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Kafi Z, Masoudi AA, Torshizi RV, Ehsani A. Copy number variations affecting growth curve parameters in a crossbred chicken population. Gene 2024; 927:148710. [PMID: 38901536 DOI: 10.1016/j.gene.2024.148710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 06/01/2024] [Accepted: 06/17/2024] [Indexed: 06/22/2024]
Abstract
Copy number variations (CNVs) are key structural variations in the genome and may contribute to phenotypic differences. In this study, we used a F2 chicken population created from reciprocal crossing between fast-growing Arian broiler line and Urmia native chickens. The chickens were genotyped by 60 K SNP BeadChip, and PennCNV algorithm was used to detect genome-wide CNVs. The growth curve parameters of W0, k, L, Wf, Wi, ti and average GR were used as phenotypic data. The association between CNV and growth curve parameters was carried out using the CNVRanger R/Bioconductor package. Five CNV regions (CNVRs) were chosen for the validation experiment using qPCR. Gene enrichment analysis was done using WebGestalt. The STRING database was used to search for significant pathways. The results identified 966 CNVs and 600 CNVRs including 468 gains, 67 losses, and 65 both events on autosomal chromosomes. Validation of the CNVRs obtained from the qPCR assay were 79 % consistent with the prediction by PennCNV. A total of 43 significant CNVs were obtained for the seven growth curve parameters. The 416 genes annotated for significant CNVs. Six genes out of 416 genes were most related to growth curve parameters. These genes were LCP2, Dock2, CD80, CYFIP1, NIPA1 and NIPA2. Some of these genes in their biological process were associated with the growth, reproduction and development of cells or organs that ultimately lead to the growth of the body. The results of the study could pave the way for better understanding the molecular process of CNVs and growth curve parameters in birds.
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Affiliation(s)
- Zeinab Kafi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
| | - Ali Akbar Masoudi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
| | - Rasoul Vaez Torshizi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
| | - Alireza Ehsani
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
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Liu X, Chen W, Huang B, Wang X, Peng Y, Zhang X, Chai W, Khan MZ, Wang C. Advancements in copy number variation screening in herbivorous livestock genomes and their association with phenotypic traits. Front Vet Sci 2024; 10:1334434. [PMID: 38274664 PMCID: PMC10808162 DOI: 10.3389/fvets.2023.1334434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 12/27/2023] [Indexed: 01/27/2024] Open
Abstract
Copy number variations (CNVs) have garnered increasing attention within the realm of genetics due to their prevalence in human, animal, and plant genomes. These structural genetic variations have demonstrated associations with a broad spectrum of phenotypic diversity, economic traits, environmental adaptations, epidemics, and other essential aspects of both plants and animals. Furthermore, CNVs exhibit extensive sequence variability and encompass a wide array of genomes. The advancement and maturity of microarray and sequencing technologies have catalyzed a surge in research endeavors pertaining to CNVs. This is particularly prominent in the context of livestock breeding, where molecular markers have gained prominence as a valuable tool in comparison to traditional breeding methods. In light of these developments, a contemporary and comprehensive review of existing studies on CNVs becomes imperative. This review serves the purpose of providing a brief elucidation of the fundamental concepts underlying CNVs, their mutational mechanisms, and the diverse array of detection methods employed to identify these structural variations within genomes. Furthermore, it seeks to systematically analyze the recent advancements and findings within the field of CNV research, specifically within the genomes of herbivorous livestock species, including cattle, sheep, horses, and donkeys. The review also highlighted the role of CNVs in shaping various phenotypic traits including growth traits, reproductive traits, pigmentation and disease resistance etc., in herbivorous livestock. The main goal of this review is to furnish readers with an up-to-date compilation of knowledge regarding CNVs in herbivorous livestock genomes. By integrating the latest research findings and insights, it is anticipated that this review will not only offer pertinent information but also stimulate future investigations into the realm of CNVs in livestock. In doing so, it endeavors to contribute to the enhancement of breeding strategies, genomic selection, and the overall improvement of herbivorous livestock production and resistance to diseases.
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Affiliation(s)
| | | | | | | | | | | | | | - Muhammad Zahoor Khan
- Liaocheng Research Institute of Donkey High-Efficiency Breeding, Liaocheng University, Liaocheng, China
| | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding, Liaocheng University, Liaocheng, China
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Jevit MJ, Castaneda C, Paria N, Das PJ, Miller D, Antczak DF, Kalbfleisch TS, Davis BW, Raudsepp T. Trio-binning of a hinny refines the comparative organization of the horse and donkey X chromosomes and reveals novel species-specific features. Sci Rep 2023; 13:20180. [PMID: 37978222 PMCID: PMC10656420 DOI: 10.1038/s41598-023-47583-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023] Open
Abstract
We generated single haplotype assemblies from a hinny hybrid which significantly improved the gapless contiguity for horse and donkey autosomal genomes and the X chromosomes. We added over 15 Mb of missing sequence to both X chromosomes, 60 Mb to donkey autosomes and corrected numerous errors in donkey and some in horse reference genomes. We resolved functionally important X-linked repeats: the DXZ4 macrosatellite and ampliconic Equine Testis Specific Transcript Y7 (ETSTY7). We pinpointed the location of the pseudoautosomal boundaries (PAB) and determined the size of the horse (1.8 Mb) and donkey (1.88 Mb) pseudoautosomal regions (PARs). We discovered distinct differences in horse and donkey PABs: a testis-expressed gene, XKR3Y, spans horse PAB with exons1-2 located in Y and exon3 in the X-Y PAR, whereas the donkey XKR3Y is Y-specific. DXZ4 had a similar ~ 8 kb monomer in both species with 10 copies in horse and 20 in donkey. We assigned hundreds of copies of ETSTY7, a sequence horizontally transferred from Parascaris and massively amplified in equids, to horse and donkey X chromosomes and three autosomes. The findings and products contribute to molecular studies of equid biology and advance research on X-linked conditions, sex chromosome regulation and evolution in equids.
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Affiliation(s)
- Matthew J Jevit
- School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Caitlin Castaneda
- School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Nandina Paria
- Texas Scottish Rite Hospital for Children, Dallas, TX, 75219, USA
| | - Pranab J Das
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
| | - Donald Miller
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, 14853, USA
| | - Douglas F Antczak
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, 14853, USA
| | - Theodore S Kalbfleisch
- Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Brian W Davis
- School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA.
| | - Terje Raudsepp
- School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA.
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Scantamburlo G, Nofziger C, Paulmichl M, Vanoni S. Genetic analysis of the equine orthologues for human CYP2D6: unraveling the complexity of the CYP2D family in horses. Front Vet Sci 2023; 10:1188633. [PMID: 37929279 PMCID: PMC10620600 DOI: 10.3389/fvets.2023.1188633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 09/25/2023] [Indexed: 11/07/2023] Open
Abstract
Introduction Because of their importance as companion animals or as racehorses, horses can be treated with various drugs. Although it is known that drug withdrawal times can vary for each horse, pharmacogenetics for these animals has not been adequately studied and requires further development. Since CYP2D6 is responsible for the metabolism of 25-30% of drugs in humans, including some used to treat horses, a study of the CYP2D family in horses was conducted to define its genetic structure as well as its expression pattern in the liver. Methods Genomic DNA extracted from venous blood and mRNA from fresh liver tissue were amplified and sequenced to analyze the genomic structure, genotype, and expression of the various enzymes that are part of the equine orthologous family for CYP2D6. Results Amplification and sequencing of the gDNA of CYP2D50, the major CYP2D6 orthologue identified in previous studies, revealed a novel putative genomic structure for this gene compared with that reported from the EquCab3.0 assembly, including the formation of a hybrid structure similar to what happens in human CYP2D6. At the mRNA level, transcripts from six different members of the equine CYP2D family were detected in horse liver. In addition, genotyping of CYP2D50 and CYP2D82 revealed the presence of several polymorphisms, six of which result in novel, nonsynonymous amino acid changes for each of the two genes. Discussion This study aimed to elucidate the pharmacogenetic analysis of the CYP2D family in horses and resulted in the identification of a novel gene structure for CYP2D50, the expression of six different members of the CYP2D family in horse liver, and several novel polymorphisms for CYP2D50 and CYP2D82.
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Choudhury MP, Wang Z, Zhu M, Teng S, Yan J, Cao S, Yi G, Liu Y, Liao Y, Tang Z. Genome-Wide Detection of Copy Number Variations Associated with Miniature Features in Horses. Genes (Basel) 2023; 14:1934. [PMID: 37895283 PMCID: PMC10606273 DOI: 10.3390/genes14101934] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Copy number variations (CNVs) are crucial structural genomic variants affecting complex traits in humans and livestock animals. The current study was designed to conduct a comprehensive comparative copy number variation analysis among three breeds, Debao (DB), Baise (BS), and Warmblood (WB), with a specific focus on identifying genomic regions associated with miniature features in horses. Using whole-genome next-generation resequencing data, we identified 18,974 CNVs across 31 autosomes. Among the breeds, we found 4279 breed-specific CNV regions (CNVRs). Baise, Debao, and Warmblood displayed 2978, 986, and 895 distinct CNVRs, respectively, with 202 CNVRs shared across all three breeds. After removing duplicates, we obtained 1545 CNVRs from 26 horse genomes. Functional annotation reveals enrichment in biological functions, including antigen processing, cell metabolism, olfactory conduction, and nervous system development. Debao horses have 970 genes overlapping with CNVRs, possibly causing their small size and mountainous adaptations. We also found that the genes GHR, SOX9, and SOX11 may be responsible for the miniature features of the Debao horse by analyzing their overlapping CNVRs. Overall, this study offers valuable insights into the widespread presence of CNVs in the horse genome. The findings contribute to mapping horse CNVs and advance research on unique miniature traits observed in the Debao horse.
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Affiliation(s)
- Md. Panir Choudhury
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 518124, China; (M.P.C.); (G.Y.); (Y.L.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Bangladesh Livestock Research Institute, Ministry of Fisheries and Livestock, Savar, Dhaka 1341, Bangladesh
| | - Zihao Wang
- Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning 530002,China; (Z.W.); (M.Z.); (S.T.); (J.Y.); (S.C.)
| | - Min Zhu
- Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning 530002,China; (Z.W.); (M.Z.); (S.T.); (J.Y.); (S.C.)
| | - Shaohua Teng
- Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning 530002,China; (Z.W.); (M.Z.); (S.T.); (J.Y.); (S.C.)
| | - Jing Yan
- Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning 530002,China; (Z.W.); (M.Z.); (S.T.); (J.Y.); (S.C.)
| | - Shuwei Cao
- Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning 530002,China; (Z.W.); (M.Z.); (S.T.); (J.Y.); (S.C.)
| | - Guoqiang Yi
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 518124, China; (M.P.C.); (G.Y.); (Y.L.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yuwen Liu
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 518124, China; (M.P.C.); (G.Y.); (Y.L.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yuying Liao
- Guangxi Veterinary Research Institute, Nanning 530001, China
| | - Zhonglin Tang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 518124, China; (M.P.C.); (G.Y.); (Y.L.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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Yu S, Liu Z, Li M, Zhou D, Hua P, Cheng H, Fan W, Xu Y, Liu D, Liang S, Zhang Y, Xie M, Tang J, Jiang Y, Hou S, Zhou Z. Resequencing of a Pekin duck breeding population provides insights into the genomic response to short-term artificial selection. Gigascience 2023; 12:giad016. [PMID: 36971291 PMCID: PMC10041536 DOI: 10.1093/gigascience/giad016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 02/04/2023] [Accepted: 02/27/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND Short-term, intense artificial selection drives fast phenotypic changes in domestic animals and leaves imprints on their genomes. However, the genetic basis of this selection response is poorly understood. To better address this, we employed the Pekin duck Z2 pure line, in which the breast muscle weight was increased nearly 3-fold after 10 generations of breeding. We denovo assembled a high-quality reference genome of a female Pekin duck of this line (GCA_003850225.1) and identified 8.60 million genetic variants in 119 individuals among 10 generations of the breeding population. RESULTS We identified 53 selected regions between the first and tenth generations, and 93.8% of the identified variations were enriched in regulatory and noncoding regions. Integrating the selection signatures and genome-wide association approach, we found that 2 regions covering 0.36 Mb containing UTP25 and FBRSL1 were most likely to contribute to breast muscle weight improvement. The major allele frequencies of these 2 loci increased gradually with each generation following the same trend. Additionally, we found that a copy number variation region containing the entire EXOC4 gene could explain 1.9% of the variance in breast muscle weight, indicating that the nervous system may play a role in economic trait improvement. CONCLUSIONS Our study not only provides insights into genomic dynamics under intense artificial selection but also provides resources for genomics-enabled improvements in duck breeding.
