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Arefnejad B, Zeinalabedini M, Talebi R, Mardi M, Ghaffari MR, Vahidi MF, Nekouei MK, Szmatoła T, Salekdeh GH. Unveiling the population genetic structure of Iranian horses breeds by whole-genome resequencing analysis. Mamm Genome 2024; 35:201-227. [PMID: 38520527 DOI: 10.1007/s00335-024-10035-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 02/14/2024] [Indexed: 03/25/2024]
Abstract
Preserving genetic diversity is pivotal for enhancing genetic improvement and facilitating adaptive responses to selection. This study focuses on identifying key genetic variants, including single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (INDELs), and copy number variants (CNVs), while exploring the genomic evolutionary connectedness among seven Iranian horses representing five indigenous breeds: Caspian, Turkemen, DareShuri, Kurdish, and Asil. Using whole-genome resequencing, we generated 2.7 Gb of sequence data, with raw reads ranging from 1.2 Gb for Caspian horses to 0.38 Gb for Turkoman horses. Post-filtering, approximately 1.9 Gb of reads remained, with ~ 1.5 Gb successfully mapped to the horse reference genome (EquCab3.0), achieving mapping rates between 76.4% (Caspian) and 98.35% (Turkoman). We identified 2,909,816 SNPs in Caspian horses, constituting around 0.1% of the genome. Notably, 71% of these SNPs were situated in intergenic regions, while 8.5 and 6.8% were located upstream and downstream, respectively. A comparative analysis of SNPs between Iranian and non-Iranian horse breeds showed that Caspian horses had the lowest number of shared SNPs with Turkoman horses. Instead, they showed a closer genetic relationship with DareShuri, Quarter, Arabian, Standardbred, and Asil breeds. Hierarchical clustering highlighted Caspian horses as a distinct cluster, underscoring their distinctive genomic signature. Caspian horses exhibit a unique genetic profile marked by an enrichment of private mutations in neurological genes, influencing sensory perception and awareness. This distinct genetic makeup shapes mating preferences and signifies a separate evolutionary trajectory. Additionally, significant non-synonymous single nucleotide polymorphisms (nsSNPs) in reproductive genes offer intervention opportunities for managing Caspian horses. These findings reveal the population genetic structure of Iranian horse breeds, contributing to the advancement of knowledge in areas such as conservation, performance traits, climate adaptation, reproduction, and resistance to diseases in equine science.
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Affiliation(s)
- Babak Arefnejad
- Department of Animal Science, University of Tehran, Karaj, Iran
| | - Mehrshad Zeinalabedini
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
| | - Reza Talebi
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Mohsen Mardi
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Mohammad Reza Ghaffari
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Mohammad Farhad Vahidi
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | | | - Tomasz Szmatoła
- Centre of Experimental and Innovative Medicine, University of Agriculture in Kraków, Al. Mickiewicza 24/28, 30-059, Kraków, Poland
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32‑083, Balice, Poland
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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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Tong H, Shao G, Wang L, Li J, Wang T, Zhang L, Lv Y, Ye F, Fu C, Jin Y. Association of a single amino acid replacement with dorsal pigmentation in a lizard from the Qinghai-Tibetan Plateau. Int J Biol Macromol 2023; 242:124907. [PMID: 37230451 DOI: 10.1016/j.ijbiomac.2023.124907] [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: 02/15/2023] [Revised: 05/08/2023] [Accepted: 05/13/2023] [Indexed: 05/27/2023]
Abstract
Reptiles can evolve adaptive colors in different environments, but relatively little is known about the genetic mechanisms. Here, we identified the MC1R gene and its association with intraspecific color variation in the lizard Phrynocephalus erythrurus. Analysis of the MC1R sequence in 143 individuals from dark South Qiangtang Plateau (SQP) and light North Qiangtang plateau (NQP) populations, revealed two amino acid sites that showed significant differences in frequency between two areas. One SNP, corresponding to Glu183Lys residue, was found to be a highly significant outlier and differentially fixed for SQP and NQP populations. This residue is located in an extracellular area in the second small extracellular loop within the secondary structure of MC1R, which represents an "attachment pocket" part of the 3D structure. Cytological expression of MC1R alleles with the Glu183Lys replacement showed a 39 % increase in intracellular agonist-induced cyclic AMP levels and a 23.18 % greater cell surface expression of MC1R protein in the SQP relative to the NQP allele. Further in silico 3D modeling and in vitro binding experiments indicated a higher MC1R-α-MSH binding for the SQP allele, and elevated melanin synthesis. We provide an overview of how a single amino acid replacement leads to fundamental changes in MC1R function, and hence shapes variation in dorsal pigmentation in lizards from different environments.
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Affiliation(s)
- Haojie Tong
- College of Life Sciences, China Jiliang University, Hangzhou 310018, PR China
| | - Gang Shao
- College of Life Sciences, China Jiliang University, Hangzhou 310018, PR China
| | - Leijie Wang
- College of Life Sciences, China Jiliang University, Hangzhou 310018, PR China
| | - Jiasheng Li
- College of Life Sciences, China Jiliang University, Hangzhou 310018, PR China
| | - Tao Wang
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Lun Zhang
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Yudie Lv
- College of Life Sciences, China Jiliang University, Hangzhou 310018, PR China
| | - Fei Ye
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Caiyun Fu
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Yuanting Jin
- College of Life Sciences, China Jiliang University, Hangzhou 310018, PR China.
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White-Springer SH, Bruemmer J, Coleman RJ. The Past, Present, and Future of Equine Science. J Equine Vet Sci 2023; 124:104297. [PMID: 37236727 DOI: 10.1016/j.jevs.2023.104297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/23/2023] [Indexed: 05/28/2023]
Abstract
A core group of 27 equine nutritionists and physiologists joined together in the late 1960s to formally address and enhance the direction of equine research, creating the Equine Nutrition and Physiology Society. In 2003, that growing society transformed into the Equine Science Society, which now serves as the preeminent, internationally recognized scientific equine organization. In recent years, it has been appreciated that equine science encompasses a wide range of focus areas, including exercise science, nutrition, genetics, reproductive physiology, teaching and extension, production and management, and mix of other specialties, qualified as biosciences. Additionally, trainees are highly valued in the society, with the clear understanding that young people are the future of equine science. Amongst tightening budgets, equine researchers must focus on timely dissemination of high-quality research studies and development of strong, interdisciplinary, cross-species, and multi-institutional collaborations to ensure sustainability of academic research programs. With a little creativity, equine science will continue to thrive for the betterment of the horse and all involved in the equine industry.
