentially expressed genes should be considered as potential candidate genes for the efficiency of gynogenesis in rainbow trout.
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Affiliation(s)
- Konrad Ocalewicz
- Department of Marine Biology and Ecology, Institute of Oceanography, Faculty of Oceanography and Geography, University of Gdansk, M. Piłsudskiego 46 Av, 81-378 Gdynia, Poland;
- Correspondence:
| | - Artur Gurgul
- Centre for Experimental and Innovative Medicine, University of Agriculture in Kraków, Rędzina 1c, 30-248 Kraków, Poland;
| | - Marcin Polonis
- Department of Marine Biology and Ecology, Institute of Oceanography, Faculty of Oceanography and Geography, University of Gdansk, M. Piłsudskiego 46 Av, 81-378 Gdynia, Poland;
| | - Stefan Dobosz
- Department of Salmonid Research, Inland Fisheries Institute in Olsztyn, Rutki, 83-330 Żukowo, Poland;
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Lepais O, Chancerel E, Boury C, Salin F, Manicki A, Taillebois L, Dutech C, Aissi A, Bacles CF, Daverat F, Launey S, Guichoux E. Fast sequence-based microsatellite genotyping development workflow. PeerJ 2020; 8:e9085. [PMID: 32411534 PMCID: PMC7204839 DOI: 10.7717/peerj.9085] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/08/2020] [Indexed: 12/21/2022] Open
Abstract
Application of high-throughput sequencing technologies to microsatellite genotyping (SSRseq) has been shown to remove many of the limitations of electrophoresis-based methods and to refine inference of population genetic diversity and structure. We present here a streamlined SSRseq development workflow that includes microsatellite development, multiplexed marker amplification and sequencing, and automated bioinformatics data analysis. We illustrate its application to five groups of species across phyla (fungi, plant, insect and fish) with different levels of genomic resource availability. We found that relying on previously developed microsatellite assay is not optimal and leads to a resulting low number of reliable locus being genotyped. In contrast, de novo ad hoc primer designs gives highly multiplexed microsatellite assays that can be sequenced to produce high quality genotypes for 20-40 loci. We highlight critical upfront development factors to consider for effective SSRseq setup in a wide range of situations. Sequence analysis accounting for all linked polymorphisms along the sequence quickly generates a powerful multi-allelic haplotype-based genotypic dataset, calling to new theoretical and analytical frameworks to extract more information from multi-nucleotide polymorphism marker systems.
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Affiliation(s)
- Olivier Lepais
- INRAE, Univ. Bordeaux, BIOGECO, Cestas, France
- INRAE, Université de Pau et Pays de l’Adour, ECOBIOP, Saint-Peé-sur-Nivelle, France
| | | | | | | | - Aurélie Manicki
- INRAE, Université de Pau et Pays de l’Adour, ECOBIOP, Saint-Peé-sur-Nivelle, France
| | - Laura Taillebois
- INRAE, Université de Pau et Pays de l’Adour, ECOBIOP, Saint-Peé-sur-Nivelle, France
| | | | | | - Cecile F.E. Bacles
- INRAE, Université de Pau et Pays de l’Adour, ECOBIOP, Saint-Peé-sur-Nivelle, France
| | | | - Sophie Launey
- INRAE, Agrocampus Ouest, ESE, Ecology and Ecosystem Health, Rennes, France
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4
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Polonis M, Jagiełło K, Dobosz S, Rożyński R, Kondraciuk P, Gurgul A, Szmatoła T, Ocalewicz K. Alterations in the rainbow trout (
Oncorhynchus mykiss
) eggs exposed to ionizing radiation during induced androgenesis. Reprod Domest Anim 2019; 54:712-718. [DOI: 10.1111/rda.13413] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/27/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Marcin Polonis
- Department of Marine Biology and Ecology, Faculty of Oceanography and Geography, Institute of Oceanography University of Gdansk Gdynia Poland
| | - Krzysztof Jagiełło
- Department of Marine Biology and Ecology, Faculty of Oceanography and Geography, Institute of Oceanography University of Gdansk Gdynia Poland
| | - Stefan Dobosz
- Department of Salmonid Research Inland Fisheries Institute in Olsztyn Rutki Poland
| | - Rafał Rożyński
- Department of Salmonid Research Inland Fisheries Institute in Olsztyn Rutki Poland
| | - Paulina Kondraciuk
- Department of Marine Biology and Ecology, Faculty of Oceanography and Geography, Institute of Oceanography University of Gdansk Gdynia Poland
| | - Artur Gurgul
- Department of Animal Molecular Biology National Research Institute of Animal Production Balice Poland
| | - Tomasz Szmatoła
- Department of Animal Molecular Biology National Research Institute of Animal Production Balice Poland
| | - Konrad Ocalewicz
- Department of Marine Biology and Ecology, Faculty of Oceanography and Geography, Institute of Oceanography University of Gdansk Gdynia Poland
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5
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Semple SL, Vo NTK, Poynter SJ, Li M, Heath DD, DeWitte-Orr SJ, Dixon B. Extracellular dsRNA induces a type I interferon response mediated via class A scavenger receptors in a novel Chinook salmon derived spleen cell line. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 89:93-101. [PMID: 30118734 DOI: 10.1016/j.dci.2018.08.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/13/2018] [Accepted: 08/13/2018] [Indexed: 06/08/2023]
Abstract
Despite increased global interest in Chinook salmon aquaculture, little is known of their viral immune defenses. This study describes the establishment and characterization of a continuous cell line derived from Chinook salmon spleen, CHSS, and its use in innate immune studies. Optimal growth was seen at 14-18 °C when grown in Leibovitz's L-15 media with 20% fetal bovine serum. DNA analyses confirmed that CHSS was Chinook salmon and genetically different from the only other available Chinook salmon cell line, CHSE-214. Unlike CHSE-214, CHSS could bind extracellular dsRNA, resulting in the rapid and robust expression of antiviral genes. Receptor/ligand blocking assays confirmed that class A scavenger receptors (SR-A) facilitated dsRNA binding and subsequent gene expression. Although both cell lines expressed three SR-A genes: SCARA3, SCARA4, and SCARA5, only CHSS appeared to have functional cell-surface SR-As for dsRNA. Collectively, CHSS is an excellent cell model to study dsRNA-mediated innate immunity in Chinook salmon.