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Affiliation(s)
- Simeng Yu
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zihua Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Ming Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Dongke Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Ping Hua
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Hong Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Wenlei Fan
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yaxi Xu
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Dapeng Liu
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Suyun Liang
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yunsheng Zhang
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ming Xie
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jing Tang
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Shuisheng Hou
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhengkui Zhou
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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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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Shilton CA, Kahler A, Roach JM, Raudsepp T, de Mestre AM. Lethal variants of equine pregnancy: is it the placenta or foetus leading the conceptus in the wrong direction? Reprod Fertil Dev 2022; 35:51-69. [PMID: 36592981 DOI: 10.1071/rd22239] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Embryonic and foetal loss remain one of the greatest challenges in equine reproductive health with 5-10% of established day 15 pregnancies and a further 5-10% of day 70 pregnancies failing to produce a viable foal. The underlying reason for these losses is variable but ultimately most cases will be attributed to pathologies of the environment of the developing embryo and later foetus, or a defect intrinsic to the embryo itself that leads to lethality at any stage of gestation right up to birth. Historically, much research has focused on the maternal endometrium, endocrine and immune responses in pregnancy and pregnancy loss, as well as infectious agents such as pathogens, and until recently very little was known about the both small and large genetic variants associated with reduced foetal viability in the horse. In this review, we first introduce key aspects of equine placental and foetal development. We then discuss incidence, risk factors and causes of pregnancy loss, with the latter focusing on genetic variants described to date that can impact equine foetal viability.
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Affiliation(s)
- Charlotte A Shilton
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, Hawkshead Lane, Herts, AL9 7TA, UK
| | - Anne Kahler
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, Hawkshead Lane, Herts, AL9 7TA, UK
| | - Jessica M Roach
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, Hawkshead Lane, Herts, AL9 7TA, UK
| | - Terje Raudsepp
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843-4458, USA
| | - Amanda M de Mestre
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, Hawkshead Lane, Herts, AL9 7TA, UK
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The Innovative Informatics Approaches of High-Throughput Technologies in Livestock: Spearheading the Sustainability and Resiliency of Agrigenomics Research. LIFE (BASEL, SWITZERLAND) 2022; 12:life12111893. [PMID: 36431028 PMCID: PMC9695872 DOI: 10.3390/life12111893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/09/2022] [Accepted: 11/14/2022] [Indexed: 11/17/2022]
Abstract
For more than a decade, next-generation sequencing (NGS) has been emerging as the mainstay of agrigenomics research. High-throughput technologies have made it feasible to facilitate research at the scale and cost required for using this data in livestock research. Scale frameworks of sequencing for agricultural and livestock improvement, management, and conservation are partly attributable to innovative informatics methodologies and advancements in sequencing practices. Genome-wide sequence-based investigations are often conducted worldwide, and several databases have been created to discover the connections between worldwide scientific accomplishments. Such studies are beginning to provide revolutionary insights into a new era of genomic prediction and selection capabilities of various domesticated livestock species. In this concise review, we provide selected examples of the current state of sequencing methods, many of which are already being used in animal genomic studies, and summarize the state of the positive attributes of genome-based research for cattle (Bos taurus), sheep (Ovis aries), pigs (Sus scrofa domesticus), horses (Equus caballus), chickens (Gallus gallus domesticus), and ducks (Anas platyrhyncos). This review also emphasizes the advantageous features of sequencing technologies in monitoring and detecting infectious zoonotic diseases. In the coming years, the continued advancement of sequencing technologies in livestock agrigenomics will significantly influence the sustained momentum toward regulatory approaches that encourage innovation to ensure continued access to a safe, abundant, and affordable food supplies for future generations.
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Davoudi P, Do DN, Rathgeber B, Colombo SM, Sargolzaei M, Plastow G, Wang Z, Karimi K, Hu G, Valipour S, Miar Y. Genome-wide detection of copy number variation in American mink using whole-genome sequencing. BMC Genomics 2022; 23:649. [PMID: 36096727 PMCID: PMC9468235 DOI: 10.1186/s12864-022-08874-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/05/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Copy number variations (CNVs) represent a major source of genetic diversity and contribute to the phenotypic variation of economically important traits in livestock species. In this study, we report the first genome-wide CNV analysis of American mink using whole-genome sequence data from 100 individuals. The analyses were performed by three complementary software programs including CNVpytor, DELLY and Manta. RESULTS A total of 164,733 CNVs (144,517 deletions and 20,216 duplications) were identified representing 5378 CNV regions (CNVR) after merging overlapping CNVs, covering 47.3 Mb (1.9%) of the mink autosomal genome. Gene Ontology and KEGG pathway enrichment analyses of 1391 genes that overlapped CNVR revealed potential role of CNVs in a wide range of biological, molecular and cellular functions, e.g., pathways related to growth (regulation of actin cytoskeleton, and cAMP signaling pathways), behavior (axon guidance, circadian entrainment, and glutamatergic synapse), lipid metabolism (phospholipid binding, sphingolipid metabolism and regulation of lipolysis in adipocytes), and immune response (Wnt signaling, Fc receptor signaling, and GTPase regulator activity pathways). Furthermore, several CNVR-harbored genes associated with fur characteristics and development (MYO5A, RAB27B, FGF12, SLC7A11, EXOC2), and immune system processes (SWAP70, FYN, ORAI1, TRPM2, and FOXO3). CONCLUSIONS This study presents the first genome-wide CNV map of American mink. We identified 5378 CNVR in the mink genome and investigated genes that overlapped with CNVR. The results suggest potential links with mink behaviour as well as their possible impact on fur quality and immune response. Overall, the results provide new resources for mink genome analysis, serving as a guideline for future investigations in which genomic structural variations are present.
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Affiliation(s)
- Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Duy Ngoc Do
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Bruce Rathgeber
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Stefanie M Colombo
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
- Select Sires Inc., Plain City, OH, USA
| | - Graham Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Zhiquan Wang
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Karim Karimi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Guoyu Hu
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Shafagh Valipour
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada.
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Copy Number Variation (CNV): A New Genomic Insight in Horses. Animals (Basel) 2022; 12:ani12111435. [PMID: 35681904 PMCID: PMC9179425 DOI: 10.3390/ani12111435] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 12/04/2022] Open
Abstract
Simple Summary This study aimed to contribute to our knowledge of CNVs, a type of genomic marker in equines, by producing, for the first time, a fine-scale characterization of the CNV regions (CNVRs) in the Pura Raza Española horse breed. We found not only the existence of a unique pattern of genomic regions enriched in CNVs in the PRE in comparison with the data available from other breeds but also the incidence of CNVs across the entire genome. Since these regions could affect the structure and dose of the genes involved, we also performed a gene ontology analysis which revealed that most of the genes overlapping in CNVRs were related to the olfactory pathways and immune response. Abstract Copy number variations (CNVs) are a new-fangled source of genetic variation that can explain changes in the phenotypes in complex traits and diseases. In recent years, their study has increased in many livestock populations. However, the study and characterization of CNVs in equines is still very limited. Our study aimed to investigate the distribution pattern of CNVs, characterize CNV regions (CNVRs), and identify the biological pathways affected by CNVRs in the Pura Raza Española (PRE) breed. To achieve this, we analyzed high-density SNP genotyping data (670,804 markers) from a large cohort of 654 PRE horses. In total, we identified 19,902 CNV segments and 1007 CNV regions in the whole population. The length of the CNVs ranged from 1.024 kb to 4.55 Mb, while the percentage of the genome covered by CNVs was 4.4%. Interestingly, duplications were more abundant than deletions and mixed CNVRs. In addition, the distribution of CNVs across the chromosomes was not uniform, with ECA12 being the chromosome with the largest percentage of its genome covered (19.2%), while the highest numbers of CNVs were found in ECA20, ECA12, and ECA1. Our results showed that 71.4% of CNVRs contained genes involved in olfactory transduction, olfactory receptor activity, and immune response. Finally, 39.1% of the CNVs detected in our study were unique when compared with CNVRs identified in previous studies. To the best of our knowledge, this is the first attempt to reveal and characterize the CNV landscape in PRE horses, and it contributes to our knowledge of CNVs in equines, thus facilitating the understanding of genetic and phenotypic variations in the species. However, further research is still needed to confirm if the CNVs observed in the PRE are also linked to variations in the specific phenotypical differences in the breed.
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12
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Wang M, Liu Y, Bi X, Ma H, Zeng G, Guo J, Guo M, Ling Y, Zhao C. Genome-Wide Detection of Copy Number Variants in Chinese Indigenous Horse Breeds and Verification of CNV-Overlapped Genes Related to Heat Adaptation of the Jinjiang Horse. Genes (Basel) 2022; 13:genes13040603. [PMID: 35456409 PMCID: PMC9033042 DOI: 10.3390/genes13040603] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 02/05/2023] Open
Abstract
In the present study, genome-wide CNVs were detected in a total of 301 samples from 10 Chinese indigenous horse breeds using the Illumina Equine SNP70 Bead Array, and the candidate genes related to adaptability to high temperature and humidity in Jinjiang horses were identified and validated. We determined a total of 577 CNVs ranging in size from 1.06 Kb to 2023.07 Kb on the 31 pairs of autosomes. By aggregating the overlapping CNVs for each breed, a total of 495 CNVRs were detected in the 10 Chinese horse breeds. As many as 211 breed-specific CNVRs were determined, of which 64 were found in the Jinjiang horse population. By removing repetitive CNV regions between breeds, a total of 239 CNVRs were identified in the Chinese indigenous horse breeds including 102 losses, 133 gains and 4 of both events (losses and gains in the same region), in which 131 CNVRs were novel and only detected in the present study compared with previous studies. The total detected CNVR length was 41.74 Mb, accounting for 1.83% of the total length of equine autosomal chromosomes. The coverage of CNVRs on each chromosome varied from 0.47% to 15.68%, with the highest coverage on ECA 12, but the highest number of CNVRs was detected on ECA1 and ECA24. A total of 229 genes overlapping with CNVRs were detected in the Jinjiang horse population, which is an indigenous horse breed unique to the southeastern coast of China exhibiting adaptability to high temperature and humidity. The functional annotation of these genes showed significant relation to cellular heat acclimation and immunity. The expression levels of the candidate genes were validated by heat shock treatment of various durations on fibroblasts of horses. The results show that the expression levels of HSPA1A were significantly increased among the different heat shock durations. The expression level of NFKBIA and SOCS4 declined from the beginning of heat shock to 2 h after heat shock and then showed a gradual increase until it reached the highest value at 6 h and 10 h of heat shock, respectively. Breed-specific CNVRs of Chinese indigenous horse breeds were revealed in the present study, and the results facilitate mapping CNVs on the whole genome and also provide valuable insights into the molecular mechanisms of adaptation to high temperature and humidity in the Jinjiang horse.