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Affiliation(s)
- Sarah H White-Springer
- Department of Animal Science, Texas A&M University and Texas A&M AgriLife Research, College Station, TX.
| | - Jason Bruemmer
- USDA-APHIS National Wildlife Research Center, Fort Collins, CO
| | - Robert J Coleman
- Department of Food and Animal Science, University of Kentucky, Lexington, KY
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5
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Arslan M. Whole-genome sequencing and genomic analysis of Norduz goat (Capra hircus). Mamm Genome 2023:10.1007/s00335-023-09990-3. [PMID: 37004528 DOI: 10.1007/s00335-023-09990-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/21/2023] [Indexed: 04/04/2023]
Abstract
Artificial and natural selective breeding of goats has resulted in many different goat breeds all around the world. Norduz goat is one of these breeds, and it is a local goat breed of Turkey. The goats are favorable due to pre-weaning viability and reproduction values compared to the regional breeds. Development in sequencing technologies has let to understand huge genomic structures and complex phenotypes. Until now, such a comprehensive study has not been carried out to understand the genomic structure of the Norduz goats, yet. In the study, the next-generation sequencing was carried out to understand the genomic structure of Norduz goat. Real-time PCR was used to evaluate prominent CNVs in the Norduz goat individuals. Whole genome of the goat was constructed with an average of 33.1X coverage level. In the stringent filtering condition, 9,757,980 SNPs, 1,536,715 InDels, and 290 CNVs were detected in the Norduz goat genome. Functional analysis of high-impact SNP variations showed that the classical complement activation biological process was affected significantly in the goat. CNVs in the goat genome were found in genes related to defense against viruses, immune response, and cell membrane transporters. It was shown that GBP2, GBP5, and mammalian ortholog GBP1, which are INF-stimulated GTPases, were found to be high copy numbers in the goats. To conclude, genetic variations mainly in immunological response processes suggest that Norduz goat is an immunologically improved goat breed and natural selection could take an important role in the genetical improvements of the goats.
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Affiliation(s)
- Mevlüt Arslan
- Department of Genetics, Faculty of Veterinary Medicine, Van Yüzüncü Yıl University, Tuşba, 65080, Van, Turkey.
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6
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Pan J, Purev C, Zhao H, Zhang Z, Wang F, Wendoule N, Qi G, Liu Y, Zhou H. Discovery of exercise-related genes and pathway analysis based on comparative genomes of Mongolian originated Abaga and Wushen horse. Open Life Sci 2022; 17:1269-1281. [PMID: 36249530 PMCID: PMC9518662 DOI: 10.1515/biol-2022-0487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/21/2022] [Accepted: 07/28/2022] [Indexed: 11/17/2022] Open
Abstract
The Mongolian horses have excellent endurance and stress resistance to adapt to the cold and harsh plateau conditions. Intraspecific genetic diversity is mainly embodied in various genetic advantages of different branches of the Mongolian horse. Since people pay progressive attention to the athletic performance of horse, we expect to guide the exercise-oriented breeding of horses through genomics research. We obtained the clean data of 630,535,376,400 bp through the entire genome second-generation sequencing for the whole blood of four Abaga horses and ten Wushen horses. Based on the data analysis of single nucleotide polymorphism, we severally detected that 479 and 943 positively selected genes, particularly exercise related, were mainly enriched on equine chromosome 4 in Abaga horses and Wushen horses, which implied that chromosome 4 may be associated with the evolution of the Mongolian horse and athletic performance. Four hundred and forty genes of positive selection were enriched in 12 exercise-related pathways and narrowed in 21 exercise-related genes in Abaga horse, which were distinguished from Wushen horse. So, we speculated that the Abaga horse may have oriented genes for the motorial mechanism and 21 exercise-related genes also provided a molecular genetic basis for exercise-directed breeding of the Mongolian horse.
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Affiliation(s)
- Jing Pan
- Faculty of Life Sciences, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, People’s Republic of China
- Department of Reproductive Medicine, Inner Mongolia Maternal and Child Health Care Hospitaly, Hohhot, Inner Mongolia Autonomous Region, People’s Republic of China
| | - Chimge Purev
- Mongolia-China Joint Laboratory of Applied Molecular Biology, “Administration of the Science Park” CSTI, Ulaanbaatar, Mongolia
| | - Hongwei Zhao
- Beijing 8omics Gene Technology Co. Ltd, Beijing, People’s Republic of China
| | - Zhipeng Zhang
- Faculty of Life Sciences, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, People’s Republic of China
| | - Feng Wang
- Faculty of Life Sciences, Nankai University, Tianjin, People’s Republic of China
| | - Nashun Wendoule
- Animal Husbandry Workstation of Ewenki Autonomous County, Hulun Buir, Inner Mongolia Autonomous Region, People’s Republic of China
| | - Guichun Qi
- Bayanta Village of Animal Husbandry and Veterinary Station of Ewenki Autonomous County, Hulun Buir, Inner Mongolia Autonomous Region, People’s Republic of China
| | - Yongbin Liu
- Sheep Collaboration and Innovation Center, Inner Mongolia Universityy, Hohhot, Inner Mongolia Autonomous Region, People’s Republic of China
| | - Huanmin Zhou
- Faculty of Life Sciences, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, People’s Republic of China
- Sheep Collaboration and Innovation Center, Inner Mongolia Universityy, Hohhot, Inner Mongolia Autonomous Region, People’s Republic of China
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Thieulent CJ, Carossino M, Balasuriya UBR, Graves K, Bailey E, Eberth J, Canisso IF, Andrews FM, Keowen ML, Go YY. Development of a TaqMan® Allelic Discrimination qPCR Assay for Rapid Detection of Equine CXCL16 Allelic Variants Associated With the Establishment of Long-Term Equine Arteritis Virus Carrier State in Stallions. Front Genet 2022; 13:871875. [PMID: 35495124 PMCID: PMC9043104 DOI: 10.3389/fgene.2022.871875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/23/2022] [Indexed: 12/02/2022] Open
Abstract
Equine arteritis virus (EAV) is the causative agent of equine viral arteritis (EVA), a respiratory, systemic, and reproductive disease of equids. Following natural infection, up to 70% of the infected stallions can remain persistently infected over 1 year (long-term persistent infection [LTPI]) and shed EAV in their semen. Thus, the LTP-infected stallions play a pivotal role in maintaining and perpetuating EAV in the equine population. Previous studies identified equine C-X-C motif chemokine ligand 16 (CXCL16) as a critical host cell factor determining LTPI in the stallion’s reproductive tract. Two alleles (CXCL16S and CXCL16r) were identified in the equine population and correlated with the susceptibility or resistance of a CD3+ T cell subpopulation in peripheral blood to in vitro EAV infection, respectively. Interestingly, CXCL16S has been linked to the establishment of LTPI in stallions, and thus, genotyping stallions based on CXCL16S/r would allow identification of those at the highest risk of establishing LTPI. Thus, we developed a TaqMan® allelic discrimination qPCR assay for the genotyping of the equine CXCL16 gene based on the identification of a single nucleotide polymorphism in position 1,073 based on NCBI gene ID: 100061442 (or position 527 based on Ensembl: ENSECAG00000018406.2) located in exon 2. One hundred and sixty horses from four breeds were screened for the CD3+ T cell susceptibility phenotype to EAV infection by flow cytometry and subsequently sequenced to determine CXCL16 allelic composition. Genotyping by Sanger sequencing determined that all horses with the resistant CD3+ T cell phenotype were homozygous for CXCL16r while horses with the susceptible CD3+ T cell phenotype carried at least one CXCL16S allele or homozygous for CXCL16S. In addition, genotypification with the TaqMan® allelic discrimination qPCR assay showed perfect agreement with Sanger sequencing and flow cytometric analysis. In conclusion, the new TaqMan® allelic discrimination genotyping qPCR assay can be used to screen prepubertal colts for the presence of the CXCL16 genotype. It is highly recommended that colts that carry the susceptible genotype (CXCL16 S/S or CXCL16S/r) are vaccinated against EAV after 6 months of age to prevent the establishment of LTPI carriers following possible natural infection with EAV.
