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Lucas SE, Yang T, Wimberly CE, Parmar KV, Hansen HM, de Smith AJ, Morimoto LM, Metayer C, Ostrom QT, Eward WC, Graves LA, Wagner LM, Wiemels JL, Spector LG, Walsh KM. Genetic variation near GRB10 associated with bone growth and osteosarcoma risk in canine and human populations. Cancer Epidemiol 2024:102599. [PMID: 38871555 DOI: 10.1016/j.canep.2024.102599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND Canine and human osteosarcoma are similar in clinical presentation and tumor genomics. Giant breed dogs experience elevated osteosarcoma incidence, and taller stature remains a consistent risk factor for human osteosarcoma. Whether evolutionarily conserved genes contribute to both human and canine osteosarcoma predisposition merits evaluation. METHODS A multi-center sample of childhood osteosarcoma patients and controls underwent genome-wide genotyping and imputation. Ancestry-adjusted SNP associations were calculated within each dataset using logistic regression, then meta-analyzed across the three datasets, totaling 1091 patients and 3026 controls. Ten regions previously associated with canine osteosarcoma risk were mapped to the human genome, spanning ∼6 Mb. We prioritized association testing of 5985 human SNPs mapping to candidate osteosarcoma risk regions detected in Irish wolfhounds, the largest dog breed studied. Secondary analyses explored 6289 additional human SNPs mapping to candidate osteosarcoma risk regions identified in Rottweilers and greyhounds. RESULTS Fourteen SNPs were associated with human osteosarcoma risk after adjustment for multiple comparisons, all within a 42 kb region of human Chromosome 7p12.1. The lead variant was rs17454681 (OR=1.25, 95 %CI: 1.12-1.39; P=4.1×10-5), and independent risk variants were not observed in conditional analyses. While the associated region spanned 2.1 Mb and contained eight genes in Irish wolfhounds, associations were localized to a 50-fold smaller region of the human genome and strongly implicate GRB10 (growth factor receptor-bound protein 10) in canine and human osteosarcoma predisposition. PheWAS analysis in UK Biobank data identified noteworthy associations of the rs17454681 risk allele with varied measures of height and pubertal timing. CONCLUSIONS Our comparative oncology analysis identified a novel human osteosarcoma risk allele near GRB10, a growth inhibitor that suppresses activated receptor tyrosine kinases including IGF1R, PDGFRB, and EGFR. Epidemiologists may benefit from leveraging cross-species comparisons to identify haplotypes in highly susceptible but genetically homogenous populations of domesticated animals, then fine-mapping these associations in diverse human populations.
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Affiliation(s)
- Sydney E Lucas
- Preston Robert Tisch Brain Tumor Center, Department of Neurosurgery, Duke University, Durham, NC, USA; Division of Pediatric Hematology/Oncology, Duke University Medical Center, Durham, NC, USA
| | - Tianzhong Yang
- Division of Biostatistics and Health Data Science, School of Public Health, University of Minnesota, Minneapolis, MN, USA; Division of Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA; Division of Pediatric Hematology/Oncology, Duke University Medical Center, Durham, NC, USA
| | - Courtney E Wimberly
- Preston Robert Tisch Brain Tumor Center, Department of Neurosurgery, Duke University, Durham, NC, USA; Division of Pediatric Hematology/Oncology, Duke University Medical Center, Durham, NC, USA
| | - Kajal V Parmar
- Preston Robert Tisch Brain Tumor Center, Department of Neurosurgery, Duke University, Durham, NC, USA; Division of Pediatric Hematology/Oncology, Duke University Medical Center, Durham, NC, USA
| | - Helen M Hansen
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA; Division of Pediatric Hematology/Oncology, Duke University Medical Center, Durham, NC, USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA; Division of Pediatric Hematology/Oncology, Duke University Medical Center, Durham, NC, USA
| | - Libby M Morimoto
- School of Public Health, University of California, Berkeley, Berkeley, CA, USA; Division of Pediatric Hematology/Oncology, Duke University Medical Center, Durham, NC, USA
| | - Catherine Metayer
- School of Public Health, University of California, Berkeley, Berkeley, CA, USA; Division of Pediatric Hematology/Oncology, Duke University Medical Center, Durham, NC, USA
| | - Quinn T Ostrom
- Preston Robert Tisch Brain Tumor Center, Department of Neurosurgery, Duke University, Durham, NC, USA; Duke Cancer Institute, Duke University, Durham, NC, USA; Division of Pediatric Hematology/Oncology, Duke University Medical Center, Durham, NC, USA
| | - William C Eward
- Duke Cancer Institute, Duke University, Durham, NC, USA; Department of Orthopaedic Surgery, Duke University, Durham, NC, USA; Division of Pediatric Hematology/Oncology, Duke University Medical Center, Durham, NC, USA
| | - Laurie A Graves
- Department of Pediatrics, Duke University, Durham, NC, USA; Division of Pediatric Hematology/Oncology, Duke University Medical Center, Durham, NC, USA
| | - Lars M Wagner
- Duke Cancer Institute, Duke University, Durham, NC, USA; Department of Pediatrics, Duke University, Durham, NC, USA; Division of Pediatric Hematology/Oncology, Duke University Medical Center, Durham, NC, USA
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA; Division of Pediatric Hematology/Oncology, Duke University Medical Center, Durham, NC, USA
| | - Logan G Spector
- Division of Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA; Division of Pediatric Hematology/Oncology, Duke University Medical Center, Durham, NC, USA
| | - Kyle M Walsh
- Preston Robert Tisch Brain Tumor Center, Department of Neurosurgery, Duke University, Durham, NC, USA; Duke Cancer Institute, Duke University, Durham, NC, USA; Department of Pediatrics, Duke University, Durham, NC, USA; Division of Pediatric Hematology/Oncology, Duke University Medical Center, Durham, NC, USA.
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2
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Cars BS, Kessler C, Hoffman EA, Côté SD, Koelsch D, Shafer ABA. Island demographics and trait associations in white-tailed deer. Heredity (Edinb) 2024:10.1038/s41437-024-00685-2. [PMID: 38802598 DOI: 10.1038/s41437-024-00685-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/29/2024] Open
Abstract
When a population is isolated and composed of few individuals, genetic drift is the paramount evolutionary force and results in the loss of genetic diversity. Inbreeding might also occur, resulting in genomic regions that are identical by descent, manifesting as runs of homozygosity (ROHs) and the expression of recessive traits. Likewise, the genes underlying traits of interest can be revealed by comparing fixed SNPs and divergent haplotypes between affected and unaffected individuals. Populations of white-tailed deer (Odocoileus virginianus) on islands of Saint Pierre and Miquelon (SPM, France) have high incidences of leucism and malocclusions, both considered genetic defects; on the Florida Keys islands (USA) deer exhibit smaller body sizes, a polygenic trait. Here we aimed to reconstruct island demography and identify the genes associated with these traits in a pseudo case-control design. The two island populations showed reduced levels of genomic diversity and a build-up of deleterious mutations compared to mainland deer; there was also significant genome-wide divergence in Key deer. Key deer showed higher inbreeding levels, but not longer ROHs, consistent with long-term isolation. We identified multiple trait-related genes in ROHs including LAMTOR2 which has links to pigmentation changes, and NPVF which is linked to craniofacial abnormalities. Our mixed approach of linking ROHs, fixed SNPs and haplotypes matched a high number (~50) of a-priori body size candidate genes in Key deer. This suite of biomarkers and candidate genes should prove useful for population monitoring, noting all three phenotypes show patterns consistent with a complex trait and non-Mendelian inheritance.
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Affiliation(s)
- Brooklyn S Cars
- Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada
- Department of Forensics, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada
| | - Camille Kessler
- Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada
| | - Eric A Hoffman
- Department of Biology, University of Central Florida, 4000, Central Florida Blvd, Orlando, FL, USA
| | - Steeve D Côté
- Département de Biologie and Centre d'Études Nordiques, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Daniel Koelsch
- Fédération des chasseurs de Saint-Pierre et Miquelon, Saint-Pierre et Miquelon, France
- Direction des Territoires de l'Alimentation et de la Mer, service Biodiversité, Saint-Pierre et Miquelon, France
| | - Aaron B A Shafer
- Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada.
- Department of Forensics, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada.
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3
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Sweetalana, Mooney JA, Szpiech ZA. Genotypic and phenotypic consequences of domestication in dogs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592072. [PMID: 38746159 PMCID: PMC11092585 DOI: 10.1101/2024.05.01.592072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Runs of homozygosity (ROH) are genomic regions that arise when two copies of an identical ancestral haplotype are inherited from parents with a recent common ancestor. In this study, we performed a novel comprehensive analysis to infer genetic diversity among dogs and quantified the association between ROH and non-disease phenotypes. We found distinct patterns of genetic diversity across clades of breed dogs and elevated levels of long ROH, compared to non- domesticated dogs. These high levels of F ROH (inbreeding coefficient) are a consequence of recent inbreeding among domesticated dogs during breed establishment. We identified statistically significant associations between F ROH and height, weight, lifespan, muscled, white head, white chest, furnish, and length of fur. After correcting for population structure, we identified more than 45 genes across the three examined quantitative traits that exceeded the threshold for suggestive significance, indicating significant polygenic inheritance for the complex quantitative phenotypes in dogs.
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4
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Heinrich J, Berger C, Berger B, Hecht W, Phillips C, Parson W. The LASSIE MPS panel: Predicting externally visible traits in dogs for forensic purposes. Forensic Sci Int Genet 2023; 66:102893. [PMID: 37290253 DOI: 10.1016/j.fsigen.2023.102893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/28/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
Predicting the outward appearance of dogs via their DNA, also known as Canine DNA Phenotyping, is a young, emerging field of research in forensic genetics. The few previous studies published in this respect were restricted to the consecutive analysis of single DNA markers, a process that is time- and sample-consuming and therefore not a viable option for limited forensic specimens. Here, we report on the development and evaluation of a Massively Parallel Sequencing (MPS) based molecular genetic assay, the LASSIE MPS Panel. This panel aims to predict externally visible as well as skeletal traits, which include coat color, coat pattern, coat structure, tail morphology, skull shape, ear shape, eye color and body size from DNA using 44 genetic markers in a single molecular genetic assay. A biostatistical naïve Bayes classification approach was applied to identify the most informative marker combinations for predicting phenotypes. Overall, the predictive performance was characterized by a very high classification success for some of the trait categories, and high to moderate success for others. The performance of the developed predictive framework was further evaluated using blind samples from three randomly selected dog individuals, whose appearance was well predicted.
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Affiliation(s)
- Josephin Heinrich
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Cordula Berger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Burkhard Berger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Werner Hecht
- Institute of Veterinary Pathology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA.
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5
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Paloma Álvarez-Rendón J, Manuel Murillo-Maldonado J, Rafael Riesgo-Escovar J. The insulin signaling pathway a century after its discovery: Sexual dimorphism in insulin signaling. Gen Comp Endocrinol 2023; 330:114146. [PMID: 36270337 DOI: 10.1016/j.ygcen.2022.114146] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 10/10/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022]
Abstract
Since practically a century ago, the insulin pathway was discovered in both vertebrates and invertebrates, implying an evolutionarily ancient origin. After a century of research, it is now clear that the insulin signal transduction pathway is a critical, flexible and pleiotropic pathway, evolving into multiple anabolic functions besides glucose homeostasis. It regulates paramount aspects of organismal well-being like growth, longevity, intermediate metabolism, and reproduction. Part of this diversification has been attained by duplications and divergence of both ligands and receptors riding on a common general signal transduction system. One of the aspects that is strikingly different is its usage in reproduction, particularly in male versus female development and fertility within the same species. This review highlights sexual divergence in metabolism and reproductive tract differences, the occurrence of sexually "exaggerated" traits, and sex size differences that are due to the sexes' differential activity/response to the insulin signaling pathway.