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Affiliation(s)
- Min Wang
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.W.); (Y.L.); (X.B.); (Y.L.)
- Equine Center, China Agricultural University, Beijing 100193, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing 100193, China
- National Engineering Laboratory for Animal Breeding, Beijing 100193, China
- Beijing Key Laboratory for Genetic Improvement of Livestock and Poultry, Beijing 100193, China
| | - Yu Liu
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.W.); (Y.L.); (X.B.); (Y.L.)
- Equine Center, China Agricultural University, Beijing 100193, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing 100193, China
- National Engineering Laboratory for Animal Breeding, Beijing 100193, China
- Beijing Key Laboratory for Genetic Improvement of Livestock and Poultry, Beijing 100193, China
| | - Xiaokun Bi
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.W.); (Y.L.); (X.B.); (Y.L.)
- Equine Center, China Agricultural University, Beijing 100193, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing 100193, China
- National Engineering Laboratory for Animal Breeding, Beijing 100193, China
- Beijing Key Laboratory for Genetic Improvement of Livestock and Poultry, Beijing 100193, China
| | - Hongying Ma
- Shaanxi Key Laboratory for Animal Conservation, Shaanxi Institute of Zoology, Xi’an 710032, China;
| | - Guorong Zeng
- Jinjiang Animal Husbandry and Veterinary Station, Quanzhou 362200, China; (G.Z.); (J.G.); (M.G.)
| | - Jintu Guo
- Jinjiang Animal Husbandry and Veterinary Station, Quanzhou 362200, China; (G.Z.); (J.G.); (M.G.)
| | - Minghao Guo
- Jinjiang Animal Husbandry and Veterinary Station, Quanzhou 362200, China; (G.Z.); (J.G.); (M.G.)
| | - Yao Ling
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.W.); (Y.L.); (X.B.); (Y.L.)
| | - Chunjiang Zhao
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.W.); (Y.L.); (X.B.); (Y.L.)
- Equine Center, China Agricultural University, Beijing 100193, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing 100193, China
- National Engineering Laboratory for Animal Breeding, Beijing 100193, China
- Beijing Key Laboratory for Genetic Improvement of Livestock and Poultry, Beijing 100193, China
- Correspondence:
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13
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Polani S, Dean M, Lichter-Peled A, Hendrickson S, Tsang S, Fang X, Feng Y, Qiao W, Avni G, Kahila Bar-Gal G. Sequence Variant in the TRIM39-RPP21 Gene Readthrough is Shared Across a Cohort of Arabian Foals Diagnosed with Juvenile Idiopathic Epilepsy. JOURNAL OF GENETIC MUTATION DISORDERS 2022; 1:103. [PMID: 35465405 PMCID: PMC9031527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Juvenile idiopathic epilepsy (JIE) is a self-limiting neurological disorder with a suspected genetic predisposition affecting young Arabian foals of the Egyptian lineage. The condition is characterized by tonic-clonic seizures with intermittent post-ictal blindness, in which most incidents are sporadic and unrecognized. This study aimed to identify genetic components shared across a local cohort of Arabian foals diagnosed with JIE via a combined whole genome and targeted resequencing approach: Initial whole genome comparisons between a small cohort of nine diagnosed foals (cases) and 27 controls from other horse breeds identified variants uniquely shared amongst the case cohort. Further validation via targeted resequencing of these variants, that pertain to non-intergenic regions, on additional eleven case individuals revealed a single 19bp deletion coupled with a triple-C insertion (Δ19InsCCC) within the TRIM39-RPP21 gene readthrough that was uniquely shared across all case individuals, and absent from three additional Arabian controls. Furthermore, we have confirmed recent findings refuting potential linkage between JIE and other inherited diseases in the Arabian lineage, and refuted the potential linkage between JIE and genes predisposing a similar disorder in human newborns. This is the first study to report a genetic variant to be shared in a sub-population cohort of Arabian foals diagnosed with JIE. Further evaluation of the sensitivity and specificity of the Δ19InsCCC allele within additional cohorts of the Arabian horse is warranted in order to validate its credibility as a marker for JIE, and to ascertain whether it has been introduced into other horse breeds by Arabian ancestry.
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Affiliation(s)
- S Polani
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - M Dean
- National Cancer Institute, Division of Cancer Epidemiology & Genetics, Laboratory of Translational Genomics, USA
| | - A Lichter-Peled
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - S Hendrickson
- Department of Biology, Shepherd University, Shepherdstown, USA
| | | | - X Fang
- BGI-Shenzhen, Shenzhen, China
| | - Y Feng
- BGI-Shenzhen, Shenzhen, China
| | - W Qiao
- BGI-Shenzhen, Shenzhen, China
| | - G Avni
- Medisoos Equine Clinic, Kibutz Magal, Israel
| | - G Kahila Bar-Gal
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
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14
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Prunier J, Carrier A, Gilbert I, Poisson W, Albert V, Taillon J, Bourret V, Côté SD, Droit A, Robert C. CNVs with adaptive potential in Rangifer tarandus: genome architecture and new annotated assembly. Life Sci Alliance 2021; 5:5/3/e202101207. [PMID: 34911809 PMCID: PMC8711850 DOI: 10.26508/lsa.202101207] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 01/13/2023] Open
Abstract
Rangifer tarandus has experienced recent drastic population size reductions throughout its circumpolar distribution and preserving the species implies genetic diversity conservation. To facilitate genomic studies of the species populations, we improved the genome assembly by combining long read and linked read and obtained a new highly accurate and contiguous genome assembly made of 13,994 scaffolds (L90 = 131 scaffolds). Using de novo transcriptome assembly of RNA-sequencing reads and similarity with annotated human gene sequences, 17,394 robust gene models were identified. As copy number variations (CNVs) likely play a role in adaptation, we additionally investigated these variations among 20 genomes representing three caribou ecotypes (migratory, boreal and mountain). A total of 1,698 large CNVs (length > 1 kb) showing a genome distribution including hotspots were identified. 43 large CNVs were particularly distinctive of the migratory and sedentary ecotypes and included genes annotated for functions likely related to the expected adaptations. This work includes the first publicly available annotation of the caribou genome and the first assembly allowing genome architecture analyses, including the likely adaptive CNVs reported here.
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Affiliation(s)
- Julien Prunier
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Quebec City, Canada
| | - Alexandra Carrier
- Département des sciences animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Quebec City, Canada
| | - Isabelle Gilbert
- Département des sciences animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Quebec City, Canada
| | - William Poisson
- Département des sciences animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Quebec City, Canada
| | - Vicky Albert
- Ministère des Forêts, de la Faune et des Parcs du Québec, Quebec City, Canada
| | - Joëlle Taillon
- Ministère des Forêts, de la Faune et des Parcs du Québec, Quebec City, Canada
| | - Vincent Bourret
- Ministère des Forêts, de la Faune et des Parcs du Québec, Quebec City, Canada
| | - Steeve D Côté
- Caribou Ungava, département de biologie, Faculté des Sciences et de Génie, Université Laval, Quebec City, Canada
| | - Arnaud Droit
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Quebec City, Canada
| | - Claude Robert
- Département des sciences animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Quebec City, Canada
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15
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Horse Clinical Cytogenetics: Recurrent Themes and Novel Findings. Animals (Basel) 2021; 11:ani11030831. [PMID: 33809432 PMCID: PMC8001954 DOI: 10.3390/ani11030831] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/12/2021] [Accepted: 03/13/2021] [Indexed: 12/17/2022] Open
Abstract
Clinical cytogenetic studies in horses have been ongoing for over half a century and clearly demonstrate that chromosomal disorders are among the most common non-infectious causes of decreased fertility, infertility, and congenital defects. Large-scale cytogenetic surveys show that almost 30% of horses with reproductive or developmental problems have chromosome aberrations, whereas abnormal karyotypes are found in only 2-5% of the general population. Among the many chromosome abnormalities reported in the horse, most are unique or rare. However, all surveys agree that there are two recurrent conditions: X-monosomy and SRY-negative XY male-to-female sex reversal, making up approximately 35% and 11% of all chromosome abnormalities, respectively. The two are signature conditions for the horse and rare or absent in other domestic species. The progress in equine genomics and the development of molecular tools, have qualitatively improved clinical cytogenetics today, allowing for refined characterization of aberrations and understanding the underlying molecular mechanisms. While cutting-edge genomics tools promise further improvements in chromosome analysis, they will not entirely replace traditional cytogenetics, which still is the most straightforward, cost-effective, and fastest approach for the initial evaluation of potential breeding animals and horses with reproductive or developmental disorders.
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16
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Laseca N, Anaya G, Peña Z, Pirosanto Y, Molina A, Demyda Peyrás S. Impaired Reproductive Function in Equines: From Genetics to Genomics. Animals (Basel) 2021; 11:393. [PMID: 33546520 PMCID: PMC7913728 DOI: 10.3390/ani11020393] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 01/29/2021] [Accepted: 01/31/2021] [Indexed: 12/15/2022] Open
Abstract
Fertility is one of the key factors in the economic and productive success of the equine industry. Despite this, studies on the genetic causes affecting reproductive performance are scarce, especially in mares, where the genetic architecture of the reproductive traits is extremely complex. Today, with the increasing availability of new genomic methodologies for this species, we are presented with an interesting opportunity to understand the genetic basis of equine reproductive disorders. These include, among others, novel techniques for detecting chromosomal abnormalities, whose association with infertility in horses was established over 50 years ago; new sequencing technologies permitting an accurate detection of point mutations influencing fertility, as well as the study of inbreeding and molecular homozygosity, which has been widely suggested as one of the main causes of low reproductive performance in horses. Finally, over the last few years, reproductive performance has also been associated with copy number variants and candidate genes detected by genome-wide association studies on fertility traits. However, such studies are still scarce, probably because they depend on the existence of large and accurate phenotypic datasets of reproductive and/or fertility traits, which are still difficult to obtain in equines.
