1
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Borja Lozano MV, Vigil Santillán B, More Montoya MJ, Morón Barraza JA, García-Serquén AL, Gutiérrez Reynoso G, Yalta-Macedo CE. Genotyping-by-sequencing reveals a high number and quality of single nucleotide polymorphisms in guinea pigs (Cavia porcellus) from the Peruvian Andes. Anim Genet 2023; 54:792-797. [PMID: 37796666 DOI: 10.1111/age.13367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/06/2023] [Accepted: 09/25/2023] [Indexed: 10/07/2023]
Abstract
Guinea pigs are a major source of animal protein for Peruvian Andean families. Despite the economic and cultural relevance of guinea pigs, their genomic characterization has been scarcely addressed. Genotyping-by-sequencing (GBS) has emerged as an affordable alternative to genotyping of livestock and native animals. Here, we report the use of GBS for single nucleotide polymorphism (SNP) discovery of traditionally raised guinea pigs from six regions of the Peruvian Andes and one group of breeding animals. The paired-end (2 × 150 bp) sequencing of 40 guinea pig DNA samples generated a mean of 6.4 million high-quality sequencing reads per sample. We obtained an average sequencing depth of 10× with an 88.5% mapping rate to the Cavia porcellus reference genome. A total of 279 965 SNPs (102 SNPs/Mbp) were identified after variant calling and quality filtering. Based on this SNP set, we assessed the genetic diversity and distance within our selected guinea pig populations. An overall average minor allele frequency of 0.13, an observed heterozygosity of 0.31, an expected heterozygosity of 0.35, and an F-value of 0.1 were obtained, while the SNP-based neighbor-joining tree suggests a closer genetic relationship between individuals from geographically close locations. We showed that GBS is a cost-effective tool for SNP discovery and genetic characterization of Peruvian guinea pig populations. Therefore, it may be considered as a suitable and affordable tool for genomic characterization of poorly studied native animal species.
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Affiliation(s)
- María Victoria Borja Lozano
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria, Lima, Peru
- Facultad de Zootecnia, Universidad Nacional Agraria La Molina, Lima, Peru
| | - Bianca Vigil Santillán
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria, Lima, Peru
| | - Manuel J More Montoya
- Facultad de Ciencias Agrarias, Universidad Nacional de San Antonio Abad del Cusco, Cusco, Peru
| | | | - Aura Liz García-Serquén
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria, Lima, Peru
| | | | - Claudia E Yalta-Macedo
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria, Lima, Peru
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2
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In Search of Species-Specific SNPs in a Non-Model Animal (European Bison ( Bison bonasus))-Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data. Animals (Basel) 2021; 11:ani11082226. [PMID: 34438684 PMCID: PMC8388393 DOI: 10.3390/ani11082226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/07/2021] [Accepted: 07/24/2021] [Indexed: 11/17/2022] Open
Abstract
The European bison is a non-model organism; thus, most of its genetic and genomic analyses have been performed using cattle-specific resources, such as BovineSNP50 BeadChip or Illumina Bovine 800 K HD Bead Chip. The problem with non-specific tools is the potential loss of evolutionary diversified information (ascertainment bias) and species-specific markers. Here, we have used a genotyping-by-sequencing (GBS) approach for genotyping 256 samples from the European bison population in Bialowieza Forest (Poland) and performed an analysis using two integrated pipelines of the STACKS software: one is de novo (without reference genome) and the other is a reference pipeline (with reference genome). Moreover, we used a reference pipeline with two different genomes, i.e., Bos taurus and European bison. Genotyping by sequencing (GBS) is a useful tool for SNP genotyping in non-model organisms due to its cost effectiveness. Our results support GBS with a reference pipeline without PCR duplicates as a powerful approach for studying the population structure and genotyping data of non-model organisms. We found more polymorphic markers in the reference pipeline in comparison to the de novo pipeline. The decreased number of SNPs from the de novo pipeline could be due to the extremely low level of heterozygosity in European bison. It has been confirmed that all the de novo/Bos taurus and Bos taurus reference pipeline obtained SNPs were unique and not included in 800 K BovineHD BeadChip.
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3
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de Jager D, Glanzmann B, Möller M, Hoal E, van Helden P, Harper C, Bloomer P. High diversity, inbreeding and a dynamic Pleistocene demographic history revealed by African buffalo genomes. Sci Rep 2021; 11:4540. [PMID: 33633171 PMCID: PMC7907399 DOI: 10.1038/s41598-021-83823-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 02/04/2021] [Indexed: 12/30/2022] Open
Abstract
Genomes retain records of demographic changes and evolutionary forces that shape species and populations. Remnant populations of African buffalo (Syncerus caffer) in South Africa, with varied histories, provide an opportunity to investigate signatures left in their genomes by past events, both recent and ancient. Here, we produce 40 low coverage (7.14×) genome sequences of Cape buffalo (S. c. caffer) from four protected areas in South Africa. Genome-wide heterozygosity was the highest for any mammal for which these data are available, while differences in individual inbreeding coefficients reflected the severity of historical bottlenecks and current census sizes in each population. PSMC analysis revealed multiple changes in Ne between approximately one million and 20 thousand years ago, corresponding to paleoclimatic changes and Cape buffalo colonisation of southern Africa. The results of this study have implications for buffalo management and conservation, particularly in the context of the predicted increase in aridity and temperature in southern Africa over the next century as a result of climate change.
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Affiliation(s)
- Deon de Jager
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa.
| | - Brigitte Glanzmann
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Eileen Hoal
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Paul van Helden
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Cindy Harper
- Veterinary Genetics Laboratory, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Paulette Bloomer
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
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4
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Belyaev's and PEI's Foxes: A Far Cry. Trends Ecol Evol 2020; 35:649-651. [PMID: 32668212 DOI: 10.1016/j.tree.2020.03.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/20/2020] [Accepted: 03/25/2020] [Indexed: 11/23/2022]
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5
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Gileta AF, Gao J, Chitre AS, Bimschleger HV, St Pierre CL, Gopalakrishnan S, Palmer AA. Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats. G3 (BETHESDA, MD.) 2020; 10:2195-2205. [PMID: 32398234 PMCID: PMC7341140 DOI: 10.1534/g3.120.401325] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 05/01/2020] [Indexed: 02/06/2023]
Abstract
The heterogeneous stock (HS) is an outbred rat population derived from eight inbred rat strains. HS rats are ideally suited for genome wide association studies; however, only a few genotyping microarrays have ever been designed for rats and none of them are currently in production. To address the need for an efficient and cost effective method of genotyping HS rats, we have adapted genotype-by-sequencing (GBS) to obtain genotype information at large numbers of single nucleotide polymorphisms (SNPs). In this paper, we have outlined the laboratory and computational steps we took to optimize double digest genotype-by-sequencing (ddGBS) for use in rats. We evaluated multiple existing computational tools and explain the workflow we have used to call and impute over 3.7 million SNPs. We have also compared various rat genetic maps, which are necessary for imputation, including a recently developed map specific to the HS. Using our approach, we obtained concordance rates of 99% with data obtained using data from a genotyping array. The principles and computational pipeline that we describe could easily be adapted for use in other species for which reliable reference genome sets are available.
