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Gao X, Gao Z, Zhang M, Qiao H, Jiang S, Zhang W, Xiong Y, Jin S, Fu H. Identifying Relationships between Glutathione S-Transferase-2 Single Nucleotide Polymorphisms and Hypoxia Tolerance and Growth Traits in Macrobrachium nipponense. Animals (Basel) 2024; 14:666. [PMID: 38473051 DOI: 10.3390/ani14050666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
Investigating hypoxia tolerance and growth trait single nucleotide polymorphisms (SNPs) in Macrobrachium nipponense is conducive to cultivating prawns with hypoxia tolerance and good growth characteristics. The glutathione S-transferase-2 gene (GST-2) has been shown to regulate hypoxia responses in M. nipponense. In this study, we identified a single GST-2 SNP in M. nipponense, and analyzed its regulatory relationship with hypoxia tolerance and growth. The GST-2 sequence was amplified with a polymerase chain reaction from 197 "Taihu Lake No. 3", "Taihu Lake No. 2", and Pearl River population samples to identify SNP loci. The full-length Mn-GST2 sequence was 2317 bp, including three exons and two introns. In total, 38 candidate SNP loci were identified from GST-2 using Mega11.0 comparisons, with most loci moderately polymorphic in terms of genetic diversity. Locus genotypes were also analyzed, and basic genetic parameters for loci were calculated using Popgene32 and PIC_CALC. The expected heterozygosity of the 38 SNP loci ranged from 0.2334 to 0.4997, with an average of 0.4107, while observed heterozygosity ranged from 0.1929 to 0.4721, with an average of 0.3401. The polymorphic information content ranged from 0.21 to 0.37. From SPSS analyses, the G+256A locus was significantly correlated with hypoxia tolerance across all three M. nipponense populations, while the SNP loci A+261C, C+898T, A+1370C, and G+1373T were significantly associated with growth traits. Further analyses revealed that the T+2017C locus was significantly correlated with hypoxia tolerance in "Taihu Lake No. 2" populations, G+256A, A+808T, C+1032T, and A+1530G loci were significantly correlated with hypoxia tolerance in "Taihu Lake No. 3" populations, while no SNP loci were correlated with hypoxia tolerance in Pearl River populations. A+1370C and G+1373T loci, which were associated with growth traits, exhibited a high degree of linkage disequilibrium (r2 = 0.89 and r2 > 0.8), suggesting potential genetic linkage. Our data suggest associations between hypoxia tolerance and growth trait SNP loci in M. nipponense, and provide valuable evidence for the genetic improvement of growth and hypoxia tolerance in this prawn species.
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Affiliation(s)
- Xuanbin Gao
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Zijian Gao
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Minglei Zhang
- Shandong Freshwater Fisheries Research Institute, Jinan 250013, China
| | - Hui Qiao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Sufei Jiang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Wenyi Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Yiwei Xiong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Shubo Jin
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Hongtuo Fu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
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Development of 84 single nucleotide polymorphism (SNP) markers for the three-spot swimming crab (Portunus sanguinolentus) by using RAD approach. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01236-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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3
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A targeted gene approach to SNP discovery in the blue (Connochaetes taurinus) and black wildebeest (C. gnou). CONSERV GENET RESOUR 2019. [DOI: 10.1007/s12686-017-0959-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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4
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Isolation and characterization of 91 single nucleotide polymorphism (SNP) markers for the blue swimming crab (Portunus pelagicus). CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0720-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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5
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Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing. Mamm Biol 2016. [DOI: 10.1016/j.mambio.2016.07.047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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6
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Hoffman JI, Thorne MAS, McEwing R, Forcada J, Ogden R. Cross-amplification and validation of SNPs conserved over 44 million years between seals and dogs. PLoS One 2013; 8:e68365. [PMID: 23874599 PMCID: PMC3712990 DOI: 10.1371/journal.pone.0068365] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Accepted: 05/28/2013] [Indexed: 01/17/2023] Open
Abstract
High-density SNP arrays developed for humans and their companion species provide a rapid and convenient tool for generating SNP data in closely-related non-model organisms, but have not yet been widely applied to phylogenetically divergent taxa. Consequently, we used the CanineHD BeadChip to genotype 24 Antarctic fur seal (Arctocephalus gazella) individuals. Despite seals and dogs having diverged around 44 million years ago, 33,324 out of 173,662 loci (19.2%) could be genotyped, of which 173 were polymorphic and clearly interpretable. Two SNPs were validated using KASP genotyping assays, with the resulting genotypes being 100% concordant with those obtained from the high-density array. Two loci were also confirmed through in silico visualisation after mapping them to the fur seal transcriptome. Polymorphic SNPs were distributed broadly throughout the dog genome and did not differ significantly in proximity to genes from either monomorphic SNPs or those that failed to cross-amplify in seals. However, the nearest genes to polymorphic SNPs were significantly enriched for functional annotations relating to energy metabolism, suggesting a possible bias towards conserved regions of the genome.