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Affiliation(s)
- Nora Laseca
- Departamento de genética, Universidad de Córdoba, Campus de Rabanales Ctra, Madrid-Cádiz, km 396, 14071 Córdoba, Spain; (N.L.); (G.A.); (Z.P.); (A.M.)
| | - Gabriel Anaya
- Departamento de genética, Universidad de Córdoba, Campus de Rabanales Ctra, Madrid-Cádiz, km 396, 14071 Córdoba, Spain; (N.L.); (G.A.); (Z.P.); (A.M.)
| | - Zahira Peña
- Departamento de genética, Universidad de Córdoba, Campus de Rabanales Ctra, Madrid-Cádiz, km 396, 14071 Córdoba, Spain; (N.L.); (G.A.); (Z.P.); (A.M.)
| | - Yamila Pirosanto
- Departamento de Producción Animal, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata 1900, Argentina;
- Consejo Superior de Investigaciones Científicas y Tecnológicas (CONICET), CCT-La Plata, La Plata 1900, Argentina
| | - Antonio Molina
- Departamento de genética, Universidad de Córdoba, Campus de Rabanales Ctra, Madrid-Cádiz, km 396, 14071 Córdoba, Spain; (N.L.); (G.A.); (Z.P.); (A.M.)
| | - Sebastián Demyda Peyrás
- Departamento de Producción Animal, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata 1900, Argentina;
- Consejo Superior de Investigaciones Científicas y Tecnológicas (CONICET), CCT-La Plata, La Plata 1900, Argentina
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17
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Klumplerova M, Splichalova P, Oppelt J, Futas J, Kohutova A, Musilova P, Kubickova S, Vodicka R, Orlando L, Horin P. Genetic diversity, evolution and selection in the major histocompatibility complex DRB and DQB loci in the family Equidae. BMC Genomics 2020; 21:677. [PMID: 32998693 PMCID: PMC7525986 DOI: 10.1186/s12864-020-07089-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 09/21/2020] [Indexed: 02/08/2023] Open
Abstract
Background The mammalian Major Histocompatibility Complex (MHC) is a genetic region containing highly polymorphic genes with immunological functions. MHC class I and class II genes encode antigen-presenting molecules expressed on the cell surface. The MHC class II sub-region contains genes expressed in antigen presenting cells. The antigen binding site is encoded by the second exon of genes encoding antigen presenting molecules. The exon 2 sequences of these MHC genes have evolved under the selective pressure of pathogens. Interspecific differences can be observed in the class II sub-region. The family Equidae includes a variety of domesticated, and free-ranging species inhabiting a range of habitats exposed to different pathogens and represents a model for studying this important part of the immunogenome. While equine MHC class II DRA and DQA loci have received attention, the genetic diversity and effects of selection on DRB and DQB loci have been largely overlooked. This study aimed to provide the first in-depth analysis of the MHC class II DRB and DQB loci in the Equidae family. Results Three DRB and two DQB genes were identified in the genomes of all equids. The genes DRB2, DRB3 and DQB3 showed high sequence conservation, while polymorphisms were more frequent at DRB1 and DQB1 across all species analyzed. DQB2 was not found in the genome of the Asiatic asses Equus hemionus kulan and E. h. onager. The bioinformatic analysis of non-zero-coverage-bases of DRB and DQB genes in 14 equine individual genomes revealed differences among individual genes. Evidence for recombination was found for DRB1, DRB2, DQB1 and DQB2 genes. Trans-species allele sharing was identified in all genes except DRB1. Site-specific selection analysis predicted genes evolving under positive selection both at DRB and DQB loci. No selected amino acid sites were identified in DQB3. Conclusions The organization of the MHC class II sub-region of equids is similar across all species of the family. Genomic sequences, along with phylogenetic trees suggesting effects of selection as well as trans-species polymorphism support the contention that pathogen-driven positive selection has shaped the MHC class II DRB/DQB sub-regions in the Equidae.
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Affiliation(s)
- Marie Klumplerova
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic.,Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic
| | - Petra Splichalova
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic.,Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic
| | - Jan Oppelt
- Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic.,Ceitec MU, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic.,National Centre for Biomolecular research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Jan Futas
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic.,Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic
| | - Aneta Kohutova
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic.,Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Petra Musilova
- Department of Genetics and Reproductive Biotechnologies, Veterinary Research Institute, Brno, Czech Republic.,Ceitec VRI, RG Animal Cytogenomics, Brno, Czech Republic
| | - Svatava Kubickova
- Department of Genetics and Reproductive Biotechnologies, Veterinary Research Institute, Brno, Czech Republic.,Ceitec VRI, RG Animal Cytogenomics, Brno, Czech Republic
| | - Roman Vodicka
- Zoo Prague, U Trojského zámku 120/3, 171 00, Praha 7, Czech Republic
| | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000, Toulouse, France.,Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K, Copenhagen, Denmark
| | - Petr Horin
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic. .,Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic.
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Abstract
The sequencing and assembly of a reference genome for the horse has been revolutionary for investigation of horse health and performance. Next-generation sequencing (NGS) methods represent a second revolution in equine genomics. Researchers can align and compare DNA and RNA sequencing data to the reference genome to explore variation that may contribute or be attributed to disease. NGS has also facilitated the translation of research discovery to clinically relevant applications. This article discusses the history and development of NGS, details some of the available sequencing platforms, and describes currently available applications in the context of both discovery and clinical settings.
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Abstract
Reproductive disorders are genetically heterogeneous and complex; available genetic tests are limited to chromosome analysis and 1 susceptibility gene. Cytogenetic analysis should be the first test to confirm or rule out chromosomal aberrations. No causative genes/mutations are known. The only available genetic test for stallion subfertility is based on a susceptibility gene FKBP6. The ongoing progress in equine genomics will improve the status of genetic testing. However, because subfertile phenotypes do not facilitate collection of large numbers of samples or pedigrees, and clinical causes of many cases remain unknown, further progress requires constructive cross-talk between geneticists, clinicians, breeders, and owners.
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Affiliation(s)
- Terje Raudsepp
- Department of Veterinary Integrative Biosciences, Molecular Cytogenetics Laboratory, Texas A&M University, College of Veterinary Medicine and Biomedical Sciences, Veterinary Research Building Room 306, 588 Raymond Stotzer Parkway, College Station, TX 77843-4458, USA.
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20
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Wang Z, Guo J, Guo Y, Yang Y, Teng T, Yu Q, Wang T, Zhou M, Zhu Q, Wang W, Zhang Q, Yang H. Genome-Wide Detection of CNVs and Association With Body Weight in Sheep Based on 600K SNP Arrays. Front Genet 2020; 11:558. [PMID: 32582291 PMCID: PMC7297042 DOI: 10.3389/fgene.2020.00558] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 05/07/2020] [Indexed: 01/30/2023] Open
Abstract
Copy number variations (CNVs) are important genomic structural variations and can give rise to significant phenotypic diversity. Herein, we used high-density 600K SNP arrays to detect CNVs in two synthetic lines of sheep (DS and SHH) and in Hu sheep (a local Chinese breed). A total of 919 CNV regions (CNVRs) were detected with a total length of 48.17 Mb, accounting for 1.96% of the sheep genome. These CNVRs consisted of 730 gains, 102 losses, and 87 complex CNVRs. These CNVRs were significantly enriched in the segmental duplication (SD) region. A CNVR-based cluster analysis of the three breeds revealed that the DS and SHH breeds share a close genetic relationship. Functional analysis revealed that some genes in these CNVRs were also significantly enriched in the olfactory transduction pathway (oas04740), including members of the OR gene family such as OR6C76, OR4Q2, and OR4K14. Using association analyses and previous gene annotations, we determined that a subset of identified genes was likely to be associated with body weight, including FOXF2, MAPK12, MAP3K11, STRBP, and C14orf132. Together, these results offer valuable information that will guide future efforts to explore the genetic basis for body weight in sheep.
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Affiliation(s)
- Zhipeng Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Jing Guo
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Yuanyuan Guo
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Yonglin Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Teng Teng
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Qian Yu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Tao Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Meng Zhou
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Qiusi Zhu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Wenwen Wang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Qin Zhang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Hua Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
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Salek Ardestani S, Aminafshar M, Zandi Baghche Maryam MB, Banabazi MH, Sargolzaei M, Miar Y. Signatures of selection analysis using whole-genome sequence data reveals novel candidate genes for pony and light horse types. Genome 2020; 63:387-396. [PMID: 32407640 DOI: 10.1139/gen-2020-0001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Natural selection and domestication have shaped modern horse populations, resulting in a vast range of phenotypically diverse breeds. Horse breeds are classified into three types (pony, light, and draft) generally based on their body type. Understanding the genetic basis of horse type variation and selective pressures related to the evolutionary trend can be particularly important for current selection strategies. Whole-genome sequences were generated for 14 pony and 32 light horses to investigate the genetic signatures of selection of the horse type in pony and light horses. In the overlapping extremes of the fixation index and nucleotide diversity results, we found novel genomic signatures of selective sweeps near key genes previously implicated in body measurements including C4ORF33, CRB1, CPN1, FAM13A, and FGF12 that may influence variation in pony and light horse types. This study contributes to a better understanding of the genetic background of differences between pony and light horse types.
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Affiliation(s)
- Siavash Salek Ardestani
- Department of Animal Science, Science and Research Branch, Islamic Azad University, Tehran 1477893855, Iran
| | - Mehdi Aminafshar
- Department of Animal Science, Science and Research Branch, Islamic Azad University, Tehran 1477893855, Iran
| | | | - Mohammad Hossein Banabazi
- Department of Biotechnology, Animal Science Research Institute of Iran, Agricultural Research, Education & Extension Organization, Karaj 3146618361, Iran
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, ON NIG 2W1, Canada.,Select Sires Inc., Plain City, OH 43064, USA
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N 5E3, Canada
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22
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Cytogenetic Mapping of 35 New Markers in the Alpaca ( Vicugna pacos). Genes (Basel) 2020; 11:genes11050522. [PMID: 32397072 PMCID: PMC7288448 DOI: 10.3390/genes11050522] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 12/11/2022] Open
Abstract
Alpaca is a camelid species of broad economic, biological and biomedical interest, and an essential part of the cultural and historical heritage of Peru. Recently, efforts have been made to improve knowledge of the alpaca genome, and its genetics and cytogenetics, to develop molecular tools for selection and breeding. Here, we report cytogenetic mapping of 35 new markers to 19 alpaca autosomes and the X chromosome. Twenty-eight markers represent alpaca SNPs, of which 17 are located inside or near protein-coding genes, two are in ncRNA genes and nine are intergenic. The remaining seven markers correspond to candidate genes for fiber characteristics (BMP4, COL1A2, GLI1, SFRP4), coat color (TYR) and development (CHD7, PAX7). The results take the tally of cytogenetically mapped markers in alpaca to 281, covering all 36 autosomes and the sex chromosomes. The new map assignments overall agree with human–camelid conserved synteny data, except for mapping BMP4 to VPA3, suggesting a hitherto unknown homology with HSA14. The findings validate, refine and correct the current alpaca assembly VicPac3.1 by anchoring unassigned sequence scaffolds, and ordering and orienting assigned scaffolds. The study contributes to the improvement in the alpaca reference genome and advances camelid molecular cytogenetics.
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23
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Characterization of A Homozygous Deletion of Steroid Hormone Biosynthesis Genes in Horse Chromosome 29 as A Risk Factor for Disorders of Sex Development and Reproduction. Genes (Basel) 2020; 11:genes11030251. [PMID: 32120906 PMCID: PMC7140900 DOI: 10.3390/genes11030251] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/21/2020] [Accepted: 02/25/2020] [Indexed: 12/24/2022] Open
Abstract
Disorders of sex development (DSD) and reproduction are not uncommon among horses, though knowledge about their molecular causes is sparse. Here we characterized a ~200 kb homozygous deletion in chromosome 29 at 29.7-29.9 Mb. The region contains AKR1C genes which function as ketosteroid reductases in steroid hormone biosynthesis, including androgens and estrogens. Mutations in AKR1C genes are associated with human DSDs. Deletion boundaries, sequence properties and gene content were studied by PCR and whole genome sequencing of select deletion homozygotes and control animals. Deletion analysis by PCR in 940 horses, including 622 with DSDs and reproductive problems and 318 phenotypically normal controls, detected 67 deletion homozygotes of which 79% were developmentally or reproductively abnormal. Altogether, 8-9% of all abnormal horses were homozygous for the deletion, with the highest incidence (9.4%) among cryptorchids. The deletion was found in ~4% of our phenotypically normal cohort, ~1% of global warmblood horses and ponies, and ~7% of draught breeds of general horse population as retrieved from published data. Based on the abnormal phenotype of the carriers, the functionally relevant gene content, and the low incidence in general population, we consider the deletion in chromosome 29 as a risk factor for equine DSDs and reproductive disorders.