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Affiliation(s)
- Alexander F Gileta
- Department of Psychiatry
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California, 92093
| | | | | | | | | | - Shyam Gopalakrishnan
- Department of Human Genetics, University of Chicago, Chicago, Illinois, 60637, and
| | - Abraham A Palmer
- Department of Psychiatry,
- Natural History Museum of Denmark, University of Copenhagen, 2200 København N, Denmark
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6
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Lord KA, Larson G, Karlsson EK. Reply to Zeder and Trut et al.: An Attractive Hypothesis in Need of Evidence. Trends Ecol Evol 2020; 35:651-652. [PMID: 32517961 DOI: 10.1016/j.tree.2020.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 02/07/2023]
Affiliation(s)
- Kathryn A Lord
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3TG, UK
| | - Elinor K Karlsson
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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7
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Simpson JH. Fear and Foxes: An Educational Primer for Use with "Anterior Pituitary Transcriptome Suggests Differences in ACTH Release in Tame and Aggressive Foxes". Genetics 2020; 215:15-24. [PMID: 32371439 PMCID: PMC7198266 DOI: 10.1534/genetics.120.303046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/26/2020] [Indexed: 01/11/2023] Open
Abstract
The way genes contribute to behavior is complicated. Although there are some single genes with large contributions, most behavioral differences are due to small effects from many interacting genes. This makes it hard to identify the genes that cause behavioral differences. Mutagenesis screens in model organisms, selective breeding experiments in animals, comparisons between related populations with different behaviors, and genome-wide association studies in humans are promising and complementary approaches to understanding the heritable aspects of complex behaviors. To connect genes to behaviors requires measuring behavioral differences, locating correlated genetic changes, determining when, where, and how these candidate genes act, and designing causative confirmatory experiments. This area of research has implications from basic discovery science to human mental health.
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Affiliation(s)
- Julie H Simpson
- Department of Molecular, Cellular and Developmental Biology and Neuroscience Research Institute, University of California, Santa Barbara, California 93106-9625
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8
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Karimi K, Farid AH, Sargolzaei M, Myles S, Miar Y. Linkage Disequilibrium, Effective Population Size and Genomic Inbreeding Rates in American Mink Using Genotyping-by-Sequencing Data. Front Genet 2020; 11:223. [PMID: 32231688 PMCID: PMC7083153 DOI: 10.3389/fgene.2020.00223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 02/26/2020] [Indexed: 12/11/2022] Open
Abstract
Knowledge of linkage disequilibrium (LD) patterns is necessary to determine the minimum density of markers required for genomic studies and to infer historical changes as well as inbreeding events in the populations. In this study, we used genotyping-by-sequencing (GBS) approach to detect single nucleotide polymorphisms (SNPs) across American mink genome and further to estimate LD, effective population size (Ne), and inbreeding rates based on excess of homozygosity (FHOM) and runs of homozygosity (ROH). A GBS assay was constructed based on the sequencing of ApeKI-digested libraries from 285 American mink using Illumina HiSeq Sequencer. Data of 13,321 SNPs located on 46 scaffolds was used to perform LD analysis. The average LD (r2 ± SD) between adjacent SNPs was 0.30 ± 0.35 over all scaffolds with an average distance of 51 kb between markers. The average r2 < 0.2 was observed at inter-marker distances of >40 kb, suggesting that at least 60,000 informative SNPs would be required for genomic selection in American mink. The Ne was estimated to be 116 at five generations ago. In addition, the most rapid decline of population size was observed between 100 and 200 generations ago. Our results showed that short extensions of homozygous genotypes (500 kb to 1 Mb) were abundant across the genome and accounted for 33% of all ROH identified. The average inbreeding coefficient based on ROH longer than 1 Mb was 0.132 ± 0.042. The estimations of FHOM ranged from −0.44 to 0.34 among different samples with an average of 0.15 over all individuals. This study provided useful insights to determine the density of SNP panel providing enough statistical power and accuracy in genomic studies of American mink. Moreover, these results confirmed that GBS approach can be considered as a useful tool for genomic studies in American mink.
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Affiliation(s)
- Karim Karimi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - A Hossain Farid
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada.,Select Sires Inc., Plain City, OH, United States
| | - Sean Myles
- Department of Plant, Food, and Environmental Sciences, Dalhousie University, Truro, NS, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
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9
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Tao R, Xu C, Wang Y, Sun X, Li C, Ma J, Hao J, Yang Q. Spatiotemporal Differentiation of Alpine Butterfly Parnassius glacialis (Papilionidae: Parnassiinae) in China: Evidence from Mitochondrial DNA and Nuclear Single Nucleotide Polymorphisms. Genes (Basel) 2020; 11:genes11020188. [PMID: 32053967 PMCID: PMC7073557 DOI: 10.3390/genes11020188] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/05/2020] [Accepted: 02/06/2020] [Indexed: 11/24/2022] Open
Abstract
The Apollo butterfly, Parnassius glacialis, is one of the most charming members of its genus and includes two subspecies locally distributed in montane areas of south-central China and Japan. In this study, we investigated the genetic structure and demographic history of P. glacialis by analyzing partial sequences of four mitochondrial genes and nuclear single nucleotide polymorphisms (SNPs) via genotyping-by-sequencing (GBS) of samples from nearly the entire known distributional range in China. The mitochondrial DNA (mtDNA) data demonstrated that a total of 39 haplotypes were present, and the species was estimated to have diverged about 0.95 million years ago during the middle Pleistocene transition into two main clades that likely formed during the Kunlun-Huanghe tectonic movement. The two clades then dispersed independently in distinct geographic areas alongside the mountainous routes in central and southern China, most likely driven by the Pleistocene glacial-interglacial cycles. Nuclear SNP analysis was generally congruent with mtDNA results at the individual level. A minor incongruence of genetic structures that was detected between mtDNA and nuclear SNP data from the Laojunshan and Tiantangzhai populations was likely due to secondary contact and male-biased dispersal. Our work demonstrates that complicated dispersal-vicariance evolutionary processes likely led to the current geographic distribution of P. glacialis in China, particularly the uplift of the Qinghai-Tibet Plateau and related climatic oscillations during the Quaternary period.
