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Ren X, Yang GL, Peng WF, Zhao YX, Zhang M, Chen ZH, Wu FA, Kantanen J, Shen M, Li MH. A genome-wide association study identifies a genomic region for the polycerate phenotype in sheep (Ovis aries). Sci Rep 2016; 6:21111. [PMID: 26883901 PMCID: PMC4756668 DOI: 10.1038/srep21111] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/18/2016] [Indexed: 01/06/2023] Open
Abstract
Horns are a cranial appendage found exclusively in Bovidae, and play important roles in accessing resources and mates. In sheep (Ovies aries), horns vary from polled to six-horned, and human have been selecting polled animals in farming and breeding. Here, we conducted a genome-wide association study on 24 two-horned versus 22 four-horned phenotypes in a native Chinese breed of Sishui Fur sheep. Together with linkage disequilibrium (LD) analyses and haplotype-based association tests, we identified a genomic region comprising 132.0–133.1 Mb on chromosome 2 that contained the top 10 SNPs (including 4 significant SNPs) and 5 most significant haplotypes associated with the polycerate phenotype. In humans and mice, this genomic region contains the HOXD gene cluster and adjacent functional genes EVX2 and KIAA1715, which have a close association with the formation of limbs and genital buds. Our results provide new insights into the genetic basis underlying variable numbers of horns and represent a new resource for use in sheep genetics and breeding.
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Affiliation(s)
- Xue Ren
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Guang-Li Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China.,Department of Life Sciences, Shangqiu Normal University, Shangqiu 476000, China
| | - Wei-Feng Peng
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Yong-Xin Zhao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Min Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Ze-Hui Chen
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China.,University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Fu-An Wu
- Bureau of Animal Husbandry and Veterinary Medicine, Sishui County, Jining 273200, China
| | - Juha Kantanen
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen 31600, Finland.,Department of Biology, University of Eastern Finland, Kuopio 70211, Finland
| | - Min Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China.,Key Laboratory of Sheep Breeding and Development Technology of Xinjiang Production and Construction Crops (XPCC), Shihezi 832000, China
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
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52
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Jonsson B, Jonsson N, Albretsen J. Environmental change influences the life history of salmon Salmo salar in the North Atlantic Ocean. JOURNAL OF FISH BIOLOGY 2016; 88:618-637. [PMID: 26725985 DOI: 10.1111/jfb.12854] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 11/04/2015] [Indexed: 06/05/2023]
Abstract
Annual mean total length (LT) of wild one-sea-winter (1SW) Atlantic salmon Salmo salar of the Norwegian River Imsa decreased from 63 to 54 cm with a corresponding decrease in condition factor (K) for cohorts migrating to sea from 1976 to 2010. The reduction in LT is associated with a 40% decline in mean individual mass, from 2 to 1·2 kg. Hatchery fish reared from parental fish of the same population exhibited similar changes from 1981 onwards. The decrease in LT correlated negatively with near-surface temperatures in the eastern Norwegian Sea, thought to be the main feeding area of the present stock. Furthermore, S. salar exhibited significant variations in the proportion of cohorts attaining maturity after only one winter in the ocean. The proportion of S. salar spawning as 1SW fish was lower both in the 1970s and after 2000 than in the 1980s and 1990s associated with a gradual decline in post-smolt growth and smaller amounts of reserve energy in the fish. In wild S. salar, there was a positive association between post-smolt growth and the sea survival back to the River Imsa for spawning. In addition, among smolt year-classes, there were significant positive correlations between wild and hatchery S. salar in LT, K and age at maturity. The present changes may be caused by ecosystem changes following the collapse and rebuilding of the pelagic fish abundance in the North Atlantic Ocean, a gradual decrease in zooplankton abundance and climate change with increasing surface temperature in the Norwegian Sea. Thus, the observed variation in the life-history traits of S. salar appears primarily associated with major changes in the pelagic food web in the ocean.