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24
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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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25
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Raudsepp T, Finno CJ, Bellone RR, Petersen JL. Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post-genome era. Anim Genet 2019; 50:569-597. [PMID: 31568563 PMCID: PMC6825885 DOI: 10.1111/age.12857] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2019] [Indexed: 12/14/2022]
Abstract
The horse reference genome from the Thoroughbred mare Twilight has been available for a decade and, together with advances in genomics technologies, has led to unparalleled developments in equine genomics. At the core of this progress is the continuing improvement of the quality, contiguity and completeness of the reference genome, and its functional annotation. Recent achievements include the release of the next version of the reference genome (EquCab3.0) and generation of a reference sequence for the Y chromosome. Horse satellite‐free centromeres provide unique models for mammalian centromere research. Despite extremely low genetic diversity of the Y chromosome, it has been possible to trace patrilines of breeds and pedigrees and show that Y variation was lost in the past approximately 2300 years owing to selective breeding. The high‐quality reference genome has led to the development of three different SNP arrays and WGSs of almost 2000 modern individual horses. The collection of WGS of hundreds of ancient horses is unique and not available for any other domestic species. These tools and resources have led to global population studies dissecting the natural history of the species and genetic makeup and ancestry of modern breeds. Most importantly, the available tools and resources, together with the discovery of functional elements, are dissecting molecular causes of a growing number of Mendelian and complex traits. The improved understanding of molecular underpinnings of various traits continues to benefit the health and performance of the horse whereas also serving as a model for complex disease across species.
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Affiliation(s)
- T Raudsepp
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Research, Texas A&M University, College Station, TX, 77843, USA
| | - C J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - R R Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.,School of Veterinary Medicine, Veterinary Genetics Laboratory, University of California-Davis, Davis, CA, 95616, USA
| | - J L Petersen
- Department of Animal Science, University of Nebraska, Lincoln, NE, 68583-0908, USA
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26
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Beeson SK, Mickelson JR, McCue ME. Exploration of fine-scale recombination rate variation in the domestic horse. Genome Res 2019; 29:1744-1752. [PMID: 31434677 PMCID: PMC6771410 DOI: 10.1101/gr.243311.118] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 08/15/2019] [Indexed: 01/17/2023]
Abstract
Total genetic map length and local recombination landscapes typically vary within and across populations. As a first step to understanding the recombination landscape in the domestic horse, we calculated population recombination rates and identified likely recombination hotspots using approximately 1.8 million SNP genotypes for 485 horses from 32 distinct breeds. The resulting breed-averaged recombination map spans 2.36 Gb and accounts for 2939.07 cM. Recombination hotspots occur once per 23.8 Mb on average and account for ∼9% of the physical map length. Regions with elevated recombination rates in the entire cohort were enriched for genes in pathways involving interaction with the environment: immune system processes (specifically, MHC class I and class II genes), responses to stimuli, and serotonin receptor pathways. We found significant correlations between differences in local recombination rates and population differentiation quantified by F ST Analysis of breed-specific maps revealed thousands of hotspot regions unique to particular breeds, as well as unique "coldspots," regions where a particular breed showed below-average recombination, whereas all other breeds had evidence of a hotspot. Finally, we identified relative enrichment (P = 5.88 × 10-27) for the in silico-predicted recognition motif for equine PR/SET domain 9 (PRDM9) in recombination hotspots. These results indicate that selective pressures and PRDM9 function contribute to variation in recombination rates across the domestic horse genome.
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Affiliation(s)
- Samantha K Beeson
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, Minnesota 55108, USA
| | - James R Mickelson
- Veterinary and Biomedical Sciences Department, University of Minnesota, St. Paul, Minnesota 55108, USA
| | - Molly E McCue
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, Minnesota 55108, USA
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27
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Corbi-Botto CM, Morales-Durand H, Zappa ME, Sadaba SA, Peral-García P, Giovambattista G, Díaz S. Genomic structural diversity in Criollo Argentino horses: Analysis of copy number variations. Gene 2019; 695:26-31. [DOI: 10.1016/j.gene.2018.12.067] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/04/2018] [Accepted: 12/27/2018] [Indexed: 12/11/2022]
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28
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Lye ZN, Purugganan MD. Copy Number Variation in Domestication. TRENDS IN PLANT SCIENCE 2019; 24:352-365. [PMID: 30745056 DOI: 10.1016/j.tplants.2019.01.003] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 05/22/2023]
Abstract
Domesticated plants have long served as excellent models for studying evolution. Many genes and mutations underlying important domestication traits have been identified, and most causal mutations appear to be SNPs. Copy number variation (CNV) is an important source of genetic variation that has been largely neglected in studies of domestication. Ongoing work demonstrates the importance of CNVs as a source of genetic variation during domestication, and during the diversification of domesticated taxa. Here, we review how CNVs contribute to evolutionary processes underlying domestication, and review examples of domestication traits caused by CNVs. We draw from examples in plant species, but also highlight cases in animal systems that could illuminate the roles of CNVs in the domestication process.
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Affiliation(s)
- Zoe N Lye
- Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, NY 10003, USA
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates.
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29
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Gabur I, Chawla HS, Snowdon RJ, Parkin IAP. Connecting genome structural variation with complex traits in crop plants. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:733-750. [PMID: 30448864 DOI: 10.1007/s00122-018-3233-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 11/07/2018] [Indexed: 05/05/2023]
Abstract
Structural genome variation is a major determinant of useful trait diversity. We describe how genome analysis methods are enabling discovery of trait-associated structural variants and their potential impact on breeding. As our understanding of complex crop genomes continues to grow, there is growing evidence that structural genome variation plays a major role in determining traits important for breeding and agriculture. Identifying the extent and impact of structural variants in crop genomes is becoming increasingly feasible with ongoing advances in the sophistication of genome sequencing technologies, particularly as it becomes easier to generate accurate long sequence reads on a genome-wide scale. In this article, we discuss the origins of structural genome variation in crops from ancient and recent genome duplication and polyploidization events and review high-throughput methods to assay such variants in crop populations in order to find associations with phenotypic traits. There is increasing evidence from such studies that gene presence-absence and copy number variation resulting from segmental chromosome exchanges may be at the heart of adaptive variation of crops to counter abiotic and biotic stress factors. We present examples from major crops that demonstrate the potential of pangenomic diversity as a key resource for future plant breeding for resilience and sustainability.
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Affiliation(s)
- Iulian Gabur
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Harmeet Singh Chawla
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N OX2, Canada
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30
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Wang H, Chai Z, Hu D, Ji Q, Xin J, Zhang C, Zhong J. A global analysis of CNVs in diverse yak populations using whole-genome resequencing. BMC Genomics 2019; 20:61. [PMID: 30658572 PMCID: PMC6339343 DOI: 10.1186/s12864-019-5451-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 01/11/2019] [Indexed: 12/01/2022] Open
Abstract
Background Genomic structural variation represents a source for genetic and phenotypic variation, which may be subject to selection during the environmental adaptation and population differentiation. Here, we described a genome-wide analysis of copy number variations (CNVs) in 16 populations of yak based on genome resequencing data and CNV-based cluster analyses of these populations. Results In total, we identified 51,461 CNV events and defined 3174 copy number variation regions (CNVRs) that covered 163.8 Mb (6.2%) of yak genome with more “loss” events than both “gain” and “both” events, and we confirmed 31 CNVRs in 36 selected yaks using quantitative PCR. Of the total 163.8 Mb CNVR coverage, a 10.8 Mb region of high-confidence CNVRs directly overlapped with the 52.9 Mb of segmental duplications, and we confirmed their uneven distributions across chromosomes. Furthermore, functional annotation indicated that the CNVR-harbored genes have a considerable variety of molecular functions, including immune response, glucose metabolism, and sensory perception. Notably, some of the identified CNVR-harbored genes associated with adaptation to hypoxia (e.g., DCC, MRPS28, GSTCD, MOGAT2, DEXI, CIITA, and SMYD1). Additionally, cluster analysis, based on either individuals or populations, showed that the CNV clustering was divided into two origins, indicating that some yak CNVs are likely to arisen independently in different populations and contribute to population difference. Conclusions Collectively, the results of the present study advanced our understanding of CNV as an important type of genomic structural variation in yak, and provide a useful genomic resource to facilitate further research on yak evolution and breeding. Electronic supplementary material The online version of this article (10.1186/s12864-019-5451-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hui Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Southwest Minzu University), Ministry of Education, Chengdu, 610000, People's Republic of China
| | - Zhixin Chai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Southwest Minzu University), Ministry of Education, Chengdu, 610000, People's Republic of China
| | - Dan Hu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Southwest Minzu University), Ministry of Education, Chengdu, 610000, People's Republic of China
| | - Qiumei Ji
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850000, People's Republic of China
| | - Jinwei Xin
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850000, People's Republic of China
| | - Chengfu Zhang
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850000, People's Republic of China
| | - Jincheng Zhong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Southwest Minzu University), Ministry of Education, Chengdu, 610000, People's Republic of China.
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31
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Goshu HA, Chu M, Xiaoyun W, Pengjia B, Zhi DX, Yan P. Genomic copy number variation of the CHKB gene alters gene expression and affects growth traits of Chinese domestic yak (Bos grunniens) breeds. Mol Genet Genomics 2019; 294:549-561. [DOI: 10.1007/s00438-018-01530-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 12/29/2018] [Indexed: 12/22/2022]
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32
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Goshu HA, Chu M, Wu X, Pengjia B, Ding XZ, Yan P. Association study and expression analysis of GPC1 gene copy number variation in Chinese Datong yak ( Bos grunniens) breed. ITALIAN JOURNAL OF ANIMAL SCIENCE 2019. [DOI: 10.1080/1828051x.2019.1586456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Habtamu Abera Goshu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, Gansu, China
- Animal Science Department, Oromia Agricultural Research Institute, Bako Agricultural Research Center, Bako, Ethiopia
| | - Min Chu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, Gansu, China
| | - Xiaoyun Wu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, Gansu, China
| | - Bao Pengjia
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, Gansu, China
| | - Xue Zhi Ding
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, Gansu, China
| | - Ping Yan
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, Gansu, China
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33
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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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Gong J, Cheng T, Wu Y, Yang X, Feng Q, Mita K. Genome-wide patterns of copy number variations in Spodoptera litura. Genomics 2018; 111:1231-1238. [PMID: 30114452 DOI: 10.1016/j.ygeno.2018.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/26/2018] [Accepted: 08/04/2018] [Indexed: 01/06/2023]
Abstract
Spodoptera litura is a polyphagous pest and can feed on more than 100 species of plants, causing great damage to agricultural production. The SNP results showed that there were gene exchanges between different regions. To explore the variations of larger segments in S. litura genome, we used genome resequencing samples from 14 regions of China, India, and Japan to study the copy number variations (CNVs). We identified 3976 CNV events and 1581 unique copy number variation regions (CNVRs) occupying the 108.5 Mb genome of S. litura. A total of 5527 genes that overlapped with CNVRs were detected. Selection signal analysis identified 19 shared CNVRs and 105 group-specific CNVRs, whose related genes were involved in various biological processes in S. litura. We constructed the first CNVs map in S. litura genome, and our findings will be valuable for understanding the genomic variations and population differences of S. litura.