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Affiliation(s)
- Come J. Thieulent
- Louisiana Animal Disease Diagnostic Laboratory and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, United States
| | - Mariano Carossino
- Louisiana Animal Disease Diagnostic Laboratory and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, United States
| | - Udeni B. R. Balasuriya
- Louisiana Animal Disease Diagnostic Laboratory and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, United States
| | - Kathryn Graves
- Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY, United States
| | - Ernest Bailey
- Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY, United States
| | - John Eberth
- Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY, United States
| | - Igor F. Canisso
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Frank M. Andrews
- Equine Health Studies Program, Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, United States
| | - Michael L. Keowen
- Equine Health Studies Program, Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, United States
| | - Yun Young Go
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine, City University of Hong Kong, Kowloon, Hong Kong SAR, China
- *Correspondence: Yun Young Go,
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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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Kharrati-Koopaee H, Ebrahimie E, Dadpasand M, Niazi A, Tian R, Esmailizadeh A. Gene network analysis to determine the effect of hypoxia-associated genes on brain damages and tumorigenesis using an avian model. J Genet Eng Biotechnol 2021; 19:100. [PMID: 34236536 PMCID: PMC8266987 DOI: 10.1186/s43141-021-00184-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/21/2021] [Indexed: 01/17/2023]
Abstract
BACKGROUND Hypoxia refers to the condition of low oxygen pressure in the atmosphere and characterization of response to hypoxia as a biological complex puzzle, is challenging. Previously, we carried out a comparative genomic study by whole genome resequencing of highland and lowland Iranian native chickens to identify genomic variants associated with hypoxia conditions. Based on our previous findings, we used chicken as a model and the identified hypoxia-associated genes were converted to human's orthologs genes to construct the informative gene network. The main goal of this study was to visualize the features of diseases due to hypoxia-associated genes by gene network analysis. RESULTS It was found that hypoxia-associated genes contained several gene networks of disorders such as Parkinson, Alzheimer, cardiomyopathy, drug toxicity, and cancers. We found that biological pathways are involved in mitochondrion dysfunctions including peroxynitrous acid production denoted in brain injuries. Lewy body and neuromelanin were reported as key symptoms in Parkinson disease. Furthermore, calmodulin, and amyloid precursor protein were detected as leader proteins in Alzheimer's diseases. Dexamethasone was reported as the candidate toxic drug under the hypoxia condition that implicates diabetes, osteoporosis, and neurotoxicity. Our results suggested DNA damages caused by the high doses of UV radiation in high-altitude conditions, were associated with breast cancer, ovarian cancer, and colorectal cancer. CONCLUSIONS Our results showed that hypoxia-associated genes were enriched in several gene networks of disorders including Parkinson, Alzheimer, cardiomyopathy, drug toxicity, and different types of cancers. Furthermore, we suggested, UV radiation and low oxygen conditions in high-altitude regions may be responsible for the variety of human diseases.
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Affiliation(s)
- Hamed Kharrati-Koopaee
- Institute of Biotechnology, Shiraz University, Shiraz, Iran.
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Esmaeil Ebrahimie
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
- Genomics Research Platform, School of Life Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Mohammad Dadpasand
- Department of Animal Science, School of Agriculture, Shiraz University, Shiraz, Iran.
| | - Ali Niazi
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
| | - Rugang Tian
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, 010031, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran.
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10
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Zhou R, Li ST, Yao WY, Xie CD, Chen Z, Zeng ZJ, Wang D, Xu K, Shen ZJ, Mu Y, Bao W, Jiang W, Li R, Liang Q, Li K. The Meishan pig genome reveals structural variation-mediated gene expression and phenotypic divergence underlying Asian pig domestication. Mol Ecol Resour 2021; 21:2077-2092. [PMID: 33825319 DOI: 10.1111/1755-0998.13396] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 03/17/2021] [Accepted: 03/29/2021] [Indexed: 01/27/2023]
Abstract
There are wide genomic and phenotypic differences between Asian and European pig breeds, yet the current reference genome is the European Duroc pig genome. A high-quality pig genome is lacking for genetic analysis of agricultural traits in Asian pigs. Here, using a hybrid approach, a high-quality reference genome (MSCAAS v1) for the Asian Meishan breed is assembled with a contig N50 size of 48.05 Mb. MSCAAS v1 outperforms the Duroc genome as a reference genome for Asian breeds. Genomic comparison reveals 49,103 structural variations (SVs) between Meishan and Duroc, 4.02% of which are Asian-specific SVs (AP-SVs). Notably, a 30-Mb hotspot for AP-SVs on chromosome X enriched for genes associated with Asian-pig-specific phenotypes is present in Asian domestic pig breeds, but absent in Asian wild boars, suggesting that Asian domestic breeds share a common ancestor. Interbreed transcriptomics reveals transcriptional suppression roles of AP-SVs in multiple tissues. Finally, transcriptional regulation in the intron of IGF2R is reported, as genomic SV (274-bp deletion) in Tibetan pig limits its growth compared to domestic pig breeds. In summary, this study provides insights regarding the genetic changes underlying pig domestication and presents a benchmark-setting resource for the utilization of agricultural valuable loci in Asian pigs.
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Affiliation(s)
- Rong Zhou
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shang-Tong Li
- National Institute of Biological Sciences (NIBS, Beijing, China
| | - Wen-Ye Yao
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chun-Di Xie
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Zhi-Jie Zeng
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Di Wang
- Novogene Bioinformatics Institute, Beijing, China
| | - Kui Xu
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhao-Ji Shen
- Guangdong Provincial key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China.,Fulcrum gene science and technology (Beijing) Ltd, Beijing, China
| | - Yulian Mu
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenbin Bao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, Beijing, China
| | - Ruiqiang Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Qiqi Liang
- Novogene Bioinformatics Institute, Beijing, China
| | - Kui Li
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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11
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Yuan C, Lu Z, Guo T, Yue Y, Wang X, Wang T, Zhang Y, Hou F, Niu C, Sun X, Zhao H, Zhu S, Liu J, Yang B. A global analysis of CNVs in Chinese indigenous fine-wool sheep populations using whole-genome resequencing. BMC Genomics 2021; 22:78. [PMID: 33485316 PMCID: PMC7825165 DOI: 10.1186/s12864-021-07387-7] [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: 10/22/2019] [Accepted: 01/13/2021] [Indexed: 12/13/2022] Open
Abstract
Background Copy number variation (CNV) is an important source of genetic variation that has a significant influence on phenotypic diversity, economically important traits and the evolution of livestock species. In this study, the genome-wide CNV distribution characteristics of 32 fine-wool sheep from three breeds were analyzed using resequencing. Results A total of 1,747,604 CNVs were detected in this study, and 7228 CNV regions (CNVR) were obtained after merging overlapping CNVs; these regions accounted for 2.17% of the sheep reference genome. The average length of the CNVRs was 4307.17 bp. “Deletion” events took place more frequently than “duplication” or “both” events. The CNVRs obtained overlapped with previously reported sheep CNVRs to variable extents (4.39–55.46%). Functional enrichment analysis showed that the CNVR-harboring genes were mainly involved in sensory perception systems, nutrient metabolism processes, and growth and development processes. Furthermore, 1855 of the CNVRs were associated with 166 quantitative trait loci (QTL), including milk QTLs, carcass QTLs, and health-related QTLs, among others. In addition, the 32 fine-wool sheep were divided into horned and polled groups to analyze for the selective sweep of CNVRs, and it was found that the relaxin family peptide receptor 2 (RXFP2) gene was strongly influenced by selection. Conclusions In summary, we constructed a genomic CNV map for Chinese indigenous fine-wool sheep using resequencing, thereby providing a valuable genetic variation resource for sheep genome research, which will contribute to the study of complex traits in sheep. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07387-7.