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Affiliation(s)
- Joseph I. Hoffman
- Department of Animal Behaviour, University of Bielefeld, Bielefeld, North Rhine-Westphalia, Germany
- * E-mail:
| | - Michael A. S. Thorne
- British Antarctic Survey, Natural Environment Research Council, High Cross, Cambridge, United Kingdom
| | - Rob McEwing
- Wildgenes Laboratory, Royal Zoological Society of Scotland, Edinburgh, United Kingdom
| | - Jaume Forcada
- British Antarctic Survey, Natural Environment Research Council, High Cross, Cambridge, United Kingdom
| | - Rob Ogden
- Wildgenes Laboratory, Royal Zoological Society of Scotland, Edinburgh, United Kingdom
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7
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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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8
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Pembleton LW, Cogan NOI, Forster JW. St
AMPP
: an R package for calculation of genetic differentiation and structure of mixed‐ploidy level populations. Mol Ecol Resour 2013; 13:946-52. [DOI: 10.1111/1755-0998.12129] [Citation(s) in RCA: 375] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 05/09/2013] [Accepted: 05/11/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Luke W. Pembleton
- Department of Environment and Primary Industries AgriBio 5 Ring Road, La Trobe University Research and Development Park Bundoora Vic. 3083 Australia
- Dairy Futures Cooperative Research Centre AgriBio 5 Ring Road, La Trobe University Research and Development Park Bundoora Vic. 3083 Australia
- La Trobe University Bundoora Vic. 3083 Australia
| | - Noel O. I. Cogan
- Department of Environment and Primary Industries AgriBio 5 Ring Road, La Trobe University Research and Development Park Bundoora Vic. 3083 Australia
- Dairy Futures Cooperative Research Centre AgriBio 5 Ring Road, La Trobe University Research and Development Park Bundoora Vic. 3083 Australia
| | - John W. Forster
- Department of Environment and Primary Industries AgriBio 5 Ring Road, La Trobe University Research and Development Park Bundoora Vic. 3083 Australia
- Dairy Futures Cooperative Research Centre AgriBio 5 Ring Road, La Trobe University Research and Development Park Bundoora Vic. 3083 Australia
- La Trobe University Bundoora Vic. 3083 Australia
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Li S, Xu S, Wan H, Ji H, Zhou K, Yang G. Genome-wide SNP and population divergence of finless porpoises. Genome Biol Evol 2013; 5:758-68. [PMID: 23563971 PMCID: PMC3641630 DOI: 10.1093/gbe/evt046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are rapidly becoming the population genomic markers in addressing ecology, evolution, and conservation issues for their high capacity to access variability across the genome. We isolated a total of 140 ideal SNPs from the finless porpoise and used 78 (under Hardy–Weinberg equilibrium) of them to conduct those issues especially for addressing population genetic differentiation. Bayesian clustering and principal component analyses all suggested that finless porpoises in Chinese waters could be divided into three distinct genetic groupings. Low levels of within-population genetic variation (mean HE = 0.3405, standard deviation = 0.1188) and significant differentiation among populations (FST = 0.1050–0.1628, P < 0.01) were confirmed. Limited gene flow was found especially between the freshwater Yangtze River porpoise and the oceanic Yellow Sea and South China Sea populations, which strongly suggested that some barriers might have restricted their genetic exchange. These evidences not only support a recent subdivision of the finless porpoise into two species but also suggest a full species status for the Yangtze finless porpoise, especially considering the significant genetic divergence between freshwater and marine porpoises, in combination with the unique distribution of Yangtze finless porpoises in freshwater and their distinctness in physiological and morphological features.