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Affiliation(s)
- Ruisong Tao
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (R.T.); (C.X.); (Y.W.)
- College of Life Sciences, Hefei Normal University, Hefei 230000, China
| | - Chang Xu
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (R.T.); (C.X.); (Y.W.)
| | - Yunliang Wang
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (R.T.); (C.X.); (Y.W.)
| | - Xiaoyan Sun
- SKLPS and Center for Excellence in Life and Paleoenvironment, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China; (X.S.); (C.L.); (J.M.)
| | - Chunxiang Li
- SKLPS and Center for Excellence in Life and Paleoenvironment, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China; (X.S.); (C.L.); (J.M.)
| | - Junye Ma
- SKLPS and Center for Excellence in Life and Paleoenvironment, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China; (X.S.); (C.L.); (J.M.)
| | - Jiasheng Hao
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (R.T.); (C.X.); (Y.W.)
- Correspondence: (J.H.); (Q.Y.)
| | - Qun Yang
- SKLPS and Center for Excellence in Life and Paleoenvironment, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China; (X.S.); (C.L.); (J.M.)
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (J.H.); (Q.Y.)
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10
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Lord KA, Larson G, Coppinger RP, Karlsson EK. The History of Farm Foxes Undermines the Animal Domestication Syndrome. Trends Ecol Evol 2019; 35:125-136. [PMID: 31810775 DOI: 10.1016/j.tree.2019.10.011] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 12/22/2022]
Abstract
The Russian Farm-Fox Experiment is the best known experimental study in animal domestication. By subjecting a population of foxes to selection for tameness alone, Dimitry Belyaev generated foxes that possessed a suite of characteristics that mimicked those found across domesticated species. This 'domestication syndrome' has been a central focus of research into the biological pathways modified during domestication. Here, we chart the origins of Belyaev's foxes in eastern Canada and critically assess the appearance of domestication syndrome traits across animal domesticates. Our results suggest that both the conclusions of the Farm-Fox Experiment and the ubiquity of domestication syndrome have been overstated. To understand the process of domestication requires a more comprehensive approach focused on essential adaptations to human-modified environments.
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Affiliation(s)
- Kathryn A Lord
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01655, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
| | - Raymond P Coppinger
- School of Cognitive Science, Hampshire College, 893 West St, Amherst, MA 01002, USA
| | - Elinor K Karlsson
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01655, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Program in Molecular Medicine, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01655, USA.
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11
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Sacks BN, Lounsberry ZT, Statham MJ. Nuclear Genetic Analysis of the Red Fox Across its Trans-Pacific Range. J Hered 2019; 109:573-584. [PMID: 29889225 DOI: 10.1093/jhered/esy028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 06/05/2018] [Indexed: 11/14/2022] Open
Abstract
The red fox (Vulpes vulpes) occurs on multiple continents in diverse habitats, making it an informative system for evolutionary genomic research. However, its phylogeography remains unclear. Previously, mitochondrial DNA and small numbers of nuclear loci provided discordant views. Both markers indicated deep divergence (~ 0.5 million years [MY]) between Eurasian and southern North American populations but differed in the apparent continental affinity of Alaskan red foxes, implying some degree of gene exchange during secondary contact (~0.1 MY). We assayed >173000 nuclear genomic sites in 52 red foxes, along with 2 Rueppell's foxes (Vulpes rueppellii) and a gray wolf (Canis lupus) using the Illumina CanineHD BeadChip. We obtained 5107 single nucleotide polymorphisms (SNPs) in the foxes. Consistent with the Afro-Eurasian origins of red foxes, genetic diversity was higher in Eurasian than North American samples. Phylogenetic trees indicated that Alaskan and southern North American red foxes formed a monophyletic group nested within the Eurasian clade. However, admixture models suggested Alaskan red foxes contained up to 40% Eurasian ancestry. We hypothesize that North American red foxes either hybridized with Eurasian foxes in Beringia at the start of the last glaciation or merged with a Beringian population after the last glaciation. Future work is needed to test between these scenarios and assess speciation.
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Affiliation(s)
- Benjamin N Sacks
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, Davis, CA.,Department of Population Health and Reproduction, University of California, Davis, Davis, CA
| | - Zachary T Lounsberry
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, Davis, CA
| | - Mark J Statham
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, Davis, CA.,Department of Population Health and Reproduction, University of California, Davis, Davis, CA
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12
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Genomic signatures of local adaptation to the degree of environmental predictability in rotifers. Sci Rep 2018; 8:16051. [PMID: 30375419 PMCID: PMC6207753 DOI: 10.1038/s41598-018-34188-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 09/27/2018] [Indexed: 11/09/2022] Open
Abstract
Environmental fluctuations are ubiquitous and thus essential for the study of adaptation. Despite this, genome evolution in response to environmental fluctuations —and more specifically to the degree of environmental predictability– is still unknown. Saline lakes in the Mediterranean region are remarkably diverse in their ecological conditions, which can lead to divergent local adaptation patterns in the inhabiting aquatic organisms. The facultatively sexual rotifer Brachionus plicatilis shows diverging local adaptation in its life-history traits in relation to estimated environmental predictability in its habitats. Here, we used an integrative approach —combining environmental, phenotypic and genomic data for the same populations– to understand the genomic basis of this diverging adaptation. Firstly, a novel draft genome for B. plicatilis was assembled. Then, genome-wide polymorphisms were studied using genotyping by sequencing on 270 clones from nine populations in eastern Spain. As a result, 4,543 high-quality SNPs were identified and genotyped. More than 90 SNPs were found to be putatively under selection with signatures of diversifying and balancing selection. Over 140 SNPs were correlated with environmental or phenotypic variables revealing signatures of local adaptation, including environmental predictability. Putative functions were associated to most of these SNPs, since they were located within annotated genes. Our results reveal associations between genomic variation and the degree of environmental predictability, providing genomic evidence of adaptation to local conditions in natural rotifer populations.