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Affiliation(s)
- Chao Yuan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Tingting Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Yaojing Yue
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Xijun Wang
- Gansu Provincial Sheep Breeding Technology Extension Station, Sunan, 734031, China
| | - Tianxiang Wang
- Gansu Provincial Sheep Breeding Technology Extension Station, Sunan, 734031, China
| | - Yajun Zhang
- Xinjiang Gongnaisi Breeding Sheep Farm, Xinyuan, 835808, China
| | - Fujun Hou
- Aohan Banner Breeding Sheep Farm, Chifeng, 024300, China
| | - Chune Niu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Xiaopin Sun
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Hongchang Zhao
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Shaohua Zhu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China.
| | - Bohui Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China.
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12
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Li B, He X, Zhao Y, Bai D, Du M, Song L, Liu Z, Yin Z, Manglai D. Transcriptome profiling of developing testes and spermatogenesis in the Mongolian horse. BMC Genet 2020; 21:46. [PMID: 32345215 PMCID: PMC7187496 DOI: 10.1186/s12863-020-00843-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 03/13/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Horse testis development and spermatogenesis are complex physiological processes. METHODS To study these processes, three immature and three mature testes were collected from the Mongolian horse, and six libraries were established using high-throughput RNA sequencing technology (RNA-Seq) to screen for genes related to testis development and spermatogenesis. RESULTS A total of 16,237 upregulated genes and 8,641 downregulated genes were detected in the testis of the Mongolian horse. These genes play important roles in different developmental stages of spermatogenesis and testicular development. Five genes with alternative splicing events that may influence spermatogenesis and development of the testis were detected. GO (Gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses were performed for functional annotation of the differentially expressed genes. Pathways related to "spermatogenesis," male gamete generation," "spermatid development" and "oocyte meiosis" were significantly involved in different stages of testis development and spermatogenesis. CONCLUSION Genes, pathways and alternative splicing events were identified with inferred functions in the process of spermatogenesis in the Mongolian horse. The identification of these differentially expressed genetic signatures improves our understanding of horse testis development and spermatogenesis.
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Affiliation(s)
- Bei Li
- College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
- lnner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Scientific Observing and Experimental Station of Equine Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Xiaolong He
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, 010031, China
| | - Yiping Zhao
- College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
- lnner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Scientific Observing and Experimental Station of Equine Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Dongyi Bai
- College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
- lnner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Scientific Observing and Experimental Station of Equine Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Ming Du
- College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
- lnner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Scientific Observing and Experimental Station of Equine Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Lianjie Song
- College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
- lnner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Scientific Observing and Experimental Station of Equine Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Zhuang Liu
- College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
- lnner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Scientific Observing and Experimental Station of Equine Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Zhenchen Yin
- College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
- lnner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Scientific Observing and Experimental Station of Equine Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Dugarjaviin Manglai
- College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China.
- lnner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China.
- Scientific Observing and Experimental Station of Equine Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China.
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13
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Whole genome detection of sequence and structural polymorphism in six diverse horses. PLoS One 2020; 15:e0230899. [PMID: 32271776 PMCID: PMC7144971 DOI: 10.1371/journal.pone.0230899] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 03/12/2020] [Indexed: 12/30/2022] Open
Abstract
The domesticated horse has played a unique role in human history, serving not just as a source of animal protein, but also as a catalyst for long-distance migration and military conquest. As a result, the horse developed unique physiological adaptations to meet the demands of both their climatic environment and their relationship with man. Completed in 2009, the first domesticated horse reference genome assembly (EquCab 2.0) produced most of the publicly available genetic variations annotations in this species. Yet, there are around 400 geographically and physiologically diverse breeds of horse. To enrich the current collection of genetic variants in the horse, we sequenced whole genomes from six horses of six different breeds: an American Miniature, a Percheron, an Arabian, a Mangalarga Marchador, a Native Mongolian Chakouyi, and a Tennessee Walking Horse, and mapped them to EquCab3.0 genome. Aside from extreme contrasts in body size, these breeds originate from diverse global locations and each possess unique adaptive physiology. A total of 1.3 billion reads were generated for the six horses with coverage between 15x to 24x per horse. After applying rigorous filtration, we identified and functionally annotated 17,514,723 Single Nucleotide Polymorphisms (SNPs), and 1,923,693 Insertions/Deletions (INDELs), as well as an average of 1,540 Copy Number Variations (CNVs) and 3,321 Structural Variations (SVs) per horse. Our results revealed putative functional variants including genes associated with size variation like LCORL gene (found in all horses), ZFAT in the Arabian, American Miniature and Percheron horses and ANKRD1 in the Native Mongolian Chakouyi horse. We detected a copy number variation in the Latherin gene that may be the result of evolutionary selection impacting thermoregulation by sweating, an important component of athleticism and heat tolerance. The newly discovered variants were formatted into user-friendly browser tracks and will provide a foundational database for future studies of the genetic underpinnings of diverse phenotypes within the horse. The domesticated horse played a unique role in human history, serving not just as a source of dietary animal protein, but also as a catalyst for long-distance migration and military conquest. As a result, the horse developed unique physiological adaptations to meet the demands of both their climatic environment and their relationship with man. Although the completion of the horse reference genome allowed for the discovery of many genetic variants, the remarkable diversity across breeds of horse calls for additional effort to quantify the complete span of genetic polymorphism within this unique species. In this work, we present genome re-sequencing and variant detection analysis for six horses belonging to six different breeds representing different morphology, origins and vary in their physiological demands and response. We identified and annotated not just single nucleotide polymorphisms (SNPs), but also insertions and deletions (INDELs), copy number variations (CNVs) and structural variations (SVs). Our results illustrate novel sources of polymorphism and highlight potentially impactful variations for phenotypes of body size and conformation. We also detected a copy number loss in the Latherin gene that could be the result of an evolutionary selection affecting thermoregulation through sweating. Our newly discovered variants were formatted into easy-to-use tracks that can be easily accessed by researchers around the globe.
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14
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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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15
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Joshi A, Chitanand M. Complete genome sequence of plant growth promoting Pseudomonas aeruginosa AJ D 2 an isolate from monocropic cotton rhizosphere. Genomics 2019; 112:1318. [PMID: 31404626 DOI: 10.1016/j.ygeno.2019.07.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/27/2019] [Accepted: 07/31/2019] [Indexed: 11/17/2022]
Abstract
A plant growth promoting Pseudomonas aeruginosa AJD 2 was isolated from monocropic cotton rhizosphere of Maharashtra state, India. The strain was identified as per physiological, biochemical and 16S rRNA gene sequencing (Accession number MG234531). The strain possess multiple functional plant growth promoting traits and antifungal activity. The genome was extracted, purified and library of avg.515 bp was prepared and sequenced by over Illumina platform. The sequenced genome was studied by using CLC workbench and NCBI pipeline using Pseudomonas aeruginosa PAO1 and Pseudomonas aeruginosa YL84 as reference assembler. The size of the genome is 6.1 Mb with 5802 genes within it. The study over strain may give an insight into its plant growth promotion mechanism.