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Affiliation(s)
- B Jonsson
- Norwegian Institute for Nature Research, Landscape Ecology Department, Gaustadalléen 21, 0349 Oslo, Norway
| | - N Jonsson
- Norwegian Institute for Nature Research, Landscape Ecology Department, Gaustadalléen 21, 0349 Oslo, Norway
| | - J Albretsen
- Institute of Marine Research, Flødevigen Research Station, Nye Flødevigveien 20, 4817 His, Norway
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53
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Wenne R, Drywa A, Kent M, Sundsaasen KK, Lien S. SNP Arrays for Species Identification in Salmonids. Methods Mol Biol 2016; 1452:97-111. [PMID: 27460372 DOI: 10.1007/978-1-4939-3774-5_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The use of SNP genotyping microarrays, developed in one species to analyze a closely related species for which genomic sequence information is scarce, enables the rapid development of a genomic resource (SNP information) without the need to develop new species-specific markers. Using large numbers of microarray SNPs offers the best chance to detect informative markers in nontarget species, markers that can very often be assayed using a lower throughput platform as is described in this paper.
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Affiliation(s)
- Roman Wenne
- Institute of Oceanology, Polish Academy of Sciences, Powstancow Warszawy 55, 81-712, Sopot, Poland.
| | - Agata Drywa
- Institute of Oceanology, Polish Academy of Sciences, Powstancow Warszawy 55, 81-712, Sopot, Poland
| | - Matthew Kent
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, IHA, Norwegian University of Life Sciences, NMBU, 1432, Ås, Norway
| | - Kristil Kindem Sundsaasen
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, IHA, Norwegian University of Life Sciences, NMBU, 1432, Ås, Norway
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, IHA, Norwegian University of Life Sciences, NMBU, 1432, Ås, Norway
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54
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Larson WA, McKinney GJ, Limborg MT, Everett MV, Seeb LW, Seeb JE. Identification of Multiple QTL Hotspots in Sockeye Salmon (Oncorhynchus nerka) Using Genotyping-by-Sequencing and a Dense Linkage Map. J Hered 2015; 107:122-33. [PMID: 26712859 DOI: 10.1093/jhered/esv099] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 11/18/2015] [Indexed: 02/01/2023] Open
Abstract
Understanding the genetic architecture of phenotypic traits can provide important information about the mechanisms and genomic regions involved in local adaptation and speciation. Here, we used genotyping-by-sequencing and a combination of previously published and newly generated data to construct sex-specific linkage maps for sockeye salmon (Oncorhynchus nerka). We then used the denser female linkage map to conduct quantitative trait locus (QTL) analysis for 4 phenotypic traits in 3 families. The female linkage map consisted of 6322 loci distributed across 29 linkage groups and was 4082 cM long, and the male map contained 2179 loci found on 28 linkage groups and was 2291 cM long. We found 26 QTL: 6 for thermotolerance, 5 for length, 9 for weight, and 6 for condition factor. QTL were distributed nonrandomly across the genome and were often found in hotspots containing multiple QTL for a variety of phenotypic traits. These hotspots may represent adaptively important regions and are excellent candidates for future research. Comparing our results with studies in other salmonids revealed several regions with overlapping QTL for the same phenotypic trait, indicating these regions may be adaptively important across multiple species. Altogether, our study demonstrates the utility of genomic data for investigating the genetic basis of important phenotypic traits. Additionally, the linkage map created here will enable future research on the genetic basis of phenotypic traits in salmon.
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Affiliation(s)
- Wesley A Larson
- From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195-5020 (Larson, McKinney, Limborg, LW Seeb, and JE Seeb); Morten T. Limborg is now at the Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen K, Denmark; Northwest Fisheries Science Center, 2725 Montlake Boulevard East, Seattle, WA, 98112 (Everett).