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Affiliation(s)
- S L Semple
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo, ON, N2L 3G1, Canada
| | - N T K Vo
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo, ON, N2L 3G1, Canada
| | - S J Poynter
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo, ON, N2L 3G1, Canada
| | - M Li
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo, ON, N2L 3G1, Canada
| | - D D Heath
- Great Lakes Institute of Environmental Research, University of Windsor, 2990 Riverside Drive, West Windsor, Ontario, N9C 1A2, Canada
| | - S J DeWitte-Orr
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, N2L 3C5, Canada; Department of Health Sciences, Wilfrid Laurier University, Waterloo, Ontario, N2L 3C5, Canada
| | - B Dixon
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo, ON, N2L 3G1, Canada.
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6
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Kleppe SA, Nordeide JT, Rudolfsen G, Figenschou L, Larsen B, Reiss K, Folstad I. No support for cryptic choice by ovarian fluid in an external fertilizer. Ecol Evol 2018; 8:11763-11774. [PMID: 30598774 PMCID: PMC6303707 DOI: 10.1002/ece3.4628] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 12/01/2022] Open
Abstract
Whether the ovarian fluid (OF) represents a selective environment influencing cryptic female choice was tested using an external fertilizer experiencing intense sperm competition and large effects of OF on sperm swimming behavior-the Arctic charr (Salvelinus alpinus). We physically separated the OF from the eggs of reproductively active females and reintroduced either their own OF or fluid from another female to the eggs. The eggs were then fertilized in vitro in a replicated split-brood design with sperm from two males under synchronized sperm competition trials, while also measuring sperm velocity of the individual males in the individual OFs. We found large effects of males, but no effect of females (i.e., eggs) on paternity, determined from microsatellites. More important, we found no effect of OF treatments on the relative paternity of the two competing males in each pair. This experimental setup does not provide support for the hypothesis that OF plays an important role as medium for cryptic female choice in charr. Power analyses revealed that our sample size is large enough to detect medium-sized changes in relative paternity (medium-sized effect sizes), but not large enough to detect small changes in relative paternity. More studies are needed before a conclusion can be drawn about OF's potential influence on paternity under sperm competition-even in charr.
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Affiliation(s)
| | | | - Geir Rudolfsen
- Faculty of Bioscience, Fishery and EconomyUiT The Arctic University of NorwayTromsøNorway
| | - Lars Figenschou
- University Library, UiT The Arctic University of NorwayTromsøNorway
| | | | - Katrin Reiss
- Faculty of Biosciences and AquacultureNord UniversityBodøNorway
| | - Ivar Folstad
- Faculty of Bioscience, Fishery and EconomyUiT The Arctic University of NorwayTromsøNorway
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7
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8
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Rubtsova GA, Ponomareva EV, Afanasiev KI, Shaikhaev EG, Kholodova MV, Pavlov SD, Zhivotovsky LA. A detection of allelic variants at microsatellite markers by using capillary and traditional electrophoresis. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416040086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Pavlov SD, Ponomareva EV, Kholodova MV, Melnikova MN, Mineeva TV. Genetic diversity of sockeye salmon Oncorhynchus nerka Walbaum of Kamchatka and the Commander Islands based on analysis of the variability of microsatellite DNA. BIOL BULL+ 2016. [DOI: 10.1134/s1062359016010131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Leggatt RA, Hollo T, Vandersteen WE, McFarlane K, Goh B, Prevost J, Devlin RH. Rearing in seawater mesocosms improves the spawning performance of growth hormone transgenic and wild-type coho salmon. PLoS One 2014; 9:e105377. [PMID: 25133780 PMCID: PMC4136866 DOI: 10.1371/journal.pone.0105377] [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: 04/09/2014] [Accepted: 07/22/2014] [Indexed: 11/18/2022] Open
Abstract
Growth hormone (GH) transgenes can significantly accelerate growth rates in fish and cause associated alterations to their physiology and behaviour. Concern exists regarding potential environmental risks of GH transgenic fish, should they enter natural ecosystems. In particular, whether they can reproduce and generate viable offspring under natural conditions is poorly understood. In previous studies, GH transgenic salmon grown under contained culture conditions had lower spawning behaviour and reproductive success relative to wild-type fish reared in nature. However, wild-type salmon cultured in equal conditions also had limited reproductive success. As such, whether decreased reproductive success of GH transgenic salmon is due to the action of the transgene or to secondary effects of culture (or a combination) has not been fully ascertained. Hence, salmon were reared in large (350,000 L), semi-natural, seawater tanks (termed mesocosms) designed to minimize effects of standard laboratory culture conditions, and the reproductive success of wild-type and GH transgenic coho salmon from mesocosms were compared with that of wild-type fish from nature. Mesocosm rearing partially restored spawning behaviour and success of wild-type fish relative to culture rearing, but remained lower overall than those reared in nature. GH transgenic salmon reared in the mesocosm had similar spawning behaviour and success as wild-type fish reared in the mesocosm when in full competition and without competition, but had lower success in male-only competition experiments. There was evidence of genotype×environmental interactions on spawning success, so that spawning success of transgenic fish, should they escape to natural systems in early life, cannot be predicted with low uncertainty. Under the present conditions, we found no evidence to support enhanced mating capabilities of GH transgenic coho salmon compared to wild-type salmon. However, it is clear that GH transgenic salmon are capable of successful spawning, and can reproduce with wild-type fish from natural systems.