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13
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Osorio-Guarín JA, Quackenbush CR, Cornejo OE. Ancestry informative alleles captured with reduced representation library sequencing in Theobroma cacao. PLoS One 2018; 13:e0203973. [PMID: 30332408 PMCID: PMC6192562 DOI: 10.1371/journal.pone.0203973] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 10/04/2018] [Indexed: 12/18/2022] Open
Abstract
As the source of chocolate, cacao has become one of the most important crops in the world. The identification of molecular markers to understand the demographic history, genetic diversity and population structure plays a pivotal role in cacao breeding programs. Here, we report the use of a modified genotyping-by-sequencing (GBS) approach for large-scale single nucleotide polymorphism (SNP) discovery and allele ancestry mapping. We identified 12,357 bi-allelic SNPs after filtering, of which, 7,009 variants were ancestry informative. The GBS approach proved to be rapid, cost-effective, and highly informative for ancestry assignment in this species.
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Affiliation(s)
- Jaime A. Osorio-Guarín
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria–Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Corey R. Quackenbush
- School of Biological Sciences, Washington State University, Pullman, WA, United States of America
| | - Omar E. Cornejo
- School of Biological Sciences, Washington State University, Pullman, WA, United States of America
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14
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Dussex N, Taylor HR, Stovall WR, Rutherford K, Dodds KG, Clarke SM, Gemmell NJ. Reduced representation sequencing detects only subtle regional structure in a heavily exploited and rapidly recolonizing marine mammal species. Ecol Evol 2018; 8:8736-8749. [PMID: 30271541 PMCID: PMC6157699 DOI: 10.1002/ece3.4411] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/17/2018] [Accepted: 05/29/2018] [Indexed: 12/20/2022] Open
Abstract
Next-generation reduced representation sequencing (RRS) approaches show great potential for resolving the structure of wild populations. However, the population structure of species that have shown rapid demographic recovery following severe population bottlenecks may still prove difficult to resolve due to high gene flow between subpopulations. Here, we tested the effectiveness of the RRS method Genotyping-By-Sequencing (GBS) for describing the population structure of the New Zealand fur seal (NZFS, Arctocephalus forsteri), a species that was heavily exploited by the 19th century commercial sealing industry and has since rapidly recolonized most of its former range from a few isolated colonies. Using 26,026 neutral single nucleotide polymorphisms (SNPs), we assessed genetic variation within and between NZFS colonies. We identified low levels of population differentiation across the species range (<1% of variation explained by regional differences) suggesting a state of near panmixia. Nonetheless, we observed subtle population substructure between West Coast and Southern East Coast colonies and a weak, but significant (p = 0.01), isolation-by-distance pattern among the eight colonies studied. Furthermore, our demographic reconstructions supported severe bottlenecks with potential 10-fold and 250-fold declines in response to Polynesian and European hunting, respectively. Finally, we were able to assign individuals treated as unknowns to their regions of origin with high confidence (96%) using our SNP data. Our results indicate that while it may be difficult to detect population structure in species that have experienced rapid recovery, next-generation markers and methods are powerful tools for resolving fine-scale structure and informing conservation and management efforts.
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Affiliation(s)
- Nicolas Dussex
- Department of AnatomyUniversity of OtagoDunedinNew Zealand
- Department of Bioinformatics and GeneticsSwedish Museum of Natural HistoryStockholmSweden
| | | | | | - Kim Rutherford
- Department of AnatomyUniversity of OtagoDunedinNew Zealand
| | - Ken G. Dodds
- Invermay Agricultural CentreAgResearchPuddle AlleyMosgielNew Zealand
| | - Shannon M. Clarke
- Invermay Agricultural CentreAgResearchPuddle AlleyMosgielNew Zealand
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15
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Eimanifar A, Brooks SA, Bustamante T, Ellis JD. Population genomics and morphometric assignment of western honey bees (Apis mellifera L.) in the Republic of South Africa. BMC Genomics 2018; 19:615. [PMID: 30111292 PMCID: PMC6094452 DOI: 10.1186/s12864-018-4998-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 08/07/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUNDS Apis mellifera scutellata and A.m. capensis (the Cape honey bee) are western honey bee subspecies indigenous to the Republic of South Africa (RSA). Both bees are important for biological and economic reasons. First, A.m. scutellata is the invasive "African honey bee" of the Americas and exhibits a number of traits that beekeepers consider undesirable. They swarm excessively, are prone to absconding (vacating the nest entirely), usurp other honey bee colonies, and exhibit heightened defensiveness. Second, Cape honey bees are socially parasitic bees; the workers can reproduce thelytokously. Both bees are indistinguishable visually. Therefore, we employed Genotyping-by-Sequencing (GBS), wing geometry and standard morphometric approaches to assess the genetic diversity and population structure of these bees to search for diagnostic markers that can be employed to distinguish between the two subspecies. RESULTS Apis mellifera scutellata possessed the highest mean number of polymorphic SNPs (among 2449 informative SNPs) with minor allele frequencies > 0.05 (Np = 88%). The RSA honey bees generated a high level of expected heterozygosity (Hexp = 0.24). The mean genetic differentiation (FST; 6.5%) among the RSA honey bees revealed that approximately 93% of the genetic variation was accounted for within individuals of these subspecies. Two genetically distinct clusters (K = 2) corresponding to both subspecies were detected by Model-based Bayesian clustering and supported by Principal Coordinates Analysis (PCoA) inferences. Selected highly divergent loci (n = 83) further reinforced a distinctive clustering of two subspecies across geographical origins, accounting for approximately 83% of the total variation in the PCoA plot. The significant correlation of allele frequencies at divergent loci with environmental variables suggested that these populations are adapted to local conditions. Only 17 of 48 wing geometry and standard morphometric parameters were useful for clustering A.m. capensis, A.m. scutellata, and hybrid individuals. CONCLUSIONS We produced a minimal set of 83 SNP loci and 17 wing geometry and standard morphometric parameters useful for identifying the two RSA honey bee subspecies by genotype and phenotype. We found that genes involved in neurology/behavior and development/growth are the most prominent heritable traits evolved in the functional evolution of honey bee populations in RSA. These findings provide a starting point for understanding the functional basis of morphological differentiations and ecological adaptations of the two honey bee subspecies in RSA.