| | - Garrett J McKinney
- From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195-5020 (Larson, McKinney, Limborg, LW Seeb, and JE Seeb); Morten T. Limborg is now at the Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen K, Denmark; Northwest Fisheries Science Center, 2725 Montlake Boulevard East, Seattle, WA, 98112 (Everett)
| | - Morten T Limborg
- From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195-5020 (Larson, McKinney, Limborg, LW Seeb, and JE Seeb); Morten T. Limborg is now at the Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen K, Denmark; Northwest Fisheries Science Center, 2725 Montlake Boulevard East, Seattle, WA, 98112 (Everett)
| | - Meredith V Everett
- From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195-5020 (Larson, McKinney, Limborg, LW Seeb, and JE Seeb); Morten T. Limborg is now at the Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen K, Denmark; Northwest Fisheries Science Center, 2725 Montlake Boulevard East, Seattle, WA, 98112 (Everett)
| | - Lisa W Seeb
- From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195-5020 (Larson, McKinney, Limborg, LW Seeb, and JE Seeb); Morten T. Limborg is now at the Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen K, Denmark; Northwest Fisheries Science Center, 2725 Montlake Boulevard East, Seattle, WA, 98112 (Everett)
| | - James E Seeb
- From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195-5020 (Larson, McKinney, Limborg, LW Seeb, and JE Seeb); Morten T. Limborg is now at the Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen K, Denmark; Northwest Fisheries Science Center, 2725 Montlake Boulevard East, Seattle, WA, 98112 (Everett)
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55
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Kardos M, Husby A, McFarlane SE, Qvarnström A, Ellegren H. Whole-genome resequencing of extreme phenotypes in collared flycatchers highlights the difficulty of detecting quantitative trait loci in natural populations. Mol Ecol Resour 2015; 16:727-41. [PMID: 26649993 DOI: 10.1111/1755-0998.12498] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 11/18/2015] [Accepted: 11/30/2015] [Indexed: 12/24/2022]
Abstract
Dissecting the genetic basis of phenotypic variation in natural populations is a long-standing goal in evolutionary biology. One open question is whether quantitative traits are determined only by large numbers of genes with small effects, or whether variation also exists in large-effect loci. We conducted genomewide association analyses of forehead patch size (a sexually selected trait) on 81 whole-genome-resequenced male collared flycatchers with extreme phenotypes, and on 415 males sampled independent of patch size and genotyped with a 50K SNP chip. No SNPs were genomewide statistically significantly associated with patch size. Simulation-based power analyses suggest that the power to detect large-effect loci responsible for 10% of phenotypic variance was <0.5 in the genome resequencing analysis, and <0.1 in the SNP chip analysis. Reducing the recombination by two-thirds relative to collared flycatchers modestly increased power. Tripling sample size increased power to >0.8 for resequencing of extreme phenotypes (N = 243), but power remained <0.2 for the 50K SNP chip analysis (N = 1245). At least 1 million SNPs were necessary to achieve power >0.8 when analysing 415 randomly sampled phenotypes. However, power of the 50K SNP chip to detect large-effect loci was nearly 0.8 in simulations with a small effective population size of 1500. These results suggest that reliably detecting large-effect trait loci in large natural populations will often require thousands of individuals and near complete sampling of the genome. Encouragingly, far fewer individuals and loci will often be sufficient to reliably detect large-effect loci in small populations with widespread strong linkage disequilibrium.
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Affiliation(s)
- Marty Kardos
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Arild Husby
- Department of Biosciences, University of Helsinki, PO Box 65, Helsinki, 00014, Finland.,Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, 7491, Norway
| | - S Eryn McFarlane
- Department of Animal Ecology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Anna Qvarnström
- Department of Animal Ecology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
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56
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Wenzel MA, Douglas A, James MC, Redpath SM, Piertney SB. The role of parasite-driven selection in shaping landscape genomic structure in red grouse (Lagopus lagopus scotica). Mol Ecol 2015; 25:324-41. [PMID: 26578090 DOI: 10.1111/mec.13473] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/09/2015] [Accepted: 11/10/2015] [Indexed: 12/25/2022]
Abstract
Landscape genomics promises to provide novel insights into how neutral and adaptive processes shape genome-wide variation within and among populations. However, there has been little emphasis on examining whether individual-based phenotype-genotype relationships derived from approaches such as genome-wide association (GWAS) manifest themselves as a population-level signature of selection in a landscape context. The two may prove irreconcilable as individual-level patterns become diluted by high levels of gene flow and complex phenotypic or environmental heterogeneity. We illustrate this issue with a case study that examines the role of the highly prevalent gastrointestinal nematode Trichostrongylus tenuis in shaping genomic signatures of selection in red grouse (Lagopus lagopus scotica). Individual-level GWAS involving 384 SNPs has previously identified five SNPs that explain variation in T. tenuis burden. Here, we examine whether these same SNPs display population-level relationships between T. tenuis burden and genetic structure across a small-scale landscape of 21 sites with heterogeneous parasite pressure. Moreover, we identify adaptive SNPs showing signatures of directional selection using F(ST) outlier analysis and relate population- and individual-level patterns of multilocus neutral and adaptive genetic structure to T. tenuis burden. The five candidate SNPs for parasite-driven selection were neither associated with T. tenuis burden on a population level, nor under directional selection. Similarly, there was no evidence of parasite-driven selection in SNPs identified as candidates for directional selection. We discuss these results in the context of red grouse ecology and highlight the broader consequences for the utility of landscape genomics approaches for identifying signatures of selection.