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Affiliation(s)
- Jéssica Paloma Álvarez-Rendón
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México (UNAM), Mexico
| | - Juan Manuel Murillo-Maldonado
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México (UNAM), Mexico
| | - Juan Rafael Riesgo-Escovar
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México (UNAM), Mexico.
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6
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Binversie EE, Momen M, Rosa GJM, Davis BW, Muir P. Across-breed genetic investigation of canine hip dysplasia, elbow dysplasia, and anterior cruciate ligament rupture using whole-genome sequencing. Front Genet 2022; 13:913354. [PMID: 36531249 PMCID: PMC9755188 DOI: 10.3389/fgene.2022.913354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022] Open
Abstract
Here, we report the use of genome-wide association study (GWAS) for the analysis of canine whole-genome sequencing (WGS) repository data using breed phenotypes. Single-nucleotide polymorphisms (SNPs) were called from WGS data from 648 dogs that included 119 breeds from the Dog10K Genomes Project. Next, we assigned breed phenotypes for hip dysplasia (Orthopedic Foundation for Animals (OFA) HD, n = 230 dogs from 27 breeds; hospital HD, n = 279 dogs from 38 breeds), elbow dysplasia (ED, n = 230 dogs from 27 breeds), and anterior cruciate ligament rupture (ACL rupture, n = 279 dogs from 38 breeds), the three most important canine spontaneous complex orthopedic diseases. Substantial morbidity is common with these diseases. Previous within- and between-breed GWAS for HD, ED, and ACL rupture using array SNPs have identified disease-associated loci. Individual disease phenotypes are lacking in repository data. There is a critical knowledge gap regarding the optimal approach to undertake categorical GWAS without individual phenotypes. We considered four GWAS approaches: a classical linear mixed model, a haplotype-based model, a binary case-control model, and a weighted least squares model using SNP average allelic frequency. We found that categorical GWAS was able to validate HD candidate loci. Additionally, we discovered novel candidate loci and genes for all three diseases, including FBX025, IL1A, IL1B, COL27A1, SPRED2 (HD), UGDH, FAF1 (ED), TGIF2 (ED & ACL rupture), and IL22, IL26, CSMD1, LDHA, and TNS1 (ACL rupture). Therefore, categorical GWAS of ancestral dog populations may contribute to the understanding of any disease for which breed epidemiological risk data are available, including diseases for which GWAS has not been performed and candidate loci remain elusive.
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Affiliation(s)
- Emily E. Binversie
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Mehdi Momen
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Guilherme J. M. Rosa
- Department of Animal and Dairy Sciences, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Brian W. Davis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Peter Muir
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States,*Correspondence: Peter Muir,
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7
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Effect of different masses, ages, and coats on the thermoregulation of dogs before and after exercise across different seasons. Vet Res Commun 2022; 47:833-847. [DOI: 10.1007/s11259-022-10045-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 11/22/2022] [Indexed: 12/02/2022]
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8
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Zhang W, Li X, Jiang Y, Zhou M, Liu L, Su S, Xu C, Li X, Wang C. Genetic architecture and selection of Anhui autochthonous pig population revealed by whole genome resequencing. Front Genet 2022; 13:1022261. [PMID: 36324508 PMCID: PMC9618877 DOI: 10.3389/fgene.2022.1022261] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/28/2022] [Indexed: 11/29/2022] Open
Abstract
The genetic resources among pigs in Anhui Province are diverse, but their value and potential have yet to be discovered. To illustrate the genetic diversity and population structure of the Anhui pigs population, we resequenced the genome of 150 pigs from six representative Anhui pigs populations and analyzed this data together with the sequencing data from 40 Asian wild boars and commercial pigs. Our results showed that Anhui pigs were divided into two distinct types based on ancestral descent: Wannan Spotted pig (WSP) and Wannan Black pig (WBP) origins from the same ancestor and the other four populations origins from another ancestor. We also identified several potential selective sweep regions associated with domestication characteristics among Anhui pigs, including reproduction-associated genes (CABS1, INSL6, MAP3K12, IGF1R, INSR, LIMK2, PATZ1, MAPK1), lipid- and meat-related genes (SNX19, MSTN, MC5R, PRKG1, CREBBP, ADCY9), and ear size genes (MSRB3 and SOX5). Therefore, these findings expand the catalogue and how these genetic differences among pigs and this newly generated data will be a valuable resource for future genetic studies and for improving genome-assisted breeding of pigs and other domesticated animals.
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9
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Morrill K, Hekman J, Li X, McClure J, Logan B, Goodman L, Gao M, Dong Y, Alonso M, Carmichael E, Snyder-Mackler N, Alonso J, Noh HJ, Johnson J, Koltookian M, Lieu C, Megquier K, Swofford R, Turner-Maier J, White ME, Weng Z, Colubri A, Genereux DP, Lord KA, Karlsson EK. Ancestry-inclusive dog genomics challenges popular breed stereotypes. Science 2022; 376:eabk0639. [PMID: 35482869 DOI: 10.1126/science.abk0639] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Behavioral genetics in dogs has focused on modern breeds, which are isolated subgroups with distinctive physical and, purportedly, behavioral characteristics. We interrogated breed stereotypes by surveying owners of 18,385 purebred and mixed-breed dogs and genotyping 2155 dogs. Most behavioral traits are heritable [heritability (h2) > 25%], and admixture patterns in mixed-breed dogs reveal breed propensities. Breed explains just 9% of behavioral variation in individuals. Genome-wide association analyses identify 11 loci that are significantly associated with behavior, and characteristic breed behaviors exhibit genetic complexity. Behavioral loci are not unusually differentiated in breeds, but breed propensities align, albeit weakly, with ancestral function. We propose that behaviors perceived as characteristic of modern breeds derive from thousands of years of polygenic adaptation that predates breed formation, with modern breeds distinguished primarily by aesthetic traits.
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Affiliation(s)
- Kathleen Morrill
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.,Morningside Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jessica Hekman
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xue Li
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.,Morningside Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jesse McClure
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Brittney Logan
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Linda Goodman
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Fauna Bio Inc., Emeryville, CA 94608, USA
| | - Mingshi Gao
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.,Morningside Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Yinan Dong
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Marjie Alonso
- The International Association of Animal Behavior Consultants, Cranberry Township, PA 16066, USA.,IAABC Foundation, Cranberry Township, PA 16066, USA
| | - Elena Carmichael
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Rice University, Houston, TX 77005, USA
| | - Noah Snyder-Mackler
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85251, USA.,School for Human Evolution and Social Change, Arizona State University, Tempe, AZ 85251, USA.,School of Life Sciences, Arizona State University, Tempe, AZ 85251, USA
| | - Jacob Alonso
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hyun Ji Noh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jeremy Johnson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Charlie Lieu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Darwin's Ark Foundation, Seattle, WA 98026, USA
| | - Kate Megquier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ross Swofford
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Michelle E White
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Zhiping Weng
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Andrés Colubri
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Kathryn A Lord
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Elinor K Karlsson
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.,Morningside Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Darwin's Ark Foundation, Seattle, WA 98026, USA.,Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
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10
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Salgado Pardo JI, Delgado Bermejo JV, González Ariza A, León Jurado JM, Marín Navas C, Iglesias Pastrana C, Martínez Martínez MDA, Navas González FJ. Candidate Genes and Their Expressions Involved in the Regulation of Milk and Meat Production and Quality in Goats ( Capra hircus). Animals (Basel) 2022; 12:ani12080988. [PMID: 35454235 PMCID: PMC9026325 DOI: 10.3390/ani12080988] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/21/2022] [Accepted: 04/07/2022] [Indexed: 12/13/2022] Open
Abstract
Simple Summary During the present decade, highly selected caprine farming has increased in popularity due to the hardiness and adaptability inherent to goats. Recent advances in genetics have enabled the improvement in goat selection efficiency. The present review explores how genetic technologies have been applied to the goat-farming sector in the last century. The main candidate genes related to economically relevant traits are reported. The major source of income in goat farming derives from the sale of milk and meat. Consequently, yield and quality must be specially considered. Meat-related traits were evaluated considering three functional groups (weight gain, carcass quality and fat profile). Milk traits were assessed in three additional functional groups (milk production, protein and fat content). Abstract Despite their pivotal position as relevant sources for high-quality proteins in particularly hard environmental contexts, the domestic goat has not benefited from the advances made in genomics compared to other livestock species. Genetic analysis based on the study of candidate genes is considered an appropriate approach to elucidate the physiological mechanisms involved in the regulation of the expression of functional traits. This is especially relevant when such functional traits are linked to economic interest. The knowledge of candidate genes, their location on the goat genetic map and the specific phenotypic outcomes that may arise due to the regulation of their expression act as a catalyzer for the efficiency and accuracy of goat-breeding policies, which in turn translates into a greater competitiveness and sustainable profit for goats worldwide. To this aim, this review presents a chronological comprehensive analysis of caprine genetics and genomics through the evaluation of the available literature regarding the main candidate genes involved in meat and milk production and quality in the domestic goat. Additionally, this review aims to serve as a guide for future research, given that the assessment, determination and characterization of the genes associated with desirable phenotypes may provide information that may, in turn, enhance the implementation of goat-breeding programs in future and ensure their sustainability.
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Affiliation(s)
- Jose Ignacio Salgado Pardo
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
| | - Juan Vicente Delgado Bermejo
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
| | - Antonio González Ariza
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
| | - José Manuel León Jurado
- Agropecuary Provincial Center of Córdoba, Provincial Council of Córdoba, 14014 Córdoba, Spain;
| | - Carmen Marín Navas
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
| | - Carlos Iglesias Pastrana
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
| | - María del Amparo Martínez Martínez
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
| | - Francisco Javier Navas González
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
- Institute of Agricultural Research and Training (IFAPA), Alameda del Obispo, 14004 Córdoba, Spain
- Correspondence: ; Tel.: +34-63-853-5046 (ext. 621262)
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11
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Sándor S, Jónás D, Tátrai K, Czeibert K, Kubinyi E. Poly(A) RNA sequencing reveals age-related differences in the prefrontal cortex of dogs. GeroScience 2022; 44:1269-1293. [PMID: 35288843 PMCID: PMC9213612 DOI: 10.1007/s11357-022-00533-3] [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: 08/24/2021] [Accepted: 02/17/2022] [Indexed: 12/02/2022] Open
Abstract
Dogs may possess a unique translational potential to investigate neural aging and dementia because they are prone to age-related cognitive decline, including an Alzheimer’s disease–like pathological condition. Yet very little is known about the molecular mechanisms underlying canine cognitive decline. The goal of the current study was to explore the transcriptomic differences between young and old dogs’ frontal cortex, which is a brain region often affected by various forms of age-related dementia in humans. RNA isolates from the frontal cortical brain area of 13 pet dogs, which represented 7 different breeds and crossbreds, were analyzed. The dogs were euthanized for medical reasons, and their bodies had been donated by their owners for scientific purposes. The poly(A) tail RNA subfraction of the total transcriptome was targeted in the sequencing analysis. Cluster analyses, differential gene expression analyses, and gene ontology analyses were carried out to assess which genes and genetic regulatory mechanisms were mostly affected by aging. Age was the most prominent factor in the clustering of the animals, indicating the presence of distinct gene expression patterns related to aging in a genetically variable population. A total of 3436 genes were found to be differentially expressed between the age groups, many of which were linked to neural function, immune system, and protein synthesis. These findings are in accordance with previous human brain aging RNA sequencing studies. Some genes were found to behave more similarly to humans than to rodents, further supporting the applicability of dogs in translational aging research.
