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Identification of Copy Number Variations in Four Horse Breed Populations in South Korea. Animals (Basel) 2022; 12:ani12243501. [PMID: 36552421 PMCID: PMC9774267 DOI: 10.3390/ani12243501] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/21/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
In this study, genome-wide CNVs were identified using a total of 469 horses from four horse populations (Jeju horses, Thoroughbreds, Jeju riding horses, and Hanla horses). We detected a total of 843 CNVRs throughout all autosomes: 281, 30, 301, and 310 CNVRs for Jeju horses, Thoroughbreds, Jeju riding horses, and Hanla horses, respectively. Of the total CNVRs, copy number losses were found to be the most abundant (48.99%), while gains and mixed CNVRs accounted for 41.04% and 9.96% of the total CNVRs, respectively. The length of the CNVRs ranged from 0.39 kb to 2.8 Mb, while approximately 7.2% of the reference horse genome assembly was covered by the total CNVRs. By comparing the CNVRs among the populations, we found a significant portion of the CNVRs (30.13%) overlapped; the highest number of shared CNVRs was between Hanla horses and Jeju riding horses. When compared with the horse CNVRs of previous studies, 26.8% of CNVRs were found to be uniquely detected in this study. The CNVRs were not randomly distributed throughout the genome; in particular, the Equus caballus autosome (ECA) 7 comprised the largest proportion of its genome (16.3%), while ECA 24 comprised the smallest (0.7%). Furthermore, functional analysis was applied to CNVRs that overlapped with genes (genic-CNVRs); these overlapping areas may be potentially associated with the olfactory pathway and nervous system. A racing performance QTL was detected in a CNVR of Thoroughbreds, Jeju riding horses, and Hanla horses, and the CNVR value was mixed for three breeds.
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2
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Yang L, Gao Y, Oswalt A, Fang L, Boschiero C, Neupane M, Sattler CG, Li CJ, Seroussi E, Xu L, Yang L, Li L, Zhang H, Rosen BD, Van Tassell CP, Zhou Y, Ma L, Liu GE. Towards the detection of copy number variation from single sperm sequencing in cattle. BMC Genomics 2022; 23:215. [PMID: 35300589 PMCID: PMC8928590 DOI: 10.1186/s12864-022-08441-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Copy number variation (CNV) has been routinely studied using bulk-cell sequencing. However, CNV is not well studied on the single-cell level except for humans and a few model organisms. RESULTS We sequenced 143 single sperms of two Holstein bulls, from which we predicted CNV events using 14 single sperms with deep sequencing. We then compared the CNV results derived from single sperms with the bulk-cell sequencing of one bull's family trio of diploid genomes. As a known CNV hotspot, segmental duplications were also predicted using the bovine ARS-UCD1.2 genome. Although the trio CNVs validated only some single sperm CNVs, they still showed a distal chromosomal distribution pattern and significant associations with segmental duplications and satellite repeats. CONCLUSION Our preliminary results pointed out future research directions and highlighted the importance of uniform whole genome amplification, deep sequence coverage, and dedicated software pipelines for CNV detection using single cell sequencing data.
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Affiliation(s)
- Liu Yang
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.,College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.,Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Adam Oswalt
- Select Sires Inc, 11740 U.S. 42 North, Plain City, OH, 43064, USA
| | - Lingzhao Fang
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Clarissa Boschiero
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - Mahesh Neupane
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | | | - Cong-Jun Li
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - Eyal Seroussi
- Agricultural Research Organization (ARO), Institute of Animal Science, HaMaccabim Road, P.O.B 15159, 7528809, Volcani CenterRishon LeTsiyon, Israel
| | - Lingyang Xu
- Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lv Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Li Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hongping Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA.
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
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3
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Identification of Copy Number Variations and Genetic Diversity in Italian Insular Sheep Breeds. Animals (Basel) 2022; 12:ani12020217. [PMID: 35049839 PMCID: PMC8773107 DOI: 10.3390/ani12020217] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 02/05/2023] Open
Abstract
Copy number variants (CNVs) are one of the major contributors to genetic diversity and phenotypic variation in livestock. The aim of this work is to identify CNVs and perform, for the first time, a CNV-based population genetics analysis with five Italian sheep breeds (Barbaresca, Comisana, Pinzirita, Sarda, and Valle del Belìce). We identified 10,207 CNVs with an average length of 1.81 Mb. The breeds showed similar mean numbers of CNVs, ranging from 20 (Sarda) to 27 (Comisana). A total of 365 CNV regions (CNVRs) were determined. The length of the CNVRs varied among breeds from 2.4 Mb to 124.1 Mb. The highest number of shared CNVRs was between Comisana and Pinzirita, and only one CNVR was shared among all breeds. Our results indicated that segregating CNVs expresses a certain degree of diversity across all breeds. Despite the low/moderate genetic differentiation among breeds, the different approaches used to disclose the genetic relationship showed that the five breeds tend to cluster in distinct groups, similar to the previous studies based on single-nucleotide polymorphism markers. Gene enrichment was described for the 37 CNVRs selected, considering the top 10%. Out of 181 total genes, 67 were uncharacterized loci. Gene Ontology analysis showed that several of these genes are involved in lipid metabolism, immune response, and the olfactory pathway. Our results corroborated previous studies and showed that CNVs represent valuable molecular resources for providing useful information for separating the population and could be further used to explore the function and evolutionary aspect of sheep genome.
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Wang X, Wang Y, Cao X, Huang Y, Li P, Lan X, Buren C, Hu L, Chen H. Copy number variations of the KAT6A gene are associated with body measurements of Chinese sheep breeds. Anim Biotechnol 2021:1-8. [PMID: 34842492 DOI: 10.1080/10495398.2021.2005616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Copy number variation (CNV) is one kind of genomic structure variations and presents as gains and losses of genomic fragments. More recently, we have made an atlas of CNV maps for livestock. In the future, it is a primary focus to determine the phenotypic effects of candidate CNVs. Lysine Acetyltransferase 6 A (KAT6A) is a protein coding gene and plays a critical role in many cellular processes. However, the effects of KAT6A CNVs on sheep body measurements remains unknown. In this study, we performed quantitative polymerase chain reaction (qPCR) to detect the presences and distributions of three CNV regions within KAT6A gene in 672 sheep from four Chinese breeds. Association analysis indicated that the three CNVs of KAT6A gene were significantly associated with body measurement(s) in Small-tailed Han sheep (STH) and Hu sheep (HU) (p < 0.05), while no effects on Large-tailed Han sheep (LTH) were observed (p > 0.05) were observed. Additionally, only one CNV was significantly associated with body measurement (body length) in Chaka sheep (CK) (p < 0.05). Our study provided evidence that the CNV(s) of KAT6A gene could be used as candidate marker(s) for molecular breedings of STH, HU, and CK breeds.
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Affiliation(s)
- Xiaogang Wang
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yiru Wang
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiukai Cao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Yongzhen Huang
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Pi Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
| | - Xianyong Lan
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Chaogetu Buren
- Animal Disease Control Center of Haixi Mongolian and Tibetan Autonomous Prefecture, Delingha, Qinghai, China
| | - Linyong Hu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
| | - Hong Chen
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,College of Animal Science, Xinjiang Agricultural University, Urumqi, China
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Serres-Armero A, Davis BW, Povolotskaya IS, Morcillo-Suarez C, Plassais J, Juan D, Ostrander EA, Marques-Bonet T. Copy number variation underlies complex phenotypes in domestic dog breeds and other canids. Genome Res 2021; 31:762-774. [PMID: 33863806 PMCID: PMC8092016 DOI: 10.1101/gr.266049.120] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 02/26/2021] [Indexed: 01/02/2023]
Abstract
Extreme phenotypic diversity, a history of artificial selection, and socioeconomic value make domestic dog breeds a compelling subject for genomic research. Copy number variation (CNV) is known to account for a significant part of inter-individual genomic diversity in other systems. However, a comprehensive genome-wide study of structural variation as it relates to breed-specific phenotypes is lacking. We have generated whole genome CNV maps for more than 300 canids. Our data set extends the canine structural variation landscape to more than 100 dog breeds, including novel variants that cannot be assessed using microarray technologies. We have taken advantage of this data set to perform the first CNV-based genome-wide association study (GWAS) in canids. We identify 96 loci that display copy number differences across breeds, which are statistically associated with a previously compiled set of breed-specific morphometrics and disease susceptibilities. Among these, we highlight the discovery of a long-range interaction involving a CNV near MED13L and TBX3, which could influence breed standard height. Integration of the CNVs with chromatin interactions, long noncoding RNA expression, and single nucleotide variation highlights a subset of specific loci and genes with potential functional relevance and the prospect to explain trait variation between dog breeds.
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Affiliation(s)
- Aitor Serres-Armero
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, Barcelona 08003, Spain
| | - Brian W Davis
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.,Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, Texas 77843, USA
| | - Inna S Povolotskaya
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Carlos Morcillo-Suarez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, Barcelona 08003, Spain
| | - Jocelyn Plassais
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - David Juan
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, Barcelona 08003, Spain
| | - Elaine A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Tomas Marques-Bonet
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, Barcelona 08003, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Catalonia 08201, Spain
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6
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Binversie EE, Baker LA, Engelman CD, Hao Z, Moran JJ, Piazza AM, Sample SJ, Muir P. Analysis of copy number variation in dogs implicates genomic structural variation in the development of anterior cruciate ligament rupture. PLoS One 2020; 15:e0244075. [PMID: 33382735 PMCID: PMC7774950 DOI: 10.1371/journal.pone.0244075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 12/02/2020] [Indexed: 11/19/2022] Open
Abstract
Anterior cruciate ligament (ACL) rupture is an important condition of the human knee. Second ruptures are common and societal costs are substantial. Canine cranial cruciate ligament (CCL) rupture closely models the human disease. CCL rupture is common in the Labrador Retriever (5.79% prevalence), ~100-fold more prevalent than in humans. Labrador Retriever CCL rupture is a polygenic complex disease, based on genome-wide association study (GWAS) of single nucleotide polymorphism (SNP) markers. Dissection of genetic variation in complex traits can be enhanced by studying structural variation, including copy number variants (CNVs). Dogs are an ideal model for CNV research because of reduced genetic variability within breeds and extensive phenotypic diversity across breeds. We studied the genetic etiology of CCL rupture by association analysis of CNV regions (CNVRs) using 110 case and 164 control Labrador Retrievers. CNVs were called from SNPs using three different programs (PennCNV, CNVPartition, and QuantiSNP). After quality control, CNV calls were combined to create CNVRs using ParseCNV and an association analysis was performed. We found no strong effect CNVRs but found 46 small effect (max(T) permutation P<0.05) CCL rupture associated CNVRs in 22 autosomes; 25 were deletions and 21 were duplications. Of the 46 CCL rupture associated CNVRs, we identified 39 unique regions. Thirty four were identified by a single calling algorithm, 3 were identified by two calling algorithms, and 2 were identified by all three algorithms. For 42 of the associated CNVRs, frequency in the population was <10% while 4 occurred at a frequency in the population ranging from 10–25%. Average CNVR length was 198,872bp and CNVRs covered 0.11 to 0.15% of the genome. All CNVRs were associated with case status. CNVRs did not overlap previous canine CCL rupture risk loci identified by GWAS. Associated CNVRs contained 152 annotated genes; 12 CNVRs did not have genes mapped to CanFam3.1. Using pathway analysis, a cluster of 19 homeobox domain transcript regulator genes was associated with CCL rupture (P = 6.6E-13). This gene cluster influences cranial-caudal body pattern formation during embryonic limb development. Clustered genes were found in 3 CNVRs on chromosome 14 (HoxA), 28 (NKX6-2), and 36 (HoxD). When analysis was limited to deletion CNVRs, the association was strengthened (P = 8.7E-16). This study suggests a component of the polygenic risk of CCL rupture in Labrador Retrievers is associated with small effect CNVs and may include aspects of stifle morphology regulated by homeobox domain transcript regulator genes.