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Affiliation(s)
- Rosalind A. Leggatt
- Fisheries and Oceans Canada, West Vancouver Laboratories, West Vancouver, BC, Canada
| | - Tanya Hollo
- Fisheries and Oceans Canada, West Vancouver Laboratories, West Vancouver, BC, Canada
| | - Wendy E. Vandersteen
- Fisheries and Oceans Canada, West Vancouver Laboratories, West Vancouver, BC, Canada
| | - Kassandra McFarlane
- Fisheries and Oceans Canada, West Vancouver Laboratories, West Vancouver, BC, Canada
| | - Benjamin Goh
- Fisheries and Oceans Canada, West Vancouver Laboratories, West Vancouver, BC, Canada
| | - Joelle Prevost
- Fisheries and Oceans Canada, West Vancouver Laboratories, West Vancouver, BC, Canada
| | - Robert H. Devlin
- Fisheries and Oceans Canada, West Vancouver Laboratories, West Vancouver, BC, Canada
- * E-mail:
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11
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Banks MA, Jacobson DP, Meusnier I, Greig CA, Rashbrook VK, Ardren WR, Smith CT, Bernier‐Latmani J, Van Sickle J, O'Malley KG. Testing advances in molecular discrimination among Chinook salmon life histories: evidence from a blind test. Anim Genet 2014; 45:412-20. [PMID: 24628286 PMCID: PMC4112815 DOI: 10.1111/age.12135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2014] [Indexed: 11/29/2022]
Abstract
The application of DNA-based markers toward the task of discriminating among alternate salmon runs has evolved in accordance with ongoing genomic developments and increasingly has enabled resolution of which genetic markers associate with important life-history differences. Accurate and efficient identification of the most likely origin for salmon encountered during ocean fisheries, or at salvage from fresh water diversion and monitoring facilities, has far-reaching consequences for improving measures for management, restoration and conservation. Near-real-time provision of high-resolution identity information enables prompt response to changes in encounter rates. We thus continue to develop new tools to provide the greatest statistical power for run identification. As a proof of concept for genetic identification improvements, we conducted simulation and blind tests for 623 known-origin Chinook salmon (Oncorhynchus tshawytscha) to compare and contrast the accuracy of different population sampling baselines and microsatellite loci panels. This test included 35 microsatellite loci (1266 alleles), some known to be associated with specific coding regions of functional significance, such as the circadian rhythm cryptochrome genes, and others not known to be associated with any functional importance. The identification of fall run with unprecedented accuracy was demonstrated. Overall, the top performing panel and baseline (HMSC21) were predicted to have a success rate of 98%, but the blind-test success rate was 84%. Findings for bias or non-bias are discussed to target primary areas for further research and resolution.
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Affiliation(s)
- Michael A. Banks
- Coastal Oregon Marine Experiment StationDepartment of Fisheries and WildlifeHatfield Marine Science CenterOregon State UniversityNewportOR97365USA
| | - David P. Jacobson
- Coastal Oregon Marine Experiment StationDepartment of Fisheries and WildlifeHatfield Marine Science CenterOregon State UniversityNewportOR97365USA
| | - Isabelle Meusnier
- Center for Biology and Management of PopulationsMontpellier34000France
| | - Carolyn A. Greig
- Department of BiosciencesCollege of ScienceSwansea UniversitySwanseaWalesSA1 1LGUK
| | - Vanessa K. Rashbrook
- UC Davis Genome Center – DNA Technologies CoreUC DavisOne Shields AveDavisCA95616USA
| | | | | | | | - John Van Sickle
- Department of Fisheries and WildlifeOregon State UniversityCorvallisOR97331USA
| | - Kathleen G. O'Malley
- Coastal Oregon Marine Experiment StationDepartment of Fisheries and WildlifeHatfield Marine Science CenterOregon State UniversityNewportOR97365USA
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12
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Moore JS, Loewen TN, Harris LN, Tallman RF. Genetic analysis of sympatric migratory ecotypes of Arctic charr Salvelinus alpinus: alternative mating tactics or reproductively isolated strategies? JOURNAL OF FISH BIOLOGY 2014; 84:145-162. [PMID: 24383802 DOI: 10.1111/jfb.12262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 09/23/2013] [Indexed: 06/03/2023]
Abstract
Three populations of Arctic charr Salvelinus alpinus from southern Baffin Island were previously identified to display variable migratory phenotypes, with an anadromous component of the population and another remaining resident in fresh water. In this study, 14 microsatellite markers were used to help distinguish between two alternative hypotheses to explain the co-existence of the two ecotypes: that the two ecotypes originate from a single population and are the result of a conditional mating tactic or that the migratory ecotypes are reproductively isolated populations utilizing alternative migratory strategies. In two of the three replicate systems, F(ST) values between the resident and anadromous individuals were non-significant, while they were significant in a third sampling location. Bayesian clustering analysis implemented in structure, however, failed to identify any within-location clustering in all three sampling locations. It is concluded from these analyses that the life-history ecotypes are most likely conditional mating tactics, rather than reproductively isolated populations. Other evidence in favour of the alternative mating tactic hypothesis is briefly reviewed, and implications for management of those populations are discussed.