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Affiliation(s)
- Sára Sándor
- Department of Ethology, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary.
| | - Dávid Jónás
- Department of Ethology, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary
| | - Kitti Tátrai
- Department of Ethology, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary.,Department of Genetics, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary
| | - Kálmán Czeibert
- Department of Ethology, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary
| | - Eniko Kubinyi
- Department of Ethology, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary
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12
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Raymond PW, Velie BD, Wade CM. Forensic DNA phenotyping: Canis familiaris breed classification and skeletal phenotype prediction using functionally significant skeletal SNPs and indels. Anim Genet 2021; 53:247-263. [PMID: 34963196 DOI: 10.1111/age.13165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/30/2021] [Accepted: 12/12/2021] [Indexed: 11/29/2022]
Abstract
This review highlights a novel application of breed identification and prediction of skeletal traits in forensic investigations using canine DNA evidence. Currently, genotyping methods used for canine breed classification involve the application of highly polymorphic short tandem repeats in addition to larger commercially available SNP arrays. Both applications face technical challenges. An additional approach to breed identification could be through genotyping SNPs and indels that characterise the array of skeletal differences displayed across domestic dog populations. Research has shown that a small number of genetic variants of large effect drive differences in skeletal phenotypes among domestic dog breeds. This feature makes functionally significant canine skeletal variants a cost-effective target for forensic investigators to classify individuals according to their breed. Further analysis of these skeletal variants would enable the prediction of external appearance. To date, functionally significant genes with genetic variants associated with differences in size, bulk, skull shape, ear shape, limb length, digit type, and tail morphology have been uncovered. Recommendations of a cost-effective genotyping method that can be readily designed and applied by forensic investigators have been given. Further advances to improve the field of canine skeletal forensic DNA phenotyping include the refinement of phenotyping methods, further biological validation of the skeletal genetic variants and establishing a publicly available database for storage of allele frequencies of the skeletal genetic variants in the wider domestic dog population.
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Affiliation(s)
- Patrick W Raymond
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Brandon D Velie
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Claire M Wade
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
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13
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Insight into the Candidate Genes and Enriched Pathways Associated with Height, Length, Length to Height Ratio and Body-Weight of Korean Indigenous Breed, Jindo Dog Using Gene Set Enrichment-Based GWAS Analysis. Animals (Basel) 2021; 11:ani11113136. [PMID: 34827868 PMCID: PMC8614278 DOI: 10.3390/ani11113136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/21/2021] [Accepted: 10/28/2021] [Indexed: 12/14/2022] Open
Abstract
As a companion and hunting dog, height, length, length to height ratio (LHR) and body-weight are the vital economic traits for Jindo dog. Human selection and targeted breeding have produced an extraordinary diversity in these traits. Therefore, the identification of causative markers, genes and pathways that help us to understand the genetic basis of this variability is essential for their selection purposes. Here, we performed a genome-wide association study (GWAS) combined with enrichment analysis on 757 dogs using 118,879 SNPs. The genomic heritability (h2) was 0.33 for height and 0.28 for weight trait in Jindo. At p-value < 5 × 10-5, ten, six, thirteen and eleven SNPs on different chromosomes were significantly associated with height, length, LHR and body-weight traits, respectively. Based on our results, HHIP, LCORL and NCAPG for height, IGFI and FGFR3 for length, DLK1 and EFEMP1 for LHR and PTPN2, IGFI and RASAL2 for weight can be the potential candidate genes because of the significant SNPs located in their intronic or upstream regions. The gene-set enrichment analysis highlighted here nine and seven overlapping significant (p < 0.05) gene ontology (GO) terms and pathways among traits. Interestingly, the highlighted pathways were related to hormone synthesis, secretion and signalling were generally involved in the metabolism, growth and development process. Our data provide an insight into the significant genes and pathways if verified further, which will have a significant effect on the breeding of the Jindo dog's population.
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14
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Brabazon DC, Callanan JJ, Nolan CM. Imprinting of canine IGF2 and H19. Anim Genet 2021; 53:108-118. [PMID: 34676575 DOI: 10.1111/age.13148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2021] [Indexed: 11/29/2022]
Abstract
Genomic imprinting occurs in therian mammals and is a phenomenon whereby the two alleles of a gene are differentially expressed, based on the sex of the parent from whom the alleles were inherited. The allelic differences in expression are the consequence of different epigenetic modifications that are established in the sperm or oocyte during gametogenesis and transmitted at fertilization to offspring. A small minority of genes is regulated in this way but they have important biological functions, and aberrant regulation of imprinted genes contributes to disease aetiology in humans and other animals. The factors driving the evolution of imprinted genes are also of considerable interest, as these genes appear to forego the benefits of diploidy. To broaden the phylogenetic analysis of genomic imprinting, we began a study of imprinted genes in the domestic dog, Canis familiaris. In this report, we show that canine IGF2 and H19 are imprinted, with parent-of origin-dependent monoallelic expression patterns in neonatal umbilical cord. We identify a putative imprint control region associated with the genes, and provide evidence for differential methylation of this region in a somatic tissue (umbilical cord) and for its hypermethylation in the male germline. Canis familiaris is fast becoming a highly informative system for elucidating disease processes and evolution, and the study of imprinted genes in this species may help in understanding how these genes contribute to the generation of morphological and behavioral diversity.
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Affiliation(s)
- D C Brabazon
- University College Dublin School of Biology and Environmental Science, Belfield, Dublin 4, Ireland
| | - J J Callanan
- University College Dublin School of Veterinary Medicine, Belfield, Dublin 4, Ireland
| | - C M Nolan
- University College Dublin School of Biology and Environmental Science, Belfield, Dublin 4, Ireland
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15
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Lyu G, Feng C, Zhu S, Ren S, Dang W, Irwin DM, Wang Z, Zhang S. Whole Genome Sequencing Reveals Signatures for Artificial Selection for Different Sizes in Japanese Primitive Dog Breeds. Front Genet 2021; 12:671686. [PMID: 34335687 PMCID: PMC8317602 DOI: 10.3389/fgene.2021.671686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/24/2021] [Indexed: 11/13/2022] Open
Abstract
Body size is an important trait in companion animals. Recently, a primitive Japanese dog breed, the Shiba Inu, has experienced artificial selection for smaller body size, resulting in the "Mame Shiba Inu" breed. To identify loci and genes that might explain the difference in the body size of these Shiba Inu dogs, we applied whole genome sequencing of pooled samples (pool-seq) on both Shiba Inu and Mame Shiba Inu. We identified a total of 13,618,261 unique SNPs in the genomes of these two breeds of dog. Using selective sweep approaches, including F ST, H p and XP-CLR with sliding windows, we identified a total of 12 genomic windows that show signatures of selection that overlap with nine genes (PRDM16, ZNF382, ZNF461, ERGIC2, ENSCAFG00000033351, CCDC61, ALDH3A2, ENSCAFG00000011141, and ENSCAFG00000018533). These results provide candidate genes and specific sites that might be associated with body size in dogs. Some of these genes are associated with body size in other mammals, but 8 of the 9 genes are novel candidate genes that need further study.
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Affiliation(s)
- Guangqi Lyu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Chunyu Feng
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Shiyu Zhu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Shuang Ren
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Wanyi Dang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Zhe Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Shuyi Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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16
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SINE Insertion in the Intron of Pig GHR May Decrease Its Expression by Acting as a Repressor. Animals (Basel) 2021; 11:ani11071871. [PMID: 34201672 PMCID: PMC8300111 DOI: 10.3390/ani11071871] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/15/2021] [Accepted: 06/19/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary GH/IGF axis genes play a central role in the regulation of skeletal accretion during development and growth, and thus represent candidate genes for growth traits. Retrotransposon insertion polymorphisms are major contributors to structural variations. They tend to generate large effect mutations resulting in variations in target gene activity and phenotype due to the fact that they carry functional elements, such as enhancers, insulators, or promoters. In the present study, RIPs in four GH/IGF axis genes (GH, GHR, IGF1, and IGF1R) were investigated by comparative genomics and PCR. Four RIPs in the GHR gene and one RIP in the IGF1 gene were identified. Further analysis revealed that one RIP in the first intron of GHR might play a role in the regulation of GHR expression by acting as a repressor. These findings contribute to the understanding of the role of RIPs in the genetic variation of GH/IGF axis genes and phenotypic variation in pigs. Abstract The genetic diversity of the GH/IGF axis genes and their association with the variation of gene expression and phenotypic traits, principally represented by SNPs, have been extensively reported. Nevertheless, the impact of retrotransposon insertion polymorphisms (RIPs) on the GH/IGF axis gene activity has not been reported. In the present study, bioinformatic prediction and PCR verification were performed to screen RIPs in four GH/IGF axis genes (GH, GHR, IGF1 and IGF1R). In total, five RIPs, including one SINE RIP in intron 3 of IGF1, one L1 RIP in intron 7 of GHR, and three SINE RIPs in intron 1, intron 5 and intron 9 of GHR, were confirmed by PCR, displaying polymorphisms in diverse breeds. Dual luciferase reporter assay revealed that the SINE insertion in intron 1 of GHR significantly repressed the GHR promoter activity in PK15, Hela, C2C12 and 3T3-L1 cells. Furthermore, qPCR results confirmed that this SINE insertion was associated with a decreased expression of GHR in the leg muscle and longissimus dorsi, indicating that it may act as a repressor involved in the regulation of GHR expression. In summary, our data revealed that RIPs contribute to the genetic variation of GH/IGF axis genes, whereby one SINE RIP in the intron 1 of GHR may decrease the expression of GHR by acting as a repressor.
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Berger C, Heinrich J, Berger B, Hecht W, Parson W. Towards Forensic DNA Phenotyping for Predicting Visible Traits in Dogs. Genes (Basel) 2021; 12:genes12060908. [PMID: 34208207 PMCID: PMC8230911 DOI: 10.3390/genes12060908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 11/16/2022] Open
Abstract
The popularity of dogs as human companions explains why these pets regularly come into focus in forensic cases such as bite attacks or accidents. Canine evidence, e.g., dog hairs, can also act as a link between the victim and suspect in a crime case due to the close contact between dogs and their owners. In line with human DNA identification, dog individualization from crime scene evidence is mainly based on the analysis of short tandem repeat (STR) markers. However, when the DNA profile does not match a reference, additional information regarding the appearance of the dog may provide substantial intelligence value. Key features of the dog's appearance, such as the body size and coat colour are well-recognizable and easy to describe even to non-dog experts, including most investigating officers and eyewitnesses. Therefore, it is reasonable to complement eyewitnesses' testimonies with externally visible traits predicted from associated canine DNA samples. Here, the feasibility and suitability of canine DNA phenotyping is explored from scratch in the form of a proof of concept study. To predict the overall appearance of an unknown dog from its DNA as accurately as possible, the following six traits were chosen: (1) coat colour, (2) coat pattern, (3) coat structure, (4) body size, (5) ear shape, and (6) tail length. A total of 21 genetic markers known for high predicting values for these traits were selected from previously published datasets, comprising 15 SNPs and six INDELS. Three of them belonged to SINE insertions. The experiments were designed in three phases. In the first two stages, the performance of the markers was tested on DNA samples from dogs with well-documented physical characteristics from different breeds. The final blind test, including dogs with initially withheld appearance information, showed that the majority of the selected markers allowed to develop composite sketches, providing a realistic impression of the tested dogs. We regard this study as the first attempt to evaluate the possibilities and limitations of forensic canine DNA phenotyping.
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Affiliation(s)
- Cordula Berger
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (J.H.); (B.B.); (W.P.)
- Correspondence: ; Tel.: +43-512-9003-70640
| | - Josephin Heinrich
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (J.H.); (B.B.); (W.P.)
| | - Burkhard Berger
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (J.H.); (B.B.); (W.P.)
| | - Werner Hecht
- Institute of Veterinary Pathology, Justus-Liebig-University Giessen, 35390 Giessen, Germany;
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (J.H.); (B.B.); (W.P.)