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Affiliation(s)
- Emily E. Binversie
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Lauren A. Baker
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Corinne D. Engelman
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Zhengling Hao
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - John J. Moran
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Alexander M. Piazza
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Susannah J. Sample
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Peter Muir
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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Li J, Fan Z, Shen F, Pendleton AL, Song Y, Xing J, Yue B, Kidd JM, Li J. Genomic Copy Number Variation Study of Nine Macaca Species Provides New Insights into Their Genetic Divergence, Adaptation, and Biomedical Application. Genome Biol Evol 2020; 12:2211-2230. [PMID: 32970804 PMCID: PMC7846157 DOI: 10.1093/gbe/evaa200] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2020] [Indexed: 02/06/2023] Open
Abstract
Copy number variation (CNV) can promote phenotypic diversification and adaptive evolution. However, the genomic architecture of CNVs among Macaca species remains scarcely reported, and the roles of CNVs in adaptation and evolution of macaques have not been well addressed. Here, we identified and characterized 1,479 genome-wide hetero-specific CNVs across nine Macaca species with bioinformatic methods, along with 26 CNV-dense regions and dozens of lineage-specific CNVs. The genes intersecting CNVs were overrepresented in nutritional metabolism, xenobiotics/drug metabolism, and immune-related pathways. Population-level transcriptome data showed that nearly 46% of CNV genes were differentially expressed across populations and also mainly consisted of metabolic and immune-related genes, which implied the role of CNVs in environmental adaptation of Macaca. Several CNVs overlapping drug metabolism genes were verified with genomic quantitative polymerase chain reaction, suggesting that these macaques may have different drug metabolism features. The CNV-dense regions, including 15 first reported here, represent unstable genomic segments in macaques where biological innovation may evolve. Twelve gains and 40 losses specific to the Barbary macaque contain genes with essential roles in energy homeostasis and immunity defense, inferring the genetic basis of its unique distribution in North Africa. Our study not only elucidated the genetic diversity across Macaca species from the perspective of structural variation but also provided suggestive evidence for the role of CNVs in adaptation and genome evolution. Additionally, our findings provide new insights into the application of diverse macaques to drug study.
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Affiliation(s)
- Jing Li
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhenxin Fan
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Feichen Shen
- Department of Human Genetics, Medical School, University of Michigan
| | | | - Yang Song
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jinchuan Xing
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway
| | - Bisong Yue
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jeffrey M Kidd
- Department of Human Genetics, Medical School, University of Michigan
| | - Jing Li
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
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Albarella S, Lorenzi LD, Rossi E, Prisco F, Riccardi MG, Restucci B, Ciotola F, Parma P. Analysis of XX SRY-Negative Sex Reversal Dogs. Animals (Basel) 2020; 10:ani10091667. [PMID: 32947906 PMCID: PMC7552623 DOI: 10.3390/ani10091667] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/02/2020] [Accepted: 09/13/2020] [Indexed: 12/14/2022] Open
Abstract
Simple Summary The study of XX SRY-negative sex reversal cases is of great interest because testicular tissue develops in these subjects in the absence of SRY gene, thus allowing us to deepen the knowledge of all the other genes involved in the development of testes and the structures related to the male reproductive apparatus. This paper reports the results of the study of four new canine disorders of sex development (DSDs) XX SRY-negative cases in which 11 copy number variations (CNVs) are observed, five of which are never described. Abstract Impaired fertility associated with disorders of sex development (DSDs) due to genetic causes in dogs are more and more frequently reported. Affected dogs are usually of specific breeds thus representing a cause of economic losses for breeders. The aim of this research is to report the clinical, cytogenetic and molecular genetic findings of four XX SRY-negative DSD dog cases. All the subjects showed a female aspect and the presence of an enlarged clitoris with a penis bone. Morphopathological analyses performed in three of the four cases showed the presence of testes in two cases and ovotestis in another. Conventional and R-banded cytogenetic techniques were applied showing that no chromosome abnormalities were involved in these DSDs. CGH arrays show the presence of 11 copy number variations (CNVs), one of which is a duplication of 458 Kb comprising the genomic region between base 17,503,928 and base 17,962,221 of chromosome 9 (CanFam3 genome assembly). This CNV, confirmed also by qPCR, includes the promoter region of SOX9 gene and could explain the observed phenotype.
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Affiliation(s)
- Sara Albarella
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via Delpino 1, 80137 Naples, Italy; (F.P.); (B.R.); (F.C.)
- Correspondence: ; Tel.: +39-081-2536502; Fax: +39-081-292981
| | - Lisa De Lorenzi
- Department of Agricultural and Environmental Sciences, Milano University, via Celoria 2, 20133 Milan, Italy; (L.D.L.); (P.P.)
| | - Elena Rossi
- Department of Molecular Medicine, Pavia University, via Forlanini 12, 27100 Pavia, Italy;
| | - Francesco Prisco
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via Delpino 1, 80137 Naples, Italy; (F.P.); (B.R.); (F.C.)
| | - Marita Georgia Riccardi
- Experimental Zooprophylactic Institute of Southern Italy, via Salute 2, 80055 Portici, Italy;
| | - Brunella Restucci
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via Delpino 1, 80137 Naples, Italy; (F.P.); (B.R.); (F.C.)
| | - Francesca Ciotola
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via Delpino 1, 80137 Naples, Italy; (F.P.); (B.R.); (F.C.)
| | - Pietro Parma
- Department of Agricultural and Environmental Sciences, Milano University, via Celoria 2, 20133 Milan, Italy; (L.D.L.); (P.P.)
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Bilyi DD, Gerdeva AА, Samoiliuk VV, Suslova NI, Yevtushenko ID. A modern look at the molecular-biological mechanisms of breast tumours in dogs. REGULATORY MECHANISMS IN BIOSYSTEMS 2020. [DOI: 10.15421/022001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
High morbidity and increase in the number of registrations of breast tumours in dogs, their wide application as biological models, discussion of numerous questions of oncogenesis, and the lack of a uniform/unified methodological approach to the study of molecular and biological mechanisms of treatment of cancer determine the relevance of the problem of cancer both in humans and in our domestic companions. The analysis of publications allowed us to establish the following patterns of carcinogenesis. The peculiarities of the biological behaviour of breast tumours depend on their pathomorphological structure. Genetic predisposition to breast cancer is characteristic only in the single breed aspect. Environmental factors are of critical relevance to carcinogenesis : chemical pollutants initiate oncogenesis indirectly – by altering the expression of several receptors, impaired endocrine balance and direct mutagenic effects. Reproductive status plays a key role in the initiation and progression of breast tumours by reducing the expression of estrogen, progesterone and prolactin receptor genes. The inflammatory response that accompanies the neoplasia process is characterized by increased production of cytokines, cyclooxygenase-2, interleukins (IL-1, IL-6, IL-8), vascular endothelial growth receptors, and impaired hemostatic status (oxidative stress), which promotes progression of disease. In breast cancer in dogs, genomic instability leads to genomic aberrations, and subsequently, mutations that support the proliferation, survival and dissemination of neoplastic cells. The initiation and progression of mammary gland tumours is provided by cancer stem cells by disrupting the regulation of precursor cell self-renewal, which also predispose to resistance to chemotherapeutic agents, radiation, and hormonal cancer therapy. The analysis of the publications revealed the major markers of carcinogenesis that could potentially be used as biological targets for the design of modern diagnostic strategies and high-performance therapeutic protocols.
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Amiri Ghanatsaman Z, Wang GD, Asadollahpour Nanaei H, Asadi Fozi M, Peng MS, Esmailizadeh A, Zhang YP. Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication. BMC Genomics 2020; 21:207. [PMID: 32131720 PMCID: PMC7057629 DOI: 10.1186/s12864-020-6619-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 02/25/2020] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we conducted whole-genome sequence analysis of three wolves and three dogs from Iran which covers the eastern part of the Fertile Crescent located in Southwest Asia where the independent domestication of most of the plants and animals has been documented and also high haplotype sharing between wolves and dog breeds has been reported. RESULTS Higher diversity was found within the wolf genome compared with the dog genome. A total number of 12.45 million SNPs were detected in all individuals (10.45 and 7.82 million SNPs were identified for all the studied wolves and dogs, respectively) and a total number of 3.49 million small Indels were detected in all individuals (3.11 and 2.24 million small Indels were identified for all the studied wolves and dogs, respectively). A total of 10,571 copy number variation regions (CNVRs) were detected across the 6 individual genomes, covering 154.65 Mb, or 6.41%, of the reference genome (canFam3.1). Further analysis showed that the distribution of deleterious variants in the dog genome is higher than the wolf genome. Also, genomic annotation results from intron and intergenic regions showed that the proportion of variations in the wolf genome is higher than that in the dog genome, while the proportion of the coding sequences and 3'-UTR in the dog genome is higher than that in the wolf genome. The genes related to the olfactory and immune systems were enriched in the set of the structural variants (SVs) identified in this work. CONCLUSIONS Our results showed more deleterious mutations and coding sequence variants in the domestic dog genome than those in wolf genome. By providing the first Iranian dog and wolf variome map, our findings contribute to understanding the genetic architecture of the dog domestication.
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Affiliation(s)
- Zeinab Amiri Ghanatsaman
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
- Yong Researchers Society, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China
| | - Hojjat Asadollahpour Nanaei
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
- Yong Researchers Society, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
| | - Masood Asadi Fozi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China.
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China.
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11
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Shen F, Kidd JM. Rapid, Paralog-Sensitive CNV Analysis of 2457 Human Genomes Using QuicK-mer2. Genes (Basel) 2020; 11:genes11020141. [PMID: 32013076 PMCID: PMC7073954 DOI: 10.3390/genes11020141] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 01/21/2020] [Accepted: 01/24/2020] [Indexed: 12/22/2022] Open
Abstract
Gene duplication is a major mechanism for the evolution of gene novelty, and copy-number variation makes a major contribution to inter-individual genetic diversity. However, most approaches for studying copy-number variation rely upon uniquely mapping reads to a genome reference and are unable to distinguish among duplicated sequences. Specialized approaches to interrogate specific paralogs are comparatively slow and have a high degree of computational complexity, limiting their effective application to emerging population-scale data sets. We present QuicK-mer2, a self-contained, mapping-free approach that enables the rapid construction of paralog-specific copy-number maps from short-read sequence data. This approach is based on the tabulation of unique k-mer sequences from short-read data sets, and is able to analyze a 20X coverage human genome in approximately 20 min. We applied our approach to newly released sequence data from the 1000 Genomes Project, constructed paralog-specific copy-number maps from 2457 unrelated individuals, and uncovered copy-number variation of paralogous genes. We identify nine genes where none of the analyzed samples have a copy number of two, 92 genes where the majority of samples have a copy number other than two, and describe rare copy number variation effecting multiple genes at the APOBEC3 locus.
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Affiliation(s)
- Feichen Shen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Jeffrey M. Kidd
- Department of Human Genetics and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Correspondence:
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12
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Solé M, Ablondi M, Binzer-Panchal A, Velie BD, Hollfelder N, Buys N, Ducro BJ, François L, Janssens S, Schurink A, Viklund Å, Eriksson S, Isaksson A, Kultima H, Mikko S, Lindgren G. Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds. BMC Genomics 2019; 20:759. [PMID: 31640551 PMCID: PMC6805398 DOI: 10.1186/s12864-019-6141-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/25/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Copy Number Variation (CNV) is a common form of genetic variation underlying animal evolution and phenotypic diversity across a wide range of species. In the mammalian genome, high frequency of CNV differentiation between breeds may be candidates for population-specific selection. However, CNV differentiation, selection and its population genetics have been poorly explored in horses. RESULTS We investigated the patterns, population variation and gene annotation of CNV using the Axiom® Equine Genotyping Array (670,796 SNPs) from a large cohort of individuals (N = 1755) belonging to eight European horse breeds, varying from draught horses to several warmblood populations. After quality control, 152,640 SNP CNVs (individual markers), 18,800 segment CNVs (consecutive SNP CNVs of same gain/loss state or both) and 939 CNV regions (CNVRs; overlapping segment CNVs by at least 1 bp) compared to the average signal of the reference (Belgian draught horse) were identified. Our analyses showed that Equus caballus chromosome 12 (ECA12) was the most enriched in segment CNV gains and losses (~ 3% average proportion of the genome covered), but the highest number of segment CNVs were detected on ECA1 and ECA20 (regardless of size). The Friesian horses showed private SNP CNV gains (> 20% of the samples) on ECA1 and Exmoor ponies displayed private SNP CNV losses on ECA25 (> 20% of the samples). The Warmblood cluster showed private SNP CNV gains located in ECA9 and Draught cluster showed private SNP CNV losses located in ECA7. The length of the CNVRs ranged from 1 kb to 21.3 Mb. A total of 10,612 genes were annotated within the CNVRs. The PANTHER annotation of these genes showed significantly under- and overrepresented gene ontology biological terms related to cellular processes and immunity (Bonferroni P-value < 0.05). We identified 80 CNVRs overlapping with known QTL for fertility, coat colour, conformation and temperament. We also report 67 novel CNVRs. CONCLUSIONS This work revealed that CNV patterns, in the genome of some European horse breeds, occurred in specific genomic regions. The results provide support to the hypothesis that high frequency private CNVs residing in genes may potentially be responsible for the diverse phenotypes seen between horse breeds.