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Affiliation(s)
- J-S Moore
- Department of Zoology and Beaty Biodiversity Research Centre and Museum, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4 Canada
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13
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Garvin MR, Saitoh K, Gharrett AJ. Application of single nucleotide polymorphisms to non-model species: a technical review. Mol Ecol Resour 2013; 10:915-34. [PMID: 21565101 DOI: 10.1111/j.1755-0998.2010.02891.x] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Single nucleotide polymorphisms (SNPs) have gained wide use in humans and model species and are becoming the marker of choice for applications in other species. Technology that was developed for work in model species may provide useful tools for SNP discovery and genotyping in non-model organisms. However, SNP discovery can be expensive, labour intensive, and introduce ascertainment bias. In addition, the most efficient approaches to SNP discovery will depend on the research questions that the markers are to resolve as well as the focal species. We discuss advantages and disadvantages of several past and recent technologies for SNP discovery and genotyping and summarize a variety of SNP discovery and genotyping studies in ecology and evolution.
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Affiliation(s)
- M R Garvin
- Fisheries Division, School of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 17101 Point Lena Loop Road, Juneau, AK 99801, USA National Research Institute of Fisheries Science, Fukuura, Kanazawa, Yokohama 236-8648 Japan
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14
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Hess MA, Rabe CD, Vogel JL, Stephenson JJ, Nelson DD, Narum SR. Supportive breeding boosts natural population abundance with minimal negative impacts on fitness of a wild population of Chinook salmon. Mol Ecol 2012; 21:5236-50. [PMID: 23025818 PMCID: PMC3490153 DOI: 10.1111/mec.12046] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 08/17/2012] [Accepted: 08/23/2012] [Indexed: 11/29/2022]
Abstract
While supportive breeding programmes strive to minimize negative genetic impacts to populations, case studies have found evidence for reduced fitness of artificially produced individuals when they reproduce in the wild. Pedigrees of two complete generations were tracked with molecular markers to investigate differences in reproductive success (RS) of wild and hatchery-reared Chinook salmon spawning in the natural environment to address questions regarding the demographic and genetic impacts of supplementation to a natural population. Results show a demographic boost to the population from supplementation. On average, fish taken into the hatchery produced 4.7 times more adult offspring, and 1.3 times more adult grand-offspring than naturally reproducing fish. Of the wild and hatchery fish that successfully reproduced, we found no significant differences in RS between any comparisons, but hatchery-reared males typically had lower RS values than wild males. Mean relative reproductive success (RRS) for hatchery F(1) females and males was 1.11 (P = 0.84) and 0.89 (P = 0.56), respectively. RRS of hatchery-reared fish (H) that mated in the wild with either hatchery or wild-origin (W) fish was generally equivalent to W × W matings. Mean RRS of H × W and H × H matings was 1.07 (P = 0.92) and 0.94 (P = 0.95), respectively. We conclude that fish chosen for hatchery rearing did not have a detectable negative impact on the fitness of wild fish by mating with them for a single generation. Results suggest that supplementation following similar management practices (e.g. 100% local, wild-origin brood stock) can successfully boost population size with minimal impacts on the fitness of salmon in the wild.
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Affiliation(s)
- Maureen A Hess
- Columbia River Inter-Tribal Fish Commission, Hagerman Fish Culture Experiment Station, Hagerman, ID 83332, USA.