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Affiliation(s)
- Marius A Wenzel
- Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Alex Douglas
- Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Marianne C James
- Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Steve M Redpath
- Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Stuart B Piertney
- Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
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57
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Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon. Nature 2015; 528:405-8. [DOI: 10.1038/nature16062] [Citation(s) in RCA: 401] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/07/2015] [Indexed: 01/14/2023]
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58
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Lal MM, Southgate PC, Jerry DR, Zenger KR. Fishing for divergence in a sea of connectivity: The utility of ddRADseq genotyping in a marine invertebrate, the black-lip pearl oyster Pinctada margaritifera. Mar Genomics 2015; 25:57-68. [PMID: 26545807 DOI: 10.1016/j.margen.2015.10.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 10/27/2015] [Accepted: 10/27/2015] [Indexed: 01/01/2023]
Abstract
Population genomic investigations on highly dispersive marine organisms typically require thousands of genome-wide SNP loci to resolve fine-scale population structure and detect signatures of selection. This information is important for species conservation efforts and stock management in both wild and captive populations, as well as genome mapping and genome wide association studies. Double digest Restriction site-Associated DNA Sequencing (ddRADseq) is a recent tool for delivering genome wide SNPs for non-model organisms. However, its application to marine invertebrate taxa has been limited, particularly given the complex and highly repetitive nature of many of these organisms' genomes. This study develops and evaluates an optimised ddRADseq technique together with associated analyses for generating genome-wide SNP data, and performs population genomic analyses to inform aquaculture and fishery management of a marine bivalve, the black-lip pearl oyster Pinctada margaritifera. A total of 5243 high-quality genome-wide SNP markers were detected, and used to assess population structure, genome diversity, detect Fst outliers and perform association testing in 156 individuals belonging to three wild and one hatchery produced populations from the Fiji Islands. Shallow but significant population structure was revealed among all wild populations (average pairwise Fst=0.046) when visualised with DAPC and an individual network analysis (NetView P), with clear evidence of a genetic bottleneck in the hatchery population (NeLD=6.1), compared to wild populations (NeLD>192.5). Fst outlier detection revealed 42-62 highly differentiated SNPs (p<0.02), while case-control association discovered up to 152 SNPs (p<0.001). Both analyses were able to successfully differentiate individuals between the orange and black tissue colour morphotypes characteristic of this species. BLAST searches revealed that five of these SNPs were associated with a melanin biosynthesis pathway, demonstrating their biological relevance. This study has produced highly informative SNP and population genomic data in P. margaritifera, and using the same approach promises to be of substantial value to a range of other non-model, broadcast-spawning or marine invertebrate taxa.
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Affiliation(s)
- Monal M Lal
- Centre for Sustainable Tropical Fisheries and Aquaculture (CSTFA), James Cook University, Townsville Campus, Townsville, QLD 4811, Australia; College of Marine and Environmental Sciences (CMES), James Cook University, Townsville Campus, Townsville, QLD 4811, Australia.
| | - Paul C Southgate
- Centre for Sustainable Tropical Fisheries and Aquaculture (CSTFA), James Cook University, Townsville Campus, Townsville, QLD 4811, Australia; College of Marine and Environmental Sciences (CMES), James Cook University, Townsville Campus, Townsville, QLD 4811, Australia.
| | - Dean R Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture (CSTFA), James Cook University, Townsville Campus, Townsville, QLD 4811, Australia; College of Marine and Environmental Sciences (CMES), James Cook University, Townsville Campus, Townsville, QLD 4811, Australia.
| | - Kyall R Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture (CSTFA), James Cook University, Townsville Campus, Townsville, QLD 4811, Australia; College of Marine and Environmental Sciences (CMES), James Cook University, Townsville Campus, Townsville, QLD 4811, Australia.
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59
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Edwards SV, Shultz AJ, Campbell-Staton SC. Next-generation sequencing and the expanding domain of phylogeography. FOLIA ZOOLOGICA 2015. [DOI: 10.25225/fozo.v64.i3.a2.2015] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Scott V. Edwards
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, U.S.A.
| | - Allison J. Shultz
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, U.S.A.
| | - Shane C. Campbell-Staton
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, U.S.A.