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16801, USA
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Kiviranta AM, Rusbridge C, Lappalainen AK, Junnila JJT, Jokinen TS. Persistent fontanelles in Chihuahuas. Part II: Association with craniocervical junction abnormalities, syringomyelia, and ventricular volume. J Vet Intern Med 2021; 35:1848-1856. [PMID: 33939205 PMCID: PMC8295681 DOI: 10.1111/jvim.16123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 12/13/2022] Open
Abstract
Background Persistent fontanelles (PFs) are, in Chihuahuas, almost ubiquitous. Furthermore, Chihuahuas are predisposed to other craniomorphological abnormalities, including syringomyelia (SM), ventriculomegaly, and craniocervical junction (CCJ) overcrowding resulting in neural tissue deviation. It is, however, undetermined if PFs are more common in dogs with these structural abnormalities, and their etiology is unknown. Hypothesis/Objectives Persistent fontanelles are more numerous and larger in Chihuahuas with low body weight, older age, SM, dilated fourth ventricle, ventriculomegaly, and CCJ overcrowding. Animals Fifty client‐owned Chihuahuas. Methods Cross‐sectional study evaluating the association of both the number of cranial sutures affected by PFs (NAS) and total fontanelle area (TFA), based on computed tomography with SM, fourth ventricle dilatation, lateral ventricle volume, and extent of neural tissue compression at the CCJ based on magnetic resonance images. Results The NASs was higher and TFA larger in dogs with low body weight (NAS: P = .007; 95% confidence interval [CI] = 0.384‐0.861; TFA: P = .002; 95% CI = −1.91 to −0.478), larger lateral ventricles (NAS: P ≤ .001; 95% CI = 1.04‐1.15; TFA: P ≤ .001; 95% CI = 0.099‐0.363), and more severe neural tissue compression at the CCJ (NAS: P ≤ .001; 95% CI = 1.26‐2.06; TFA: P = .03; 95% CI = 0.066‐1.13). Similarly, dogs with SM (NAS: P = .004; 95% CI = 1.26‐3.32; TFA: mean ± SD, 130 ± 217 mm2; P = .05) had higher NAS and larger TFA than did dogs without SM (43.7 ± 61.0 mm2). Age was not associated with NAS (P = .81; 95% CI = 0.989‐1.01) or TFA (P = .33; 95% CI = −0.269 to 0.092). Conclusions and Clinical Importance Persistent fontanelles are associated with small size, SM, ventriculomegaly, and CCJ overcrowding.
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Affiliation(s)
- Anna-Mariam Kiviranta
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Clare Rusbridge
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom.,Fitzpatrick Referrals Halfway Lane, Eashing Godalming, Surrey, United Kingdom
| | - Anu K Lappalainen
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | | | - Tarja S Jokinen
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
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19
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Yan CC, Zhang XS, Zhou L, Yang Q, Zhou M, Zhang LW, Xing JC, Yan ZF, Price M, Li J, Yue BS, Fan ZX. Effects of aging on gene expression in blood of captive Tibetan macaques ( Macaca thibetana) and comparisons with expression in humans. Zool Res 2021; 41:557-563. [PMID: 32746507 PMCID: PMC7475009 DOI: 10.24272/j.issn.2095-8137.2020.092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Changes in gene expression occur as animals, including primates, age. Macaques have long been used as a model species for primate evolution and biomedical studies. Here, to study gene expression in Tibetan macaques (Macaca thibetana, TMs) and its differences to humans, we applied RNA-Seq to obtain the blood transcriptomes of 24 TMs. In total, 2 523 age-associated differentially expressed genes (DEGs) were identified. Several pathways and processes that regulate aging, including the FoxO signaling pathway, autophagy, and platelet activation, were significantly enriched in the up-regulated DEGs. Two significantly age-related modules were identified by weighted gene co-expression network analysis (WGCNA). The TMs and humans shared 279 common DEGs, including 111 up-regulated and 141 down-regulated genes with advancing age in the same expression direction. However, 27 age-related DEGs presented the opposite expression direction in TMs as that in humans. For example, INPPL1, with inhibitory effects on the B cell receptor signaling pathway, was up-regulated in humans but down-regulated in TMs. In general, our study suggests that aging is a critical factor affecting gene expression in the captive TM population. The similarities and differences in gene expression patterns between TMs and humans could provide new insights into primate evolution and benefit TM model development.
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Affiliation(s)
- Chao-Chao Yan
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Xin-Shang Zhang
- Institute of Laboratory Animal Sciences, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan 610212, China
| | - Liang Zhou
- Institute of Laboratory Animal Sciences, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan 610212, China
| | - Qiao Yang
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Min Zhou
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Lin-Wan Zhang
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Jin-Chuan Xing
- Department of Genetics, Rutgers, State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Zhi-Feng Yan
- Institute of Laboratory Animal Sciences, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan 610212, China
| | - Megan Price
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Jing Li
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Bi-Song Yue
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Zhen-Xin Fan
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China. E-mail:
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20
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Zhou E, Lui J. Physiological regulation of bone length and skeletal proportion in mammals. Exp Physiol 2020; 106:389-395. [PMID: 33369789 DOI: 10.1113/ep089086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 12/11/2020] [Indexed: 11/08/2022]
Abstract
NEW FINDINGS What is the topic of this review? Mechanisms regulating bone length and skeletal proportions What advances does it highlight? The study of differential bone length between leg and finger bones, metatarsals of the Egyptian jerboa and genomic analysis of giraffes. ABSTRACT Among mammalian species, skeletal structures vary greatly in size and shape, leading to a dramatic variety of body sizes and proportions. How different bones grow to different lengths, whether among different species, different individuals of the same species, or even in different anatomical parts of our the body, has always been a fascinating subject of research in biology and physiology. In the current review, we focus on some of the recent advances in the field and discuss how these provided important new insights into the mechanisms regulating bone length and skeletal proportions.
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Affiliation(s)
- Elaine Zhou
- Section on Growth and Development, National Institute of Child Health and Human Development, NIH, Bethesda, Maryland, USA
| | - Julian Lui
- Section on Growth and Development, National Institute of Child Health and Human Development, NIH, Bethesda, Maryland, USA
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21
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Nijhout HF, Kudla AM, Hazelwood CC. Genetic assimilation and accommodation: Models and mechanisms. Curr Top Dev Biol 2020; 141:337-369. [PMID: 33602492 DOI: 10.1016/bs.ctdb.2020.11.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genetic assimilation and genetic accommodation are mechanisms by which novel phenotypes are produced and become established in a population. Novel characters may be fixed and canalized so they are insensitive to environmental variation, or can be plastic and adaptively responsive to environmental variation. In this review we explore the various theories that have been proposed to explain the developmental origin and evolution of novel phenotypes and the mechanisms by which canalization and phenotypic plasticity evolve. These theories and models range from conceptual to mathematical and have taken different views of how genes and environment contribute to the development and evolution of the properties of phenotypes. We will argue that a deeper and more nuanced understanding of genetic accommodation requires a recognition that phenotypes are not static entities but are dynamic system properties with no fixed deterministic relationship between genotype and phenotype. We suggest a mechanistic systems-view of development that allows one to incorporate both genes and environment in a common model, and that enables both quantitative analysis and visualization of the evolution of canalization and phenotypic plasticity.
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Affiliation(s)
| | - Anna M Kudla
- Department of Biology, Duke University, Durham, NC, United States
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22
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Vea IM, Shingleton AW. Network-regulated organ allometry: The developmental regulation of morphological scaling. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2020; 10:e391. [PMID: 32567243 DOI: 10.1002/wdev.391] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/30/2020] [Accepted: 05/23/2020] [Indexed: 12/11/2022]
Abstract
Morphological scaling relationships, or allometries, describe how traits grow coordinately and covary among individuals in a population. The developmental regulation of scaling is essential to generate correctly proportioned adults across a range of body sizes, while the mis-regulation of scaling may result in congenital birth defects. Research over several decades has identified the developmental mechanisms that regulate the size of individual traits. Nevertheless, we still have poor understanding of how these mechanisms work together to generate correlated size variation among traits in response to environmental and genetic variation. Conceptually, morphological scaling can be generated by size-regulatory factors that act directly on multiple growing traits (trait-autonomous scaling), or indirectly via hormones produced by central endocrine organs (systemically regulated scaling), and there are a number of well-established examples of such mechanisms. There is much less evidence, however, that genetic and environmental variation actually acts on these mechanisms to generate morphological scaling in natural populations. More recent studies indicate that growing organs can themselves regulate the growth of other organs in the body. This suggests that covariation in trait size can be generated by network-regulated scaling mechanisms that respond to changes in the growth of individual traits. Testing this hypothesis, and one of the main challenges of understanding morphological scaling, requires connecting mechanisms elucidated in the laboratory with patterns of scaling observed in the natural world. This article is categorized under: Establishment of Spatial and Temporal Patterns > Regulation of Size, Proportion, and Timing Comparative Development and Evolution > Organ System Comparisons Between Species.
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Affiliation(s)
- Isabelle M Vea
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Alexander W Shingleton
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
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Bannasch DL, Baes CF, Leeb T. Genetic Variants Affecting Skeletal Morphology in Domestic Dogs. Trends Genet 2020; 36:598-609. [PMID: 32487495 DOI: 10.1016/j.tig.2020.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 12/25/2022]
Abstract
Purebred dog breeds provide a powerful resource for the discovery of genetic variants affecting skeletal morphology. Domesticated and subsequently purebred dogs have undergone strong artificial selection for a broad range of skeletal variation, which include both the size and shapes of their bones. While the phenotypic variation between breeds is high, within-breed morphological variation is typically low. Approaches for defining genetic variants associated with canine morphology include quantitative within-breed analyses, as well as across-breed analyses, using breed standards as proxies for individual measurements. The ability to identify variants across the genomes of individual dogs can now be paired with precise measures of morphological variation to define the genetic interactions and the phenotypic effect of variants on skeletal morphology.
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Affiliation(s)
- Danika L Bannasch
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA.
| | - Christine F Baes
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada; Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
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24
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Yang Q, Chen H, Ye J, Liu C, Wei R, Chen C, Huang L. Genetic Diversity and Signatures of Selection in 15 Chinese Indigenous Dog Breeds Revealed by Genome-Wide SNPs. Front Genet 2019; 10:1174. [PMID: 31803243 PMCID: PMC6872681 DOI: 10.3389/fgene.2019.01174] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/24/2019] [Indexed: 01/01/2023] Open
Abstract
There are dozens of recognized indigenous dog breeds in China. However, these breeds have not had extensive studies to describe their population structure, genomic linkage disequilibrium (LD) patterns, and selection signatures. Here, we systematically surveyed the genomes of 157 unrelated dogs that were from 15 diverse Chinese dog breeds. Canine 170K SNP chips were used to compare the genomic structures of Chinese and Western dogs. The genotyping data of 170K SNP chips in Western dogs were downloaded from the LUPA (a European initiative of canine genome project) database. Chinese indigenous dogs had lower LD and shorter accumulative runs of homozygosity (ROH) in the genome. The genetic distances between individuals within each Chinese breed were larger than those within Western breeds. Chinese indigenous and Western dog breeds were clearly differentiated into two separate clades revealed by the PCA and NJ-tree. We found evidence for historical introgression of Western dogs into Chinese Kazakhstan shepherd and Mongolia Xi dogs. We suggested that Greenland sledge dog, Papillon, and European Eurasier have Chinese dog lineages. Selection sweep analysis identified genome-wide selection signatures of each Chinese breed and three breed groups. We highlighted several genes including EPAS1 and DNAH9 that show signatures of natural selection in Qinghai-Tibetan plateau dogs and are likely important for genetic adaptation to high altitude. Comparison of our findings with previous reports suggested RBP7, NMNAT1, SLC2A5, and H6PD that exhibit signatures of natural selection in Chinese mountain hounds as promising candidate genes for the traits of endurance and night vision, and NOL8, KRT9, RORB, and CAMTA1 that show signals of selection in Xi dogs might be candidate genes influencing dog running speed. The results about genomic and population structures, and selection signatures of Chinese dog breeds reinforce the conclusion that Chinese indigenous dogs with great variations of phenotypes are important resources for identifying genes responsible for complex traits.