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15
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Loridon K, Burgarella C, Chantret N, Martins F, Gouzy J, Prospéri JM, Ronfort J. Single-nucleotide polymorphism discovery and diversity in the model legume Medicago truncatula. Mol Ecol Resour 2012; 13:84-95. [PMID: 23017123 DOI: 10.1111/1755-0998.12021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 08/16/2012] [Accepted: 08/20/2012] [Indexed: 01/09/2023]
Abstract
Extensive genomic resources are available in the model legume Medicago truncatula. Here, we present the discovery and design of the first array of single-nucleotide polymorphism (SNP) markers in M. truncatula through large-scale Sanger resequencing of genomic fragments spanning the genome, in a diverse panel of 16 M. truncatula accessions. Both anonymous fragments and fragments targeting candidate genes for flowering phenology and symbiosis were surveyed for nucleotide variation in almost 230 kb of unique genomic regions. A set of 384 SNP markers was designed for an Illumina's GoldenGate assay, genotyped on a collection of 192 inbred lines (CC192) representing the geographical range of the species and used to survey the diversity of two natural populations. Finally, 86% of the tested SNPs were of high quality and exhibited polymorphism in the CC192 collection. Even at the population level, we detected polymorphism for more than 50% of the selected SNPs. Analysis of the allele frequency spectrum in the CC192 showed a reduced ascertainment bias, mostly limited to very rare alleles (frequency <0.01). The substantial polymorphism detected at the species and population levels, the high marker quality and the potential to survey large samples of individuals make this set of SNP markers a valuable tool to improve our understanding of the effect of demographic and selective factors that shape the natural genetic diversity within the selfing species Medicago truncatula.
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Affiliation(s)
- Karine Loridon
- INRA, UMR AGAP, 2 place Pierre Viala, F-34060, Montpellier Cedex 1, France.
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16
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LIN JOCELYNE, HILBORN RAY, QUINN THOMASP, HAUSER LORENZ. Self-sustaining populations, population sinks or aggregates of strays: chum (Oncorhynchus keta) and Chinook salmon (Oncorhynchus tshawytscha) in the Wood River system, Alaska. Mol Ecol 2011; 20:4925-37. [DOI: 10.1111/j.1365-294x.2011.05334.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Vandersteen W, Biro P, Harris L, Devlin R. Introgression of domesticated alleles into a wild trout genotype and the impact on seasonal survival in natural lakes. Evol Appl 2011; 5:76-88. [PMID: 25568031 DOI: 10.1111/j.1752-4571.2011.00210.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 09/03/2011] [Indexed: 11/28/2022] Open
Abstract
We tested the fitness consequences of introgression of fast-growing domesticated fish into a wild population. Fry from wild and domesticated rainbow trout (Oncorhynchus mykiss) crosses, F1 hybrids, and first- and second-generation backcrosses were released into two natural lakes. Parentage analysis using microsatellite loci facilitated the identification of survivors, so fitness was estimated in nature from the first-feeding stage. Results indicated that under certain conditions, domesticated fish survived at least as well as wild fish within the same environment. Relative growth and survival of the crosses, however, were highly dependent on environment. During the first summer, fastest-growing crosses had the highest survival, but this trend was reversed after one winter and another summer. Although the F1 hybrids showed evidence of outbreeding depression because of the disruption of local adaptation, there was little evidence of outbreeding depression in the backcrosses, and the second-generation backcrosses exhibited a wild-type phenotype. This information is relevant for assessing the multigenerational risk of escaped or released domesticated fish should they successfully interbreed with wild populations and provides information on how to minimize detrimental impacts of a conservation breeding and/or management programme. These data also further understanding of the selection pressures in nature that maintain submaximal rates of growth.
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Affiliation(s)
- Wendy Vandersteen
- Centre for Aquaculture and Environmental Research, Fisheries & Oceans Canada West Vancouver, BC, Canada
| | - Pete Biro
- Centre for Integrative Ecology, Deakin University Waurn Ponds, Vic., Australia
| | - Les Harris
- Centre for Aquaculture and Environmental Research, Fisheries & Oceans Canada West Vancouver, BC, Canada ; Fisheries & Oceans Canada Winnipeg, MB, Canada
| | - Robert Devlin
- Centre for Aquaculture and Environmental Research, Fisheries & Oceans Canada West Vancouver, BC, Canada
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DeHaan PW, Brenkman SJ, Adams B, Crain P. Genetic Population Structure of Olympic Peninsula Bull Trout Populations and Implications for Elwha Dam Removal. NORTHWEST SCIENCE 2011. [DOI: 10.3955/046.085.0305] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Mel'nikova MN, Senchukova AL, Pavlov SD. Designing of new population genetic markers based on intersatellite DNA variation for Parasalmo (Oncorhynchus) mykiss. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2011; 435:400-3. [PMID: 21221893 DOI: 10.1134/s0012496610060086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Indexed: 11/23/2022]
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MEEUWIG MICHAELH, GUY CHRISTOPHERS, KALINOWSKI STEVENT, FREDENBERG WADEA. Landscape influences on genetic differentiation among bull trout populations in a stream-lake network. Mol Ecol 2010; 19:3620-33. [DOI: 10.1111/j.1365-294x.2010.04655.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Rexroad CE, Vallejo RL. Estimates of linkage disequilibrium and effective population size in rainbow trout. BMC Genet 2009; 10:83. [PMID: 20003428 PMCID: PMC2800115 DOI: 10.1186/1471-2156-10-83] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Accepted: 12/14/2009] [Indexed: 12/19/2022] Open
Abstract
Background The use of molecular genetic technologies for broodstock management and selective breeding of aquaculture species is becoming increasingly more common with the continued development of genome tools and reagents. Several laboratories have produced genetic maps for rainbow trout to aid in the identification of loci affecting phenotypes of interest. These maps have resulted in the identification of many quantitative/qualitative trait loci affecting phenotypic variation in traits associated with albinism, disease resistance, temperature tolerance, sex determination, embryonic development rate, spawning date, condition factor and growth. Unfortunately, the elucidation of the precise allelic variation and/or genes underlying phenotypic diversity has yet to be achieved in this species having low marker densities and lacking a whole genome reference sequence. Experimental designs which integrate segregation analyses with linkage disequilibrium (LD) approaches facilitate the discovery of genes affecting important traits. To date the extent of LD has been characterized for humans and several agriculturally important livestock species but not for rainbow trout. Results We observed that the level of LD between syntenic loci decayed rapidly at distances greater than 2 cM which is similar to observations of LD in other agriculturally important species including cattle, sheep, pigs and chickens. However, in some cases significant LD was also observed up to 50 cM. Our estimate of effective population size based on genome wide estimates of LD for the NCCCWA broodstock population was 145, indicating that this population will respond well to high selection intensity. However, the range of effective population size based on individual chromosomes was 75.51 - 203.35, possibly indicating that suites of genes on each chromosome are disproportionately under selection pressures. Conclusions Our results indicate that large numbers of markers, more than are currently available for this species, will be required to enable the use of genome-wide integrated mapping approaches aimed at identifying genes of interest in rainbow trout.