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Affiliation(s)
- Shuzhen Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, China
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10
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A targeted gene approach to SNP discovery in the White Rhino (Ceratotherium simum). CONSERV GENET RESOUR 2013. [DOI: 10.1007/s12686-012-9783-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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11
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Hancock‐Hanser BL, Frey A, Leslie MS, Dutton PH, Archer FI, Morin PA. Targeted multiplex next‐generation sequencing: advances in techniques of mitochondrial and nuclear
DNA
sequencing for population genomics. Mol Ecol Resour 2013; 13:254-68. [DOI: 10.1111/1755-0998.12059] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 11/30/2012] [Accepted: 12/06/2012] [Indexed: 11/27/2022]
Affiliation(s)
- Brittany L. Hancock‐Hanser
- Protected Resources Division Southwest Fisheries Science Center National Marine Fisheries Service, NOAA 8901 La Jolla Shores Drive La Jolla CA 92037 USA
| | - Amy Frey
- Protected Resources Division Southwest Fisheries Science Center National Marine Fisheries Service, NOAA 8901 La Jolla Shores Drive La Jolla CA 92037 USA
| | - Matthew S. Leslie
- Scripps Institution of Oceanography University of California San Diego 9500 Gilman Drive, MC 0202 La Jolla CA 92093 USA
| | - Peter H. Dutton
- Protected Resources Division Southwest Fisheries Science Center National Marine Fisheries Service, NOAA 8901 La Jolla Shores Drive La Jolla CA 92037 USA
| | - Frederick I. Archer
- Protected Resources Division Southwest Fisheries Science Center National Marine Fisheries Service, NOAA 8901 La Jolla Shores Drive La Jolla CA 92037 USA
| | - Phillip A. Morin
- Protected Resources Division Southwest Fisheries Science Center National Marine Fisheries Service, NOAA 8901 La Jolla Shores Drive La Jolla CA 92037 USA
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12
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Two different high throughput sequencing approaches identify thousands of de novo genomic markers for the genetically depleted Bornean elephant. PLoS One 2012. [PMID: 23185354 PMCID: PMC3504023 DOI: 10.1371/journal.pone.0049533] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
High throughput sequencing technologies are being applied to an increasing number of model species with a high-quality reference genome. The application and analyses of whole-genome sequence data in non-model species with no prior genomic information are currently under way. Recent sequencing technologies provide new opportunities for gathering genomic data in natural populations, laying the empirical foundation for future research in the field of conservation and population genomics. Here we present the case study of the Bornean elephant, which is the most endangered subspecies of Asian elephant and exhibits very low genetic diversity. We used two different sequencing platforms, the Roche 454 FLX (shotgun) and Illumina, GAIIx (Restriction site associated DNA, RAD) to evaluate the feasibility of the two methodologies for the discovery of de novo markers (single nucleotide polymorphism, SNPs and microsatellites) using low coverage data. Approximately, 6,683 (shotgun) and 14,724 (RAD) SNPs were detected within our elephant sequence dataset. Genotyping of a representative sample of 194 SNPs resulted in a SNP validation rate of ∼ 83 to 94% and 17% of the loci were polymorphic with a low diversity (Ho = 0.057). Different numbers of microsatellites were identified through shotgun (27,226) and RAD (868) techniques. Out of all di-, tri-, and tetra-microsatellite loci, 1,706 loci had sufficient flanking regions (shotgun) while only 7 were found with RAD. All microsatellites were monomorphic in the Bornean but polymorphic in another elephant subspecies. Despite using different sample sizes, and the well known differences in the two platforms used regarding sequence length and throughput, the two approaches showed high validation rate. The approaches used here for marker development in a threatened species demonstrate the utility of high throughput sequencing technologies as a starting point for the development of genomic tools in a non-model species and in particular for a species with low genetic diversity.
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Vollmer NL, Rosel PE. Developing genomic resources for the common bottlenose dolphin (
Tursiops truncatus
): isolation and characterization of 153 single nucleotide polymorphisms and 53 genotyping assays. Mol Ecol Resour 2012; 12:1124-32. [DOI: 10.1111/1755-0998.12008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 07/24/2012] [Accepted: 07/28/2012] [Indexed: 01/24/2023]
Affiliation(s)
- N. L. Vollmer
- Department of Biology University of Louisiana at Lafayette P.O. Box 42451 Lafayette LA 70504 USA
- NOAA National Marine Fisheries Service Southeast Fisheries Science Center 646 Cajundome Blvd. Suite 234 Lafayette LA 70506 USA
| | - P. E. Rosel
- NOAA National Marine Fisheries Service Southeast Fisheries Science Center 646 Cajundome Blvd. Suite 234 Lafayette LA 70506 USA
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14
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Ma H, Ma Q, Ma C, Ma L. Isolation and characterization of gene-derived single nucleotide polymorphism (SNP) markers in Scylla paramamosain. BIOCHEM SYST ECOL 2011. [DOI: 10.1016/j.bse.2011.05.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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15
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MESNICK SARAHL, TAYLOR BARBARAL, ARCHER FREDERICKI, MARTIEN KARENK, TREVIÑO SERGIOESCORZA, HANCOCK-HANSER BRITTANYL, MORENO MEDINA SANDRACAROLINA, PEASE VICTORIAL, ROBERTSON KELLYM, STRALEY JANICEM, BAIRD ROBINW, CALAMBOKIDIS JOHN, SCHORR GREGORYS, WADE PAUL, BURKANOV VLADIMIR, LUNSFORD CHRISR, RENDELL LUKE, MORIN PHILLIPA. Sperm whale population structure in the eastern and central North Pacific inferred by the use of single-nucleotide polymorphisms, microsatellites and mitochondrial DNA. Mol Ecol Resour 2011; 11 Suppl 1:278-98. [DOI: 10.1111/j.1755-0998.2010.02973.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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16