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Affiliation(s)
- Marina Solé
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Michela Ablondi
- Department of Veterinary Science, Università di Parma, Parma, Italy
| | - Amrei Binzer-Panchal
- Department of Medical Sciences, Array and Analysis Facility, Uppsala University, Uppsala, Sweden
| | - Brandon D Velie
- Faculty of Life and Environmental Science, University of Sydney, Sydney, NSW, Australia
| | - Nina Hollfelder
- Department of Medical Sciences, Array and Analysis Facility, Uppsala University, Uppsala, Sweden
| | - Nadine Buys
- Livestock Genetics, Department of Biosystems, KU Leuven, 3001, Leuven, Belgium
| | - Bart J Ducro
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, the Netherlands
| | - Liesbeth François
- Livestock Genetics, Department of Biosystems, KU Leuven, 3001, Leuven, Belgium
| | - Steven Janssens
- Livestock Genetics, Department of Biosystems, KU Leuven, 3001, Leuven, Belgium
| | - Anouk Schurink
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, the Netherlands.,Centre for Genetic Resources, the Netherlands (CGN), Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, the Netherlands
| | - Åsa Viklund
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Susanne Eriksson
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anders Isaksson
- Department of Medical Sciences, Array and Analysis Facility, Uppsala University, Uppsala, Sweden
| | - Hanna Kultima
- Department of Medical Sciences, Array and Analysis Facility, Uppsala University, Uppsala, Sweden
| | - Sofia Mikko
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Gabriella Lindgren
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Livestock Genetics, Department of Biosystems, KU Leuven, 3001, Leuven, Belgium
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13
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Huckaby AC, Granum CS, Carey MA, Szlachta K, Al-Barghouthi B, Wang YH, Guler JL. Complex DNA structures trigger copy number variation across the Plasmodium falciparum genome. Nucleic Acids Res 2019; 47:1615-1627. [PMID: 30576466 PMCID: PMC6393310 DOI: 10.1093/nar/gky1268] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 12/04/2018] [Accepted: 12/07/2018] [Indexed: 02/06/2023] Open
Abstract
Antimalarial resistance is a major obstacle in the eradication of the human malaria parasite, Plasmodium falciparum. Genome amplifications, a type of DNA copy number variation (CNV), facilitate overexpression of drug targets and contribute to parasite survival. Long monomeric A/T tracks are found at the breakpoints of many Plasmodium resistance-conferring CNVs. We hypothesize that other proximal sequence features, such as DNA hairpins, act with A/T tracks to trigger CNV formation. By adapting a sequence analysis pipeline to investigate previously reported CNVs, we identified breakpoints in 35 parasite clones with near single base-pair resolution. Using parental genome sequence, we predicted the formation of stable hairpins within close proximity to all future breakpoint locations. Especially stable hairpins were predicted to form near five shared breakpoints, establishing that the initiating event could have occurred at these sites. Further in-depth analyses defined characteristics of these 'trigger sites' across the genome and detected signatures of error-prone repair pathways at the breakpoints. We propose that these two genomic signals form the initial lesion (hairpins) and facilitate microhomology-mediated repair (A/T tracks) that lead to CNV formation across this highly repetitive genome. Targeting these repair pathways in P. falciparum may be used to block adaptation to antimalarial drugs.
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Affiliation(s)
- Adam C Huckaby
- Department of Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Claire S Granum
- Department of Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Maureen A Carey
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia Health System, Charlottesville, VA 22908, USA.,Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Karol Szlachta
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Basel Al-Barghouthi
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA.,Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Jennifer L Guler
- Department of Biology, University of Virginia, Charlottesville, VA 22908, USA.,Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville, VA 22908, USA
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14
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Keel BN, Nonneman DJ, Lindholm-Perry AK, Oliver WT, Rohrer GA. A Survey of Copy Number Variation in the Porcine Genome Detected From Whole-Genome Sequence. Front Genet 2019; 10:737. [PMID: 31475038 PMCID: PMC6707380 DOI: 10.3389/fgene.2019.00737] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 07/12/2019] [Indexed: 12/11/2022] Open
Abstract
Copy number variations (CNVs) are gains and losses of large regions of genomic sequence between individuals of a species. Although CNVs have been associated with various phenotypic traits in humans and other species, the extent to which CNVs impact phenotypic variation remains unclear. In swine, as well as many other species, relatively little is understood about the frequency of CNV in the genome, sizes, locations, and other chromosomal properties. In this work, we identified and characterized CNV by utilizing whole-genome sequence from 240 members of an intensely phenotyped experimental swine herd at the U.S. Meat Animal Research Center (USMARC). These animals included all 24 of the purebred founding boars (12 Duroc and 12 Landrace), 48 of the founding Yorkshire-Landrace composite sows, 109 composite animals from generations 4 through 9, 29 composite animals from generation 15, and 30 purebred industry boars (15 Landrace and 15 Yorkshire) used as sires in generations 10 through 15. Using a combination of split reads, paired-end mapping, and read depth approaches, we identified a total of 3,538 copy number variable regions (CNVRs), including 1,820 novel CNVRs not reported in previous studies. The CNVRs covered 0.94% of the porcine genome and overlapped 1,401 genes. Gene ontology analysis identified that CNV-overlapped genes were enriched for functions related to organism development. Additionally, CNVRs overlapped with many known quantitative trait loci (QTL). In particular, analysis of QTL previously identified in the USMARC herd showed that CNVRs were most overlapped with reproductive traits, such as age of puberty and ovulation rate, and CNVRs were significantly enriched for reproductive QTL.
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Affiliation(s)
- Brittney N Keel
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Dan J Nonneman
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States
| | | | - William T Oliver
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Gary A Rohrer
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States
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15
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Di Gerlando R, Mastrangelo S, Sardina MT, Ragatzu M, Spaterna A, Portolano B, Biscarini F, Ciampolini R. A Genome-Wide Detection of Copy Number Variations Using SNP Genotyping Arrays in Braque Français Type Pyrénées Dogs. Animals (Basel) 2019; 9:E77. [PMID: 30832273 PMCID: PMC6466271 DOI: 10.3390/ani9030077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/21/2019] [Accepted: 02/28/2019] [Indexed: 01/07/2023] Open
Abstract
Copy number variants (CNVs) are an important source of genetic variation complementary to single nucleotide polymorphisms (SNPs). Only few studies have been conducted in dogs on CNVs derived from high-density SNP array data, and many canine breeds still remain uncharacterized, e.g., the Braque Français, type Pyrénées breed (BRA). Therefore, in an effort to more comprehensively investigate the canine genome for CNVs, we used a high-density SNP array (170 K) to discover CNVs in BRA. The CNV regions (CNVRs) were identified through the merging of two different CNVRs datasets, obtained separately from SNP data using the PennCNV and SVS software. A total of 45 stringent CNVRs, ranging from 3.5 kb to 458,716 kb in length were detected in 26 dog samples. Results overlapped moderately in comparison with previous studies on CNVs in dogs, leading to the identification of 16 novel CNVRs. A total of 159 genes were annotated in the CNVRs detected with stringent quality criteria in particular high classification stringency and false discovery rate correction. The gene ontology enrichment analysis provided information on biological processes and cellular components related to muscle structure development and muscle cell differentiation. Considering that BRA is a breed used for speed in hunting and retrieval, for the ability to find feathered game, and for pointing, we can hypothesize that selection for such hunting behavior could have driven, at least in part, the presence of these genes into the CNVRs.
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Affiliation(s)
- Rosalia Di Gerlando
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy.
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy.
| | - Maria Teresa Sardina
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy.
| | - Marco Ragatzu
- Club Italiano Braque Français Type Pyrénées, 58011 Capalbio, Italy.
| | - Andrea Spaterna
- Scuola di Scienze Mediche Veterinarie, University of Camerino, 62024 Matelica, Italy.
- Centro interuniversitario di ricerca e di consulenza sulla genetica e la clinica del cane, 62024, Matelica, MC, Italy.
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy.
| | - Filippo Biscarini
- Consiglio Nazionale delle Ricerche-Istituto di Biologia e Biotecnologia Agraria, 20133 Milano, Italy.
| | - Roberta Ciampolini
- Centro interuniversitario di ricerca e di consulenza sulla genetica e la clinica del cane, 62024, Matelica, MC, Italy.
- Dipartimento di Scienze Veterinarie, University of Pisa, 56100 Pisa, Italy.
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16
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Mortlock SA, Williamson P, Khatkar MS. Copy number variation and variant discovery in Bullmastiff dogs. Anim Genet 2019; 50:177-181. [PMID: 30793343 DOI: 10.1111/age.12754] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2018] [Indexed: 01/05/2023]
Abstract
Identification of genomic variants within dogs is important for understanding genetic factors contributing to breed diversity and phenotypic traits. This study aimed to identify sources of variation in the Bullmastiff using high-density signal intensity and whole-genome sequence data. Close to 3000 copy number variants (CNVs) were identified in Bullmastiff dogs using Canine HD BeadChip data. When CNVs were collated, 82 CNV regions (CNVRs) were detected, 50% in transcribed regions encompassing 432 genes. Fifty of the CNVRs detected have not been reported in other breeds and represent potential breed-specific variants. A proportion of the CNVR variants with predicted modifying effects on gene pathways may contribute to breed traits. Approximately 5 million putative variants per dog, inclusive of single nucleotide polymorphisms (SNPs), multi-nucleotide polymorphisms (MNPs) and insertion and deletions (INDELs), were identified from DNA sequence data on a small number of animals. Identification of genetic variants in the Bullmastiff highlights sources of variation in the breed and molecular markers that will assist in future trait and disease investigations in dogs.
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Affiliation(s)
- S-A Mortlock
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camperdown, NSW, 2006, Australia.,School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - P Williamson
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camperdown, NSW, 2006, Australia.,School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - M S Khatkar
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camperdown, NSW, 2006, Australia
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17
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Wang GD, Shao XJ, Bai B, Wang J, Wang X, Cao X, Liu YH, Wang X, Yin TT, Zhang SJ, Lu Y, Wang Z, Wang L, Zhao W, Zhang B, Ruan J, Zhang YP. Structural variation during dog domestication: insights from gray wolf and dhole genomes. Natl Sci Rev 2019; 6:110-122. [PMID: 34694297 PMCID: PMC8291444 DOI: 10.1093/nsr/nwy076] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 06/27/2018] [Accepted: 07/17/2018] [Indexed: 12/11/2022] Open
Abstract
Several processes like phenotypic evolution, disease susceptibility and environmental adaptations, which fashion the domestication of animals, are largely attributable to structural variations (SVs) in the genome. Here, we present high-quality draft genomes of the gray wolf (Canis lupus) and dhole (Cuon alpinus) with scaffold N50 of 6.04 Mb and 3.96 Mb, respectively. Sequence alignment comprising genomes of three canid species reveals SVs specific to the dog, particularly 16 315 insertions, 2565 deletions, 443 repeats, 16 inversions and 15 translocations. Functional annotation of the dog SVs associated with genes indicates their enrichments in energy metabolisms, neurological processes and immune systems. Interestingly, we identify and verify at population level an insertion fully covering a copy of the AKR1B1 (Aldo-Keto Reductase Family 1 Member B) transcript. Transcriptome analysis reveals a high level of expression of the new AKR1B1 copy in the small intestine and liver, implying an increase in de novo fatty acid synthesis and antioxidant ability in dog compared to gray wolf, likely in response to dietary shifts during the agricultural revolution. For the first time, we report a comprehensive analysis of the evolutionary dynamics of SVs during the domestication step of dogs. Our findings demonstrate that retroposition can birth new genes to facilitate domestication, and affirm the importance of large-scale genomic variants in domestication studies.