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Affiliation(s)
- Caird E Rexroad
- USDA/ARS National Center for Cool and Cold Water Aquaculture, Leetown, West Virginia 25430, USA.
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22
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DeHaan PW, Schwabe LT, Ardren WR. Spatial patterns of hybridization between bull trout, Salvelinus confluentus, and brook trout, Salvelinus fontinalis in an Oregon stream network. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9937-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Rexroad CE, Palti Y, Gahr SA, Vallejo RL. A second generation genetic map for rainbow trout (Oncorhynchus mykiss). BMC Genet 2008; 9:74. [PMID: 19019240 PMCID: PMC2605456 DOI: 10.1186/1471-2156-9-74] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Accepted: 11/19/2008] [Indexed: 11/14/2022] Open
Abstract
Background Genetic maps characterizing the inheritance patterns of traits and markers have been developed for a wide range of species and used to study questions in biomedicine, agriculture, ecology and evolutionary biology. The status of rainbow trout genetic maps has progressed significantly over the last decade due to interest in this species in aquaculture and sport fisheries, and as a model research organism for studies related to carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition. We constructed a second generation genetic map for rainbow trout using microsatellite markers to facilitate the identification of quantitative trait loci for traits affecting aquaculture production efficiency and the extraction of comparative information from the genome sequences of model fish species. Results A genetic map ordering 1124 microsatellite loci spanning a sex-averaged distance of 2927.10 cM (Kosambi) and having 2.6 cM resolution was constructed by genotyping 10 parents and 150 offspring from the National Center for Cool and Cold Water Aquaculture (NCCCWA) reference family mapping panel. Microsatellite markers, representing pairs of loci resulting from an evolutionarily recent whole genome duplication event, identified 180 duplicated regions within the rainbow trout genome. Microsatellites associated with genes through expressed sequence tags or bacterial artificial chromosomes produced comparative assignments with tetraodon, zebrafish, fugu, and medaka resulting in assignments of homology for 199 loci. Conclusion The second generation NCCCWA genetic map provides an increased microsatellite marker density and quantifies differences in recombination rate between the sexes in outbred populations. It has the potential to integrate with cytogenetic and other physical maps, identifying paralogous regions of the rainbow trout genome arising from the evolutionarily recent genome duplication event, and anchoring a comparative map with the zebrafish, medaka, tetraodon, and fugu genomes. This resource will facilitate the identification of genes affecting traits of interest through fine mapping and positional cloning of candidate genes.
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Affiliation(s)
- Caird E Rexroad
- USDA/ARS National Center for Cool and Cold Water Aquaculture, Leetown, West Virginia, USA.
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Beacham TD, Spilsted B, Le KD, Wetklo M. Population structure and stock identification of chum salmon (Oncorhynchus keta) from British Columbia determined with microsatellite DNA variation. CAN J ZOOL 2008. [DOI: 10.1139/z08-079] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Variation at 14 microsatellite loci was surveyed in 205 populations of chum salmon ( Oncorhynchus keta (Walbaum in Artedi, 1792)) from British Columbia to determine population structure and the possible application of microsatellites to estimate stock composition of chum salmon in mixed-stock fisheries. The genetic differentiation index (FST) over all populations and loci was 0.016, with individual locus values ranging from 0.006 to 0.059. Sixteen regional stocks were defined in British Columbia for stock identification applications. Analysis of simulated fishery samples suggested that accurate and precise regional estimates of stock composition should be produced when the microsatellites were used to estimate stock compositions. The main stocks that constitute the October 2007 samples of migrating chum salmon through Johnstone Strait in southern British Columbia were Fraser River (45%–64%), southern British Columbia mainland (22%), and east coast Vancouver Island (13%–28%), within the range of those to be expected in samples from Johnstone Strait. Microsatellites have the ability to provide fine-scale resolution of stock composition in British Columbia coastal fisheries.