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Affiliation(s)
- Qianyong Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China.,Jiangxi Provincial Key Laboratory for Police Dog Breeding and Behavioral Science, Nanchang Police Dog Base, Nanchang, China
| | - Hao Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Junhua Ye
- Jiangxi Provincial Key Laboratory for Police Dog Breeding and Behavioral Science, Nanchang Police Dog Base, Nanchang, China
| | - Chenlong Liu
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Rongxing Wei
- Jiangxi Provincial Key Laboratory for Police Dog Breeding and Behavioral Science, Nanchang Police Dog Base, Nanchang, China
| | - Congying Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Lusheng Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
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Okada H, Yagi R, Gardeux V, Deplancke B, Hafen E. Sex-dependent and sex-independent regulatory systems of size variation in natural populations. Mol Syst Biol 2019; 15:e9012. [PMID: 31777173 PMCID: PMC6878047 DOI: 10.15252/msb.20199012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 10/29/2019] [Accepted: 10/30/2019] [Indexed: 11/21/2022] Open
Abstract
Size of organs/organisms is a polygenic trait. Many of the growth-regulatory genes constitute conserved growth signaling pathways. However, how these multiple genes are orchestrated at the systems level to attain the natural variation in size including sexual size dimorphism is mostly unknown. Here we take a multi-layered systems omics approach to study size variation in the Drosophila wing. We show that expression levels of many critical growth regulators such as Wnt and TGFβ pathway components significantly differ between sexes but not between lines exhibiting size differences within each sex, suggesting a primary role of these regulators in sexual size dimorphism. Only a few growth genes including a receptor of steroid hormone ecdysone exhibit association with between-line size differences. In contrast, we find that between-line size variation is largely regulated by genes with a diverse range of cellular functions, most of which have never been implicated in growth. In addition, we show that expression quantitative trait loci (eQTLs) linked to these novel growth regulators accurately predict population-wide, between-line wing size variation. In summary, our study unveils differential gene regulatory systems that control wing size variation between and within sexes.
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Affiliation(s)
- Hirokazu Okada
- Institute of Molecular Systems BiologyETH ZurichZürichSwitzerland
| | - Ryohei Yagi
- Institute of Molecular Systems BiologyETH ZurichZürichSwitzerland
| | - Vincent Gardeux
- Laboratory of Systems Biology and GeneticsInstitute of BioengineeringSchool of Life SciencesEcole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Bart Deplancke
- Laboratory of Systems Biology and GeneticsInstitute of BioengineeringSchool of Life SciencesEcole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Ernst Hafen
- Institute of Molecular Systems BiologyETH ZurichZürichSwitzerland
- Faculty of ScienceUniversity of ZurichZurichSwitzerland
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26
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Sándor S, Kubinyi E. Genetic Pathways of Aging and Their Relevance in the Dog as a Natural Model of Human Aging. Front Genet 2019; 10:948. [PMID: 31681409 PMCID: PMC6813227 DOI: 10.3389/fgene.2019.00948] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 09/05/2019] [Indexed: 12/15/2022] Open
Abstract
Aging research has experienced a burst of scientific efforts in the last decades as the growing ratio of elderly people has begun to pose an increased burden on the healthcare and pension systems of developed countries. Although many breakthroughs have been reported in understanding the cellular mechanisms of aging, the intrinsic and extrinsic factors that contribute to senescence on higher biological levels are still barely understood. The dog, Canis familiaris, has already served as a valuable model of human physiology and disease. The possible role the dog could play in aging research is still an open question, although utilization of dogs may hold great promises as they naturally develop age-related cognitive decline, with behavioral and histological characteristics very similar to those of humans. In this regard, family dogs may possess unmatched potentials as models for investigations on the complex interactions between environmental, behavioral, and genetic factors that determine the course of aging. In this review, we summarize the known genetic pathways in aging and their relevance in dogs, putting emphasis on the yet barely described nature of certain aging pathways in canines. Reasons for highlighting the dog as a future aging and gerontology model are also discussed, ranging from its unique evolutionary path shared with humans, its social skills, and the fact that family dogs live together with their owners, and are being exposed to the same environmental effects.
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Affiliation(s)
- Sára Sándor
- Department of Ethology, Eötvös Loránd University, Budapest, Hungary
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27
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Imputation of canine genotype array data using 365 whole-genome sequences improves power of genome-wide association studies. PLoS Genet 2019; 15:e1008003. [PMID: 31525180 PMCID: PMC6762211 DOI: 10.1371/journal.pgen.1008003] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 09/26/2019] [Accepted: 08/19/2019] [Indexed: 12/11/2022] Open
Abstract
Genomic resources for the domestic dog have improved with the widespread adoption of a 173k SNP array platform and updated reference genome. SNP arrays of this density are sufficient for detecting genetic associations within breeds but are underpowered for finding associations across multiple breeds or in mixed-breed dogs, where linkage disequilibrium rapidly decays between markers, even though such studies would hold particular promise for mapping complex diseases and traits. Here we introduce an imputation reference panel, consisting of 365 diverse, whole-genome sequenced dogs and wolves, which increases the number of markers that can be queried in genome-wide association studies approximately 130-fold. Using previously genotyped dogs, we show the utility of this reference panel in identifying potentially novel associations, including a locus on CFA20 significantly associated with cranial cruciate ligament disease, and fine-mapping for canine body size and blood phenotypes, even when causal loci are not in strong linkage disequilibrium with any single array marker. This reference panel resource will improve future genome-wide association studies for canine complex diseases and other phenotypes. Complex traits are controlled by more than one gene and as such are difficult to map. For complex trait mapping in the domestic dog, researchers use the current array of 173,000 variants, with only minimal success. Here, we use a method called imputation to increase the number of variants–from 173,000 to 24 million–that can be queried in canine association studies. We use sequence data from the whole genomes of 365 dogs and wolves to accurately predict variants, in a separate cohort of dogs, that are not present on the array. Using dog body size, blood phenotypes, and a common orthopedic disease that involves rupture of the cranial cruciate ligament, we show that the increase in variants results in an increase in mapping power, through the identification of new associations and the narrowing of regions of interest. This imputation panel is particularly important because of its usefulness in improving complex trait mapping in the dog, which has significant implications for discovery of variants in humans with similar diseases.
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28
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Ostrander EA, Wang GD, Larson G, vonHoldt BM, Davis BW, Jagannathan V, Hitte C, Wayne RK, Zhang YP. Dog10K: an international sequencing effort to advance studies of canine domestication, phenotypes and health. Natl Sci Rev 2019; 6:810-824. [PMID: 31598383 PMCID: PMC6776107 DOI: 10.1093/nsr/nwz049] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/14/2019] [Accepted: 04/09/2019] [Indexed: 12/18/2022] Open
Abstract
Dogs are the most phenotypically diverse mammalian species, and they possess more known heritable disorders than any other non-human mammal. Efforts to catalog and characterize genetic variation across well-chosen populations of canines are necessary to advance our understanding of their evolutionary history and genetic architecture. To date, no organized effort has been undertaken to sequence the world's canid populations. The Dog10K Consortium (http://www.dog10kgenomes.org) is an international collaboration of researchers from across the globe who will generate 20× whole genomes from 10 000 canids in 5 years. This effort will capture the genetic diversity that underlies the phenotypic and geographical variability of modern canids worldwide. Breeds, village dogs, niche populations and extended pedigrees are currently being sequenced, and de novo assemblies of multiple canids are being constructed. This unprecedented dataset will address the genetic underpinnings of domestication, breed formation, aging, behavior and morphological variation. More generally, this effort will advance our understanding of human and canine health.
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Affiliation(s)
- Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford OX1 3TG, UK
| | - Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544-1014, USA
| | - Brian W Davis
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77840, USA
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern CH-3001, Switzerland
| | | | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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29
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Smith SP, Phillips JB, Johnson ML, Abbot P, Capra JA, Rokas A. Genome-wide association analysis uncovers variants for reproductive variation across dog breeds and links to domestication. Evol Med Public Health 2019; 2019:93-103. [PMID: 31263560 PMCID: PMC6592264 DOI: 10.1093/emph/eoz015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 05/09/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND AND OBJECTIVES The diversity of eutherian reproductive strategies has led to variation in many traits, such as number of offspring, age of reproductive maturity and gestation length. While reproductive trait variation has been extensively investigated and is well established in mammals, the genetic loci contributing to this variation remain largely unknown. The domestic dog, Canis lupus familiaris is a powerful model for studies of the genetics of inherited disease due to its unique history of domestication. To gain insight into the genetic basis of reproductive traits across domestic dog breeds, we collected phenotypic data for four traits, cesarean section rate, litter size, stillbirth rate and gestation length, from primary literature and breeders' handbooks. METHODOLOGY By matching our phenotypic data to genomic data from the Cornell Veterinary Biobank, we performed genome-wide association analyses for these four reproductive traits, using body mass and kinship among breeds as covariates. RESULTS We identified 12 genome-wide significant associations between these traits and genetic loci, including variants near CACNA2D3 with gestation length, MSRB3 and MSANTD1 with litter size, SMOC2 with cesarean section rate and UFM1 with stillbirth rate. A few of these loci, such as CACNA2D3 and MSRB3, have been previously implicated in human reproductive pathologies, whereas others have been associated with domestication-related traits, including brachycephaly (SMOC2) and coat curl (KRT71). CONCLUSIONS AND IMPLICATIONS We hypothesize that the artificial selection that gave rise to dog breeds also influenced the observed variation in their reproductive traits. Overall, our work establishes the domestic dog as a system for studying the genetics of reproductive biology and disease. LAY SUMMARY The genetic contributors to variation in mammalian reproductive traits remain largely unknown. We took advantage of the domestic dog, a powerful model system, to test for associations between genome-wide variants and four reproductive traits (cesarean section rate, litter size, stillbirth rate and gestation length) that vary extensively across breeds. We identified associations at a dozen loci, including ones previously associated with domestication-related traits, suggesting that selection on dog breeds also influenced their reproductive traits.
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Affiliation(s)
- Samuel P Smith
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37203, USA
- Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
| | - Julie B Phillips
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37203, USA
- Department of Biological Sciences, Cumberland University, Lebanon, TN 37087, USA
| | - Maddison L Johnson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37203, USA
| | - Patrick Abbot
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37203, USA
| | - John A Capra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37203, USA
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37203, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37203, USA
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37203, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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30
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Whole genome sequencing of canids reveals genomic regions under selection and variants influencing morphology. Nat Commun 2019; 10:1489. [PMID: 30940804 PMCID: PMC6445083 DOI: 10.1038/s41467-019-09373-w] [Citation(s) in RCA: 178] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 03/06/2019] [Indexed: 01/14/2023] Open
Abstract
Domestic dog breeds are characterized by an unrivaled diversity of morphologic traits and breed-associated behaviors resulting from human selective pressures. To identify the genetic underpinnings of such traits, we analyze 722 canine whole genome sequences (WGS), documenting over 91 million single nucleotide and small indels, creating a large catalog of genomic variation for a companion animal species. We undertake both selective sweep analyses and genome wide association studies (GWAS) inclusive of over 144 modern breeds, 54 wild canids and a hundred village dogs. Our results identify variants of strong impact associated with 16 phenotypes, including body weight variation which, when combined with existing data, explain greater than 90% of body size variation in dogs. We thus demonstrate that GWAS and selection scans performed with WGS are powerful complementary methods for expanding the utility of companion animal systems for the study of mammalian growth and biology. Being man’s best friend, dogs have been bred and selected for certain morphologic traits and breed-associated behaviours. Here, Plassais et al. analyse 722 canine whole genome sequences including modern breeds, wild canids and village dogs by GWAS and search for signatures of selection.