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Affiliation(s)
- Amin Eimanifar
- Honey Bee Research and Extension Laboratory, Entomology and Nematology Department, University of Florida, Gainesville, Florida, 32611-0620 USA
| | - Samantha A. Brooks
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611 USA
| | - Tomas Bustamante
- Honey Bee Research and Extension Laboratory, Entomology and Nematology Department, University of Florida, Gainesville, Florida, 32611-0620 USA
| | - James D. Ellis
- Honey Bee Research and Extension Laboratory, Entomology and Nematology Department, University of Florida, Gainesville, Florida, 32611-0620 USA
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16
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Kukekova AV, Johnson JL, Xiang X, Feng S, Liu S, Rando HM, Kharlamova AV, Herbeck Y, Serdyukova NA, Xiong Z, Beklemischeva V, Koepfli KP, Gulevich RG, Vladimirova AV, Hekman JP, Perelman PL, Graphodatsky AS, O'Brien SJ, Wang X, Clark AG, Acland GM, Trut LN, Zhang G. Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours. Nat Ecol Evol 2018; 2:1479-1491. [PMID: 30082739 DOI: 10.1038/s41559-018-0611-6] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 06/18/2018] [Indexed: 12/30/2022]
Abstract
Strains of red fox (Vulpes vulpes) with markedly different behavioural phenotypes have been developed in the famous long-term selective breeding programme known as the Russian farm-fox experiment. Here we sequenced and assembled the red fox genome and re-sequenced a subset of foxes from the tame, aggressive and conventional farm-bred populations to identify genomic regions associated with the response to selection for behaviour. Analysis of the re-sequenced genomes identified 103 regions with either significantly decreased heterozygosity in one of the three populations or increased divergence between the populations. A strong positional candidate gene for tame behaviour was highlighted: SorCS1, which encodes the main trafficking protein for AMPA glutamate receptors and neurexins and suggests a role for synaptic plasticity in fox domestication. Other regions identified as likely to have been under selection in foxes include genes implicated in human neurological disorders, mouse behaviour and dog domestication. The fox represents a powerful model for the genetic analysis of affiliative and aggressive behaviours that can benefit genetic studies of behaviour in dogs and other mammals, including humans.
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Affiliation(s)
- Anna V Kukekova
- Animal Sciences Department, College of ACES, University of Illinois at Urbana, Champaign, IL, USA.
| | - Jennifer L Johnson
- Animal Sciences Department, College of ACES, University of Illinois at Urbana, Champaign, IL, USA
| | - Xueyan Xiang
- China National Genebank, BGI -Shenzhen, Shenzhen, China
| | - Shaohong Feng
- China National Genebank, BGI -Shenzhen, Shenzhen, China
| | - Shiping Liu
- China National Genebank, BGI -Shenzhen, Shenzhen, China
| | - Halie M Rando
- Animal Sciences Department, College of ACES, University of Illinois at Urbana, Champaign, IL, USA
| | - Anastasiya V Kharlamova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Yury Herbeck
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Natalya A Serdyukova
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Zijun Xiong
- China National Genebank, BGI -Shenzhen, Shenzhen, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Violetta Beklemischeva
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington DC, USA.,Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, Saint Petersburg, Russia
| | - Rimma G Gulevich
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anastasiya V Vladimirova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Jessica P Hekman
- Animal Sciences Department, College of ACES, University of Illinois at Urbana, Champaign, IL, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Polina L Perelman
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Aleksander S Graphodatsky
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, Saint Petersburg, Russia.,Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Xu Wang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.,Department of Pathobiology, Auburn University, Auburn, AL, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Gregory M Acland
- Baker Institute for Animal Health, Cornell University, College of Veterinary Medicine, Ithaca, NY, USA
| | - Lyudmila N Trut
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Guojie Zhang
- China National Genebank, BGI -Shenzhen, Shenzhen, China. .,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. .,Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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17
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Rando HM, Farré M, Robson MP, Won NB, Johnson JL, Buch R, Bastounes ER, Xiang X, Feng S, Liu S, Xiong Z, Kim J, Zhang G, Trut LN, Larkin DM, Kukekova AV. Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly. Genes (Basel) 2018; 9:E308. [PMID: 29925783 PMCID: PMC6027122 DOI: 10.3390/genes9060308] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 05/19/2018] [Accepted: 06/04/2018] [Indexed: 01/08/2023] Open
Abstract
The genome of a red fox (Vulpes vulpes) was recently sequenced and assembled using next-generation sequencing (NGS). The assembly is of high quality, with 94X coverage and a scaffold N50 of 11.8 Mbp, but is split into 676,878 scaffolds, some of which are likely to contain assembly errors. Fragmentation and misassembly hinder accurate gene prediction and downstream analysis such as the identification of loci under selection. Therefore, assembly of the genome into chromosome-scale fragments was an important step towards developing this genomic model. Scaffolds from the assembly were aligned to the dog reference genome and compared to the alignment of an outgroup genome (cat) against the dog to identify syntenic sequences among species. The program Reference-Assisted Chromosome Assembly (RACA) then integrated the comparative alignment with the mapping of the raw sequencing reads generated during assembly against the fox scaffolds. The 128 sequence fragments RACA assembled were compared to the fox meiotic linkage map to guide the construction of 40 chromosomal fragments. This computational approach to assembly was facilitated by prior research in comparative mammalian genomics, and the continued improvement of the red fox genome can in turn offer insight into canid and carnivore chromosome evolution. This assembly is also necessary for advancing genetic research in foxes and other canids.
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Affiliation(s)
- Halie M Rando
- Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Marta Farré
- Department of Comparative Biomedical Science, Royal Veterinary College, London NW1 0TU, UK.
| | - Michael P Robson
- Department of Computer Science, College of Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Naomi B Won
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Jennifer L Johnson
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Ronak Buch
- Department of Computer Science, College of Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Estelle R Bastounes
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Xueyan Xiang
- China National Genebank, BGI -Shenzhen, Shenzhen 518083, Guangdong, China.
| | - Shaohong Feng
- China National Genebank, BGI -Shenzhen, Shenzhen 518083, Guangdong, China.
| | - Shiping Liu
- China National Genebank, BGI -Shenzhen, Shenzhen 518083, Guangdong, China.
| | - Zijun Xiong
- China National Genebank, BGI -Shenzhen, Shenzhen 518083, Guangdong, China.
| | - Jaebum Kim
- Department of Stem Cell and Regenerative Biology, Konkuk University, Seoul 05029, Korea.
| | - Guojie Zhang
- China National Genebank, BGI -Shenzhen, Shenzhen 518083, Guangdong, China.