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Affiliation(s)
- 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
| | - Xiu-Juan Shao
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Bing Bai
- Medical Faculty, Kunming University of Science and Technology, Kunming 650504, China
- Department of Pediatrics, the First People's Hospital of Yunnan Province, Kunming 650032, China
| | - Junlong Wang
- College of Pharmacology, Soochow University, Suzhou 215123, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xiaobo Wang
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xue Cao
- Department of Laboratory Animal Science, Kunming Medical University, Kunming 650500, China
| | - Yan-Hu Liu
- Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Xuan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Shao-Jie Zhang
- Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Yan Lu
- Beijing Zoo, Beijing 100044, China
| | | | - Lu Wang
- Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Wenming Zhao
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bing Zhang
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jue Ruan
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Ya-Ping Zhang
- 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
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18
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Pendleton AL, Shen F, Taravella AM, Emery S, Veeramah KR, Boyko AR, Kidd JM. Comparison of village dog and wolf genomes highlights the role of the neural crest in dog domestication. BMC Biol 2018; 16:64. [PMID: 29950181 PMCID: PMC6022502 DOI: 10.1186/s12915-018-0535-2] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/23/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Domesticated from gray wolves between 10 and 40 kya in Eurasia, dogs display a vast array of phenotypes that differ from their ancestors, yet mirror other domesticated animal species, a phenomenon known as the domestication syndrome. Here, we use signatures persisting in dog genomes to identify genes and pathways possibly altered by the selective pressures of domestication. RESULTS Whole-genome SNP analyses of 43 globally distributed village dogs and 10 wolves differentiated signatures resulting from domestication rather than breed formation. We identified 246 candidate domestication regions containing 10.8 Mb of genome sequence and 429 genes. The regions share haplotypes with ancient dogs, suggesting that the detected signals are not the result of recent selection. Gene enrichments highlight numerous genes linked to neural crest and central nervous system development as well as neurological function. Read depth analysis suggests that copy number variation played a minor role in dog domestication. CONCLUSIONS Our results identify genes that act early in embryogenesis and can confer phenotypes distinguishing domesticated dogs from wolves, such as tameness, smaller jaws, floppy ears, and diminished craniofacial development as the targets of selection during domestication. These differences reflect the phenotypes of the domestication syndrome, which can be explained by alterations in the migration or activity of neural crest cells during development. We propose that initial selection during early dog domestication was for behavior, a trait influenced by genes which act in the neural crest, which secondarily gave rise to the phenotypes of modern dogs.
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Affiliation(s)
- Amanda L Pendleton
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Feichen Shen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Angela M Taravella
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sarah Emery
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Adam R Boyko
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, 14853, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.
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19
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Serres-Armero A, Povolotskaya IS, Quilez J, Ramirez O, Santpere G, Kuderna LFK, Hernandez-Rodriguez J, Fernandez-Callejo M, Gomez-Sanchez D, Freedman AH, Fan Z, Novembre J, Navarro A, Boyko A, Wayne R, Vilà C, Lorente-Galdos B, Marques-Bonet T. Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing. BMC Genomics 2017; 18:977. [PMID: 29258433 PMCID: PMC5735816 DOI: 10.1186/s12864-017-4318-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 11/17/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Whole genome re-sequencing data from dogs and wolves are now commonly used to study how natural and artificial selection have shaped the patterns of genetic diversity. Single nucleotide polymorphisms, microsatellites and variants in mitochondrial DNA have been interrogated for links to specific phenotypes or signals of domestication. However, copy number variation (CNV), despite its increasingly recognized importance as a contributor to phenotypic diversity, has not been extensively explored in canids. RESULTS Here, we develop a new accurate probabilistic framework to create fine-scale genomic maps of segmental duplications (SDs), compare patterns of CNV across groups and investigate their role in the evolution of the domestic dog by using information from 34 canine genomes. Our analyses show that duplicated regions are enriched in genes and hence likely possess functional importance. We identify 86 loci with large CNV differences between dogs and wolves, enriched in genes responsible for sensory perception, immune response, metabolic processes, etc. In striking contrast to the observed loss of nucleotide diversity in domestic dogs following the population bottlenecks that occurred during domestication and breed creation, we find a similar proportion of CNV loci in dogs and wolves, suggesting that other dynamics are acting to particularly select for CNVs with potentially functional impacts. CONCLUSIONS This work is the first comparison of genome wide CNV patterns in domestic and wild canids using whole-genome sequencing data and our findings contribute to study the impact of novel kinds of genetic changes on the evolution of the domestic dog.
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Affiliation(s)
- Aitor Serres-Armero
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Inna S Povolotskaya
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Javier Quilez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Oscar Ramirez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain.,Vetgenomics, 08193, Barcelona, Spain
| | - Gabriel Santpere
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain.,Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Lukas F K Kuderna
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Jessica Hernandez-Rodriguez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Marcos Fernandez-Callejo
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Daniel Gomez-Sanchez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Adam H Freedman
- UCLA, Department of Ecology and Evolutionary Biology, Los Angeles, CA, 90095, USA
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - John Novembre
- UCLA, Department of Ecology and Evolutionary Biology, Los Angeles, CA, 90095, USA
| | - Arcadi Navarro
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Catalonia, Spain
| | - Adam Boyko
- Cornell University, Department of Biological Statistics and Computational Biology, New York, NY, 14853, USA
| | - Robert Wayne
- UCLA, Department of Ecology and Evolutionary Biology, Los Angeles, CA, 90095, USA
| | - Carles Vilà
- Estación Biológica de Doñana EBD-CSIC, Department of Integrative Ecology, 41092, Sevilla, Spain
| | - Belen Lorente-Galdos
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain. .,Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.
| | - Tomas Marques-Bonet
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain. .,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .,Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Catalonia, Spain.
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20
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Dolatabadian A, Patel DA, Edwards D, Batley J. Copy number variation and disease resistance in plants. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:2479-2490. [PMID: 29043379 DOI: 10.1007/s00122-017-2993-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 09/27/2017] [Indexed: 05/06/2023]
Abstract
Plant genome diversity varies from single nucleotide polymorphisms to large-scale deletions, insertions, duplications, or re-arrangements. These re-arrangements of sequences resulting from duplication, gains or losses of DNA segments are termed copy number variations (CNVs). During the last decade, numerous studies have emphasized the importance of CNVs as a factor affecting human phenotype; in particular, CNVs have been associated with risks for several severe diseases. In plants, the exploration of the extent and role of CNVs in resistance against pathogens and pests is just beginning. Since CNVs are likely to be associated with disease resistance in plants, an understanding of the distribution of CNVs could assist in the identification of novel plant disease-resistance genes. In this paper, we review existing information about CNVs; their importance, role and function, as well as their association with disease resistance in plants.
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Affiliation(s)
- Aria Dolatabadian
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia
| | - Dhwani Apurva Patel
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia.
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21
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Yang L, Xu L, Zhu B, Niu H, Zhang W, Miao J, Shi X, Zhang M, Chen Y, Zhang L, Gao X, Gao H, Li L, Liu GE, Li J. Genome-wide analysis reveals differential selection involved with copy number variation in diverse Chinese Cattle. Sci Rep 2017; 7:14299. [PMID: 29085051 PMCID: PMC5662686 DOI: 10.1038/s41598-017-14768-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 10/12/2017] [Indexed: 12/20/2022] Open
Abstract
Copy number variations (CNVs) are defined as deletions, insertions, and duplications between two individuals of a species. To investigate the diversity and population-genetic properties of CNVs and their diverse selection patterns, we performed a genome-wide CNV analysis using high density SNP array in Chinese native cattle. In this study, we detected a total of 13,225 CNV events and 3,356 CNV regions (CNVRs), overlapping with 1,522 annotated genes. Among them, approximately 71.43 Mb of novel CNVRs were detected in the Chinese cattle population for the first time, representing the unique genomic resources in cattle. A new V i statistic was proposed to estimate the region-specific divergence in CNVR for each group based on unbiased estimates of pairwise V ST . We obtained 12 and 62 candidate CNVRs at the top 1% and top 5% of genome-wide V i value thresholds for each of four groups (North, Northwest, Southwest and South). Moreover, we identified many lineage-differentiated CNV genes across four groups, which were associated with several important molecular functions and biological processes, including metabolic process, response to stimulus, immune system, and others. Our findings provide some insights into understanding lineage-differentiated CNVs under divergent selection in the Chinese native cattle.
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Affiliation(s)
- Liu Yang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Lingyang Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Bo Zhu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Hong Niu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wengang Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jian Miao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Xinping Shi
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,College of Animal Science and Technology, Agricultural University of Hebei, Baoding, Hebei, 071001, China
| | - Ming Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yan Chen
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lupei Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xue Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Huijiang Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Li Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland, 20705, USA
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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22
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Sohrabi SS, Mohammadabadi M, Wu DD, Esmailizadeh A. Detection of breed-specific copy number variations in domestic chicken genome. Genome 2017; 61:7-14. [PMID: 28961404 DOI: 10.1139/gen-2017-0016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Copy number variations (CNVs) are important large-scale variants. They are widespread in the genome and may contribute to phenotypic variation. Detection and characterization of CNVs can provide new insights into the genetic basis of important traits. Here, we perform whole-genome short read sequence analysis to identify CNVs in two indigenous and commercial chicken breeds to evaluate the impact of the identified CNVs on breed-specific traits. After filtration, a total of 12 955 CNVs spanning (on average) about 9.42% of the chicken genome were found that made up 5467 CNV regions (CNVRs). Chicken quantitative trait loci (QTL) datasets and Ensembl gene annotations were used as resources for the estimation of potential phenotypic effects of our CNVRs on breed-specific traits. In total, 34% of our detected CNVRs were also detected in earlier CNV studies. These CNVRs partly overlap several previously reported QTL and gene ontology terms associated with some important traits, including shank length QTL in Creeper-specific CNVRs and body weight and egg production characteristics, as well as muscle and body organ growth, in the Arian commercial breed. Our findings provide new insights into the genomic structure of the chicken genome for an improved understanding of the potential roles of CNVRs in differentiating between breeds or lines.
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Affiliation(s)
- Saeed S Sohrabi
- a Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran.,b Young Researchers Society, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
| | - Mohammadreza Mohammadabadi
- a Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
| | - Dong-Dong Wu
- c State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,d Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Ali Esmailizadeh
- a Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran.,c State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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23
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Structural Variation Shapes the Landscape of Recombination in Mouse. Genetics 2017; 206:603-619. [PMID: 28592499 DOI: 10.1534/genetics.116.197988] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/13/2017] [Indexed: 01/02/2023] Open
Abstract
Meiotic recombination is an essential feature of sexual reproduction that ensures faithful segregation of chromosomes and redistributes genetic variants in populations. Multiparent populations such as the Diversity Outbred (DO) mouse stock accumulate large numbers of crossover (CO) events between founder haplotypes, and thus present a unique opportunity to study the role of genetic variation in shaping the recombination landscape. We obtained high-density genotype data from [Formula: see text] DO mice, and localized 2.2 million CO events to intervals with a median size of 28 kb. The resulting sex-averaged genetic map of the DO population is highly concordant with large-scale (order 10 Mb) features of previously reported genetic maps for mouse. To examine fine-scale (order 10 kb) patterns of recombination in the DO, we overlaid putative recombination hotspots onto our CO intervals. We found that CO intervals are enriched in hotspots compared to the genomic background. However, as many as [Formula: see text] of CO intervals do not overlap any putative hotspots, suggesting that our understanding of hotspots is incomplete. We also identified coldspots encompassing 329 Mb, or [Formula: see text] of observable genome, in which there is little or no recombination. In contrast to hotspots, which are a few kilobases in size, and widely scattered throughout the genome, coldspots have a median size of 2.1 Mb and are spatially clustered. Coldspots are strongly associated with copy-number variant (CNV) regions, especially multi-allelic clusters, identified from whole-genome sequencing of 228 DO mice. Genes in these regions have reduced expression, and epigenetic features of closed chromatin in male germ cells, which suggests that CNVs may repress recombination by altering chromatin structure in meiosis. Our findings demonstrate how multiparent populations, by bridging the gap between large-scale and fine-scale genetic mapping, can reveal new features of the recombination landscape.
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24
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Hu XS, Yeh FC, Hu Y, Deng LT, Ennos RA, Chen X. High mutation rates explain low population genetic divergence at copy-number-variable loci in Homo sapiens. Sci Rep 2017; 7:43178. [PMID: 28225073 PMCID: PMC5320550 DOI: 10.1038/srep43178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 01/19/2017] [Indexed: 11/09/2022] Open
Abstract
Copy-number-variable (CNV) loci differ from single nucleotide polymorphic (SNP) sites in size, mutation rate, and mechanisms of maintenance in natural populations. It is therefore hypothesized that population genetic divergence at CNV loci will differ from that found at SNP sites. Here, we test this hypothesis by analysing 856 CNV loci from the genomes of 1184 healthy individuals from 11 HapMap populations with a wide range of ancestry. The results show that population genetic divergence at the CNV loci is generally more than three times lower than at genome-wide SNP sites. Populations generally exhibit very small genetic divergence (Gst = 0.05 ± 0.049). The smallest divergence is among African populations (Gst = 0.0081 ± 0.0025), with increased divergence among non-African populations (Gst = 0.0217 ± 0.0109) and then among African and non-African populations (Gst = 0.0324 ± 0.0064). Genetic diversity is high in African populations (~0.13), low in Asian populations (~0.11), and intermediate in the remaining 11 populations. Few significant linkage disequilibria (LDs) occur between the genome-wide CNV loci. Patterns of gametic and zygotic LDs indicate the absence of epistasis among CNV loci. Mutation rate is about twice as large as the migration rate in the non-African populations, suggesting that the high mutation rates play dominant roles in producing the low population genetic divergence at CNV loci.