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31
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Asadollahpour Nanaei H, Ayatollahi Mehrgardi A, Esmailizadeh A. Comparative population genomics unveils candidate genes for athletic performance in Hanoverians. Genome 2019; 62:279-285. [DOI: 10.1139/gen-2018-0151] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Equine athletes have a genetic heritage that has been evolved for millions of years, which provides an opportunity to study the genetics of locomotion pattern and performance in mammals. The Hanoverian, a breed originating in Germany, is arguably among the most athletic of horse breeds, as well as possessing a balanced character and beautiful appearance. Here, we compared the whole genomes of Hanoverian with three other horse breeds (Akhal-Teke, Franches-Montagnes, and Standardbred), using the fixation index (Fst) and cross-population composite likelihood ratio (XP-CLR) methods for testing the multi-locus allele frequency differentiation between populations. We identified 299 and 485 positively selected genes using the Fst and XP-CLR methods, respectively. Further functional analyses showed that the ACTA1 gene is potentially involved in athletic performance in the Hanoverian breed, consistent with its role observed in human population. In addition, three other loci on chromosomes 1 and 20 were identified to be potentially involved in equine physical performance. The selected candidate genes identified in this study may be useful in current breeding efforts to develop improved breeds in regard to athletic performance.
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Affiliation(s)
- Hojjat Asadollahpour Nanaei
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran
| | - Ahmad Ayatollahi Mehrgardi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran
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Chen L, Peng W, Kong S, Pu F, Chen B, Zhou Z, Feng J, Li X, Xu P. Genetic Mapping of Head Size Related Traits in Common Carp ( Cyprinus carpio). Front Genet 2018; 9:448. [PMID: 30356829 PMCID: PMC6190898 DOI: 10.3389/fgene.2018.00448] [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: 08/28/2017] [Accepted: 09/18/2018] [Indexed: 12/23/2022] Open
Abstract
Head size is important economic trait for many aquaculture fish which is directly linked to their carcass yield. The genetic basis of head size trait remains unclear in many widely cultured fish species. Common carp (Cyprinus carpio) is one of the most widely studied fish due to its importance on both economic and environmental aspects. In this study, we performed genome-wide association study using 433 Yellow River carp individuals from multiple families to identify loci and genes potentially associated with head size related traits including head length (HL), head length/body length ratio (HBR), eye diameter (ED), and eye cross (EC). QTL mapping was utilized to filter the effects of population stratification and improve power for the candidates identification in the largest surveyed family with a published genetic linkage map. Twelve SNPs showed significant for head size traits in GWAS and 18 QTLs were identified in QTL mapping. Our study combining both GWAS and QTL mapping could compensate the deficiency from each other and advance our understanding of head size traits in common carp. To acquire a better understanding of the correlation between head size and body growth, we also performed comparisons between QTLs of head size traits and growth-related traits. Candidate genes underlying head size traits were identified surrounding the significant SNPs, including parvalbumin, srpk2, fsrp5, igf1, igf3, grb10, igf1r, notch2, sfrp2. Many of these genes have been identified with potential functions on bone formation and growth. Igf1 was a putative gene associated with both head size and body growth in Yellow River carp. The teleost-specific igf3 was a candidate head size related gene, related to both HL and HBR. Our study also indicated the importance of Igf signaling pathway for both growth and head size determination in common carp, which could be potentially used in future selective breeding in common carp as well as other species.
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Affiliation(s)
- Lin Chen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,College of Fisheries, Henan Normal University, Xinxiang, China
| | - Wenzhu Peng
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Shengnan Kong
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,College of Fisheries, Henan Normal University, Xinxiang, China
| | - Fei Pu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Baohua Chen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Zhixiong Zhou
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Jianxin Feng
- Henan Academy of Fishery Sciences, Zhengzhou, China
| | - Xuejun Li
- College of Fisheries, Henan Normal University, Xinxiang, China
| | - Peng Xu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Bourgeois B, Watts K, Thomas DM, Carmichael O, Hu FB, Heo M, Hall JE, Heymsfield SB. Associations between height and blood pressure in the United States population. Medicine (Baltimore) 2017; 96:e9233. [PMID: 29390353 PMCID: PMC5815765 DOI: 10.1097/md.0000000000009233] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The mechanisms linking short stature with an increase in cardiovascular and cerebrovascular disease risk remain elusive. This study tested the hypothesis that significant associations are present between height and blood pressure in a representative sample of the US adult population.Participants were 12,988 men and women from a multiethnic sample (age ≥ 18 years) evaluated in the 1999 to 2006 National Health and Nutrition Examination Survey who were not taking antihypertensive medications and who had complete height, weight, % body fat, and systolic and diastolic arterial blood pressure (SBP and DBP) measurements; mean arterial blood pressure and pulse pressure (MBP and PP) were calculated. Multiple regression models for men and women were developed with each blood pressure as dependent variable and height, age, race/ethnicity, body mass index, % body fat, socioeconomic status, activity level, and smoking history as potential independent variables.Greater height was associated with significantly lower SBP and PP, and higher DBP (all P < .001) in combined race/ethnic-sex group models beginning in the 4th decade. Predicted blood pressure differences between people who are short and tall increased thereafter with greater age except for MBP. Socioeconomic status, activity level, and smoking history did not consistently contribute to blood pressure prediction models.Height-associated blood pressure effects were present in US adults who appeared in the 4th decade and increased in magnitude with greater age thereafter. These observations, in the largest and most diverse population sample evaluated to date, provide support for postulated mechanisms linking adult stature with cardiovascular and cerebrovascular disease risk.
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Affiliation(s)
| | - Krista Watts
- Department of mathematical sciences, United States Military Academy, West Point, NY
| | - Diana M. Thomas
- Department of mathematical sciences, United States Military Academy, West Point, NY
| | - Owen Carmichael
- Pennington Biomedical Research Center, LSU System, Baton Rouge, LA
| | - Frank B. Hu
- Department of Nutrition and Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
| | | | - John E. Hall
- Departments of Physiology and Biophysics and Mississippi Center for Obesity Research, University of Mississippi Medical Center, Jackson, MS
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34
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Ostrander EA, Wayne RK, Freedman AH, Davis BW. Demographic history, selection and functional diversity of the canine genome. Nat Rev Genet 2017; 18:705-720. [DOI: 10.1038/nrg.2017.67] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Expression Profiles of IGF-1R Gene and Polymorphisms of its Regulatory Regions in Different Pig Breeds. Protein J 2017; 35:231-6. [PMID: 27229719 DOI: 10.1007/s10930-016-9666-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Insulin like growth factor 1 receptor (IGF-1R) is a candidate gene for growth and carcass traits in regulating animal growth, metabolism and endocrine. It is widely expressed in liver, muscle, bone tissues where the IGF-1R functions as a factor that promotes cell growth. In this study, the protein expression level of IGF-1R gene in liver and muscle tissues of three periods (birth, weaning and adult) of three pig breeds (BamaXiang pigs (BM), Tibetan pigs (TM) and Junmu No.1 pigs (JM)) were tested by western blot. SNPs within the regulatory region of pig IGF-1R gene were detected using direct sequencing and then the genotypes were identified through AS-PCR approach. Results showed expression profiles of IGF-1R gene between liver and muscle tissues were different and significant differences were also found among pig breeds. In the same time, four SNPs were detected in the regulatory region of IGF-1R gene, among which the genotype frequency of three (g.-1468G > C, g.-1192 C > T and g.330,424 C > T) were significantly different among the pig breeds. BM tended to heterozygous (GC/CT) of the anterior two loci, while TM and JM preferred the other two homozygotes respectively. For the g.330,424 C > T, all pig breeds were tended to be the heterozygous. In conclusion, the SNPs with different genotype distribution among the three pig breeds may explain the gene expression difference between the different pig breeds.
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Plassais J, Rimbault M, Williams FJ, Davis BW, Schoenebeck JJ, Ostrander EA. Analysis of large versus small dogs reveals three genes on the canine X chromosome associated with body weight, muscling and back fat thickness. PLoS Genet 2017; 13:e1006661. [PMID: 28257443 PMCID: PMC5357063 DOI: 10.1371/journal.pgen.1006661] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/17/2017] [Accepted: 02/26/2017] [Indexed: 12/21/2022] Open
Abstract
Domestic dog breeds display significant diversity in both body mass and skeletal size, resulting from intensive selective pressure during the formation and maintenance of modern breeds. While previous studies focused on the identification of alleles that contribute to small skeletal size, little is known about the underlying genetics controlling large size. We first performed a genome-wide association study (GWAS) using the Illumina Canine HD 170,000 single nucleotide polymorphism (SNP) array which compared 165 large-breed dogs from 19 breeds (defined as having a Standard Breed Weight (SBW) >41 kg [90 lb]) to 690 dogs from 69 small breeds (SBW ≤41 kg). We identified two loci on the canine X chromosome that were strongly associated with large body size at 82-84 megabases (Mb) and 101-104 Mb. Analyses of whole genome sequencing (WGS) data from 163 dogs revealed two indels in the Insulin Receptor Substrate 4 (IRS4) gene at 82.2 Mb and two additional mutations, one SNP and one deletion of a single codon, in Immunoglobulin Superfamily member 1 gene (IGSF1) at 102.3 Mb. IRS4 and IGSF1 are members of the GH/IGF1 and thyroid pathways whose roles include determination of body size. We also found one highly associated SNP in the 5'UTR of Acyl-CoA Synthetase Long-chain family member 4 (ACSL4) at 82.9 Mb, a gene which controls the traits of muscling and back fat thickness. We show by analysis of sequencing data from 26 wolves and 959 dogs representing 102 domestic dog breeds that skeletal size and body mass in large dog breeds are strongly associated with variants within IRS4, ACSL4 and IGSF1.
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Affiliation(s)
- Jocelyn Plassais
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Maud Rimbault
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Falina J. Williams
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Brian W. Davis
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jeffrey J. Schoenebeck
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Elaine A. Ostrander
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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Unusual life cycle and impact on microfibril assembly of ADAMTS17, a secreted metalloprotease mutated in genetic eye disease. Sci Rep 2017; 7:41871. [PMID: 28176809 PMCID: PMC5296908 DOI: 10.1038/srep41871] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 12/28/2016] [Indexed: 01/30/2023] Open
Abstract
Secreted metalloproteases have diverse roles in the formation, remodeling, and the destruction of extracellular matrix. Recessive mutations in the secreted metalloprotease ADAMTS17 cause ectopia lentis and short stature in humans with Weill-Marchesani-like syndrome and primary open angle glaucoma and ectopia lentis in dogs. Little is known about this protease or its connection to fibrillin microfibrils, whose major component, fibrillin-1, is genetically associated with ectopia lentis and alterations in height. Fibrillin microfibrils form the ocular zonule and are present in the drainage apparatus of the eye. We show that recombinant ADAMTS17 has unique characteristics and an unusual life cycle. It undergoes rapid autocatalytic processing in trans after its secretion from cells. Secretion of ADAMTS17 requires O-fucosylation and its autocatalytic activity does not depend on propeptide processing by furin. ADAMTS17 binds recombinant fibrillin-2 but not fibrillin-1 and does not cleave either. It colocalizes to fibrillin-1 containing microfibrils in cultured fibroblasts and suppresses fibrillin-2 (FBN2) incorporation in microfibrils, in part by transcriptional downregulation of Fbn2 mRNA expression. RNA in situ hybridization detected Adamts17 expression in specific structures in the eye, skeleton and other organs, where it may regulate the fibrillin isoform composition of microfibrils.