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Affiliation(s)
- Terry D. Beacham
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
- Fisheries and Oceans Canada, 417-2nd Avenue West, Prince Rupert, BC V8J 1G8, Canada
| | - Brian Spilsted
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
- Fisheries and Oceans Canada, 417-2nd Avenue West, Prince Rupert, BC V8J 1G8, Canada
| | - Khai D. Le
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
- Fisheries and Oceans Canada, 417-2nd Avenue West, Prince Rupert, BC V8J 1G8, Canada
| | - Michael Wetklo
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
- Fisheries and Oceans Canada, 417-2nd Avenue West, Prince Rupert, BC V8J 1G8, Canada
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25
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Campbell NR, Narum SR. Quantitative PCR assessment of microsatellite and SNP genotyping with variable quality DNA extracts. CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9661-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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NARUM S, BANKS M, BEACHAM T, BELLINGER M, CAMPBELL M, DEKONING J, ELZ A, GUTHRIEIII C, KOZFKAY C, MILLER K, MORAN P, PHILLIPS R, SEEB L, SMITH C, WARHEIT K, YOUNG S, GARZA J. Differentiating salmon populations at broad and fine geographical scales with microsatellites and single nucleotide polymorphisms. Mol Ecol 2008; 17:3464-77. [DOI: 10.1111/j.1365-294x.2008.03851.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Nichols KM, Broman KW, Sundin K, Young JM, Wheeler PA, Thorgaard GH. Quantitative trait loci x maternal cytoplasmic environment interaction for development rate in Oncorhynchus mykiss. Genetics 2007; 175:335-47. [PMID: 17057232 PMCID: PMC1774986 DOI: 10.1534/genetics.106.064311] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Accepted: 10/02/2006] [Indexed: 11/18/2022] Open
Abstract
Effects of maternal cytoplasmic environment (MCE) on development rate in rainbow trout were evaluated within a quantitative trait loci (QTL) analysis framework. Previous research had identified QTL for development rate in doubled haploid (DH) progeny produced from a cross between the Oregon State University (OSU) and the Swanson (SW) River rainbow trout clonal lines. In this study, progeny for QTL mapping were produced from a cross between the OSU and Clearwater (CW) River clonal lines. Doubled haploids were produced from the OSU x CW F1 by androgenesis using eggs from different females (or MCEs); with androgenesis, the maternal nuclear genome was destroyed by irradiation and diploidy was restored by blocking the first embryonic cleavage by heat shock. All embryos were incubated at the same temperature and development rate quantified as time to hatch. Using a linkage map constructed primarily with AFLP markers, QTL mapping was performed, including MCE covariates and QTL x MCE effects in models for testing. The major QTL for development rate in the OSU x SW cross overlaps with the major QTL found in this OSU x CW cross; effects at this locus were the same across MCEs. Both MCE and QTL x MCE effects contribute to variability in development rate, but QTL x MCE were minor and detected only at small-effect QTL.
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Affiliation(s)
- Krista M Nichols
- School of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, Washington 99164-4236, USA.
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Microsatellite variation reveals weak genetic structure and retention of genetic variability in threatened Chinook salmon (Oncorhynchus tshawytscha) within a Snake River watershed. CONSERV GENET 2006. [DOI: 10.1007/s10592-006-9155-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Small MP, Frye AE, Von Bargen JF, Young SF. Genetic Structure of Chum Salmon (Oncorhynchus keta) Populations in the Lower Columbia River: Are Chum Salmon in Cascade Tributaries Remnant Populations? CONSERV GENET 2006. [DOI: 10.1007/s10592-005-7967-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Gahr SA, Rodriguez MF, Rexroad CE. Identification and expression profile of the ID gene family in the rainbow trout (Oncorhynchus mykiss). ACTA ACUST UNITED AC 2005; 1729:64-73. [PMID: 15866514 DOI: 10.1016/j.bbaexp.2005.03.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2005] [Revised: 02/23/2005] [Accepted: 03/26/2005] [Indexed: 11/17/2022]
Abstract
ID proteins are negative regulators of basic helix-loop-helix transcription factors governing growth and development in mammals. However, little is known about the ID gene function and expression in fish. We report the identification and characterization of two new rainbow trout ID genes (ID1D and ID2B) and extend our expression analyses of two previously identified ID genes (ID1A and ID2A). Phylogenetic analyses indicate an evolutionary relationship between ID1A and ID1D and between ID1B and ID1C, suggesting a mechanism of divergence throughout salmonid evolution. To access the expression of these genes in adult and developing fish, we measured the relative transcript abundance of four ID1 and two ID2 genes by real-time PCR. ID1 transcripts were expressed in a variety of tissues and the ID1 paralogues showed similar patterns of expression, whereas the ID2 paralogues were differentially expressed. To access the role of the ID genes during embryonic development, gene expression was measured at early (day 0 and day 2), mid (day 9 and day 18) and late (day 30 and day 50) embryonic development. ID1A and ID1D expression remained unchanged throughout embryonic development, while ID1B and ID1C were lowest during early, highest at mid, and decreased during late embryonic development. The ID2 transcripts revealed the highest expression in unfertilized eggs and day 2 embryos, and remained low throughout the remainder of embryonic development. The sequence analyses and gene expression patterns implicate gene and genome duplication in rainbow trout ID gene evolution and suggest an extensive role for the IDs in rainbow trout growth and development.