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Affiliation(s)
- Xin-Sheng Hu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong 510642, China.,College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong 510642, China
| | - Francis C Yeh
- Department of Renewable Resources, 751 General Service Building, University of Alberta, Edmonton, AB T6G 2H1, Canada
| | - Yang Hu
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2S4, Canada
| | - Li-Ting Deng
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong 510642, China.,College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong 510642, China
| | - Richard A Ennos
- Institute of Evolutionary Biology, Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, Edinburgh EH 9 3JT, United Kingdom
| | - Xiaoyang Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong 510642, China.,College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong 510642, China
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25
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Keel BN, Lindholm-Perry AK, Snelling WM. Evolutionary and Functional Features of Copy Number Variation in the Cattle Genome. Front Genet 2016; 7:207. [PMID: 27920798 PMCID: PMC5118444 DOI: 10.3389/fgene.2016.00207] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 11/08/2016] [Indexed: 01/18/2023] Open
Abstract
Genomic structural variations are an important source of genetic diversity. Copy number variations (CNVs), gains and losses of large regions of genomic sequence between individuals of a species, have been associated with a wide variety of phenotypic traits. However, in cattle, as well as many other species, relatively little is understood about CNV, including frequency of CNVs in the genome, sizes, and locations, chromosomal properties, and evolutionary processes acting to shape CNV. In this work, we focused on copy number variation in the bovine genome, with the aim to detect CNVs in Bos taurus coding sequence and explore potential evolutionary mechanisms shaping these CNV. We identified and characterized CNV regions by utilizing exome sequence from 175 influential sires used in the Germplasm Evaluation project, representing 10 breeds. We examined various evolutionary and functional aspects of these CNVs, including selective constraint on CNV-overlapped genes, centrality of CNV genes in protein-protein interaction networks, and tissue-specific expression of CNV genes. Patterns of CNV in the Bos taurus genome reveal that reduced functional constraint and mutational bias may play a prominent role in shaping this type of structural variation.
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Affiliation(s)
- Brittney N Keel
- Agricultural Research Service (USDA), Meat Animal Research Center Clay Center, NE, USA
| | | | - Warren M Snelling
- Agricultural Research Service (USDA), Meat Animal Research Center Clay Center, NE, USA
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26
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Keel BN, Keele JW, Snelling WM. Genome-wide copy number variation in the bovine genome detected using low coverage sequence of popular beef breeds,. Anim Genet 2016; 48:141-150. [DOI: 10.1111/age.12519] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2016] [Indexed: 12/19/2022]
Affiliation(s)
- B. N. Keel
- USDA; ARS; U.S. Meat Animal Research Center; Clay Center NE 68933 USA
| | - J. W. Keele
- USDA; ARS; U.S. Meat Animal Research Center; Clay Center NE 68933 USA
| | - W. M. Snelling
- USDA; ARS; U.S. Meat Animal Research Center; Clay Center NE 68933 USA
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27
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Zapata I, Serpell JA, Alvarez CE. Genetic mapping of canine fear and aggression. BMC Genomics 2016; 17:572. [PMID: 27503363 PMCID: PMC4977763 DOI: 10.1186/s12864-016-2936-3] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 07/13/2016] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Fear/anxiety and anger/aggression greatly influence health, quality of life and social interactions. They are a huge burden to wellbeing, and personal and public economics. However, while much is known about the physiology and neuroanatomy of such emotions, little is known about their genetics - most importantly, why some individuals are more susceptible to pathology under stress. RESULTS We conducted genomewide association (GWA) mapping of breed stereotypes for many fear and aggression traits across several hundred dogs from diverse breeds. We confirmed those findings using GWA in a second cohort of partially overlapping breeds. Lastly, we used the validated loci to create a model that effectively predicted fear and aggression stereotypes in a third group of dog breeds that were not involved in the mapping studies. We found that i) known IGF1 and HMGA2 loci variants for small body size are associated with separation anxiety, touch-sensitivity, owner directed aggression and dog rivalry; and ii) two loci, between GNAT3 and CD36 on chr18, and near IGSF1 on chrX, are associated with several traits, including touch-sensitivity, non-social fear, and fear and aggression that are directed toward unfamiliar dogs and humans. All four genome loci are among the most highly evolutionarily-selected in dogs, and each of those was previously shown to be associated with morphological traits. We propose that the IGF1 and HMGA2 loci are candidates for identical variation being associated with both behavior and morphology. In contrast, we show that the GNAT3-CD36 locus has distinct variants for behavior and morphology. The chrX region is a special case due to its extensive linkage disequilibrium (LD). Our evidence strongly suggests that sociability (which we propose is associated with HS6ST2) and fear/aggression are two distinct GWA loci within this LD block on chrX, but there is almost perfect LD between the peaks for fear/aggression and animal size. CONCLUSIONS We have mapped many canine fear and aggression traits to single haplotypes at the GNAT3-CD36 and IGSF1 loci. CD36 is widely expressed, but areas of the amygdala and hypothalamus are among the brain regions with highest enrichment; and CD36-knockout mice are known to have significantly increased anxiety and aggression. Both of the other genes have very high tissue-specificity and are very abundantly expressed in brain regions that comprise the core anatomy of fear and aggression - the amygdala to hypothalamic-pituitary-adrenal (HPA) axis. We propose that reduced-fear variants at these loci may have been involved in the domestication process.
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Affiliation(s)
- Isain Zapata
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205 USA
| | - James A. Serpell
- Center for the Interaction of Animals and Society, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Carlos E. Alvarez
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205 USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210 USA
- Department of Veterinary Clinical Sciences, The Ohio State University College of Veterinary Medicine, Columbus, OH 43210 USA
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28
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Kader A, Liu X, Dong K, Song S, Pan J, Yang M, Chen X, He X, Jiang L, Ma Y. Identification of copy number variations in three Chinese horse breeds using 70K single nucleotide polymorphism BeadChip array. Anim Genet 2016; 47:560-9. [PMID: 27440410 DOI: 10.1111/age.12451] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2016] [Indexed: 02/06/2023]
Abstract
Copy number variation (CNV), an essential form of genetic variation, has been increasingly recognized as one promising genetic marker in the analysis of animal genomes. Here, we used the Equine 70K single nucleotide polymorphism genotyping array for the genome-wide detection of CNVs in 96 horses from three diverse Chinese breeds: Debao pony (DB), Mongolian horse (MG) and Yili horse (YL). A total of 287 CNVs were determined and merged into 122 CNV regions (CNVRs) ranging from 199 bp to 2344 kb in size and distributed in a heterogeneous manner on chromosomes. These CNVRs were integrated with seven existing reports to generate a composite genome-wide dataset of 1558 equine CNVRs, revealing 69 (56.6%) novel CNVRs. The majority (69.7%) of the 122 CNVRs overlapped with 438 genes, whereas 30.3% were located in intergenic regions. Most of these genes were associated with common CNVRs, which were shared by divergent horse breeds. As many as 60, 42 and 91 genes overlapping with the breed-specific ss were identified in DB, MG and YL respectively. Among these genes, FGF11, SPEM1, PPARG, CIDEB, HIVEP1 and GALR may have potential relevance to breed-specific traits. These findings provide valuable information for understanding the equine genome and facilitating association studies of economically important traits with equine CNVRs in the future.
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Affiliation(s)
- Adiljan Kader
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China.,Xinjiang Academy of Animal Science, Urumqi, Xinjiang, 83000, China
| | - Xuexue Liu
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China
| | - Kunzhe Dong
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China.,United States Department of Agriculture, Agricultural Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI, 48823, USA
| | - Shen Song
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China.,Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100094, China
| | - Jianfei Pan
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China
| | - Min Yang
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China
| | - Xiaofei Chen
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China
| | - Xiaohong He
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China
| | - Lin Jiang
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China.
| | - Yuehui Ma
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China.
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Hu XS, Hu Y, Chen X. Testing neutrality at copy-number-variable loci under the finite-allele and finite-site models. Theor Popul Biol 2016; 112:1-13. [PMID: 27423854 DOI: 10.1016/j.tpb.2016.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 07/05/2016] [Accepted: 07/06/2016] [Indexed: 02/01/2023]
Abstract
Copy-number variation (CNV) is an important form of DNA structural variation because a certain proportion of genomes in many eukaryotic species can contribute to such variations. Owing to the differences between CNVs and single nucleotide polymorphisms (SNPs) in size, mutation rate and maintaining mechanism, it is more realistic to characterize CNV evolution under the finite-allele and finite-site models. Here, we propose a method to test multiple CNVs neutrality under the finite-allele and finite-site models and the assumption of mutation-drift process. The statistical property of the method is evaluated through Monte Carlo simulations under the effects of the sample size, the scaled mutation rates, the number of CNVs, the population demographic change, and selection. Different from Tajima's D test, a bootstrap or a permutation approach is suggested to conduct a neutrality test. Application of this method is illustrated using the diploid CNV genotypes measured in discrete copy numbers in 11 HapMap phase III populations. The results show that the mutation-drift process can explain the variation of genome-wide CNVs among 1184 individuals (856 CNVs, ∼0.02Mb on average in size), irrespective of the historical demographic changes. Patterns from allele-frequency-spectrum analysis also support the hypothesis of neutral CNVs. Our results suggest that most human chromosomal changes in healthy individuals via unbalanced rearrangements of the segments with certain sizes are neutral.
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Affiliation(s)
- Xin-Sheng Hu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong 510642, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangdong 510642, China; Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX13RB, United Kingdom.
| | - Yang Hu
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2S4, Canada
| | - Xiaoyang Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong 510642, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangdong 510642, China.
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30
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Comparative analyses across cattle genders and breeds reveal the pitfalls caused by false positive and lineage-differential copy number variations. Sci Rep 2016; 6:29219. [PMID: 27381368 PMCID: PMC4933914 DOI: 10.1038/srep29219] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 06/14/2016] [Indexed: 12/31/2022] Open
Abstract
We compared CNV region (CNVR) results derived from 1,682 Nellore cattle with equivalent results derived from our previous analysis of Bovine HapMap samples. By comparing CNV segment frequencies between different genders and groups, we identified 9 frequent, false positive CNVRs with a total length of 0.8 Mbp that were likely caused by assembly errors. Although there was a paucity of lineage specific events, we did find one 54 kb deletion on chr5 significantly enriched in Nellore cattle. A few highly frequent CNVRs present in both datasets were detected within genomic regions containing olfactory receptor, ATP-binding cassette, and major histocompatibility complex genes. We further evaluated their impacts on downstream bioinformatics and CNV association analyses. Our results revealed pitfalls caused by false positive and lineage-differential copy number variations and will increase the accuracy of future CNV studies in both taurine and indicine cattle.
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31
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da Silva VH, Regitano LCDA, Geistlinger L, Pértille F, Giachetto PF, Brassaloti RA, Morosini NS, Zimmer R, Coutinho LL. Genome-Wide Detection of CNVs and Their Association with Meat Tenderness in Nelore Cattle. PLoS One 2016; 11:e0157711. [PMID: 27348523 PMCID: PMC4922624 DOI: 10.1371/journal.pone.0157711] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 06/03/2016] [Indexed: 12/20/2022] Open
Abstract
Brazil is one of the largest beef producers and exporters in the world with the Nelore breed representing the vast majority of Brazilian cattle (Bos taurus indicus). Despite the great adaptability of the Nelore breed to tropical climate, meat tenderness (MT) remains to be improved. Several factors including genetic composition can influence MT. In this article, we report a genome-wide analysis of copy number variation (CNV) inferred from Illumina® High Density SNP-chip data for a Nelore population of 723 males. We detected >2,600 CNV regions (CNVRs) representing ≈6.5% of the genome. Comparing our results with previous studies revealed an overlap in ≈1400 CNVRs (>50%). A total of 1,155 CNVRs (43.6%) overlapped 2,750 genes. They were enriched for processes involving guanosine triphosphate (GTP), previously reported to influence skeletal muscle physiology and morphology. Nelore CNVRs also overlapped QTLs for MT reported in other breeds (8.9%, 236 CNVRs) and from a previous study with this population (4.1%, 109 CNVRs). Two CNVRs were also proximal to glutathione metabolism genes that were previously associated with MT. Genome-wide association study of CN state with estimated breeding values derived from meat shear force identified 6 regions, including a region on BTA3 that contains genes of the cAMP and cGMP pathway. Ten CNVRs that overlapped regions associated with MT were successfully validated by qPCR. Our results represent the first comprehensive CNV study in Bos taurus indicus cattle and identify regions in which copy number changes are potentially of importance for the MT phenotype.