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Affiliation(s)
- Abhijeet Joshi
- Department of Microbiology, Netaji Subhaschandra Bose College Nanded, India.
| | - Manjusha Chitanand
- Department of Microbiology, Netaji Subhaschandra Bose College Nanded, India
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16
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McGivney BA, Hernandez B, Katz LM, MacHugh DE, McGovern SP, Parnell AC, Wiencko HL, Hill EW. A genomic prediction model for racecourse starts in the Thoroughbred horse. Anim Genet 2019; 50:347-357. [PMID: 31257665 DOI: 10.1111/age.12798] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2019] [Indexed: 12/26/2022]
Abstract
Durability traits in Thoroughbred horses are heritable, economically valuable and may affect horse welfare. The aims of this study were to test the hypotheses that (i) durability traits are heritable and (ii) genetic data may be used to predict a horse's potential to have a racecourse start. Heritability for the phenotype 'number of 2- and 3-year-old starts' was estimated to be h m 2 = 0.11 ± 0.02 (n = 4499). A genome-wide association study identified SNP contributions to the trait. The neurotrimin (NTM), opioid-binding protein/cell adhesion molecule like (OPCML) and prolylcarboxypeptidase (PRCP) genes were identified as candidate genes associated with the trait. NTM functions in brain development and has been shown to have been selected during the domestication of the horse. PRCP is an established expression quantitative trait locus involved in the interaction between voluntary exercise and body composition in mice. We hypothesise that variation at these loci contributes to the motivation of the horse to exercise, which may influence its response to the demands of the training and racing environment. A random forest with mixed effects (RFME) model identified a set of SNPs that contributed to 24.7% of the heritable variation in the trait. In an independent validation set (n = 528 horses), the cohort with high genetic potential for a racecourse start had significantly fewer unraced horses (16% unraced) than did low (27% unraced) potential horses and had more favourable race outcomes among those that raced. Therefore, the information from SNPs included in the model may be used to predict horses with a greater chance of a racecourse start.
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Affiliation(s)
- B A McGivney
- Plusvital Ltd, The Highline, Dun Laoghaire Industrial Estate, Dun Laoghaire, Dublin, Ireland
| | - B Hernandez
- Prolego Scientific, Nova UCD, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland.,The Irish Longitudinal Study on Aging (TILDA), Trinity College Dublin, Dublin, D02 PN40, Ireland
| | - L M Katz
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - D E MacHugh
- UCD Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland.,UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - S P McGovern
- Plusvital Ltd, The Highline, Dun Laoghaire Industrial Estate, Dun Laoghaire, Dublin, Ireland
| | - A C Parnell
- Prolego Scientific, Nova UCD, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland.,School of Mathematics and Statistics, Insight Centre for Data Analytics, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - H L Wiencko
- Plusvital Ltd, The Highline, Dun Laoghaire Industrial Estate, Dun Laoghaire, Dublin, Ireland
| | - E W Hill
- Plusvital Ltd, The Highline, Dun Laoghaire Industrial Estate, Dun Laoghaire, Dublin, Ireland.,UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
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17
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Kharrati-Koopaee H, Ebrahimie E, Dadpasand M, Niazi A, Esmailizadeh A. Genomic analysis reveals variant association with high altitude adaptation in native chickens. Sci Rep 2019; 9:9224. [PMID: 31239472 PMCID: PMC6592930 DOI: 10.1038/s41598-019-45661-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 03/12/2019] [Indexed: 01/10/2023] Open
Abstract
Native chickens are endangered genetic resources that are kept by farmers for different purposes. Native chickens distributed in a wide range of altitudes, have developed adaptive mechanisms to deal with hypoxia. For the first time, we report variants associated with high-altitude adaptation in Iranian native chickens by whole genome sequencing of lowland and highland chickens. We found that these adaptive variants are involved in DNA repair, organs development, immune response and histone binding. Amazingly, signature selection analysis demonstrated that differential variants are adaptive in response to hypoxia and are not due to other evolutionary pressures. Cellular component analysis of variants showed that mitochondrion is the most important organelle for hypoxia adaptation. A total of 50 variants was detected in mtDNA for highland and lowland chickens. High-altitude associated with variant discovery highlighted the importance of COX3, a gene involved in cell respiration, in hypoxia adaptation. The results of study suggest that MIR6644-2 is involved in hypoxia and high-altitude adaptations by regulation of embryo development. Finally, 3877 novel SNVs including the mtDNA ones, were submitted to EBI (PRJEB24944). Whole-genome sequencing and variant discovery of native chickens provided novel insights about adaptation mechanisms and highlights the importance of valuable genomic variants in chickens.
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Affiliation(s)
| | - Esmaeil Ebrahimie
- Institute of Biotechnology, School of Agriculture, Shiraz University, Shiraz, Iran.
- The University of Adelaide, School of Animal and Veterinary Sciences, Adelaide, South Australia, Australia.
- School of Information Technology and Mathematical Science, Division of Information Technology, Engineering and the Environment, University of South Australia, South Australia, Adelaide, Australia.
- Genomics Research Platform, School of Life Sciences, La Trobe University, Melbourne, Victoria, Australia.
| | - Mohammad Dadpasand
- Department of Animal science, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Ali Niazi
- Institute of Biotechnology, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Ali Esmailizadeh
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences No. 32 Jiaochang Donglu, Kunming, Yunnan, 650223, P.R. China.
- Department of Animal science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran.
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18
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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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19
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Felkel S, Vogl C, Rigler D, Dobretsberger V, Chowdhary BP, Distl O, Fries R, Jagannathan V, Janečka JE, Leeb T, Lindgren G, McCue M, Metzger J, Neuditschko M, Rattei T, Raudsepp T, Rieder S, Rubin CJ, Schaefer R, Schlötterer C, Thaller G, Tetens J, Velie B, Brem G, Wallner B. The horse Y chromosome as an informative marker for tracing sire lines. Sci Rep 2019; 9:6095. [PMID: 30988347 PMCID: PMC6465346 DOI: 10.1038/s41598-019-42640-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 04/04/2019] [Indexed: 12/31/2022] Open
Abstract
Analysis of the Y chromosome is the best-established way to reconstruct paternal family history in humans. Here, we applied fine-scaled Y-chromosomal haplotyping in horses with biallelic markers and demonstrate the potential of our approach to address the ancestry of sire lines. We de novo assembled a draft reference of the male-specific region of the Y chromosome from Illumina short reads and then screened 5.8 million basepairs for variants in 130 specimens from intensively selected and rural breeds and nine Przewalski's horses. Among domestic horses we confirmed the predominance of a young'crown haplogroup' in Central European and North American breeds. Within the crown, we distinguished 58 haplotypes based on 211 variants, forming three major haplogroups. In addition to two previously characterised haplogroups, one observed in Arabian/Coldblooded and the other in Turkoman/Thoroughbred horses, we uncovered a third haplogroup containing Iberian lines and a North African Barb Horse. In a genealogical showcase, we distinguished the patrilines of the three English Thoroughbred founder stallions and resolved a historic controversy over the parentage of the horse 'Galopin', born in 1872. We observed two nearly instantaneous radiations in the history of Central and Northern European Y-chromosomal lineages that both occurred after domestication 5,500 years ago.