- Section for Ecology and Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
| | - Lyudmila N Trut
- Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
| | - Denis M Larkin
- Department of Comparative Biomedical Science, Royal Veterinary College, London NW1 0TU, UK.
| | - Anna V Kukekova
- Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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18
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Anterior Pituitary Transcriptome Suggests Differences in ACTH Release in Tame and Aggressive Foxes. G3-GENES GENOMES GENETICS 2018; 8:859-873. [PMID: 29378821 PMCID: PMC5844307 DOI: 10.1534/g3.117.300508] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Domesticated species exhibit a suite of behavioral, endocrinological, and morphological changes referred to as "domestication syndrome." These changes may include a reduction in reactivity of the hypothalamic-pituitary-adrenal (HPA) axis and specifically reduced adrenocorticotropic hormone release from the anterior pituitary. To investigate the biological mechanisms targeted during domestication, we investigated gene expression in the pituitaries of experimentally domesticated foxes (Vulpes vulpes). RNA was sequenced from the anterior pituitary of six foxes selectively bred for tameness ("tame foxes") and six foxes selectively bred for aggression ("aggressive foxes"). Expression, splicing, and network differences identified between the two lines indicated the importance of genes related to regulation of exocytosis, specifically mediated by cAMP, organization of pseudopodia, and cell motility. These findings provide new insights into biological mechanisms that may have been targeted when these lines of foxes were selected for behavior and suggest new directions for research into HPA axis regulation and the biological underpinnings of domestication.
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19
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Ashbrook DG, Mulligan MK, Williams RW. Post-genomic behavioral genetics: From revolution to routine. GENES, BRAIN, AND BEHAVIOR 2018; 17:e12441. [PMID: 29193773 PMCID: PMC5876106 DOI: 10.1111/gbb.12441] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/02/2017] [Accepted: 11/20/2017] [Indexed: 12/16/2022]
Abstract
What was once expensive and revolutionary-full-genome sequence-is now affordable and routine. Costs will continue to drop, opening up new frontiers in behavioral genetics. This shift in costs from the genome to the phenome is most notable in large clinical studies of behavior and associated diseases in cohorts that exceed hundreds of thousands of subjects. Examples include the Women's Health Initiative (www.whi.org), the Million Veterans Program (www. RESEARCH va.gov/MVP), the 100 000 Genomes Project (genomicsengland.co.uk) and commercial efforts such as those by deCode (www.decode.com) and 23andme (www.23andme.com). The same transition is happening in experimental neuro- and behavioral genetics, and sample sizes of many hundreds of cases are becoming routine (www.genenetwork.org, www.mousephenotyping.org). There are two major consequences of this new affordability of massive omics datasets: (1) it is now far more practical to explore genetic modulation of behavioral differences and the key role of gene-by-environment interactions. Researchers are already doing the hard part-the quantitative analysis of behavior. Adding the omics component can provide powerful links to molecules, cells, circuits and even better treatment. (2) There is an acute need to highlight and train behavioral scientists in how best to exploit new omics approaches. This review addresses this second issue and highlights several new trends and opportunities that will be of interest to experts in animal and human behaviors.
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Affiliation(s)
- D G Ashbrook
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Sciences Center, College of Medicine, Memphis, Tennessee
| | - M K Mulligan
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Sciences Center, College of Medicine, Memphis, Tennessee
| | - R W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Sciences Center, College of Medicine, Memphis, Tennessee
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20
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Boschiero C, Moreira GCM, Gheyas AA, Godoy TF, Gasparin G, Mariani PDSC, Paduan M, Cesar ASM, Ledur MC, Coutinho LL. Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines. BMC Genomics 2018; 19:83. [PMID: 29370772 PMCID: PMC5785814 DOI: 10.1186/s12864-018-4444-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 01/10/2018] [Indexed: 12/13/2022] Open
Abstract
Background Meat and egg-type chickens have been selected for several generations for different traits. Artificial and natural selection for different phenotypes can change frequency of genetic variants, leaving particular genomic footprints throghtout the genome. Thus, the aims of this study were to sequence 28 chickens from two Brazilian lines (meat and white egg-type) and use this information to characterize genome-wide genetic variations, identify putative regions under selection using Fst method, and find putative pathways under selection. Results A total of 13.93 million SNPs and 1.36 million INDELs were identified, with more variants detected from the broiler (meat-type) line. Although most were located in non-coding regions, we identified 7255 intolerant non-synonymous SNPs, 512 stopgain/loss SNPs, 1381 frameshift and 1094 non-frameshift INDELs that may alter protein functions. Genes harboring intolerant non-synonymous SNPs affected metabolic pathways related mainly to reproduction and endocrine systems in the white-egg layer line, and lipid metabolism and metabolic diseases in the broiler line. Fst analysis in sliding windows, using SNPs and INDELs separately, identified over 300 putative regions of selection overlapping with more than 250 genes. For the first time in chicken, INDEL variants were considered for selection signature analysis, showing high level of correlation in results between SNP and INDEL data. The putative regions of selection signatures revealed interesting candidate genes and pathways related to important phenotypic traits in chicken, such as lipid metabolism, growth, reproduction, and cardiac development. Conclusions In this study, Fst method was applied to identify high confidence putative regions under selection, providing novel insights into selection footprints that can help elucidate the functional mechanisms underlying different phenotypic traits relevant to meat and egg-type chicken lines. In addition, we generated a large catalog of line-specific and common genetic variants from a Brazilian broiler and a white egg layer line that can be used for genomic studies involving association analysis with phenotypes of economic interest to the poultry industry. Electronic supplementary material The online version of this article (10.1186/s12864-018-4444-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Clarissa Boschiero
- Animal Biotechnology Laboratory, Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, 13418-900, Brazil. .,Noble Reserch Institute, 2510 Sam Noble Parkway, Ardmore, Oklahoma, 73401, USA.