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60
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Ayllon F, Kjærner-Semb E, Furmanek T, Wennevik V, Solberg MF, Dahle G, Taranger GL, Glover KA, Almén MS, Rubin CJ, Edvardsen RB, Wargelius A. The vgll3 Locus Controls Age at Maturity in Wild and Domesticated Atlantic Salmon (Salmo salar L.) Males. PLoS Genet 2015; 11:e1005628. [PMID: 26551894 PMCID: PMC4638356 DOI: 10.1371/journal.pgen.1005628] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 10/05/2015] [Indexed: 11/25/2022] Open
Abstract
Wild and domesticated Atlantic salmon males display large variation for sea age at sexual maturation, which varies between 1-5 years. Previous studies have uncovered a genetic predisposition for variation of age at maturity with moderate heritability, thus suggesting a polygenic or complex nature of this trait. The aim of this study was to identify associated genetic loci, genes and ultimately specific sequence variants conferring sea age at maturity in salmon. We performed a genome wide association study (GWAS) using a pool sequencing approach (20 individuals per river and phenotype) of male salmon returning to rivers as sexually mature either after one sea winter (2009) or three sea winters (2011) in six rivers in Norway. The study revealed one major selective sweep, which covered 76 significant SNPs in which 74 were found in a 370 kb region of chromosome 25. Genotyping other smolt year classes of wild and domesticated salmon confirmed this finding. Genotyping domesticated fish narrowed the haplotype region to four SNPs covering 2386 bp, containing the vgll3 gene, including two missense mutations explaining 33-36% phenotypic variation. A single locus was found to have a highly significant role in governing sea age at maturation in this species. The SNPs identified may be both used as markers to guide breeding for late maturity in salmon aquaculture and in monitoring programs of wild salmon. Interestingly, a SNP in proximity of the VGLL3 gene in humans (Homo sapiens), has previously been linked to age at puberty suggesting a conserved mechanism for timing of puberty in vertebrates.
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Affiliation(s)
| | - Erik Kjærner-Semb
- Institute of Marine Research, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | | | | | | | - Geir Dahle
- Institute of Marine Research, Bergen, Norway
| | | | - Kevin A. Glover
- Institute of Marine Research, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | - Markus Sällman Almén
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Carl J Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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61
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Aykanat T, Johnston SE, Orell P, Niemelä E, Erkinaro J, Primmer CR. Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population. Mol Ecol 2015; 24:5158-74. [DOI: 10.1111/mec.13383] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 09/04/2015] [Accepted: 09/09/2015] [Indexed: 01/13/2023]
Affiliation(s)
- Tutku Aykanat
- Division of Genetics and Physiology; Department of Biology; University of Turku; Itäinen Pitkäkatu 4 Turku FI-20520 Finland
| | - Susan E. Johnston
- Division of Genetics and Physiology; Department of Biology; University of Turku; Itäinen Pitkäkatu 4 Turku FI-20520 Finland
- Institute of Evolutionary Biology; University of Edinburgh; Charlotte Auerbach Road Edinburgh EH9 3FL UK
| | - Panu Orell
- Natural Resources Institute Finland; Utsjoki FI-99980 Finland
| | - Eero Niemelä
- Natural Resources Institute Finland; Utsjoki FI-99980 Finland
| | - Jaakko Erkinaro
- Natural Resources Institute Finland; Utsjoki FI-99980 Finland
| | - Craig R. Primmer
- Division of Genetics and Physiology; Department of Biology; University of Turku; Itäinen Pitkäkatu 4 Turku FI-20520 Finland
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62
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Genome-wide SNP loci reveal novel insights into koala (Phascolarctos cinereus) population variability across its range. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0784-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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63
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Brieuc MSO, Ono K, Drinan DP, Naish KA. Integration of Random Forest with population-based outlier analyses provides insight on the genomic basis and evolution of run timing in Chinook salmon (Oncorhynchus tshawytscha). Mol Ecol 2015; 24:2729-46. [PMID: 25913096 DOI: 10.1111/mec.13211] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 04/15/2015] [Accepted: 04/21/2015] [Indexed: 01/11/2023]
Abstract
Anadromous Chinook salmon populations vary in the period of river entry at the initiation of adult freshwater migration, facilitating optimal arrival at natal spawning. Run timing is a polygenic trait that shows evidence of rapid parallel evolution in some lineages, signifying a key role for this phenotype in the ecological divergence between populations. Studying the genetic basis of local adaptation in quantitative traits is often impractical in wild populations. Therefore, we used a novel approach, Random Forest, to detect markers linked to run timing across 14 populations from contrasting environments in the Columbia River and Puget Sound, USA. The approach permits detection of loci of small effect on the phenotype. Divergence between populations at these loci was then examined using both principle component analysis and FST outlier analyses, to determine whether shared genetic changes resulted in similar phenotypes across different lineages. Sequencing of 9107 RAD markers in 414 individuals identified 33 predictor loci explaining 79.2% of trait variance. Discriminant analysis of principal components of the predictors revealed both shared and unique evolutionary pathways in the trait across different lineages, characterized by minor allele frequency changes. However, genome mapping of predictor loci also identified positional overlap with two genomic outlier regions, consistent with selection on loci of large effect. Therefore, the results suggest selective sweeps on few loci and minor changes in loci that were detected by this study. Use of a polygenic framework has provided initial insight into how divergence in a trait has occurred in the wild.