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Comparative analysis of DNA methylome and transcriptome of skeletal muscle in lean-, obese-, and mini-type pigs. Sci Rep 2017; 7:39883. [PMID: 28045116 PMCID: PMC5206674 DOI: 10.1038/srep39883] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 11/29/2016] [Indexed: 02/07/2023] Open
Abstract
DNA methylation plays a pivotal role in biological processes by affecting gene expression. However, how DNA methylation mediates phenotype difference of skeletal muscle between lean-, obese-, and mini-type pigs remains unclear. We systematically carried out comparative analysis of skeletal muscle by integrating analysis of genome-wide DNA methylation, mRNA, lncRNA and miRNA profiles in three different pig breeds (obese-type Tongcheng, lean-type Landrace, and mini-type Wuzhishan pigs). We found that the differentially methylated genes (DMGs) were significantly associated with lipid metabolism, oxidative stress and muscle development. Among the identified DMGs, 253 genes were related to body-size and obesity. A set of lncRNAs and mRNAs including UCP3, FHL1, ANK1, HDAC4, and HDAC5 exhibited inversely changed DNA methylation and expression level; these genes were associated with oxidation reduction, fatty acid metabolism and cell proliferation. Gene regulatory networks involved in phenotypic variation of skeletal muscle were related to lipid metabolism, cellular movement, skeletal muscle development, and the p38 MAPK signaling pathway. DNA methylation potentially influences the propensity for obesity and body size by affecting gene expression in skeletal muscle. Our findings provide an abundant information of epigenome and transcriptome that will be useful for animal breeding and biomedical research.
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Dwarfism and Altered Craniofacial Development in Rabbits Is Caused by a 12.1 kb Deletion at the HMGA2 Locus. Genetics 2016; 205:955-965. [PMID: 27986804 DOI: 10.1534/genetics.116.196667] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 12/05/2016] [Indexed: 12/19/2022] Open
Abstract
The dwarf phenotype characterizes the smallest of rabbit breeds and is governed largely by the effects of a single dwarfing allele with an incompletely dominant effect on growth. Dwarf rabbits typically weigh under 1 kg and have altered craniofacial morphology. The dwarf allele is recessive lethal and dwarf homozygotes die within a few days of birth. The dwarf phenotype is expressed in heterozygous individuals and rabbits from dwarf breeds homozygous for the wild-type allele are normal, although smaller when compared to other breeds. Here, we show that the dwarf allele constitutes a ∼12.1 kb deletion overlapping the promoter region and first three exons of the HMGA2 gene leading to inactivation of this gene. HMGA2 has been frequently associated with variation in body size across species. Homozygotes for null alleles are viable in mice but not in rabbits and probably not in humans. RNA-sequencing analysis of rabbit embryos showed that very few genes (4-29 genes) were differentially expressed among the three HMGA2/dwarf genotypes, suggesting that dwarfism and inviability in rabbits are caused by modest changes in gene expression. Our results show that HMGA2 is critical for normal expression of IGF2BP2, which encodes an RNA-binding protein. Finally, we report a catalog of regions of elevated genetic differentiation between dwarf and normal-size rabbits, including LCORL-NCAPG, STC2, HOXD cluster, and IGF2BP2 Levels and patterns of genetic diversity at the LCORL-NCAPG locus further suggest that small size in dwarf breeds was enhanced by crosses with wild rabbits. Overall, our results imply that small size in dwarf rabbits results from a large effect, loss-of-function (LOF) mutation in HMGA2 combined with polygenic selection.
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Bøtkjær JA, Borgbo T, Kløverpris S, Noer PR, Oxvig C, Andersen CY. Effect of pregnancy-associated plasma protein-A (PAPP-A) single-nucleotide polymorphisms on the level and activity of PAPP-A and the hormone profile in fluid from normal human small antral follicles. Fertil Steril 2016; 106:1778-1786.e8. [PMID: 27793387 DOI: 10.1016/j.fertnstert.2016.09.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 08/10/2016] [Accepted: 09/07/2016] [Indexed: 01/06/2023]
Abstract
OBJECTIVE To reveal a possible relationship between two single nucleotide polymorphisms (SNPs) in PAPP-A-1224 (rs7020782) and 327 (rs12375498)-and the level and activity of PAPP-A in follicular fluid (FF) of human small antral follicles, and to analyze the intrafollicular hormone levels. DESIGN Laboratory investigation. SETTING University hospital. PATIENT(S) Fifty volunteer women who contributed a total of 210 samples of FF from normal small antral follicles. INTERVENTION(S) Genotyping and measurement of antigen levels of steroids, PAPP-A, stanniocalcin-2 (STC2), and antimüllerian hormone (AMH) plus activity of PAPP-A toward insulin-like growth factor binding protein 4 (IGFBP-4). MAIN OUTCOME MEASURE(S) Measurement of PAPP-A levels and hormones with enzyme-linked immunosorbent assay (ELISA) and PAPP-A activity toward radiolabeled IGFBP-4. RESULT(S) Women homozygous for the minor C allele of the 1224 SNP showed a statistically significantly lower level of PAPP-A protein and activity in FF compared with women carrying the major A allele. These women also displayed nonsignificant reduced levels of estradiol and increased levels of AMH and androgen. A statistically significant correlation between FF levels of PAPP-A activity and the molar ratio of PAPP-A/STC2 was obtained. The 327 SNP did not show statistically significant associations. CONCLUSION(S) This study presents a statistically significant effect of the 1224 SNP on the level and activity of PAPP-A in human follicles, suggesting that the FF level of bioactive insulin-like growth factor depends on the genotype. We observed STC2 to be an important regulator of PAPP-A in human FF. The 1224 SNP has previously been associated with recurrent pregnancy loss, so further evaluation of an underlying mechanism including aberrant control of insulin-like growth factor activity is warranted.
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Affiliation(s)
- Jane Alrø Bøtkjær
- Laboratory of Reproductive Biology, Juliane Marie Centre for Women, Children and Reproduction, Copenhagen University Hospital, Copenhagen University, Copenhagen, Denmark.
| | - Tanni Borgbo
- Laboratory of Reproductive Biology, Juliane Marie Centre for Women, Children and Reproduction, Copenhagen University Hospital, Copenhagen University, Copenhagen, Denmark
| | - Søren Kløverpris
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Pernille Rimmer Noer
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Claus Oxvig
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Claus Yding Andersen
- Laboratory of Reproductive Biology, Juliane Marie Centre for Women, Children and Reproduction, Copenhagen University Hospital, Copenhagen University, Copenhagen, Denmark
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Jimenez AG. Physiological underpinnings in life-history trade-offs in man’s most popular selection experiment: the dog. J Comp Physiol B 2016; 186:813-27. [DOI: 10.1007/s00360-016-1002-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/05/2016] [Accepted: 05/17/2016] [Indexed: 10/21/2022]
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Penso-Dolfin L, Swofford R, Johnson J, Alföldi J, Lindblad-Toh K, Swarbreck D, Moxon S, Di Palma F. An Improved microRNA Annotation of the Canine Genome. PLoS One 2016; 11:e0153453. [PMID: 27119849 PMCID: PMC4847789 DOI: 10.1371/journal.pone.0153453] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/30/2016] [Indexed: 01/14/2023] Open
Abstract
The domestic dog, Canis familiaris, is a valuable model for studying human diseases. The publication of the latest Canine genome build and annotation, CanFam3.1 provides an opportunity to enhance our understanding of gene regulation across tissues in the dog model system. In this study, we used the latest dog genome assembly and small RNA sequencing data from 9 different dog tissues to predict novel miRNAs in the dog genome, as well as to annotate conserved miRNAs from the miRBase database that were missing from the current dog annotation. We used both miRCat and miRDeep2 algorithms to computationally predict miRNA loci. The resulting, putative hairpin sequences were analysed in order to discard false positives, based on predicted secondary structures and patterns of small RNA read alignments. Results were further divided into high and low confidence miRNAs, using the same criteria. We generated tissue specific expression profiles for the resulting set of 811 loci: 720 conserved miRNAs, (207 of which had not been previously annotated in the dog genome) and 91 novel miRNA loci. Comparative analyses revealed 8 putative homologues of some novel miRNA in ferret, and one in microbat. All miRNAs were also classified into the genic and intergenic categories, based on the Ensembl RefSeq gene annotation for CanFam3.1. This additionally allowed us to identify four previously undescribed MiRtrons among our total set of miRNAs. We additionally annotated piRNAs, using proTRAC on the same input data. We thus identified 263 putative clusters, most of which (211 clusters) were found to be expressed in testis. Our results represent an important improvement of the dog genome annotation, paving the way to further research on the evolution of gene regulation, as well as on the contribution of post-transcriptional regulation to pathological conditions.
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Affiliation(s)
- Luca Penso-Dolfin
- Vertebrate and Health Genomics, The Genome Analysis Centre, Norwich, United Kingdom
| | - Ross Swofford
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jeremy Johnson
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jessica Alföldi
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Kerstin Lindblad-Toh
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - David Swarbreck
- Regulatory Genomics, The Genome Analysis Centre, Norwich, United Kingdom
| | - Simon Moxon
- Regulatory Genomics, The Genome Analysis Centre, Norwich, United Kingdom
- * E-mail: (SM); (DFP)
| | - Federica Di Palma
- Vertebrate and Health Genomics, The Genome Analysis Centre, Norwich, United Kingdom
- * E-mail: (SM); (DFP)
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Charruau P, Johnston RA, Stahler DR, Lea A, Snyder-Mackler N, Smith DW, vonHoldt BM, Cole SW, Tung J, Wayne RK. Pervasive Effects of Aging on Gene Expression in Wild Wolves. Mol Biol Evol 2016; 33:1967-78. [PMID: 27189566 DOI: 10.1093/molbev/msw072] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Gene expression levels change as an individual ages and responds to environmental conditions. With the exception of humans, such patterns have principally been studied under controlled conditions, overlooking the array of developmental and environmental influences that organisms encounter under conditions in which natural selection operates. We used high-throughput RNA sequencing (RNA-Seq) of whole blood to assess the relative impacts of social status, age, disease, and sex on gene expression levels in a natural population of gray wolves (Canis lupus). Our findings suggest that age is broadly associated with gene expression levels, whereas other examined factors have minimal effects on gene expression patterns. Further, our results reveal evolutionarily conserved signatures of senescence, such as immunosenescence and metabolic aging, between wolves and humans despite major differences in life history and environment. The effects of aging on gene expression levels in wolves exhibit conservation with humans, but the more rapid expression differences observed in aging wolves is evolutionarily appropriate given the species' high level of extrinsic mortality due to intraspecific aggression. Some expression changes that occur with age can facilitate physical age-related changes that may enhance fitness in older wolves. However, the expression of these ancestral patterns of aging in descendant modern dogs living in highly modified domestic environments may be maladaptive and cause disease. This work provides evolutionary insight into aging patterns observed in domestic dogs and demonstrates the applicability of studying natural populations to investigate the mechanisms of aging.