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Affiliation(s)
- Jiao Gong
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Tingcai Cheng
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, 2, Tiansheng Road, Beibei, Chongqing 400715, China.
| | - Yuqian Wu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Xi Yang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Qili Feng
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, South China Normal University, Guangzhou 510631, China
| | - Kazuei Mita
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
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Neuhauser S, Handler J, Schelling C, Pieńkowska-Schelling A. Disorder of Sexual Development in a Mare with an Unusual Tentative Mosaic Karyotype: 63,X/64,Xdel(Y). Sex Dev 2018; 12:232-238. [PMID: 30071527 DOI: 10.1159/000490861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2018] [Indexed: 11/19/2022] Open
Abstract
The present report describes a 4-year-old Trakehner mare which was referred to the clinic for a breeding soundness evaluation. Clinical, histological, and postmortem examination revealed an underdeveloped genital tract, the absence of a cervix uteri, and small inactive ovaries without male gonadal tissue. Blood lymphocyte analysis revealed an unusual mosaic karyotype consisting of 2 cell lines. For the majority of cells (70%), monosomy X (63,X) was observed. The remaining cells (30%) contained 64 chromosomes including one X chromosome and a small rudimentary Y chromosome consisting mostly of heterochromatin. The centromere was retained, but its full functionality was questionable. PCR analysis revealed that the entire male-specific region of Y (Yq14), including the SRY gene, was deleted. It remained unclear if the pseudoautosomal region (Yq15) and parts of the heterochromatic region (Yq13) were affected by this deletion. The phenotype of the mare with this disorder of sex development associated with sex chromosome abnormalities is genetically comparable to 63,X monosomy which fully explains the clinical findings.
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Schurink A, da Silva VH, Velie BD, Dibbits BW, Crooijmans RPMA, Franҫois L, Janssens S, Stinckens A, Blott S, Buys N, Lindgren G, Ducro BJ. Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity. BMC Genet 2018; 19:49. [PMID: 30060732 PMCID: PMC6065148 DOI: 10.1186/s12863-018-0657-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 07/19/2018] [Indexed: 12/04/2022] Open
Abstract
Background Many common and relevant diseases affecting equine welfare have yet to be tested regarding structural variants such as copy number variations (CNVs). CNVs make up a substantial proportion of total genetic variability in populations of many species, resulting in more sequence differences between individuals than SNPs. Associations between CNVs and disease phenotypes have been established in several species, but equine CNV studies have been limited. Aim of this study was to identify CNVs and to perform a genome-wide association (GWA) study in Friesian horses to identify genomic loci associated with insect bite hypersensitivity (IBH), a common seasonal allergic dermatitis observed in many horse breeds worldwide. Results Genotypes were obtained using the Axiom® Equine Genotyping Array containing 670,796 SNPs. After quality control of genotypes, 15,041 CNVs and 5350 CNV regions (CNVRs) were identified in 222 Friesian horses. Coverage of the total genome by CNVRs was 11.2% with 49.2% of CNVRs containing genes. 58.0% of CNVRs were novel (i.e. so far only identified in Friesian horses). A SNP- and CNV-based GWA analysis was performed, where about half of the horses were affected by IBH. The SNP-based analysis showed a highly significant association between the MHC region on ECA20 and IBH in Friesian horses. Associations between the MHC region on ECA20 and IBH were also detected based on the CNV-based analysis. However, CNVs associated with IBH in Friesian horses were not often in close proximity to SNPs identified to be associated with IBH. Conclusions CNVs were identified in a large sample of the Friesian horse population, thereby contributing to our knowledge on CNVs in horses and facilitating our understanding of the equine genome and its phenotypic expression. A clear association was identified between the MHC region on ECA20 and IBH in Friesian horses based on both SNP- and CNV-based GWA studies. These results imply that MHC contributes to IBH sensitivity in Friesian horses. Although subsequent analyses are needed for verification, nucleotide differences, as well as more complex structural variations like CNVs, seem to contribute to IBH sensitivity. IBH should be considered as a common disease with a complex genomic architecture. Electronic supplementary material The online version of this article (10.1186/s12863-018-0657-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anouk Schurink
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, the Netherlands.
| | - Vinicius H da Silva
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, the Netherlands.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 75007, Uppsala, Sweden.,Department of Animal Ecology, Netherlands Institute of Ecology, NIOO-KNAW, 6708, PB, Wageningen, the Netherlands
| | - Brandon D Velie
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 75007, Uppsala, Sweden
| | - Bert W Dibbits
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, the Netherlands
| | - Richard P M A Crooijmans
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, the Netherlands
| | - Liesbeth Franҫois
- KU Leuven, Department of Biosystems, Livestock Genetics, P.O. Box 2456, 3001, Heverlee, Belgium
| | - Steven Janssens
- KU Leuven, Department of Biosystems, Livestock Genetics, P.O. Box 2456, 3001, Heverlee, Belgium
| | - Anneleen Stinckens
- KU Leuven, Department of Biosystems, Livestock Genetics, P.O. Box 2456, 3001, Heverlee, Belgium
| | - Sarah Blott
- Reproductive Biology, Faculty of Medicine and Health Sciences, The University of Nottingham, Leicestershire, LE12 5RD, UK
| | - Nadine Buys
- KU Leuven, Department of Biosystems, Livestock Genetics, P.O. Box 2456, 3001, Heverlee, Belgium
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 75007, Uppsala, Sweden
| | - Bart J Ducro
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, the Netherlands
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Alkhilaiwi F, Wang L, Zhou D, Raudsepp T, Ghosh S, Paul S, Palechor-Ceron N, Brandt S, Luff J, Liu X, Schlegel R, Yuan H. Long-term expansion of primary equine keratinocytes that maintain the ability to differentiate into stratified epidermis. Stem Cell Res Ther 2018; 9:181. [PMID: 29973296 PMCID: PMC6032561 DOI: 10.1186/s13287-018-0918-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/25/2018] [Accepted: 06/04/2018] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Skin injuries in horses frequently lead to chronic wounds that lack a keratinocyte cover essential for healing. The limited proliferation of equine keratinocytes using current protocols has limited their use for regenerative medicine. Previously, equine induced pluripotent stem cells (eiPSCs) have been produced, and eiPSCs could be differentiated into equine keratinocytes suitable for stem cell-based skin constructs. However, the procedure is technically challenging and time-consuming. The present study was designed to evaluate whether conditional reprogramming (CR) could expand primary equine keratinocytes rapidly in an undifferentiated state but retain their ability to differentiate normally and form stratified epithelium. METHODS Conditional reprogramming was used to isolate and propagate two equine keratinocyte cultures. PCR and FISH were employed to evaluate the equine origin of the cells and karyotyping to perform a chromosomal count. FACS analysis and immunofluorescence were used to determine the purity of equine keratinocytes and their proliferative state. Three-dimensional air-liquid interphase method was used to test the ability of cells to differentiate and form stratified squamous epithelium. RESULTS Conditional reprogramming was an efficient method to isolate and propagate two equine keratinocyte cultures. Cells were propagated at the rate of 2.39 days/doubling for more than 40 population doublings. A feeder-free culture method was also developed for long-term expansion. Rock-inhibitor is critical for both feeder and feeder-free conditions and for maintaining the proliferating cells in a stem-like state. PCR and FISH validated equine-specific markers in the cultures. Karyotyping showed normal equine 64, XY chromosomes. FACS using pan-cytokeratin antibodies showed a pure population of keratinocytes. When ROCK inhibitor was withdrawn and the cells were transferred to a three-dimensional air-liquid culture, they formed a well-differentiated stratified squamous epithelium, which was positive for terminal differentiation markers. CONCLUSIONS Our results prove that conditional reprogramming is the first method that allows for the rapid and continued in vitro propagation of primary equine keratinocytes. These unlimited supplies of autologous cells could be used to generate transplants without the risk of immune rejection. This offers the opportunity for treating recalcitrant horse wounds using autologous transplantation.
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Affiliation(s)
- Faris Alkhilaiwi
- Department of Pathology, Georgetown University Medical School, Washington, DC 20057 USA
- Department of Oncology, Georgetown University Medical School, Washington, DC 20057 USA
- Department of Biochemistry and Molecular Biology, Georgetown University Medical School, Washington, DC 20057 USA
- College of Pharmacy, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Liqing Wang
- Department of Pathology, Georgetown University Medical School, Washington, DC 20057 USA
| | - Dan Zhou
- Department of Pathology, Georgetown University Medical School, Washington, DC 20057 USA
| | - Terje Raudsepp
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX USA
| | - Sharmila Ghosh
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX USA
| | - Siddartha Paul
- Department of Pathology, Georgetown University Medical School, Washington, DC 20057 USA
| | - Nancy Palechor-Ceron
- Department of Pathology, Georgetown University Medical School, Washington, DC 20057 USA
| | - Sabine Brandt
- Equine Clinic, VetOMICs Core Facility, Veterinary University Vienna, Vienna, Austria
| | - Jennifer Luff
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC USA
| | - Xuefeng Liu
- Department of Pathology, Georgetown University Medical School, Washington, DC 20057 USA
| | - Richard Schlegel
- Department of Pathology, Georgetown University Medical School, Washington, DC 20057 USA
| | - Hang Yuan
- Department of Pathology, Georgetown University Medical School, Washington, DC 20057 USA
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Bhanuprakash V, Chhotaray S, Pruthviraj DR, Rawat C, Karthikeyan A, Panigrahi M. Copy number variation in livestock: A mini review. Vet World 2018; 11:535-541. [PMID: 29805222 PMCID: PMC5960796 DOI: 10.14202/vetworld.2018.535-541] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 03/31/2018] [Indexed: 01/22/2023] Open
Abstract
Copy number variation (CNV) is a phenomenon in which sections of the genome, ranging from one kilo base pair (Kb) to several million base pairs (Mb), are repeated and the number of repeats vary between the individuals in a population. It is an important source of genetic variation in an individual which is now being utilized rather than single nucleotide polymorphisms (SNPs), as it covers the more genomic region. CNVs alter the gene expression and change the phenotype of an individual due to deletion and duplication of genes in the copy number variation regions (CNVRs). Earlier, researchers extensively utilized SNPs as the main source of genetic variation. But now, the focus is on identification of CNVs associated with complex traits. With the recent advances and reduction in the cost of sequencing, arrays are developed for genotyping which cover the maximum number of SNPs at a time that can be used for detection of CNVRs and underlying quantitative trait loci (QTL) for the complex traits to accelerate genetic improvement. CNV studies are also being carried out to understand the evolutionary mechanism in the domestication of livestock and their adaptation to the different environmental conditions. The main aim of the study is to review the available data on CNV and its role in genetic variation among the livestock.
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Affiliation(s)
- V Bhanuprakash
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly - 243122, Uttar Pradesh, India
| | - Supriya Chhotaray
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly - 243122, Uttar Pradesh, India
| | - D R Pruthviraj
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly - 243122, Uttar Pradesh, India
| | - Chandrakanta Rawat
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly - 243122, Uttar Pradesh, India
| | - A Karthikeyan
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly - 243122, Uttar Pradesh, India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly - 243122, Uttar Pradesh, India
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Karimi K, Esmailizadeh A, Wu DD, Gondro C. Mapping of genome-wide copy number variations in the Iranian indigenous cattle using a dense SNP data set. ANIMAL PRODUCTION SCIENCE 2018. [DOI: 10.1071/an16384] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The objective of this study was to present the first map of the copy number variations (CNVs) in Iranian indigenous cattle based on a high-density single nucleotide polymorphism (SNP) dataset. A total of 90 individuals were genotyped using the Illumina BovineHD BeadChip containing 777 962 SNPs. The QuantiSNP algorithm was used to perform a genome-wide CNV detection across autosomal genome. After merging the overlapping CNV, a total of 221 CNV regions were identified encompassing 36.4 Mb or 1.44% of the bovine autosomal genome. The length of the CNV regions ranged from 3.5 to 2252.8 Kb with an average of 163.8 Kb. These regions included 147 loss (66.52%) and 74 gain (33.48%) events containing a total of 637 annotated Ensembl genes. Gene ontology analysis revealed that most of genes in the CNV regions were involved in environmental responses, disease susceptibility and immune system functions. Furthermore, 543 of these genes corresponded to the human orthologous genes, which involved in a wide range of biological functions. Altogether, 73% of the 221 CNV regions overlapped either completely or partially with those previously reported in other cattle studies. Moreover, novel CNV regions involved several quantitative trait loci (QTL)-related to adaptative traits of Iranian indigenous cattle. These results provided a basis to conduct future studies on association between CNV regions and phenotypic variations in the Iranian indigenous cattle.