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Affiliation(s)
- Marine S O Brieuc
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98195-5020, USA
| | - Kotaro Ono
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98195-5020, USA
| | - Daniel P Drinan
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98195-5020, USA
| | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98195-5020, USA
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Wenzel MA, James MC, Douglas A, Piertney SB. Genome-wide association and genome partitioning reveal novel genomic regions underlying variation in gastrointestinal nematode burden in a wild bird. Mol Ecol 2015; 24:4175-92. [PMID: 26179597 DOI: 10.1111/mec.13313] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 06/23/2015] [Accepted: 07/03/2015] [Indexed: 02/06/2023]
Abstract
Identifying the genetic architecture underlying complex phenotypes is a notoriously difficult problem that often impedes progress in understanding adaptive eco-evolutionary processes in natural populations. Host-parasite interactions are fundamentally important drivers of evolutionary processes, but a lack of understanding of the genes involved in the host's response to chronic parasite insult makes it particularly difficult to understand the mechanisms of host life history trade-offs and the adaptive dynamics involved. Here, we examine the genetic basis of gastrointestinal nematode (Trichostrongylus tenuis) burden in 695 red grouse (Lagopus lagopus scotica) individuals genotyped at 384 genome-wide SNPs. We first use genome-wide association to identify individual SNPs associated with nematode burden. We then partition genome-wide heritability to identify chromosomes with greater heritability than expected from gene content, due to harbouring a multitude of additive SNPs with individually undetectable effects. We identified five SNPs on five chromosomes that accounted for differences of up to 556 worms per bird, but together explained at best 4.9% of the phenotypic variance. These SNPs were closely linked to genes representing a range of physiological processes including the immune system, protein degradation and energy metabolism. Genome partitioning indicated genome-wide heritability of up to 29% and three chromosomes with excess heritability of up to 4.3% (total 8.9%). These results implicate SNPs and novel genomic regions underlying nematode burden in this system and suggest that this phenotype is somewhere between being based on few large-effect genes (oligogenic) and based on a large number of genes with small individual but large combined effects (polygenic).