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Affiliation(s)
- Sabine Felkel
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Claus Vogl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | - Doris Rigler
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | - Viktoria Dobretsberger
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | | | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, 30559, Germany
| | - Ruedi Fries
- Lehrstuhl fuer Tierzucht, Technische Universitaet Muenchen, Freising, 85354, Germany
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - Jan E Janečka
- Department of Biological Sciences, Duquesne University, Pittsburgh, 15282, USA
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
- Department of Biosystems, KU Leuven, Leuven, 3001, Belgium
| | - Molly McCue
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, MN, 55108, USA
| | - Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, 30559, Germany
| | | | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Terje Raudsepp
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843-4458, USA
| | - Stefan Rieder
- Agroscope, Swiss National Stud Farm, Avenches, 1580, Switzerland
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, 75123, Sweden
| | - Robert Schaefer
- Agroscope, Swiss National Stud Farm, Avenches, 1580, Switzerland
| | - Christian Schlötterer
- Institut fuer Populationsgenetik, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, University of Kiel, Kiel, 24098, Germany
| | - Jens Tetens
- Institute of Animal Breeding and Husbandry, University of Kiel, Kiel, 24098, Germany
- Functional Breeding Group, Department of Animal Sciences, Georg-August-University Göttingen, Göttingen, 37077, Germany
| | - Brandon Velie
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
- School of Life and Environmental Sciences, University of Sydney, Sydney, 2006, Australia
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | - Barbara Wallner
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria.
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20
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Seong HS, Kim NY, Kim DC, Hwang NH, Son DH, Shin JS, Lee JH, Chung WH, Choi JW. Whole genome sequencing analysis of horse populations inhabiting the Korean Peninsula and Przewalski's horse. Genes Genomics 2019; 41:621-628. [PMID: 30941726 DOI: 10.1007/s13258-019-00795-w] [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] [Received: 10/14/2018] [Accepted: 02/11/2019] [Indexed: 12/30/2022]
Abstract
BACKGROUND The Jeju horse is an indigenous horse breed in Korea. However, there is a severe lack of genomic studies on Korean horse breeds. OBJECTIVE The objective of this study was to report genomic characteristics of domestic horse populations that inhabit South Korea (Jeju, Jeju crossbred, and Thoroughbred) and a wild horse breed (Przewalski's horse). RESULTS Using the equine reference genome assembly (EquCab 2.0), more than ~ 6.5 billion sequence reads were successfully mapped, which generated an average of 40.87-fold coverage throughout the genome. Using these data, we detected a total of 12.88 million SNPs, of which 73.7% were found to be novel. All the detected SNPs were deeply annotated to retrieve SNPs in gene regions using the RefSeq and Ensemble gene sets. Approximately 27% of the total SNPs were located within genes, whereas the remaining 73% were found in intergenic regions. Using 129,776 coding SNPs, we retrieved a total of 49,171 nonsynonymous SNPs in 12,351 genes. Furthermore, we identified a total of 10,770 deleterious nonsynonymous SNPs which are predicted to affect protein structure or function. CONCLUSION We showed numerous genomic variants from domestic and wild horse breeds. These results provide a valuable resource for further studies on functions of SNP-containing genes, and can aid in determining the molecular basis underlying variation in economically important traits of horses.
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Affiliation(s)
- Ha-Seung Seong
- College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Nam-Young Kim
- Subtropical Animal Research Institute, National Institute of Animal Science, RDA, Jeju, 690-150, Republic of Korea
| | - Dae Cheol Kim
- Jeju Special Self-Governing Province Livestock Promotion, Jeju, Republic of Korea
| | - Nam-Hyun Hwang
- College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Da-Hye Son
- College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Jong Suh Shin
- College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Joon-Hee Lee
- Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Won-Hyong Chung
- Division of Food Functionality Research, Research Group of Healthcare, Wanju-gun, 55365, Republic of Korea.
| | - Jung-Woo Choi
- College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
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21
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Khalkhali-Evrigh R, Hafezian SH, Hedayat-Evrigh N, Farhadi A, Bakhtiarizadeh MR. Genetic variants analysis of three dromedary camels using whole genome sequencing data. PLoS One 2018; 13:e0204028. [PMID: 30235280 PMCID: PMC6147446 DOI: 10.1371/journal.pone.0204028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 08/31/2018] [Indexed: 12/27/2022] Open
Abstract
Whole genome wide identification and annotation of genetic variations in camels is in its first steps. The aim of this study was the identification of genome wide variants, functional annotations of them and enrichment analysis of affected genes using whole genome sequencing data of three dromedary camels. The genomes of two Iranian female dromedary camels that mostly used to produce meat and milk were sequenced to 41.9-fold and 38.6-fold coverage. A total of 4,727,238 single-nucleotide polymorphisms (SNPs) and 692,908 indels (insertions and deletions) were found by mapping raw reads to the dromedary reference assembly (GenBank Accession: GCA_000767585.1). In-silico functional annotation of the discovered variants in under study samples revealed that most SNPs (2,305,738; 48.78%) and indels (339,756; 49.03%) were located in intergenic regions. A comparison of the identified SNPs with those of the African camel (BioProject Accession: PRJNA269274) indicated that they had 993,474 SNPs in common. We found 15,168 non-synonymous SNPs in the shared variants of the three camels that could affect gene function and protein structure. Obtained results revealed that there were 7085, 6271 and 4688 non-synonymous SNPs among the 3436, 3058 and 2882 genes in the specific gene sets of Yazd dromedary, Trod dromedary and African dromedary, respectively. The list of genes predicted to be affected by non-synonymous variants in different individuals was subjected to gene ontology (GO) enrichment analysis.