| | - Gabriel Costa Monteiro Moreira
- Animal Biotechnology Laboratory, Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, 13418-900, Brazil
| | - Almas Ara Gheyas
- Department of Genetics and Genomics, The Roslin Institute and Royal School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Thaís Fernanda Godoy
- Animal Biotechnology Laboratory, Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, 13418-900, Brazil
| | - Gustavo Gasparin
- Animal Biotechnology Laboratory, Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, 13418-900, Brazil
| | - Pilar Drummond Sampaio Corrêa Mariani
- Animal Biotechnology Laboratory, Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, 13418-900, Brazil
| | - Marcela Paduan
- Animal Biotechnology Laboratory, Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, 13418-900, Brazil
| | - Aline Silva Mello Cesar
- Animal Biotechnology Laboratory, Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, 13418-900, Brazil
| | | | - Luiz Lehmann Coutinho
- Animal Biotechnology Laboratory, Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, 13418-900, Brazil
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21
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Theofanopoulou C, Gastaldon S, O’Rourke T, Samuels BD, Messner A, Martins PT, Delogu F, Alamri S, Boeckx C. Self-domestication in Homo sapiens: Insights from comparative genomics. PLoS One 2017; 12:e0185306. [PMID: 29045412 PMCID: PMC5646786 DOI: 10.1371/journal.pone.0185306] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/11/2017] [Indexed: 02/07/2023] Open
Abstract
This study identifies and analyzes statistically significant overlaps between selective sweep screens in anatomically modern humans and several domesticated species. The results obtained suggest that (paleo-)genomic data can be exploited to complement the fossil record and support the idea of self-domestication in Homo sapiens, a process that likely intensified as our species populated its niche. Our analysis lends support to attempts to capture the "domestication syndrome" in terms of alterations to certain signaling pathways and cell lineages, such as the neural crest.
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Affiliation(s)
- Constantina Theofanopoulou
- Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain
- Universitat de Barcelona Institute for Complex Systems, Barcelona, Spain
| | - Simone Gastaldon
- Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain
- School of Psychology, University of Padova, Padova, Italy
| | - Thomas O’Rourke
- Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain
| | - Bridget D. Samuels
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, United States of America
| | - Angela Messner
- Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain
| | | | - Francesco Delogu
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Saleh Alamri
- Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain
| | - Cedric Boeckx
- Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain
- Universitat de Barcelona Institute for Complex Systems, Barcelona, Spain
- ICREA, Barcelona, Spain
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22
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Mazzatenta A, Carluccio A, Robbe D, Giulio CD, Cellerino A. The companion dog as a unique translational model for aging. Semin Cell Dev Biol 2017; 70:141-153. [DOI: 10.1016/j.semcdb.2017.08.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 08/06/2017] [Accepted: 08/07/2017] [Indexed: 10/19/2022]
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23
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Furuta T, Ashikari M, Jena KK, Doi K, Reuscher S. Adapting Genotyping-by-Sequencing for Rice F2 Populations. G3 (BETHESDA, MD.) 2017; 7:881-893. [PMID: 28082325 PMCID: PMC5345719 DOI: 10.1534/g3.116.038190] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 01/09/2017] [Indexed: 12/30/2022]
Abstract
Rapid and cost-effective genotyping of large mapping populations can be achieved by sequencing a reduced representation of the genome of every individual in a given population, and using that information to generate genetic markers. A customized genotyping-by-sequencing (GBS) pipeline was developed to genotype a rice F2 population from a cross of Oryza sativa ssp. japonica cv. Nipponbare and the African wild rice species O. longistaminata While most GBS pipelines aim to analyze mainly homozygous populations, we attempted to genotype a highly heterozygous F2 population. We show how species- and population-specific improvements of established protocols can drastically increase sample throughput and genotype quality. Using as few as 50,000 reads for some individuals (134,000 reads on average), we were able to generate up to 8154 informative SNP markers in 1081 F2 individuals. Additionally, the effects of enzyme choice, read coverage, and data postprocessing are evaluated. Using GBS-derived markers, we were able to assemble a genetic map of 1536 cM. To demonstrate the usefulness of our GBS pipeline, we determined quantitative trait loci (QTL) for the number of tillers. We were able to map four QTL to chromosomes 1, 3, 4, and 8, and partially confirm their effects using introgression lines. We provide an example of how to successfully use GBS with heterozygous F2 populations. By using the comparatively low-cost MiSeq platform, we show that the GBS method is flexible and cost-effective, even for smaller laboratories.
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Affiliation(s)
- Tomoyuki Furuta
- Bioscience and Biotechnology Center, Nagoya University, 464-8601, Japan
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, 464-8601, Japan
| | - Kshirod K Jena
- Plant Breeding Division, International Rice Research Institute, 1301 Manila, Philippines
| | - Kazuyuki Doi
- Associated Field Science and Research Center, Nagoya University, 470-0151, Japan
| | - Stefan Reuscher
- Bioscience and Biotechnology Center, Nagoya University, 464-8601, Japan
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Genetics of Interactive Behavior in Silver Foxes (Vulpes vulpes). Behav Genet 2016; 47:88-101. [PMID: 27757730 DOI: 10.1007/s10519-016-9815-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 08/27/2016] [Indexed: 10/20/2022]
Abstract
Individuals involved in a social interaction exhibit different behavioral traits that, in combination, form the individual's behavioral responses. Selectively bred strains of silver foxes (Vulpes vulpes) demonstrate markedly different behaviors in their response to humans. To identify the genetic basis of these behavioral differences we constructed a large F2 population including 537 individuals by cross-breeding tame and aggressive fox strains. 98 fox behavioral traits were recorded during social interaction with a human experimenter in a standard four-step test. Patterns of fox behaviors during the test were evaluated using principal component (PC) analysis. Genetic mapping identified eight unique significant and suggestive QTL. Mapping results for the PC phenotypes from different test steps showed little overlap suggesting that different QTL are involved in regulation of behaviors exhibited in different behavioral contexts. Many individual behavioral traits mapped to the same genomic regions as PC phenotypes. This provides additional information about specific behaviors regulated by these loci. Further, three pairs of epistatic loci were also identified for PC phenotypes suggesting more complex genetic architecture of the behavioral differences between the two strains than what has previously been observed.