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Affiliation(s)
- Scott A Gahr
- United States Department of Agriculture, Agriculture Research Service, National Center for Cool and Cold Water Aquaculture, 11861 Leetown Road, Kearneysville, WV 25430, USA
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Gahr SA, Palti Y, Rexroad CE. Genomic characterization of a novel pair of ID genes in the rainbow trout (Oncorhynchus mykiss). Anim Genet 2004; 35:317-20. [PMID: 15265072 DOI: 10.1111/j.1365-2052.2004.01142.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ID (inhibitors of DNA binding/differentiation) proteins represent a family of dominant negative regulators of the basic helix-loop-helix transcription factors whose activities result in delayed cell differentiation and prolonged proliferation. A pair of expressed sequence tag clones with homologies to the ID proteins were identified and used to screen a rainbow trout bacterial artificial chromosome (BAC) library to identify clones containing homologues sequences. Phylogenetic analysis of the predicted amino acid sequences revealed close similarities to the rainbow trout ID1 protein, the genes were therefore classified as rainbow trout ID1B and ID1C. Genome characterization based on BAC sequencing showed each gene to have two exons separated by a small intron. The genes are 83% similar in their transcribed regions, yet they are only 64 and 65% similar in the upstream and downstream sequences, respectively. Using reverse transcription polymerase chain reaction, we found both genes to be expressed in a variety of tissues in the adult rainbow trout.
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Affiliation(s)
- S A Gahr
- United Stated Department of Agriculture, Agriculture Research Service, National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, USA
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Nichols KM, Young WP, Danzmann RG, Robison BD, Rexroad C, Noakes M, Phillips RB, Bentzen P, Spies I, Knudsen K, Allendorf FW, Cunningham BM, Brunelli J, Zhang H, Ristow S, Drew R, Brown KH, Wheeler PA, Thorgaard GH. A consolidated linkage map for rainbow trout (Oncorhynchus mykiss). Anim Genet 2003; 34:102-15. [PMID: 12648093 DOI: 10.1046/j.1365-2052.2003.00957.x] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Androgenetic doubled haploid progeny produced from a cross between the Oregon State University and Arlee clonal rainbow trout (Oncorhynchus mykiss) lines, used for a previous published rainbow trout map, were used to update the map with the addition of more amplified fragment length polymorphic (AFLP) markers, microsatellites, type I and allozyme markers. We have added more than 900 markers, bringing the total number to 1359 genetic markers and the sex phenotype including 799 EcoRI AFLPs, 174 PstI AFLPs, 226 microsatellites, 72 VNTR, 38 SINE markers, 29 known genes, 12 minisatellites, five RAPDs, and four allozymes. Thirty major linkage groups were identified. Synteny of linkage groups in our map with the outcrossed microsatellite map has been established for all except one linkage group in this doubled haploid cross. Putative homeologous relationships among linkage groups, resulting from the autotetraploid nature of the salmonid genome, have been revealed based on the placement of duplicated microsatellites and type I loci.
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Affiliation(s)
- K M Nichols
- School of Biological Sciences, Washington State University, Pullman, WA, USA
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Palti Y, Danzmann RG, Rexroad CE. Characterization and mapping of 19 polymorphic microsatellite markers for rainbow trout (Oncorhynchus mykiss). Anim Genet 2003; 34:153-6. [PMID: 12648105 DOI: 10.1046/j.1365-2052.2003.00965_7.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Y Palti
- National Center for Cool and Cold Water Aquaculture, USDA-ARS, 11876 Leetown Road, Kearneysville, WV 25430, USA.
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Palti Y, Fincham MR, Rexroad CE. Characterization of 38 polymorphic microsatellite markers for rainbow trout (Oncorhynchus mykiss). ACTA ACUST UNITED AC 2002. [DOI: 10.1046/j.1471-8286.2002.00274.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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37
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Thorgaard GH, Bailey GS, Williams D, Buhler DR, Kaattari SL, Ristow SS, Hansen JD, Winton JR, Bartholomew JL, Nagler JJ, Walsh PJ, Vijayan MM, Devlin RH, Hardy RW, Overturf KE, Young WP, Robison BD, Rexroad C, Palti Y. Status and opportunities for genomics research with rainbow trout. Comp Biochem Physiol B Biochem Mol Biol 2002; 133:609-46. [PMID: 12470823 DOI: 10.1016/s1096-4959(02)00167-7] [Citation(s) in RCA: 141] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The rainbow trout (Oncorhynchus mykiss) is one of the most widely studied of model fish species. Extensive basic biological information has been collected for this species, which because of their large size relative to other model fish species are particularly suitable for studies requiring ample quantities of specific cells and tissue types. Rainbow trout have been widely utilized for research in carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition. They are distinctive in having evolved from a relatively recent tetraploid event, resulting in a high incidence of duplicated genes. Natural populations are available and have been well characterized for chromosomal, protein, molecular and quantitative genetic variation. Their ease of culture, and experimental and aquacultural significance has led to the development of clonal lines and the widespread application of transgenic technology to this species. Numerous microsatellites have been isolated and two relatively detailed genetic maps have been developed. Extensive sequencing of expressed sequence tags has begun and four BAC libraries have been developed. The development and analysis of additional genomic sequence data will provide distinctive opportunities to address problems in areas such as evolution of the immune system and duplicate genes.
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Affiliation(s)
- Gary H Thorgaard
- School of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164-4236, USA.
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