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Affiliation(s)
- Reza Khalkhali-Evrigh
- Department of Animal Breeding and Genetics, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - Seyed Hasan Hafezian
- Department of Animal Breeding and Genetics, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - Nemat Hedayat-Evrigh
- Department of Animal Science, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
- * E-mail:
| | - Ayoub Farhadi
- Department of Animal Breeding and Genetics, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
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22
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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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23
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Pereira GL, Chud TC, Bernardes PA, Venturini GC, Chardulo LA, Curi RA. Genotype Imputation and Accuracy Evaluation in Racing Quarter Horses Genotyped Using Different Commercial SNP Panels. J Equine Vet Sci 2017. [DOI: 10.1016/j.jevs.2017.07.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Schaefer RJ, Schubert M, Bailey E, Bannasch DL, Barrey E, Bar-Gal GK, Brem G, Brooks SA, Distl O, Fries R, Finno CJ, Gerber V, Haase B, Jagannathan V, Kalbfleisch T, Leeb T, Lindgren G, Lopes MS, Mach N, da Câmara Machado A, MacLeod JN, McCoy A, Metzger J, Penedo C, Polani S, Rieder S, Tammen I, Tetens J, Thaller G, Verini-Supplizi A, Wade CM, Wallner B, Orlando L, Mickelson JR, McCue ME. Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds. BMC Genomics 2017; 18:565. [PMID: 28750625 PMCID: PMC5530493 DOI: 10.1186/s12864-017-3943-8] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 07/13/2017] [Indexed: 12/30/2022] Open
Abstract
Background To date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole genome sequences has created the opportunity to develop a next generation, high-density equine SNP array. Results Using whole genome sequence from 153 individuals representing 24 distinct breeds collated by the equine genomics community, we cataloged over 23 million de novo discovered genetic variants. Leveraging genotype data from individuals with both whole genome sequence, and genotypes from lower-density, legacy SNP arrays, a subset of ~5 million high-quality, high-density array candidate SNPs were selected based on breed representation and uniform spacing across the genome. Considering probe design recommendations from a commercial vendor (Affymetrix, now Thermo Fisher Scientific) a set of ~2 million SNPs were selected for a next-generation high-density SNP chip (MNEc2M). Genotype data were generated using the MNEc2M array from a cohort of 332 horses from 20 breeds and a lower-density array, consisting of ~670 thousand SNPs (MNEc670k), was designed for genotype imputation. Conclusions Here, we document the steps taken to design both the MNEc2M and MNEc670k arrays, report genomic and technical properties of these genotyping platforms, and demonstrate the imputation capabilities of these tools for the domestic horse. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3943-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Robert J Schaefer
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ernest Bailey
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, USA
| | - Danika L Bannasch
- School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Eric Barrey
- Unité de Génétique Animale et Biologie Intégrative- UMR1313, INRA, Université Paris-Saclay, AgroParisTech, 78350, Jouy-en-Josas, France
| | - Gila Kahila Bar-Gal
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Koret School of Veterinary Medicine, The Hebrew University, 76100, Rehovot, Israel
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Samantha A Brooks
- Department of Animal Science, University of Florida, Gainesville, FL, USA
| | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine, Hannover, Germany
| | - Ruedi Fries
- Lehrstuhl für Tierzucht der Technischen Universität München, Liesel-Beckmann-Strasse 1, 85354, Freising, Germany
| | - Carrie J Finno
- School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Vinzenz Gerber
- Swiss Institute of Equine Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, and Agroscope, Länggassstrasse 124, 3001, Bern, Switzerland
| | - Bianca Haase
- School of Life and Environmental Sciences, Faculty of Veterinary Science, University of Sydney, Regimental Drive, B19-301 RMC Gunn, Sydney, NSW, 2006, Australia
| | | | - Ted Kalbfleisch
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
| | - Tosso Leeb
- Institute of Genetics, University of Bern, 3001, Bern, Switzerland
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Maria Susana Lopes
- Biotechnology Centre of Azores, University of Azores, Angra do heroísmo, Portugal
| | - Núria Mach
- Unité de Génétique Animale et Biologie Intégrative- UMR1313, INRA, Université Paris-Saclay, AgroParisTech, 78350, Jouy-en-Josas, France
| | | | - James N MacLeod
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, USA
| | - Annette McCoy
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Champaign, IL, 61802, USA
| | - Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine, Hannover, Germany
| | - Cecilia Penedo
- Veterinary Genetics Laboratory, University of California Davis, Davis, CA, USA
| | - Sagi Polani
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Koret School of Veterinary Medicine, The Hebrew University, 76100, Rehovot, Israel
| | - Stefan Rieder
- Agroscope, Swiss National Stud Farm, 1580, Avenches, Switzerland
| | - Imke Tammen
- School of Life and Environmental Sciences, Faculty of Veterinary Science, University of Sydney, Regimental Drive, B19-301 RMC Gunn, Sydney, NSW, 2006, Australia
| | - Jens Tetens
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, Hermann-Rodewald-Strasse 6, 24098, Kiel, Germany.,Department of Animal Sciences, Functional Breeding Group, Georg-August University Göttingen, Burckhardtweg 2, 37077, Göttingen, Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, Hermann-Rodewald-Strasse 6, 24098, Kiel, Germany
| | - Andrea Verini-Supplizi
- Department of Veterinary Medicine - Sport Horse Research Centre, University of Perugia, Perugia, Italy
| | - Claire M Wade
- School of Life and Environmental Sciences, Faculty of Veterinary Science, University of Sydney, Regimental Drive, B19-301 RMC Gunn, Sydney, NSW, 2006, Australia
| | - Barbara Wallner
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000, Toulouse, France
| | - James R Mickelson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Molly E McCue
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA.
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25
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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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26
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Ma Q, Liu X, Pan J, Ma L, Ma Y, He X, Zhao Q, Pu Y, Li Y, Jiang L. Genome-wide detection of copy number variation in Chinese indigenous sheep using an ovine high-density 600 K SNP array. Sci Rep 2017; 7:912. [PMID: 28424525 PMCID: PMC5430420 DOI: 10.1038/s41598-017-00847-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 03/16/2017] [Indexed: 12/21/2022] Open
Abstract
Copy number variants (CNVs) represent a form of genomic structural variation underlying phenotypic diversity. In this study, we used the Illumina Ovine SNP 600 K BeadChip array for genome-wide detection of CNVs in 48 Chinese Tan sheep. A total of 1,296 CNV regions (CNVRs), ranging from 1.2 kb to 2.3 Mb in length, were detected, representing approximately 4.7% of the entire ovine genome (Oar_v3.1). We combined our findings with five existing CNVR reports to generate a composite genome-wide dataset of 4,321 CNVRs, which revealed 556 (43%) novel CNVRs. Subsequently, ten novel CNVRs were randomly chosen for further quantitative real-time PCR (qPCR) confirmation, and eight were successfully validated. Gene functional enrichment revealed that these CNVRs cluster into Gene Ontology (GO) categories of homeobox and embryonic skeletal system morphogenesis. One CNVR overlapping with the homeobox transcription factor DLX3 and previously shown to be associated with curly hair in sheep was identified as the candidate CNV for the special curly fleece phenotype in Tan sheep. We constructed a Chinese indigenous sheep genomic CNV map based on the Illumina Ovine SNP 600 K BeadChip array, providing an important addition to published sheep CNVs, which will be helpful for future investigations of the genomic structural variations underlying traits of interest in sheep.
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Affiliation(s)
- Qing Ma
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, 75002, China
| | - Xuexue Liu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Jianfei Pan
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Lina Ma
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, 75002, China
| | - Yuehui Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Xiaohong He
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Qianjun Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Yabin Pu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Yingkang Li
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, 75002, China.
| | - Lin Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China. .,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Road, Beijing, 100193, China.
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Jiang J, Gao Y, Hou Y, Li W, Zhang S, Zhang Q, Sun D. Whole-Genome Resequencing of Holstein Bulls for Indel Discovery and Identification of Genes Associated with Milk Composition Traits in Dairy Cattle. PLoS One 2016; 11:e0168946. [PMID: 28030618 PMCID: PMC5193355 DOI: 10.1371/journal.pone.0168946] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 12/08/2016] [Indexed: 11/18/2022] Open
Abstract
The use of whole-genome resequencing to obtain more information on genetic variation could produce a range of benefits for the dairy cattle industry, especially with regard to increasing milk production and improving milk composition. In this study, we sequenced the genomes of eight Holstein bulls from four half- or full-sib families, with high and low estimated breeding values (EBVs) of milk protein percentage and fat percentage at an average effective depth of 10×, using Illumina sequencing. Over 0.9 million nonredundant short insertions and deletions (indels) [1–49 base pairs (bp)] were obtained. Among them, 3,625 indels that were polymorphic between the high and low groups of bulls were revealed and subjected to further analysis. The vast majority (76.67%) of these indels were novel. Follow-up validation assays confirmed that most (70%) of the randomly selected indels represented true variations. The indels that were polymorphic between the two groups were annotated based on the cattle genome sequence assembly (UMD3.1.69); as a result, nearly 1,137 of them were found to be located within 767 annotated genes, only 5 (0.138%) of which were located in exons. Then, by integrated analysis of the 767 genes with known quantitative trait loci (QTL); significant single-nucleotide polymorphisms (SNPs) previously identified by genome-wide association studies (GWASs) to be associated with bovine milk protein and fat traits; and the well-known pathways involved in protein, fat synthesis, and metabolism, we identified a total of 11 promising candidate genes potentially affecting milk composition traits. These were FCGR2B, CENPE, RETSAT, ACSBG2, NFKB2, TBC1D1, NLK, MAP3K1, SLC30A2, ANGPT1 and UGDH. Our findings provide a basis for further study and reveal key genes for milk composition traits in dairy cattle.