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Bimber BN, Raboin MJ, Letaw J, Nevonen KA, Spindel JE, McCouch SR, Cervera-Juanes R, Spindel E, Carbone L, Ferguson B, Vinson A. Whole-genome characterization in pedigreed non-human primates using genotyping-by-sequencing (GBS) and imputation. BMC Genomics 2016; 17:676. [PMID: 27558348 PMCID: PMC4997765 DOI: 10.1186/s12864-016-2966-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Accepted: 07/22/2016] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Rhesus macaques are widely used in biomedical research, but the application of genomic information in this species to better understand human disease is still in its infancy. Whole-genome sequence (WGS) data in large pedigreed macaque colonies could provide substantial experimental power for genetic discovery, but the collection of WGS data in large cohorts remains a formidable expense. Here, we describe a cost-effective approach that selects the most informative macaques in a pedigree for 30X WGS, followed by low-cost genotyping-by-sequencing (GBS) at 30X on the remaining macaques in order to generate sparse genotype data at high accuracy. Dense variants from the selected macaques with WGS data are then imputed into macaques having only sparse GBS data, resulting in dense genome-wide genotypes throughout the pedigree. RESULTS We developed GBS for the macaque genome using a digestion with PstI, followed by sequencing of size-selected fragments at 30X coverage. From GBS sequence data collected on all individuals in a 16-member pedigree, we characterized high-confidence genotypes at 22,455 single nucleotide variant (SNV) sites that were suitable for guiding imputation of dense sequence data from WGS. To characterize dense markers for imputation, we performed WGS at 30X coverage on nine of the 16 individuals, yielding 10,193,425 high-confidence SNVs. To validate the use of GBS data for facilitating imputation, we initially focused on chromosome 19 as a test case, using an optimized panel of 833 sparse, evenly-spaced markers from GBS and 5,010 dense markers from WGS. Using the method of "Genotype Imputation Given Inheritance" (GIGI), we evaluated the effects on imputation accuracy of 3 different strategies for selecting individuals for WGS, including 1) using "GIGI-Pick" to select the most informative individuals, 2) using the most recent generation, or 3) using founders only. We also evaluated the effects on imputation accuracy of using a range of from 1 to 9 WGS individuals for imputation. We found that the GIGI-Pick algorithm for selection of WGS individuals outperformed common heuristic approaches, and that genotype numbers and accuracy improved very little when using >5 WGS individuals for imputation. Informed by our findings, we used 4 macaques with WGS data to impute variants at up to 7,655,491 sites spanning all 20 autosomes in the 12 remaining macaques, based on their GBS genotypes at only 17,158 loci. Using a strict confidence threshold, we imputed an average of 3,680,238 variants per individual at >99 % accuracy, or an average 4,458,883 variants per individual at a more relaxed threshold, yielding >97 % accuracy. CONCLUSIONS We conclude that an optimal tradeoff between genotype accuracy, number of imputed genotypes, and overall cost exists at the ratio of one individual selected for WGS using the GIGI-Pick algorithm, per 3-5 relatives selected for GBS. This approach makes feasible the collection of accurate, dense genome-wide sequence data in large pedigreed macaque cohorts without the need for more expensive WGS data on all individuals.
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Affiliation(s)
- Benjamin N Bimber
- Primate Genetics Section, Oregon National Primate Research Center, Beaverton, OR, USA.,Oregon Health & Science University, Portland, OR, USA
| | - Michael J Raboin
- Primate Genetics Section, Oregon National Primate Research Center, Beaverton, OR, USA.,Oregon Health & Science University, Portland, OR, USA
| | - John Letaw
- Primate Genetics Section, Oregon National Primate Research Center, Beaverton, OR, USA.,Oregon Health & Science University, Portland, OR, USA
| | - Kimberly A Nevonen
- Primate Genetics Section, Oregon National Primate Research Center, Beaverton, OR, USA.,Oregon Health & Science University, Portland, OR, USA
| | - Jennifer E Spindel
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, USA
| | - Susan R McCouch
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, USA
| | - Rita Cervera-Juanes
- Primate Genetics Section, Oregon National Primate Research Center, Beaverton, OR, USA.,Oregon Health & Science University, Portland, OR, USA
| | - Eliot Spindel
- Primate Genetics Section, Oregon National Primate Research Center, Beaverton, OR, USA.,Oregon Health & Science University, Portland, OR, USA
| | - Lucia Carbone
- Primate Genetics Section, Oregon National Primate Research Center, Beaverton, OR, USA.,Oregon Health & Science University, Portland, OR, USA
| | - Betsy Ferguson
- Primate Genetics Section, Oregon National Primate Research Center, Beaverton, OR, USA.,Oregon Health & Science University, Portland, OR, USA
| | - Amanda Vinson
- Primate Genetics Section, Oregon National Primate Research Center, Beaverton, OR, USA. .,Oregon Health & Science University, Portland, OR, USA.
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Summers CF, Gulliford CM, Carlson CH, Lillis JA, Carlson MO, Cadle-Davidson L, Gent DH, Smart CD. Identification of Genetic Variation between Obligate Plant Pathogens Pseudoperonospora cubensis and P. humuli Using RNA Sequencing and Genotyping-By-Sequencing. PLoS One 2015; 10:e0143665. [PMID: 26599440 PMCID: PMC4658093 DOI: 10.1371/journal.pone.0143665] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/06/2015] [Indexed: 12/29/2022] Open
Abstract
RNA sequencing (RNA-seq) and genotyping-by-sequencing (GBS) were used for single nucleotide polymorphism (SNP) identification from two economically important obligate plant pathogens, Pseudoperonospora cubensis and P. humuli. Twenty isolates of P. cubensis and 19 isolates of P. humuli were genotyped using RNA-seq and GBS. Principle components analysis (PCA) of each data set showed genetic separation between the two species. Additionally, results supported previous findings that P. cubensis isolates from squash are genetically distinct from cucumber and cantaloupe isolates. A PCA-based procedure was used to identify SNPs correlated with the separation of the two species, with 994 and 4,231 PCA-correlated SNPs found within the RNA-seq and GBS data, respectively. The corresponding unigenes (n = 800) containing these potential species-specific SNPs were then annotated and 135 putative pathogenicity genes, including 3 effectors, were identified. The characterization of genes containing SNPs differentiating these two closely related downy mildew species may contribute to the development of improved detection and diagnosis strategies and improve our understanding of host specificity pathways.
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Affiliation(s)
- Carly F. Summers
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, New York, United States of America
| | - Colwyn M. Gulliford
- Cornell Laboratory for Accelerator-based Sciences and Education, Cornell University, Ithaca, New York, United States of America
| | - Craig H. Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, New York, United States of America
| | - Jacquelyn A. Lillis
- United States Department of Agriculture Agricultural Research Service, Grape Genetics Research Unit, Geneva, New York, United States of America
| | - Maryn O. Carlson
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, New York, United States of America
| | - Lance Cadle-Davidson
- United States Department of Agriculture Agricultural Research Service, Grape Genetics Research Unit, Geneva, New York, United States of America
| | - David H. Gent
- United States Department of Agriculture Agricultural Research Service, Forage Seed and Cereal Research Unit and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Christine D. Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, New York, United States of America
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