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Affiliation(s)
- Vinicius Henrique da Silva
- Animal Biotechnology Laboratory, Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
- * E-mail: (LLC); (VHS)
| | | | - Ludwig Geistlinger
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München (LMU), Amalienstrasse 17, 80333, München, Germany
| | - Fábio Pértille
- Animal Biotechnology Laboratory, Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | | | - Ricardo Augusto Brassaloti
- Animal Biotechnology Laboratory, Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - Natália Silva Morosini
- Animal Biotechnology Laboratory, Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - Ralf Zimmer
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München (LMU), Amalienstrasse 17, 80333, München, Germany
| | - Luiz Lehmann Coutinho
- Animal Biotechnology Laboratory, Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
- * E-mail: (LLC); (VHS)
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32
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Olsson M, Kierczak M, Karlsson Å, Jabłońska J, Leegwater P, Koltookian M, Abadie J, De Citres CD, Thomas A, Hedhammar Å, Tintle L, Lindblad-Toh K, Meadows JRS. Absolute quantification reveals the stable transmission of a high copy number variant linked to autoinflammatory disease. BMC Genomics 2016; 17:299. [PMID: 27107962 PMCID: PMC4841964 DOI: 10.1186/s12864-016-2619-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/13/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Dissecting the role copy number variants (CNVs) play in disease pathogenesis is directly reliant on accurate methods for quantification. The Shar-Pei dog breed is predisposed to a complex autoinflammatory disease with numerous clinical manifestations. One such sign, recurrent fever, was previously shown to be significantly associated with a novel, but unstable CNV (CNV_16.1). Droplet digital PCR (ddPCR) offers a new mechanism for CNV detection via absolute quantification with the promise of added precision and reliability. The aim of this study was to evaluate ddPCR in relation to quantitative PCR (qPCR) and to assess the suitability of the favoured method as a genetic test for Shar-Pei Autoinflammatory Disease (SPAID). RESULTS One hundred and ninety-six individuals were assayed using both PCR methods at two CNV positions (CNV_14.3 and CNV_16.1). The digital method revealed a striking result. The CNVs did not follow a continuum of alleles as previously reported, rather the alleles were stable and pedigree analysis showed they adhered to Mendelian segregation. Subsequent analysis of ddPCR case/control data confirmed that both CNVs remained significantly associated with the subphenotype of fever, but also to the encompassing SPAID complex (p < 0.001). In addition, harbouring CNV_16.1 allele five (CNV_16.1|5) resulted in a four-fold increase in the odds for SPAID (p < 0.001). The inclusion of a genetic marker for CNV_16.1 in a genome-wide association test revealed that this variant explained 9.7 % of genetic variance and 25.8 % of the additive genetic heritability of this autoinflammatory disease. CONCLUSIONS This data shows the utility of the ddPCR method to resolve cryptic copy number inheritance patterns and so open avenues of genetic testing. In its current form, the ddPCR test presented here could be used in canine breeding to reduce the number of homozygote CNV_16.1|5 individuals and thereby to reduce the prevalence of disease in this breed.
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Affiliation(s)
- M Olsson
- Department of Medicine, Rheumatology Unit, Karolinska Institute, Stockholm, Sweden
| | - M Kierczak
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Å Karlsson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - J Jabłońska
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - P Leegwater
- Department of Clinical Sciences of Companion Animals, Utrecht University, Utrecht, Netherlands
| | - M Koltookian
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | - J Abadie
- LUNAM University, Oniris, AMaROC Unit, Nantes, F-44307, France
| | | | - A Thomas
- ANTAGENE Animal Genetics Laboratory, La Tour de Salvagny, Lyon, 69, France
| | - Å Hedhammar
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - L Tintle
- Wurtsboro Veterinary Clinic, Wurtsboro, New York, USA
| | - K Lindblad-Toh
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Broad Institute of MIT and Harvard, Boston, MA, USA
| | - J R S Meadows
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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33
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Bai Z, Chen J, Liao Y, Wang M, Liu R, Ge S, Wing RA, Chen M. The impact and origin of copy number variations in the Oryza species. BMC Genomics 2016; 17:261. [PMID: 27025496 PMCID: PMC4812662 DOI: 10.1186/s12864-016-2589-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 03/15/2016] [Indexed: 02/16/2023] Open
Abstract
Background Copy number variation (CNV), a complex genomic rearrangement, has been extensively studied in humans and other organisms. In plants, CNVs of several genes were found to be responsible for various important traits; however, the cause and consequence of CNVs remains largely unknown. Recently released next-generation sequencing (NGS) data provide an opportunity for a genome-wide study of CNVs in rice. Results Here, by an NGS-based approach, we generated a CNV map comprising 9,196 deletions compared to the reference genome ‘Nipponbare’. Using Oryza glaberrima as the outgroup, 80 % of the CNV events turned out to be insertions in Nipponbare. There were 2,806 annotated genes affected by these CNV events. We experimentally validated 28 functional CNV genes including OsMADS56, BPH14, OsDCL2b and OsMADS30, implying that CNVs might have contributed to phenotypic variations in rice. Most CNV genes were found to be located in non-co-linear positions by comparison to O. glaberrima. One of the origins of these non-co-linear genes was genomic duplications caused by transposon activity or double-strand break repair. Comprehensive analysis of mutation mechanisms suggested an abundance of CNVs formed by non-homologous end-joining and mobile element insertion. Conclusions This study showed the impact and origin of copy number variations in rice on a genomic scale. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2589-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zetao Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinfeng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yi Liao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Meijiao Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rong Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Science, University of Arizona, Tucson, AZ, 85721, USA
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
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34
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Reiter T, Jagoda E, Capellini TD. Dietary Variation and Evolution of Gene Copy Number among Dog Breeds. PLoS One 2016; 11:e0148899. [PMID: 26863414 PMCID: PMC4749313 DOI: 10.1371/journal.pone.0148899] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 01/24/2016] [Indexed: 01/11/2023] Open
Abstract
Prolonged human interactions and artificial selection have influenced the genotypic and phenotypic diversity among dog breeds. Because humans and dogs occupy diverse habitats, ecological contexts have likely contributed to breed-specific positive selection. Prior to the advent of modern dog-feeding practices, there was likely substantial variation in dietary landscapes among disparate dog breeds. As such, we investigated one type of genetic variant, copy number variation, in three metabolic genes: glucokinase regulatory protein (GCKR), phytanol-CoA 2-hydroxylase (PHYH), and pancreatic α-amylase 2B (AMY2B). These genes code for proteins that are responsible for metabolizing dietary products that originate from distinctly different food types: sugar, meat, and starch, respectively. After surveying copy number variation among dogs with diverse dietary histories, we found no correlation between diet and positive selection in either GCKR or PHYH. Although it has been previously demonstrated that dogs experienced a copy number increase in AMY2B relative to wolves during or after the dog domestication process, we demonstrate that positive selection continued to act on amylase copy number in dog breeds that consumed starch-rich diets in time periods after domestication. Furthermore, we found that introgression with wolves is not responsible for deterioration of positive selection on AMY2B among diverse dog breeds. Together, this supports the hypothesis that the amylase copy number expansion is found universally in dogs.
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Affiliation(s)
- Taylor Reiter
- Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, MA, 02138, United States of America
| | - Evelyn Jagoda
- Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, MA, 02138, United States of America
| | - Terence D. Capellini
- Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, MA, 02138, United States of America
- * E-mail:
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35
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Xie J, Li R, Li S, Ran X, Wang J, Jiang J, Zhao P. Identification of Copy Number Variations in Xiang and Kele Pigs. PLoS One 2016; 11:e0148565. [PMID: 26840413 PMCID: PMC4740446 DOI: 10.1371/journal.pone.0148565] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 01/19/2016] [Indexed: 12/24/2022] Open
Abstract
Xiang and Kele pigs are two well-known local Chinese pig breeds that possess rich genetic resources and have enormous economic and scientific value. We performed a comprehensive genomic analysis of the copy number variations (CNVs) in these breeds. CNVs are one of the most important forms of genomic variation and have profound effects on phenotypic variation. In this study, PorcineSNP60 genotyping data from 98 Xiang pigs and 22 Kele pigs were used to identify CNVs. In total, 172 candidate CNV regions (CNVRs) were identified, ranging from 3.19 kb to 8175.26 kb and covering 80.41 Mb of the pig genome. Approximately 56.40% (97/172) of the CNVRs overlapped with those identified in seven previous studies, and 43.60% (75/172) of the identified CNVRs were novel. Of the identified CNVRs, 82 (47 gain, 33 loss, and two gain-loss events that covered 4.58 Mb of the pig genome) were found only in a Xiang population with a large litter size. In contrast, 13 CNVRs (8 gain and 5 loss events) were unique to a Xiang population with small litter sizes, and 30 CNVRs (14 loss and 16 gain events) were unique to Kele pigs. The CNVRs span approximately 660 annotated Sus scrofa genes that are significantly enriched for specific biological functions, such as sensory perception, cognition, reproduction, ATP biosynthetic processes, and neurological processes. Many CNVR-associated genes, particularly the genes involved in reproductive traits, differed between the Xiang populations with large and small litter sizes, and these genes warrant further investigation due to their importance in determining the reproductive performance of Xiang pigs. Our results provide meaningful information about genomic variation, which may be useful in future assessments of the associations between CNVs and important phenotypes in Xiang and Kele pigs to ultimately help protect these rare breeds.
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Affiliation(s)
- Jian Xie
- Institute of Agro-Bioengineering and College of Life Sciences, Guizhou University, Guiyang, China
| | - Rongrong Li
- Institute of Agro-Bioengineering and College of Life Sciences, Guizhou University, Guiyang, China
| | - Sheng Li
- Institute of Agro-Bioengineering and College of Life Sciences, Guizhou University, Guiyang, China
| | - Xueqin Ran
- College of animal Science, Guizhou University, Guiyang, China
- * E-mail: (XQR); (JFW)
| | - Jiafu Wang
- Institute of Agro-Bioengineering and College of Life Sciences, Guizhou University, Guiyang, China
- * E-mail: (XQR); (JFW)
| | - Jicai Jiang
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Pengju Zhao
- College of Animal Science and Technology, China Agricultural University, Beijing, China
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36
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Sasaki S, Watanabe T, Nishimura S, Sugimoto Y. Genome-wide identification of copy number variation using high-density single-nucleotide polymorphism array in Japanese Black cattle. BMC Genet 2016; 17:26. [PMID: 26809925 PMCID: PMC4727303 DOI: 10.1186/s12863-016-0335-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 01/14/2016] [Indexed: 12/12/2022] Open
Abstract
Background Copy number variation (CNV) is an important source of genetic variability associated with phenotypic variation and disease susceptibility. Comprehensive genome-wide CNV maps provide valuable information for genetic and functional studies. To identify CNV in Japanese Black cattle, we performed a genome-wide autosomal screen using genomic data from 1,481 animals analyzed with the Illumina Bovine High-Density (HD) BeadChip Array (735,293 single-nucleotide polymorphisms (SNPs) with an average marker interval of 3.4 kb on the autosomes). Results We identified a total of 861 CNV regions (CNVRs) across all autosomes, which covered 43.65 Mb of the UMD3.1 genome assembly and corresponded to 1.74 % of the 29 bovine autosomes. Overall, 35 % of the CNVRs were present at a frequency of > 1 % in 1,481 animals. The estimated lengths of CNVRs ranged from 1.1 kb to 1.4 Mb, with an average of 50.7 kb. The average number of CNVR events per animal was 35. Comparisons with previously reported cattle CNV showed that 72 % of the CNVR calls detected in this study were within or overlapped with known CNVRs. Experimentally, three CNVRs were validated using quantitative PCR, and one CNVR was validated using PCR with flanking primers for the deleted region. Out of the 861 CNVRs, 390 contained 717 Ensembl-annotated genes significantly enriched for stimulus response, cellular defense response, and immune response in the Gene Ontology (GO) database. To associate genes contained in CNVRs with phenotypes, we converted 560 bovine Ensembl gene IDs to their 438 orthologous associated mouse gene IDs, and 195 of these mouse orthologous genes were categorized into 1,627 phenotypes in the Mouse Genome Informatics (MGI) database. Conclusions We identified 861 CNVRs in 1,481 Japanese Black cattle using the Illumina BovineHD BeadChip Array. The genes contained in CNVRs were characterized using GO analysis and the mouse orthologous genes were characterized using the MGI database. The comprehensive genome-wide CNVRs map will facilitate identification of genetic variation and disease-susceptibility alleles in Japanese Black cattle. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0335-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shinji Sasaki
- National Livestock Breeding Center, Odakura, Nishigo, Fukushima, 961-8511, Japan.
| | - Toshio Watanabe
- National Livestock Breeding Center, Odakura, Nishigo, Fukushima, 961-8511, Japan.
| | - Shota Nishimura
- Shirakawa Institute of Animal Genetics, Japan Livestock Technology Association, Odakura, Nishigo, Fukushima, 961-8061, Japan.
| | - Yoshikazu Sugimoto
- Shirakawa Institute of Animal Genetics, Japan Livestock Technology Association, Odakura, Nishigo, Fukushima, 961-8061, Japan.