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40
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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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Letaief R, Rebours E, Grohs C, Meersseman C, Fritz S, Trouilh L, Esquerré D, Barbieri J, Klopp C, Philippe R, Blanquet V, Boichard D, Rocha D, Boussaha M. Identification of copy number variation in French dairy and beef breeds using next-generation sequencing. Genet Sel Evol 2017; 49:77. [PMID: 29065859 PMCID: PMC5655909 DOI: 10.1186/s12711-017-0352-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 10/17/2017] [Indexed: 11/15/2022] Open
Abstract
Background Copy number variations (CNV) are known to play a major role in genetic variability and disease pathogenesis in several species including cattle. In this study, we report the identification and characterization of CNV in eight French beef and dairy breeds using whole-genome sequence data from 200 animals. Bioinformatics analyses to search for CNV were carried out using four different but complementary tools and we validated a subset of the CNV by both in silico and experimental approaches.
Results We report the identification and localization of 4178 putative deletion-only, duplication-only and CNV regions, which cover 6% of the bovine autosomal genome; they were validated by two in silico approaches and/or experimentally validated using array-based comparative genomic hybridization and single nucleotide polymorphism genotyping arrays. The size of these variants ranged from 334 bp to 7.7 Mb, with an average size of ~ 54 kb. Of these 4178 variants, 3940 were deletions, 67 were duplications and 171 corresponded to both deletions and duplications, which were defined as potential CNV regions. Gene content analysis revealed that, among these variants, 1100 deletions and duplications encompassed 1803 known genes, which affect a wide spectrum of molecular functions, and 1095 overlapped with known QTL regions. Conclusions Our study is a large-scale survey of CNV in eight French dairy and beef breeds. These CNV will be useful to study the link between genetic variability and economically important traits, and to improve our knowledge on the genomic architecture of cattle. Electronic supplementary material The online version of this article (doi:10.1186/s12711-017-0352-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rabia Letaief
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78352, Jouy-en-Josas, France.
| | - Emmanuelle Rebours
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78352, Jouy-en-Josas, France
| | - Cécile Grohs
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78352, Jouy-en-Josas, France
| | - Cédric Meersseman
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78352, Jouy-en-Josas, France.,GMA, INRA, Université de Limoges, UMR1061, Unité Génétique Moléculaire Animale, 123 avenue Albert Thomas, 87060, Limoges Cedex, France
| | - Sébastien Fritz
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78352, Jouy-en-Josas, France.,Allice, Maison Nationale des Eleveurs, 75012, Paris, France
| | - Lidwine Trouilh
- LISBP, CNRS, INRA, INSA, Université de Toulouse, Toulouse, France
| | - Diane Esquerré
- GenPhySE, INRA, Université de Toulouse INPT ENSAT, Université de Toulouse INPT ENVT, 52627, Castanet-Tolosan, France
| | - Johanna Barbieri
- GenPhySE, INRA, Université de Toulouse INPT ENSAT, Université de Toulouse INPT ENVT, 52627, Castanet-Tolosan, France
| | | | - Romain Philippe
- GMA, INRA, Université de Limoges, UMR1061, Unité Génétique Moléculaire Animale, 123 avenue Albert Thomas, 87060, Limoges Cedex, France
| | - Véronique Blanquet
- GMA, INRA, Université de Limoges, UMR1061, Unité Génétique Moléculaire Animale, 123 avenue Albert Thomas, 87060, Limoges Cedex, France
| | - Didier Boichard
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78352, Jouy-en-Josas, France
| | - Dominique Rocha
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78352, Jouy-en-Josas, France
| | - Mekki Boussaha
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78352, Jouy-en-Josas, France
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Pawlina-Tyszko K, Gurgul A, Szmatoła T, Ropka-Molik K, Semik-Gurgul E, Klukowska-Rötzler J, Koch C, Mählmann K, Bugno-Poniewierska M. Genomic landscape of copy number variation and copy neutral loss of heterozygosity events in equine sarcoids reveals increased instability of the sarcoid genome. Biochimie 2017; 140:122-132. [PMID: 28743673 DOI: 10.1016/j.biochi.2017.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/20/2017] [Indexed: 12/20/2022]
Abstract
Although they are the most common neoplasms in equids, sarcoids are not fully characterized at the molecular level. Therefore, the objective of this study was to characterize the landscape of structural rearrangements, such as copy number variation (CNV) and copy neutral loss of heterozygosity (cnLOH), in the genomes of sarcoid tumor cells. This information will not only broaden our understanding of the characteristics of this genome but will also improve the general knowledge of this tumor and the mechanisms involved in its generation. To this end, Equine SNP64K Illumina microarrays were applied along with bioinformatics tools dedicated for signal intensity analysis. The analysis revealed increased instability of the genome of sarcoid cells compared with unaltered skin tissue samples, which was manifested by the prevalence of CNV and cnLOH events. Many of the identified CNVs overlapped with the other research results, but the simultaneously observed variability in the number and sizes of detected aberrations indicated a need for further studies and the development of more reliable bioinformatics algorithms. The functional analysis of genes co-localized with the identified aberrations revealed that these genes are engaged in vital cellular processes. In addition, a number of these genes directly contribute to neoplastic transformation. Furthermore, large numbers of cnLOH events identified in the sarcoids suggested that they may play no less significant roles than CNVs in the carcinogenesis of this tumor. Thus, our results indicate the importance of cnLOH and CNV in equine sarcoid oncogenesis and present a direction of future research.
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Affiliation(s)
- Klaudia Pawlina-Tyszko
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - Artur Gurgul
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - Tomasz Szmatoła
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - Katarzyna Ropka-Molik
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - Ewelina Semik-Gurgul
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - Jolanta Klukowska-Rötzler
- Division of Pedriatric Hematology/Oncology, Department of Clinical Research, University of Bern, Murtenstrasse 35, 3008, Bern, Switzerland; Department of Emergency Medicine, University Hospital Bern, Inselspital, 3010, Bern, Switzerland.
| | - Christoph Koch
- Swiss Institute of Equine Medicine ISME, Faculty of Veterinary Medicine, University of Bern and Agroscope, Länggassstrasse 124c, Postfach 8466, CH-3001, Bern, Switzerland.
| | - Kathrin Mählmann
- Swiss Institute of Equine Medicine ISME, Faculty of Veterinary Medicine, University of Bern and Agroscope, Länggassstrasse 124c, Postfach 8466, CH-3001, Bern, Switzerland; Equine Clinic: Surgery and Radiology, Department of Veterinary Medicine, Free University of Berlin, Oertzenweg 19b, 14163, Berlin, Germany.
| | - Monika Bugno-Poniewierska
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
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Ricard A, Robert C, Blouin C, Baste F, Torquet G, Morgenthaler C, Rivière J, Mach N, Mata X, Schibler L, Barrey E. Endurance Exercise Ability in the Horse: A Trait with Complex Polygenic Determinism. Front Genet 2017; 8:89. [PMID: 28702049 PMCID: PMC5488500 DOI: 10.3389/fgene.2017.00089] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 06/09/2017] [Indexed: 12/17/2022] Open
Abstract
Endurance horses are able to run at more than 20 km/h for 160 km (in bouts of 30-40 km). This level of performance is based on intense aerobic metabolism, effective body heat dissipation and the ability to endure painful exercise. The known heritabilities of endurance performance and exercise-related physiological traits in Arabian horses suggest that adaptation to extreme endurance exercise is influenced by genetic factors. The objective of the present genome-wide association study (GWAS) was to identify single nucleotide polymorphisms (SNPs) related to endurance racing performance in 597 Arabian horses. The performance traits studied were the total race distance, average race speed and finishing status (qualified, eliminated or retired). We used three mixed models that included a fixed allele or genotype effect and a random, polygenic effect. Quantile-quantile plots were acceptable, and the regression coefficients for actual vs. expected log10p-values ranged from 0.865 to 1.055. The GWAS revealed five significant quantitative trait loci (QTL) corresponding to 6 SNPs on chromosomes 6, 1, 7, 16, and 29 (two SNPs) with corrected p-values from 1.7 × 10-6 to 1.8 × 10-5. Annotation of these 5 QTL revealed two genes: sortilin-related VPS10-domain-containing receptor 3 (SORCS3) on chromosome 1 is involved in protein trafficking, and solute carrier family 39 member 12 (SLC39A12) on chromosome 29 is active in zinc transport and cell homeostasis. These two coding genes could be involved in neuronal tissues (CNS). The other QTL on chromosomes 6, 7, and 16 may be involved in the regulation of the gene expression through non-coding RNAs, CpG islands and transcription factor binding sites. On chromosome 6, a new candidate equine long non-coding RNA (KCNQ1OT1 ortholog: opposite antisense transcript 1 of potassium voltage-gated channel subfamily Q member 1 gene) was predicted in silico and validated by RT-qPCR in primary cultures of equine myoblasts and fibroblasts. This lncRNA could be one element of the cardiac rhythm regulation. Our GWAS revealed that equine performance during endurance races is a complex polygenic trait, and is partially governed by at least 5 QTL: two coding genes involved in neuronal tissues and three other loci with many regulatory functions such as slowing down heart rate.