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Affiliation(s)
- Marius A Wenzel
- Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Marianne C James
- Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Alex Douglas
- Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Stuart B Piertney
- Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
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Graham CF, Glenn TC, McArthur AG, Boreham DR, Kieran T, Lance S, Manzon RG, Martino JA, Pierson T, Rogers SM, Wilson JY, Somers CM. Impacts of degraded
DNA
on restriction enzyme associated
DNA
sequencing (
RADS
eq). Mol Ecol Resour 2015; 15:1304-15. [DOI: 10.1111/1755-0998.12404] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 03/04/2015] [Accepted: 03/06/2015] [Indexed: 12/01/2022]
Affiliation(s)
- Carly F. Graham
- Department of Biology University of Regina Regina Saskatchewan S4S 0A2 Canada
| | - Travis C. Glenn
- College of Public Health University of Georgia Athens GA 30602 USA
| | - Andrew G. McArthur
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences DeGroote School of Medicine McMaster University 1280 Main Street West Hamilton Ontario L8S 4K1 Canada
| | - Douglas R. Boreham
- Medical Sciences Northern Ontario School of Medicine Greater Sudbury Ontario P0M Canada
| | - Troy Kieran
- College of Public Health University of Georgia Athens GA 30602 USA
| | - Stacey Lance
- Savannah River Ecology Laboratory University of Georgia Athens GA 30602 USA
| | - Richard G. Manzon
- Department of Biology University of Regina Regina Saskatchewan S4S 0A2 Canada
| | - Jessica A. Martino
- Department of Biology University of Regina Regina Saskatchewan S4S 0A2 Canada
| | - Todd Pierson
- College of Public Health University of Georgia Athens GA 30602 USA
| | - Sean M. Rogers
- Department of Biological Sciences University of Calgary Calgary Alberta T2N 1N4 Canada
| | - Joanna Y. Wilson
- Department of Biology McMaster University Hamilton Ontario L8S 4M1 Canada
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66
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Genome-wide association study (GWAS) for growth rate and age at sexual maturation in Atlantic salmon (Salmo salar). PLoS One 2015; 10:e0119730. [PMID: 25757012 PMCID: PMC4355585 DOI: 10.1371/journal.pone.0119730] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 01/25/2015] [Indexed: 11/26/2022] Open
Abstract
Early sexual maturation is considered a serious drawback for Atlantic salmon aquaculture as it retards growth, increases production times and affects flesh quality. Although both growth and sexual maturation are thought to be complex processes controlled by several genetic and environmental factors, selection for these traits has been continuously accomplished since the beginning of Atlantic salmon selective breeding programs. In this genome-wide association study (GWAS) we used a 6.5K single-nucleotide polymorphism (SNP) array to genotype ∼480 individuals from the Cermaq Canada broodstock program and search for SNPs associated with growth and age at sexual maturation. Using a mixed model approach we identified markers showing a significant association with growth, grilsing (early sexual maturation) and late sexual maturation. The most significant associations were found for grilsing, with markers located in Ssa10, Ssa02, Ssa13, Ssa25 and Ssa12, and for late maturation with markers located in Ssa28, Ssa01 and Ssa21. A lower level of association was detected with growth on Ssa13. Candidate genes, which were linked to these genetic markers, were identified and some of them show a direct relationship with developmental processes, especially for those in association with sexual maturation. However, the relatively low power to detect genetic markers associated with growth (days to 5 kg) in this GWAS indicates the need to use a higher density SNP array in order to overcome the low levels of linkage disequilibrium observed in Atlantic salmon before the information can be incorporated into a selective breeding program.
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67
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Limborg MT, Waples RK, Seeb JE, Seeb LW. Temporally isolated lineages of pink salmon reveal unique signatures of selection on distinct pools of standing genetic variation. J Hered 2014; 105:741-51. [PMID: 25292170 DOI: 10.1093/jhered/esu063] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A species' genetic diversity bears the marks of evolutionary processes that have occurred throughout its history. However, robust detection of selection in wild populations is difficult and often impeded by lack of replicate tests. Here, we investigate selection in pink salmon (Oncorhynchus gorbuscha) using genome scans coupled with inference from a haploid-assisted linkage map. Pink salmon have a strict 2-year semelparous life history which has resulted in temporally isolated (allochronic) lineages that remain sympatric through sharing of spawning habitats in alternate years. The lineages differ in a range of adaptive traits, suggesting different genetic backgrounds. We used genotyping by sequencing of haploids to generate a high-density linkage map with 7035 loci and screened an existing panel of 8036 loci for signatures of selection. The linkage map enabled identification of novel genomic regions displaying signatures of parallel selection shared between lineages. Furthermore, 24 loci demonstrated divergent selection and differences in genetic diversity between lineages, suggesting that adaptation in the 2 lineages has arisen from different pools of standing genetic variation. Findings have implications for understanding asynchronous population abundances as well as predicting future ecosystem impacts from lineage-specific responses to climate change.
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Affiliation(s)
- Morten T Limborg
- From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA 98195 (Limborg, Waples, Seeb, Seeb); and the National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark (Limborg).
| | - Ryan K Waples
- From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA 98195 (Limborg, Waples, Seeb, Seeb); and the National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark (Limborg)
| | - James E Seeb
- From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA 98195 (Limborg, Waples, Seeb, Seeb); and the National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark (Limborg)
| | - Lisa W Seeb
- From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA 98195 (Limborg, Waples, Seeb, Seeb); and the National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark (Limborg)
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