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37
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Copy number variation in the region harboring SOX9 gene in dogs with testicular/ovotesticular disorder of sex development (78,XX; SRY-negative). Sci Rep 2015; 5:14696. [PMID: 26423656 PMCID: PMC4589768 DOI: 10.1038/srep14696] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 09/04/2015] [Indexed: 11/09/2022] Open
Abstract
Although the disorder of sex development in dogs with female karyotype (XX DSD) is quite common, its molecular basis is still unclear. Among mutations underlying XX DSD in mammals are duplication of a long sequence upstream of the SOX9 gene (RevSex) and duplication of the SOX9 gene (also observed in dogs). We performed a comparative analysis of 16 XX DSD and 30 control female dogs, using FISH and MLPA approaches. Our study was focused on a region harboring SOX9 and a region orthologous to the human RevSex (CanRevSex), which was located by in silico analysis downstream of SOX9. Two highly polymorphic copy number variable regions (CNVRs): CNVR1 upstream of SOX9 and CNVR2 encompassing CanRevSex were identified. Although none of the detected copy number variants were specific to either affected or control animals, we observed that the average number of copies in CNVR1 was higher in XX DSD. No copy variation of SOX9 was observed. Our extensive studies have excluded duplication of SOX9 as the common cause of XX DSD in analyzed samples. However, it remains possible that the causative mutation is hidden in highly polymorphic CNVR1.
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38
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Rossi E, Radi O, De Lorenzi L, Iannuzzi A, Camerino G, Zuffardi O, Parma P. A Revised Genome Assembly of the Region 5′ to Canine SOX9 Includes the RevSex Orthologous Region. Sex Dev 2015; 9:155-61. [DOI: 10.1159/000435871] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2015] [Indexed: 11/19/2022] Open
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39
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Roode SC, Rotroff D, Avery AC, Suter SE, Bienzle D, Schiffman JD, Motsinger-Reif A, Breen M. Genome-wide assessment of recurrent genomic imbalances in canine leukemia identifies evolutionarily conserved regions for subtype differentiation. Chromosome Res 2015; 23:681-708. [PMID: 26037708 DOI: 10.1007/s10577-015-9475-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/02/2015] [Accepted: 05/05/2015] [Indexed: 11/30/2022]
Abstract
Leukemia in dogs is a heterogeneous disease with survival ranging from days to years, depending on the subtype. Strides have been made in both human and canine leukemia to improve classification and understanding of pathogenesis through immunophenotyping, yet classification and choosing appropriate therapy remains challenging. In this study, we assessed 123 cases of canine leukemia (28 ALLs, 24 AMLs, 25 B-CLLs, and 46 T-CLLs) using high-resolution oligonucleotide array comparative genomic hybridization (oaCGH) to detect DNA copy number alterations (CNAs). For the first time, such data were used to identify recurrent CNAs and inclusive genes that may be potential drivers of subtype-specific pathogenesis. We performed predictive modeling to identify CNAs that could reliably differentiate acute subtypes (ALL vs. AML) and chronic subtypes (B-CLL vs. T-CLL) and used this model to differentiate cases with up to 83.3 and 95.8 % precision, respectively, based on CNAs at only one to three genomic regions. In addition, CGH datasets for canine and human leukemia were compared to reveal evolutionarily conserved copy number changes between species, including the shared gain of HSA 21q in ALL and ∼25 Mb of shared gain of HSA 12 and loss of HSA 13q14 in CLL. These findings support the use of canine leukemia as a relevant in vivo model for human leukemia and justify the need to further explore the conserved genomic regions of interest for their clinical impact.
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Affiliation(s)
- Sarah C Roode
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - Daniel Rotroff
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - Anne C Avery
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Science, Colorado State University, Fort Collins, CO, USA
| | - Steven E Suter
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA.,Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC, USA.,Cancer Genetics Program, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Dorothee Bienzle
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
| | - Joshua D Schiffman
- Department of Pediatrics, University of Utah, Salt Lake City, UT, USA.,Department of Oncological Sciences, Center for Children's Cancer Research, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Alison Motsinger-Reif
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC, USA.,Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC, USA
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA. .,Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC, USA. .,Cancer Genetics Program, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
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40
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Radke DW, Lee C. Adaptive potential of genomic structural variation in human and mammalian evolution. Brief Funct Genomics 2015; 14:358-68. [PMID: 26003631 DOI: 10.1093/bfgp/elv019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Because phenotypic innovations must be genetically heritable for biological evolution to proceed, it is natural to consider new mutation events as well as standing genetic variation as sources for their birth. Previous research has identified a number of single-nucleotide polymorphisms that underlie a subset of adaptive traits in organisms. However, another well-known class of variation, genomic structural variation, could have even greater potential to produce adaptive phenotypes, due to the variety of possible types of alterations (deletions, insertions, duplications, among others) at different genomic positions and with variable lengths. It is from these dramatic genomic alterations, and selection on their phenotypic consequences, that adaptations leading to biological diversification could be derived. In this review, using studies in humans and other mammals, we highlight examples of how phenotypic variation from structural variants might become adaptive in populations and potentially enable biological diversification. Phenotypic change arising from structural variants will be described according to their immediate effect on organismal metabolic processes, immunological response and physical features. Study of population dynamics of segregating structural variation can therefore provide a window into understanding current and historical biological diversification.
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Dauchot N, Raulier P, Maudoux O, Notté C, Draye X, Van Cutsem P. Loss of function of 1-FEH IIb has more impact on post-harvest inulin degradation in Cichorium intybus than copy number variation of its close paralog 1-FEH IIa. FRONTIERS IN PLANT SCIENCE 2015; 6:455. [PMID: 26157446 PMCID: PMC4477480 DOI: 10.3389/fpls.2015.00455] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 06/03/2015] [Indexed: 05/20/2023]
Abstract
Key Message: The loss of mini-exon 2 in the 1-FEH IIb glycosyl-hydrolase results in a putative non-functional allele. This loss of function has a strong impact on the susceptibility to post-harvest inulin depolymerization. Significant variation of copy number was identified in its close paralog 1-FEH IIa, but no quantitative effect of copy number on carbohydrates-related phenotypes was detected. Inulin polyfructan is the second most abundant storage carbohydrate in flowering plants. After harvest, it is depolymerized by fructan exohydrolases (FEHs) as an adaptive response to end-season cold temperatures. In chicory, the intensity of this depolymerization differs between cultivars but also between individuals within a cultivar. Regarding this phenotypic variability, we recently identified statistically significant associations between inulin degradation and genetic polymorphisms located in three FEHs. We present here new results of a systematic analysis of copy number variation (CNV) in five key members of the chicory (Cichorium intybus) GH32 multigenic family, including three FEH genes and the two inulin biosynthesis genes: 1-SST and 1-FFT. qPCR analysis identified a significant variability of relative copy number only in the 1-FEH IIa gene. However, this CNV had no quantitative effect. Instead, cloning of the full length gDNA of a close paralogous sequence (1-FEH IIb) identified a 1028 bp deletion in lines less susceptible to post-harvest inulin depolymerization. This region comprises a 9 bp mini-exon containing one of the three conserved residues of the active site. This results in a putative non-functional 1-FEH IIb allele and an observed lower inulin depolymerization. Extensive genotyping confirmed that the loss of mini-exon 2 in 1-FEH IIb and the previously identified 47 bp duplication located in the 3'UTR of 1-FEH IIa belong to a single haplotype, both being statistically associated with reduced susceptibility to post-harvest inulin depolymerization. Emergence of these haplotypes is discussed.
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Affiliation(s)
- Nicolas Dauchot
- Research Unit in Plant Biology, University of NamurNamur, Belgium
- *Correspondence: Nicolas Dauchot, Research Unit in Plant Biology, University of Namur,rue de Bruxelles 61, 5000 Namur, Belgium,
| | - Pierre Raulier
- Earth and Life Institute, Université Catholique de LouvainLouvain-la-Neuve, Belgium
| | | | | | - Xavier Draye
- Earth and Life Institute, Université Catholique de LouvainLouvain-la-Neuve, Belgium
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Abstract
We constructed a 400K WG tiling oligoarray for the horse and applied it for the discovery of copy number variations (CNVs) in 38 normal horses of 16 diverse breeds, and the Przewalski horse. Probes on the array represented 18,763 autosomal and X-linked genes, and intergenic, sub-telomeric and chrY sequences. We identified 258 CNV regions (CNVRs) across all autosomes, chrX and chrUn, but not in chrY. CNVs comprised 1.3% of the horse genome with chr12 being most enriched. American Miniature horses had the highest and American Quarter Horses the lowest number of CNVs in relation to Thoroughbred reference. The Przewalski horse was similar to native ponies and draft breeds. The majority of CNVRs involved genes, while 20% were located in intergenic regions. Similar to previous studies in horses and other mammals, molecular functions of CNV-associated genes were predominantly in sensory perception, immunity and reproduction. The findings were integrated with previous studies to generate a composite genome-wide dataset of 1476 CNVRs. Of these, 301 CNVRs were shared between studies, while 1174 were novel and require further validation. Integrated data revealed that to date, 41 out of over 400 breeds of the domestic horse have been analyzed for CNVs, of which 11 new breeds were added in this study. Finally, the composite CNV dataset was applied in a pilot study for the discovery of CNVs in 6 horses with XY disorders of sexual development. A homozygous deletion involving AKR1C gene cluster in chr29 in two affected horses was considered possibly causative because of the known role of AKR1C genes in testicular androgen synthesis and sexual development. While the findings improve and integrate the knowledge of CNVs in horses, they also show that for effective discovery of variants of biomedical importance, more breeds and individuals need to be analyzed using comparable methodological approaches. Genomes of individuals in a species vary in many ways, one of which is DNA copy number variation (CNV). This includes deletions, duplications, and complex rearrangements typically larger than 50 base-pairs. CNVs are part of normal genetic variation contributing to phenotypic diversity but can also be pathogenic and associated with diseases and disorders. In order to distinguish between the two, detailed knowledge about CNVs in the species of interest is needed. Here we studied the genomes of 38 normal horses of 16 diverse breeds, and identified 258 CNV regions. We integrated our findings with previously published horse CNVs and generated a composite dataset of ∼1400 CNVRs. Despite this large number, our analysis shows that CNV research in horses needs further improvement because the current data are based on 10% of horse breeds and that most CNVRs are study-specific and require validation. Finally, we analyzed CNVs in horses with disorders of sexual development and found in two male pseudo-hermaphrodites a large deletion disrupting a group of genes involved in sex hormone metabolism and sexual differentiation. The findings underline the possible role of CNVs in complex disorders such as development and reproduction.
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Rossi E, Radi O, De Lorenzi L, Vetro A, Groppetti D, Bigliardi E, Luvoni GC, Rota A, Camerino G, Zuffardi O, Parma P. Sox9 duplications are a relevant cause of Sry-negative XX sex reversal dogs. PLoS One 2014; 9:e101244. [PMID: 25010117 PMCID: PMC4091935 DOI: 10.1371/journal.pone.0101244] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 06/04/2014] [Indexed: 01/06/2023] Open
Abstract
Sexual development in mammals is based on a complicated and delicate network of genes and hormones that have to collaborate in a precise manner. The dark side of this pathway is represented by pathological conditions, wherein sexual development does not occur properly either in the XX and the XY background. Among them a conundrum is represented by the XX individuals with at least a partial testis differentiation even in absence of SRY. This particular condition is present in various mammals including the dog. Seven dogs characterized by XX karyotype, absence of SRY gene, and testicular tissue development were analysed by Array-CGH. In two cases the array-CGH analysis detected an interstitial heterozygous duplication of chromosome 9. The duplication contained the SOX9 coding region. In this work we provide for the first time a causative mutation for the XXSR condition in the dog. Moreover this report supports the idea that the dog represents a good animal model for the study of XXSR condition caused by abnormalities in the SOX9 locus.