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Affiliation(s)
- Anne Ricard
- Institut National de la Recherche Agronomique, AgroParisTech, Université Paris Saclay, Département Sciences du Vivant, UMR 1313 Génétique Animale et Biologie IntégrativeJouy-en-Josas, France
- Institut Français du Cheval et de l'Equitation, Département Recherche et InnovationExmes, France
| | - Céline Robert
- Institut National de la Recherche Agronomique, AgroParisTech, Université Paris Saclay, Département Sciences du Vivant, UMR 1313 Génétique Animale et Biologie IntégrativeJouy-en-Josas, France
- Ecole Nationale Vétérinaire d'AlfortMaisons Alfort, France
| | - Christine Blouin
- Institut National de la Recherche Agronomique, AgroParisTech, Université Paris Saclay, Département Sciences du Vivant, UMR 1313 Génétique Animale et Biologie IntégrativeJouy-en-Josas, France
| | - Fanny Baste
- Institut National de la Recherche Agronomique, AgroParisTech, Université Paris Saclay, Département Sciences du Vivant, UMR 1313 Génétique Animale et Biologie IntégrativeJouy-en-Josas, France
| | - Gwendoline Torquet
- Institut National de la Recherche Agronomique, AgroParisTech, Université Paris Saclay, Département Sciences du Vivant, UMR 1313 Génétique Animale et Biologie IntégrativeJouy-en-Josas, France
| | - Caroline Morgenthaler
- Institut National de la Recherche Agronomique, AgroParisTech, Université Paris Saclay, Département Sciences du Vivant, UMR 1313 Génétique Animale et Biologie IntégrativeJouy-en-Josas, France
| | - Julie Rivière
- Institut National de la Recherche Agronomique, AgroParisTech, Université Paris Saclay, Département Sciences du Vivant, UMR 1313 Génétique Animale et Biologie IntégrativeJouy-en-Josas, France
| | - Nuria Mach
- Institut National de la Recherche Agronomique, AgroParisTech, Université Paris Saclay, Département Sciences du Vivant, UMR 1313 Génétique Animale et Biologie IntégrativeJouy-en-Josas, France
| | - Xavier Mata
- Institut National de la Recherche Agronomique, AgroParisTech, Université Paris Saclay, Département Sciences du Vivant, UMR 1313 Génétique Animale et Biologie IntégrativeJouy-en-Josas, France
| | - Laurent Schibler
- Institut National de la Recherche Agronomique, AgroParisTech, Université Paris Saclay, Département Sciences du Vivant, UMR 1313 Génétique Animale et Biologie IntégrativeJouy-en-Josas, France
| | - Eric Barrey
- Institut National de la Recherche Agronomique, AgroParisTech, Université Paris Saclay, Département Sciences du Vivant, UMR 1313 Génétique Animale et Biologie IntégrativeJouy-en-Josas, France
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Li BJ, Li HL, Meng Z, Zhang Y, Lin H, Yue GH, Xia JH. Copy Number Variations in Tilapia Genomes. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:11-21. [PMID: 28168542 DOI: 10.1007/s10126-017-9733-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/23/2016] [Indexed: 06/06/2023]
Abstract
Discovering the nature and pattern of genome variation is fundamental in understanding phenotypic diversity among populations. Although several millions of single nucleotide polymorphisms (SNPs) have been discovered in tilapia, the genome-wide characterization of larger structural variants, such as copy number variation (CNV) regions has not been carried out yet. We conducted a genome-wide scan for CNVs in 47 individuals from three tilapia populations. Based on 254 Gb of high-quality paired-end sequencing reads, we identified 4642 distinct high-confidence CNVs. These CNVs account for 1.9% (12.411 Mb) of the used Nile tilapia reference genome. A total of 1100 predicted CNVs were found overlapping with exon regions of protein genes. Further association analysis based on linear model regression found 85 CNVs ranging between 300 and 27,000 base pairs significantly associated to population types (R 2 > 0.9 and P > 0.001). Our study sheds first insights on genome-wide CNVs in tilapia. These CNVs among and within tilapia populations may have functional effects on phenotypes and specific adaptation to particular environments.
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Affiliation(s)
- Bi Jun Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Hong Lian Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zining Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yong Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Haoran Lin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Gen Hua Yue
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| | - Jun Hong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
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45
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Abstract
The association between chromosomal abnormalities and reduced fertility in domestic animals is well recorded and has been studied for decades. Chromosome aberrations directly affect meiosis, gametogenesis, and the viability of zygotes and embryos. In some instances, balanced structural rearrangements can be transmitted, causing fertility problems in subsequent generations. Here, we aim to give a comprehensive overview of the current status and future prospects of clinical cytogenetics of animal reproduction by focusing on the advances in molecular cytogenetics during the genomics era. We describe how advancing knowledge about animal genomes has improved our understanding of connections between gross structural or molecular chromosome variations and reproductive disorders. Further, we expand on a key area of reproduction genetics: cytogenetics of animal gametes and embryos. Finally, we describe how traditional cytogenetics is interfacing with advanced genomics approaches, such as array technologies and next-generation sequencing, and speculate about the future prospects.
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Affiliation(s)
- Terje Raudsepp
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-4458;
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46
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Duplication of chicken defensin7 gene generated by gene conversion and homologous recombination. Proc Natl Acad Sci U S A 2016; 113:13815-13820. [PMID: 27849592 DOI: 10.1073/pnas.1616948113] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Defensins constitute an evolutionary conserved family of cationic antimicrobial peptides that play a key role in host innate immune responses to infection. Defensin genes generally reside in complex genomic regions that are prone to structural variation, and defensin genes exhibit extensive copy number variation in humans and in other species. Copy number variation of defensin genes was examined in inbred lines of Leghorn and Fayoumi chickens, and a duplication of defensin7 was discovered in the Fayoumi breed. Analysis of junction sequences confirmed the occurrence of a simple tandem duplication of defensin7 with sequence identity at the junction, suggesting nonallelic homologous recombination between defensin7 and defensin6 The duplication event generated two chimeric promoters that are best explained by gene conversion followed by homologous recombination. Expression of defensin7 was not elevated in animals with two genes despite both genes being transcribed in the tissues examined. Computational prediction of promoter regions revealed the presence of several putative transcription factor binding sites generated by the duplication event. These data provide insight into the evolution and possible function of large gene families and specifically, the defensins.
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47
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Steenwyk JL, Soghigian JS, Perfect JR, Gibbons JG. Copy number variation contributes to cryptic genetic variation in outbreak lineages of Cryptococcus gattii from the North American Pacific Northwest. BMC Genomics 2016; 17:700. [PMID: 27590805 PMCID: PMC5009542 DOI: 10.1186/s12864-016-3044-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 08/24/2016] [Indexed: 12/13/2022] Open
Abstract
Background Copy number variants (CNVs) are a class of structural variants (SVs) and are defined as fragments of DNA that are present at variable copy number in comparison with a reference genome. Recent advances in bioinformatics methodologies and sequencing technologies have enabled the high-resolution quantification of genome-wide CNVs. In pathogenic fungi SVs have been shown to alter gene expression, influence host specificity, and drive fungicide resistance, but little attention has focused specifically on CNVs. Using publicly available sequencing data, we identified 90 isolates across 212 Cryptococcus gattii genomes that belong to the VGII subgroups responsible for the recent deadly outbreaks in the North American Pacific Northwest. We generated CNV profiles for each sample to investigate the prevalence and function of CNV in C. gattii. Results We identified eight genetic clusters among publicly available Illumina whole genome sequence data from 212 C. gattii isolates through population structure analysis. Three clusters represent the VGIIa, VGIIb, and VGIIc subgroups from the North American Pacific Northwest. CNV was bioinformatically predicted and affected ~300–400 Kilobases (Kb) of the C. gattii VGII subgroup genomes. Sixty-seven loci, encompassing 58 genes, showed highly divergent patterns of copy number variation between VGII subgroups. Analysis of PFam domains within divergent CN variable genes revealed enrichment of protein domains associated with transport, cell wall organization and external encapsulating structure. Conclusions CNVs may contribute to pathological and phenotypic differences observed between the C. gattii VGIIa, VGIIb, and VGIIc subpopulations. Genes overlapping with population differentiated CNVs were enriched for several virulence related functional terms. These results uncover novel candidate genes to examine the genetic and functional underpinnings of C. gattii pathogenicity. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3044-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jacob L Steenwyk
- Biology Department, Clark University, 950 Main Street, Worcester, MA, USA.,Current address: Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - John S Soghigian
- Biology Department, Clark University, 950 Main Street, Worcester, MA, USA.,Current address: Department of Environmental Sciences, The Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | - John R Perfect
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - John G Gibbons
- Biology Department, Clark University, 950 Main Street, Worcester, MA, USA.
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48
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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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49
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Zhang X, Wang K, Wang L, Yang Y, Ni Z, Xie X, Shao X, Han J, Wan D, Qiu Q. Genome-wide patterns of copy number variation in the Chinese yak genome. BMC Genomics 2016; 17:379. [PMID: 27206476 PMCID: PMC4875690 DOI: 10.1186/s12864-016-2702-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 05/06/2016] [Indexed: 12/02/2022] Open
Abstract
Background Copy number variation (CNV) represents an important source of genetic divergence that can produce drastic phenotypic differences and may therefore be subject to selection during domestication and environmental adaptation. To investigate the evolutionary dynamics of CNV in the yak genome, we used a read depth approach to detect CNV based on genome resequencing data from 14 wild and 65 domestic yaks and determined CNV regions related to domestication and adaptations to high-altitude. Results We identified 2,634 CNV regions (CNVRs) comprising a total of 153 megabases (5.7 % of the yak genome) and 3,879 overlapping annotated genes. Comparison between domestic and wild yak populations identified 121 potentially selected CNVRs, harboring genes related to neuronal development, reproduction, nutrition and energy metabolism. In addition, we found 85 CNVRs that are significantly different between domestic yak living in high- and low-altitude areas, including three genes related to hypoxia response and six related to immune defense. This analysis shows that genic CNVs may play an important role in phenotypic changes during yak domestication and adaptation to life at high-altitude. Conclusions We present the first refined CNV map for yak along with comprehensive genomic analysis of yak CNV. Our results provide new insights into the genetic basis of yak domestication and adaptation to living in a high-altitude environment, as well as a valuable genetic resource that will facilitate future CNV association studies of important traits in yak and other bovid species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2702-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiao Zhang
- State Key Laboratory of Grassland Agroecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Kun Wang
- State Key Laboratory of Grassland Agroecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Lizhong Wang
- State Key Laboratory of Grassland Agroecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agroecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Zhengqiang Ni
- State Key Laboratory of Grassland Agroecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Xiuyue Xie
- State Key Laboratory of Grassland Agroecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Xuemin Shao
- State Key Laboratory of Grassland Agroecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Jin Han
- State Key Laboratory of Grassland Agroecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Dongshi Wan
- State Key Laboratory of Grassland Agroecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China.
| | - Qiang Qiu
- State Key Laboratory of Grassland Agroecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China.
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50
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Ghosh S, Das PJ, McQueen CM, Gerber V, Swiderski CE, Lavoie JP, Chowdhary BP, Raudsepp T. Analysis of genomic copy number variation in equine recurrent airway obstruction (heaves). Anim Genet 2016; 47:334-44. [PMID: 26932307 DOI: 10.1111/age.12426] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2016] [Indexed: 12/18/2022]
Abstract
We explored the involvement of genomic copy number variants (CNVs) in susceptibility to recurrent airway obstruction (RAO), or heaves-an asthmalike inflammatory disease in horses. Analysis of 16 RAO-susceptible (cases) and six RAO-resistant (control) horses on a custom-made whole-genome 400K equine tiling array identified 245 CNV regions (CNVRs), 197 previously known and 48 new, distributed on all horse autosomes and the X chromosome. Among the new CNVRs, 30 were exclusively found in RAO cases and were further analyzed by quantitative PCR, including additional cases and controls. Suggestive association (P = 0.03; corrected P = 0.06) was found between RAO and a loss on chromosome 5 involving NME7, a gene necessary for ciliary functions in lungs and involved in primary ciliary dyskinesia in humans. The CNVR could be a potential marker for RAO susceptibility but needs further study in additional RAO cohorts. Other CNVRs were not associated with RAO, although several involved genes of interest, such as SPI2/SERPINA1 from the serpin gene family, which are associated with chronic obstructive pulmonary disease and asthma in humans. The SPI2/SERPINA1 CNVR showed striking variation among horses, but it was not significantly different between RAO cases and controls. The findings provide baseline information on the relationship between CNVs and RAO susceptibility. Discovery of new CNVs and the use of a larger population of RAO-affected and control horses are needed to shed more light on their significance in modulating this complex and heterogeneous disease.
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Affiliation(s)
- S Ghosh
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA
| | - P J Das
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA.,National Research Centre on Yak (ICAR), Dirang, Arunachal Pradesh, 790101, India
| | - C M McQueen
- Department of Large Animal Clinical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - V Gerber
- Department of Veterinary Medicine, University of Bern, Bern, Switzerland
| | - C E Swiderski
- Department of Clinical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - J-P Lavoie
- Department of Clinical Sciences, University of Montreal, Montreal, QC, J2S 7C6, Canada
| | - B P Chowdhary
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA.,New Research Complex, Qatar University, Doha, 2713, Qatar
| | - T Raudsepp
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA
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