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Affiliation(s)
- Pauline Charruau
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles
| | - Rachel A Johnston
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles
| | - Daniel R Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park
| | | | | | - Douglas W Smith
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park
| | | | - Steven W Cole
- Department of Medicine, University of California, Los Angeles Cousins Center for Psychoneuroimmunology, Semel Institute, University of California, Los Angeles
| | - Jenny Tung
- Department of Biology, Duke University Department of Evolutionary Anthropology, Duke University
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles
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Freedman AH, Schweizer RM, Ortega-Del Vecchyo D, Han E, Davis BW, Gronau I, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Ramirez O, Hormozdiari F, Alkan C, Vilà C, Squire K, Geffen E, Kusak J, Boyko AR, Parker HG, Lee C, Tadigotla V, Siepel A, Bustamante CD, Harkins TT, Nelson SF, Marques-Bonet T, Ostrander EA, Wayne RK, Novembre J. Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs. PLoS Genet 2016; 12:e1005851. [PMID: 26943675 PMCID: PMC4778760 DOI: 10.1371/journal.pgen.1005851] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/18/2016] [Indexed: 12/31/2022] Open
Abstract
Controlling for background demographic effects is important for accurately identifying loci that have recently undergone positive selection. To date, the effects of demography have not yet been explicitly considered when identifying loci under selection during dog domestication. To investigate positive selection on the dog lineage early in the domestication, we examined patterns of polymorphism in six canid genomes that were previously used to infer a demographic model of dog domestication. Using an inferred demographic model, we computed false discovery rates (FDR) and identified 349 outlier regions consistent with positive selection at a low FDR. The signals in the top 100 regions were frequently centered on candidate genes related to brain function and behavior, including LHFPL3, CADM2, GRIK3, SH3GL2, MBP, PDE7B, NTAN1, and GLRA1. These regions contained significant enrichments in behavioral ontology categories. The 3rd top hit, CCRN4L, plays a major role in lipid metabolism, that is supported by additional metabolism related candidates revealed in our scan, including SCP2D1 and PDXC1. Comparing our method to an empirical outlier approach that does not directly account for demography, we found only modest overlaps between the two methods, with 60% of empirical outliers having no overlap with our demography-based outlier detection approach. Demography-aware approaches have lower-rates of false discovery. Our top candidates for selection, in addition to expanding the set of neurobehavioral candidate genes, include genes related to lipid metabolism, suggesting a dietary target of selection that was important during the period when proto-dogs hunted and fed alongside hunter-gatherers.
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Affiliation(s)
- Adam H. Freedman
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America
- * E-mail:
| | - Rena M. Schweizer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Diego Ortega-Del Vecchyo
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Eunjung Han
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Brian W. Davis
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ilan Gronau
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | | | | | - Zhenxin Fan
- Key Laboratory of Bioresources and Ecoenvironment, Sichuan University, Chengdu, China
| | - Peter Marx
- Department of Measurement and Information Systems, Budapest University of Technology and Economics, Budapest, Hungary
| | - Belen Lorente-Galdos
- ICREA at Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Oscar Ramirez
- ICREA at Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Farhad Hormozdiari
- Department of Computer Science, University of California, Los Angeles, Los Angeles, California, United States of America
| | | | - Carles Vilà
- Estación Biológia de Doñana EBD-CSIC, Sevilla, Spain
| | - Kevin Squire
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Eli Geffen
- Department of Zoology, Tel Aviv University, Tel Aviv, Israel
| | - Josip Kusak
- Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Adam R. Boyko
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, United States of America
| | - Heidi G. Parker
- ICREA at Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Clarence Lee
- Life Technologies, Foster City, California, United States of America
| | - Vasisht Tadigotla
- Life Technologies, Foster City, California, United States of America
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | | | | | - Stanley F. Nelson
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Tomas Marques-Bonet
- ICREA at Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Centro Nacional de Analisis Genomico (CNAG/PCB), Baldiri Reixach 4–8, Barcelona, Spain
| | - Elaine A. Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - John Novembre
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America
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45
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Complex disease and phenotype mapping in the domestic dog. Nat Commun 2016; 7:10460. [PMID: 26795439 PMCID: PMC4735900 DOI: 10.1038/ncomms10460] [Citation(s) in RCA: 177] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/11/2015] [Indexed: 12/17/2022] Open
Abstract
The domestic dog is becoming an increasingly valuable model species in medical genetics, showing particular promise to advance our understanding of cancer and orthopaedic disease. Here we undertake the largest canine genome-wide association study to date, with a panel of over 4,200 dogs genotyped at 180,000 markers, to accelerate mapping efforts. For complex diseases, we identify loci significantly associated with hip dysplasia, elbow dysplasia, idiopathic epilepsy, lymphoma, mast cell tumour and granulomatous colitis; for morphological traits, we report three novel quantitative trait loci that influence body size and one that influences fur length and shedding. Using simulation studies, we show that modestly larger sample sizes and denser marker sets will be sufficient to identify most moderate- to large-effect complex disease loci. This proposed design will enable efficient mapping of canine complex diseases, most of which have human homologues, using far fewer samples than required in human studies. The domestic dog is an important model organism for our understanding of cancer and other diseases. Here the authors conduct a genome-wide association study across multiple breeds and identify novel loci significantly associated with several complex diseases and morphological traits.
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46
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Cagan A, Blass T. Identification of genomic variants putatively targeted by selection during dog domestication. BMC Evol Biol 2016; 16:10. [PMID: 26754411 PMCID: PMC4710014 DOI: 10.1186/s12862-015-0579-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 12/22/2015] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Dogs [Canis lupus familiaris] were the first animal species to be domesticated and continue to occupy an important place in human societies. Recent studies have begun to reveal when and where dog domestication occurred. While much progress has been made in identifying the genetic basis of phenotypic differences between dog breeds we still know relatively little about the genetic changes underlying the phenotypes that differentiate all dogs from their wild progenitors, wolves [Canis lupus]. In particular, dogs generally show reduced aggression and fear towards humans compared to wolves. Therefore, selection for tameness was likely a necessary prerequisite for dog domestication. With the increasing availability of whole-genome sequence data it is possible to try and directly identify the genetic variants contributing to the phenotypic differences between dogs and wolves. RESULTS We analyse the largest available database of genome-wide polymorphism data in a global sample of dogs 69 and wolves 7. We perform a scan to identify regions of the genome that are highly differentiated between dogs and wolves. We identify putatively functional genomic variants that are segregating or at high frequency [> = 0.75 Fst] for alternative alleles between dogs and wolves. A biological pathways analysis of the genes containing these variants suggests that there has been selection on the 'adrenaline and noradrenaline biosynthesis pathway', well known for its involvement in the fight-or-flight response. We identify 11 genes with putatively functional variants fixed for alternative alleles between dogs and wolves. The segregating variants in these genes are strong candidates for having been targets of selection during early dog domestication. CONCLUSIONS We present the first genome-wide analysis of the different categories of putatively functional variants that are fixed or segregating at high frequency between a global sampling of dogs and wolves. We find evidence that selection has been strongest around non-synonymous variants. Strong selection in the initial stages of dog domestication appears to have occurred on multiple genes involved in the fight-or-flight response, particularly in the catecholamine synthesis pathway. Different alleles in some of these genes have been associated with behavioral differences between modern dog breeds, suggesting an important role for this pathway at multiple stages in the domestication process.
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Affiliation(s)
- Alex Cagan
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany.
| | - Torsten Blass
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany.
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Levy DL, Heald R. Biological Scaling Problems and Solutions in Amphibians. Cold Spring Harb Perspect Biol 2015; 8:a019166. [PMID: 26261280 DOI: 10.1101/cshperspect.a019166] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Size is a primary feature of biological systems that varies at many levels, from the organism to its constituent cells and subcellular structures. Amphibians populate some of the extremes in biological size and have provided insight into scaling mechanisms, upper and lower size limits, and their physiological significance. Body size variation is a widespread evolutionary tactic among amphibians, with miniaturization frequently correlating with direct development that occurs without a tadpole stage. The large genomes of salamanders lead to large cell sizes that necessitate developmental modification and morphological simplification. Amphibian extremes at the cellular level have provided insight into mechanisms that accommodate cell-size differences. Finally, how organelles scale to cell size between species and during development has been investigated at the molecular level, because subcellular scaling can be recapitulated using Xenopus in vitro systems.
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Affiliation(s)
- Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071
| | - Rebecca Heald
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
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Parker HG, Gilbert SF. From caveman companion to medical innovator: genomic insights into the origin and evolution of domestic dogs. ACTA ACUST UNITED AC 2015; 5:239-255. [PMID: 28490917 DOI: 10.2147/agg.s57678] [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: 11/23/2022]
Abstract
The phenotypic and behavioral diversity of the domestic dog has yet to be matched by any other mammalian species. In their current form, which comprises more than 350 populations known as breeds, there is a size range of two orders of magnitude and morphological features reminiscent of not only different species but also different phylogenetic families. The range of both appearance and behavior found in the dog is the product of millennia of human interference, and though humans created the diversity it remains a point of fascination to both lay and scientific communities. In this review we summarize the current understanding of the history of dog domestication based on molecular data. We will examine the ways that canine genetic and genomic studies have evolved and look at examples of dog genetics in the light of human disease.
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Affiliation(s)
- Heidi G Parker
- National Human Genome Research Institute, National Institutes of Health, Bethesda MD, 20892 USA
| | - Samuel F Gilbert
- National Human Genome Research Institute, National Institutes of Health, Bethesda MD, 20892 USA
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Dong Y, Zhang X, Xie M, Arefnezhad B, Wang Z, Wang W, Feng S, Huang G, Guan R, Shen W, Bunch R, McCulloch R, Li Q, Li B, Zhang G, Xu X, Kijas JW, Salekdeh GH, Wang W, Jiang Y. Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication. BMC Genomics 2015; 16:431. [PMID: 26044654 PMCID: PMC4455334 DOI: 10.1186/s12864-015-1606-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 05/01/2015] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Domestic goats (Capra hircus) have been selected to play an essential role in agricultural production systems, since being domesticated from their wild progenitor, bezoar (Capra aegagrus). A detailed understanding of the genetic consequences imparted by the domestication process remains a key goal of evolutionary genomics. RESULTS We constructed the reference genome of bezoar and sequenced representative breeds of domestic goats to search for genomic changes that likely have accompanied goat domestication and breed formation. Thirteen copy number variation genes associated with coat color were identified in domestic goats, among which ASIP gene duplication contributes to the generation of light coat-color phenotype in domestic goats. Analysis of rapidly evolving genes identified genic changes underlying behavior-related traits, immune response and production-related traits. CONCLUSION Based on the comparison studies of copy number variation genes and rapidly evolving genes between wild and domestic goat, our findings and methodology shed light on the genetic mechanism of animal domestication and will facilitate future goat breeding.
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Affiliation(s)
- Yang Dong
- Kunming University of Science and Technology, Kunming, 650093, China.
- CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China.
| | - Xiaolei Zhang
- CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China.
| | - Min Xie
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Babak Arefnezhad
- Agricultural Biotechnology Research Institute of Iran, Karaj, Iran.
| | - Zongji Wang
- BGI-Shenzhen, Shenzhen, 518083, China.
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China.
| | | | | | | | - Rui Guan
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Wenjing Shen
- CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China.
| | - Rowan Bunch
- CSIRO, Agriculture Flagship, Brisbane, 4065, QLD, Australia.
| | | | - Qiye Li
- BGI-Shenzhen, Shenzhen, 518083, China.
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
| | - Bo Li
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Guojie Zhang
- BGI-Shenzhen, Shenzhen, 518083, China.
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - James W Kijas
- CSIRO, Agriculture Flagship, Brisbane, 4065, QLD, Australia.
| | - Ghasem Hosseini Salekdeh
- Agricultural Biotechnology Research Institute of Iran, Karaj, Iran.
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
| | - Wen Wang
- CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China.
| | - Yu Jiang
- CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China.
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
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Davies KT, Tsagkogeorga G, Bennett NC, Dávalos LM, Faulkes CG, Rossiter SJ. Molecular evolution of growth hormone and insulin-like growth factor 1 receptors in long-lived, small-bodied mammals. Gene 2014; 549:228-36. [DOI: 10.1016/j.gene.2014.07.061] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 07/16/2014] [Accepted: 07/23/2014] [Indexed: 10/25/2022]
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