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Affiliation(s)
- Elena Rossi
- Department of Molecular Medicine, Pavia University, Pavia, Italy
| | - Orietta Radi
- Department of Molecular Medicine, Pavia University, Pavia, Italy
| | - Lisa De Lorenzi
- Department of Agricultural and Environmental Sciences, Milan University, Milan, Italy
| | - Annalisa Vetro
- Biotechnology Research Laboratories, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Debora Groppetti
- Department of Veterinary Science and Public Health, Milan University, Milan, Italy
| | - Enrico Bigliardi
- Department of Veterinary Science, Parma University, Parma, Italy
| | - Gaia Cecilia Luvoni
- Department of Health, Animal Science and Food Safety, Milan University, Milan, Italy
| | - Ada Rota
- Department of Veterinary Science, Torino University, Torino, Italy
| | | | - Orsetta Zuffardi
- Department of Molecular Medicine, Pavia University, Pavia, Italy
| | - Pietro Parma
- Department of Agricultural and Environmental Sciences, Milan University, Milan, Italy
- * E-mail:
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Ekenstedt KJ, Oberbauer AM. Inherited epilepsy in dogs. Top Companion Anim Med 2014; 28:51-8. [PMID: 24070682 DOI: 10.1053/j.tcam.2013.07.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 07/01/2013] [Indexed: 12/15/2022]
Abstract
Epilepsy is the most common neurologic disease in dogs and many forms are considered to have a genetic basis. In contrast, some seizure disorders are also heritable, but are not technically defined as epilepsy. Investigation of true canine epilepsies has uncovered genetic associations in some cases, however, many remain unexplained. Gene mutations have been described for 2 forms of canine epilepsy: primary epilepsy (PE) and progressive myoclonic epilepsies. To date, 9 genes have been described to underlie progressive myoclonic epilepsies in several dog breeds. Investigations into genetic PE have been less successful, with only 1 causative gene described. Genetic testing as an aid to diagnosis, prognosis, and breeding decisions is available for these 10 forms. Additional studies utilizing genome-wide tools have identified PE loci of interest; however, specific genetic tests are not yet developed. Many studies of dog breeds with PE have failed to identify genes or loci of interest, suggesting that, similar to what is seen in many human genetic epilepsies, inheritance is likely complex, involving several or many genes, and reflective of environmental interactions. An individual dog's response to therapeutic intervention for epilepsy may also be genetically complex. Although the field of inherited epilepsy has faced challenges, particularly with PE, newer technologies contribute to further advances.
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Affiliation(s)
- Kari J Ekenstedt
- Department of Animal and Food Science, College of Agriculture, Food, and Environmental Sciences, University of Wisconsin - River Falls, River Falls, WI, USA.
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Zhang H, Du ZQ, Dong JQ, Wang HX, Shi HY, Wang N, Wang SZ, Li H. Detection of genome-wide copy number variations in two chicken lines divergently selected for abdominal fat content. BMC Genomics 2014; 15:517. [PMID: 24962627 PMCID: PMC4092215 DOI: 10.1186/1471-2164-15-517] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 06/19/2014] [Indexed: 12/13/2022] Open
Abstract
Background The chicken (Gallus gallus) is an important model organism that bridges the evolutionary gap between mammals and other vertebrates. Copy number variations (CNVs) are a form of genomic structural variation widely distributed in the genome. CNV analysis has recently gained greater attention and momentum, as the identification of CNVs can contribute to a better understanding of traits important to both humans and other animals. To detect chicken CNVs, we genotyped 475 animals derived from two broiler chicken lines divergently selected for abdominal fat content using chicken 60 K SNP array, which is a high-throughput method widely used in chicken genomics studies. Results Using PennCNV algorithm, we detected 438 and 291 CNVs in the lean and fat lines, respectively, corresponding to 271 and 188 CNV regions (CNVRs), which were obtained by merging overlapping CNVs. Out of these CNVRs, 99% were confirmed also by the CNVPartition program. These CNVRs covered 40.26 and 30.60 Mb of the chicken genome in the lean and fat lines, respectively. Moreover, CNVRs included 176 loss, 68 gain and 27 both (i.e. loss and gain within the same region) events in the lean line, and 143 loss, 25 gain and 20 both events in the fat line. Ten CNVRs were chosen for the validation experiment using qPCR method, and all of them were confirmed in at least one qPCR assay. We found a total of 886 genes located within these CNVRs, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed they could play various roles in a number of biological processes. Integrating the results of CNVRs, known quantitative trait loci (QTL) and selective sweeps for abdominal fat content suggested that some genes (including SLC9A3, GNAL, SPOCK3, ANXA10, HELIOS, MYLK, CCDC14, SPAG9, SOX5, VSNL1, SMC6, GEN1, MSGN1 and ZPAX) may be important for abdominal fat deposition in the chicken. Conclusions Our study provided a genome-wide CNVR map of the chicken genome, thereby contributing to our understanding of genomic structural variations and their potential roles in abdominal fat content in the chicken. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-517) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin 150030, P,R China.
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Analysis of structural diversity in wolf-like canids reveals post-domestication variants. BMC Genomics 2014; 15:465. [PMID: 24923435 PMCID: PMC4070573 DOI: 10.1186/1471-2164-15-465] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 06/06/2014] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Although a variety of genetic changes have been implicated in causing phenotypic differences among dogs, the role of copy number variants (CNVs) and their impact on phenotypic variation is still poorly understood. Further, very limited knowledge exists on structural variation in the gray wolf, the ancestor of the dog, or other closely related wild canids. Documenting CNVs variation in wild canids is essential to identify ancestral states and variation that may have appeared after domestication. RESULTS In this work, we genotyped 1,611 dog CNVs in 23 wolf-like canids (4 purebred dogs, one dingo, 15 gray wolves, one red wolf, one coyote and one golden jackal) to identify CNVs that may have arisen after domestication. We have found an increase in GC-rich regions close to the breakpoints and around 1 kb away from them suggesting that some common motifs might be associated with the formation of CNVs. Among the CNV regions that showed the largest differentiation between dogs and wild canids we found 12 genes, nine of which are related to two known functions associated with dog domestication; growth (PDE4D, CRTC3 and NEB) and neurological function (PDE4D, EML5, ZNF500, SLC6A11, ELAVL2, RGS7 and CTSB). CONCLUSIONS Our results provide insight into the evolution of structural variation in canines, where recombination is not regulated by PRDM9 due to the inactivation of this gene. We also identified genes within the most differentiated CNV regions between dogs and wolves, which could reflect selection during the domestication process.
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Identification of genomic loci associated with Rhodococcus equi susceptibility in foals. PLoS One 2014; 9:e98710. [PMID: 24892408 PMCID: PMC4043894 DOI: 10.1371/journal.pone.0098710] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 05/04/2014] [Indexed: 11/30/2022] Open
Abstract
Pneumonia caused by Rhodococcus equi is a common cause of disease and death in foals. Although agent and environmental factors contribute to the incidence of this disease, the genetic factors influencing the clinical outcomes of R. equi pneumonia are ill-defined. Here, we performed independent single nucleotide polymorphism (SNP)- and copy number variant (CNV)-based genome-wide association studies to identify genomic loci associated with R. equi pneumonia in foals. Foals at a large Quarter Horse breeding farm were categorized into 3 groups: 1) foals with R. equi pneumonia (clinical group [N = 43]); 2) foals with ultrasonographic evidence of pulmonary lesions that never developed clinical signs of pneumonia (subclinical group [N = 156]); and, 3) foals without clinical signs or ultrasonographic evidence of pneumonia (unaffected group [N = 49]). From each group, 24 foals were randomly selected and used for independent SNP- and CNV-based genome-wide association studies (GWAS). The SNP-based GWAS identified a region on chromosome 26 that had moderate evidence of association with R. equi pneumonia when comparing clinical and subclinical foals. A joint analysis including all study foals revealed a 3- to 4-fold increase in odds of disease for a homozygous SNP within the associated region when comparing the clinical group with either of the other 2 groups of foals or their combination. The region contains the transient receptor potential cation channel, subfamily M, member 2 (TRPM2) gene, which is involved in neutrophil function. No associations were identified in the CNV-based GWAS. Collectively, these data identify a region on chromosome 26 associated with R. equi pneumonia in foals, providing evidence that genetic factors may indeed contribute to this important disease of foals.
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Molin AM, Berglund J, Webster MT, Lindblad-Toh K. Genome-wide copy number variant discovery in dogs using the CanineHD genotyping array. BMC Genomics 2014; 15:210. [PMID: 24640994 PMCID: PMC4234435 DOI: 10.1186/1471-2164-15-210] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 03/13/2014] [Indexed: 12/23/2022] Open
Abstract
Background Substantial contribution to phenotypic diversity is accounted for by copy number variants (CNV). In human, as well as other species, the effect of CNVs range from benign to directly disease-causing which motivates the continued investigations of CNVs. Previous canine genome-wide screenings for CNVs have been performed using high-resolution comparative genomic hybridisation arrays which have contributed with a detailed catalogue of CNVs. Here, we present the first CNV investigation in dogs based on the recently reported CanineHD 170 K genotyping array. The hitherto largest dataset in canine CNV discovery was assessed, 351 dogs from 30 different breeds, enabling identification of novel CNVs and a thorough characterisation of breed-specific CNVs. Results A stringent procedure identified 72 CNV regions with the smallest size of 38 kb and of the 72 CNV regions, 38 overlapped 148 annotated genes. A total of 29 novel CNV regions were found containing 44 genes. Furthermore, 15 breed specific CNV regions were identified of which 14 were novel and some of them overlapped putative disease susceptibility genes. In addition, the human ortholog of 23 canine copy number variable genes identified herein has been previously suggested to be dosage-sensitive in human. Conclusions The present study evaluated the performance of the CanineHD in detecting CNVs and extends the current catalogue of canine CNV regions with several dozens of novel CNV regions. These novel CNV regions, which harbour candidate genes that possibly contribute to phenotypic variation in dogs or to disease-susceptibility, are a rich resource for future investigations.
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Affiliation(s)
- Anna-Maja Molin
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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General assessment of copy number variation in normal and tumor tissues of the domestic dog (Canis lupus familiaris). J Appl Genet 2014; 55:353-63. [PMID: 24573641 DOI: 10.1007/s13353-014-0201-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 01/10/2014] [Accepted: 02/04/2014] [Indexed: 12/22/2022]
Abstract
In recent years, characterization of a copy number variation (CNV) of the genomic DNA has provided evidence for the relationship of this type of genetic variation with the occurrence of a broad spectrum of diseases, including cancer lesions. Copy number variants (CNVs) also occur in the genomes of healthy individuals as a result of abnormal recombination processes in germ cells and have a hereditary character contributing to the natural genetic diversity. Recent image analysis methods and advanced computational techniques allow for identification of CNVs using SNPs genotyping microarrays based on the analysis of signal intensity observed for markers located in the specific genomic regions. In this study we used CanineHD BeadChip assay (Illumina) to identify both natural and cancer-induced CNVs in the genomes of different dog breeds and in different cancer types occurring in this species. The obtained results showed that structural aberrations are a common phenomenon arising during a tumor progression and are more complex and widespread in tumors of mesenchymal tissue origin than in epithelial tissue originating tumors. The tumor derived CNVs, in comparison to healthy samples, were characterized by larger sizes of regions, higher number of amplifications, and in some cases encompassed genes with potential effect on tumor progression.
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Machado HE, Jui G, Joyce DA, Reilly CRL, Lunt DH, Renn SCP. Gene duplication in an African cichlid adaptive radiation. BMC Genomics 2014; 15:161. [PMID: 24571567 PMCID: PMC3944005 DOI: 10.1186/1471-2164-15-161] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 02/19/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene duplication is a source of evolutionary innovation and can contribute to the divergence of lineages; however, the relative importance of this process remains to be determined. The explosive divergence of the African cichlid adaptive radiations provides both a model for studying the general role of gene duplication in the divergence of lineages and also an exciting foray into the identification of genomic features that underlie the dramatic phenotypic and ecological diversification in this particular lineage. We present the first genome-wide study of gene duplication in African cichlid fishes, identifying gene duplicates in three species belonging to the Lake Malawi adaptive radiation (Metriaclima estherae, Protomelas similis, Rhamphochromis "chilingali") and one closely related species from a non-radiated riverine lineage (Astatotilapia tweddlei). RESULTS Using Astatotilapia burtoni as reference, microarray comparative genomic hybridization analysis of 5689 genes reveals 134 duplicated genes among the four cichlid species tested. Between 51 and 55 genes were identified as duplicated in each of the three species from the Lake Malawi radiation, representing a 38%-49% increase in number of duplicated genes relative to the non-radiated lineage (37 genes). Duplicated genes include several that are involved in immune response, ATP metabolism and detoxification. CONCLUSIONS These results contribute to our understanding of the abundance and type of gene duplicates present in cichlid fish lineages. The duplicated genes identified in this study provide candidates for the analysis of functional relevance with regard to phenotype and divergence. Comparative sequence analysis of gene duplicates can address the role of positive selection and adaptive evolution by gene duplication, while further study across the phylogenetic range of cichlid radiations (and more generally in other adaptive radiations) will determine whether the patterns of gene duplication seen in this study consistently accompany rapid radiation.
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Affiliation(s)
| | | | | | | | | | - Suzy C P Renn
- Department of Biology, Reed College, Portland, OR 97202, USA.
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