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RODEN SUZANNEE, DUTTON PETERH, MORIN PHILLIPA. Characterization of single nucleotide polymorphism markers for the green sea turtle (Chelonia mydas). Mol Ecol Resour 2009; 9:1055-60. [DOI: 10.1111/j.1755-0998.2009.02573.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Amaral AR, Silva MC, Möller LM, Beheregaray LB, Coelho MM. Anonymous nuclear markers for cetacean species. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9903-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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18
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Roden SE, Dutton PH, Morin PA. AFLP Fragment Isolation Technique as a Method to Produce Random Sequences for Single Nucleotide Polymorphism Discovery in the Green Turtle, Chelonia mydas. J Hered 2009; 100:390-3. [DOI: 10.1093/jhered/esn108] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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19
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SNP discovery based on CATS and genotyping in the finless porpoise (Neophocaena phocaenoides). CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9882-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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20
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MORIN PHILLIPA, MARTIEN KARENK, TAYLOR BARBARAL. Assessing statistical power of SNPs for population structure and conservation studies. Mol Ecol Resour 2009; 9:66-73. [DOI: 10.1111/j.1755-0998.2008.02392.x] [Citation(s) in RCA: 172] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Slate J, Gratten J, Beraldi D, Stapley J, Hale M, Pemberton JM. Gene mapping in the wild with SNPs: guidelines and future directions. Genetica 2008; 136:97-107. [PMID: 18780148 DOI: 10.1007/s10709-008-9317-z] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2008] [Accepted: 08/18/2008] [Indexed: 10/21/2022]
Abstract
One of the biggest challenges facing evolutionary biologists is to identify and understand loci that explain fitness variation in natural populations. This review describes how genetic (linkage) mapping with single nucleotide polymorphism (SNP) markers can lead to great progress in this area. Strategies for SNP discovery and SNP genotyping are described and an overview of how to model SNP genotype information in mapping studies is presented. Finally, the opportunity afforded by new generation sequencing and typing technologies to map fitness genes by genome-wide association studies is discussed.
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Affiliation(s)
- Jon Slate
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.
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22
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O'Corry-Crowe G. Climate change and the molecular ecology of Arctic marine mammals. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2008; 18:S56-S76. [PMID: 18494363 DOI: 10.1890/06-0795.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Key to predicting likely consequences of future climate change for Arctic marine mammals is developing a detailed understanding of how these species use their environment today and how they were affected by past climate-induced environmental change. Genetic analyses are uniquely placed to address these types of questions. Molecular genetic approaches are being used to determine distribution and migration patterns, dispersal and breeding behavior, population structure and abundance over time, and the effects of past and present climate change in Arctic marine mammals. A review of published studies revealed that population subdivision, dispersal, and gene flow in Arctic marine mammals was shaped primarily by evolutionary history, geography, sea ice, and philopatry to predictable, seasonally available resources. A meta-analysis of data from 38 study units across seven species found significant relationships between neutral genetic diversity and population size and climate region, revealing that small, isolated subarctic populations tend to harbor lower diversity than larger Arctic populations. A few small populations had substantially lower diversity than others. By contrast, other small populations retain substantial neutral diversity despite extensive population declines in the 19th and 20th centuries. The evolutionary and contemporary perspectives gained from these studies can be used to model the consequences of different climate projections for individual behavior and population structure and ultimately individual fitness and population viability. Future research should focus on: (1) the use of ancient-DNA techniques to directly reconstruct population histories through the analysis of historical and prehistorical material, (2) the use of genomic technologies to identify, map, and survey genes that directly influence fitness, (3) long-term studies to monitor populations and investigate evolution in contemporary time, (4) further Arctic-wide, multispecies analyses, preferably across different taxa and trophic levels, and (5) the use of genetic parameters in population and species risk analyses.
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Affiliation(s)
- Gregory O'Corry-Crowe
- Southwest Fisheries Science Center, 8604 La Jolla Shores Drive, La Jolla, California 92037, USA.
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23
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MORIN PHILLIPA, MCCARTHY MELISSA. Highly accurate SNP genotyping from historical and low-quality samples. ACTA ACUST UNITED AC 2007. [DOI: 10.1111/j.1471-8286.2007.01804.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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