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Affiliation(s)
- Jianping Jiang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Yahui Gao
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Yali Hou
- Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Wenhui Li
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Shengli Zhang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Qin Zhang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Dongxiao Sun
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
- * E-mail:
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28
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Leegwater PA, Vos-Loohuis M, Ducro BJ, Boegheim IJ, van Steenbeek FG, Nijman IJ, Monroe GR, Bastiaansen JWM, Dibbits BW, van de Goor LH, Hellinga I, Back W, Schurink A. Dwarfism with joint laxity in Friesian horses is associated with a splice site mutation in B4GALT7. BMC Genomics 2016; 17:839. [PMID: 27793082 PMCID: PMC5084406 DOI: 10.1186/s12864-016-3186-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 10/22/2016] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Inbreeding and population bottlenecks in the ancestry of Friesian horses has led to health issues such as dwarfism. The limbs of dwarfs are short and the ribs are protruding inwards at the costochondral junction, while the head and back appear normal. A striking feature of the condition is the flexor tendon laxity that leads to hyperextension of the fetlock joints. The growth plates of dwarfs display disorganized and thickened chondrocyte columns. The aim of this study was to identify the gene defect that causes the recessively inherited trait in Friesian horses to understand the disease process at the molecular level. RESULTS We have localized the genetic cause of the dwarfism phenotype by a genome wide approach to a 3 Mb region on the p-arm of equine chromosome 14. The DNA of two dwarfs and one control Friesian horse was sequenced completely and we identified the missense mutation ECA14:g.4535550C > T that cosegregated with the phenotype in all Friesians analyzed. The mutation leads to the amino acid substitution p.(Arg17Lys) of xylosylprotein beta 1,4-galactosyltransferase 7 encoded by B4GALT7. The protein is one of the enzymes that synthesize the tetrasaccharide linker between protein and glycosaminoglycan moieties of proteoglycans of the extracellular matrix. The mutation not only affects a conserved arginine codon but also the last nucleotide of the first exon of the gene and we show that it impedes splicing of the primary transcript in cultured fibroblasts from a heterozygous horse. As a result, the level of B4GALT7 mRNA in fibroblasts from a dwarf is only 2 % compared to normal levels. Mutations in B4GALT7 in humans are associated with Ehlers-Danlos syndrome progeroid type 1 and Larsen of Reunion Island syndrome. Growth retardation and ligamentous laxity are common manifestations of these syndromes. CONCLUSIONS We suggest that the identified mutation of equine B4GALT7 leads to the typical dwarfism phenotype in Friesian horses due to deficient splicing of transcripts of the gene. The mutated gene implicates the extracellular matrix in the regular organization of chrondrocyte columns of the growth plate. Conservation of individual amino acids may not be necessary at the protein level but instead may reflect underlying conservation of nucleotide sequence that are required for efficient splicing.
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Affiliation(s)
- Peter A Leegwater
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, PO Box 80154, NL-3508 TD, Utrecht, The Netherlands.
| | - Manon Vos-Loohuis
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, PO Box 80154, NL-3508 TD, Utrecht, The Netherlands
| | - Bart J Ducro
- Animal Breeding and Genomics Centre, Wageningen University, PO Box 338, NL-6700 AH, Wageningen, The Netherlands
| | - Iris J Boegheim
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, PO Box 80154, NL-3508 TD, Utrecht, The Netherlands.,Department of Equine Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 112-114, NL-3584 CM, Utrecht, The Netherlands
| | - Frank G van Steenbeek
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, PO Box 80154, NL-3508 TD, Utrecht, The Netherlands
| | - Isaac J Nijman
- Department of Medical Genetics, University Medical Center Utrecht, PO Box 85090, NL-3508 AB, Utrecht, The Netherlands
| | - Glen R Monroe
- Department of Medical Genetics, University Medical Center Utrecht, PO Box 85090, NL-3508 AB, Utrecht, The Netherlands
| | - John W M Bastiaansen
- Animal Breeding and Genomics Centre, Wageningen University, PO Box 338, NL-6700 AH, Wageningen, The Netherlands
| | - Bert W Dibbits
- Animal Breeding and Genomics Centre, Wageningen University, PO Box 338, NL-6700 AH, Wageningen, The Netherlands
| | - Leanne H van de Goor
- Dr. van Haeringen Laboratorium B.V., PO Box 408, NL-6700 AK, Wageningen, The Netherlands
| | - Ids Hellinga
- Koninklijke Vereniging "het Friesch Paarden-Stamboek", PO Box 624, NL-9200 AP, Drachten, The Netherlands
| | - Willem Back
- Department of Equine Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 112-114, NL-3584 CM, Utrecht, The Netherlands.,Department of Surgery and Anaesthesiology of Domestic Animals, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820, Merelbeke, Belgium
| | - Anouk Schurink
- Animal Breeding and Genomics Centre, Wageningen University, PO Box 338, NL-6700 AH, Wageningen, The Netherlands
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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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30
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Lee JH, Song KD, Kim JM, Leem HK, Park KD. Identification of genes with nonsynonymous SNP in Jeju horse by whole-genome resequencing reveals a functional role for immune response. J Anim Sci 2016; 94:895-901. [PMID: 27065251 DOI: 10.2527/jas.2014-8488] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Jeju horse (Natural Monument number 347) is a breed of horse that has experienced long-term isolation and domestication in Jeju Island, South Korea. We evaluated genetic features of this breed, including SNP, by whole-genome resequencing using an Illumina HiSeq 2000. A total of 5,986,852 SNP were identified in 4 Jeju horses and were divided into homozygous and heterozygous SNP (2,357,099 and 3,629,753 SNP, respectively). It revealed that 63.8% of these SNP resided in intergenic regions. Immune response genes with nonsynonymous SNP were overrepresented in Jeju horses as evidenced by Gene Ontology clustering. Among these genes, Toll-like receptors (TLR) are highly enriched. Comparing TLR genes between Jeju horses and the Przewalski's horse, and genes showed "possibly damaging" mutations in several regions by analysis with PolyPhen-2. These results provide a framework for further genetic studies in Jeju horse by domestication. Furthermore, research on functions of SNP-associated genes would aid in understanding the molecular genetic variation of horse breeds.
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31
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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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McQueen CM, Dindot SV, Foster MJ, Cohen ND. Genetic Susceptibility to Rhodococcus equi. J Vet Intern Med 2015; 29:1648-59. [PMID: 26340305 PMCID: PMC4895676 DOI: 10.1111/jvim.13616] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/29/2015] [Accepted: 08/10/2015] [Indexed: 02/02/2023] Open
Abstract
Rhodococcus equi pneumonia is a major cause of morbidity and mortality in neonatal foals. Much effort has been made to identify preventative measures and new treatments for R. equi with limited success. With a growing focus in the medical community on understanding the genetic basis of disease susceptibility, investigators have begun to evaluate the interaction of the genetics of the foal with R. equi. This review describes past efforts to understand the genetic basis underlying R. equi susceptibility and tolerance. It also highlights the genetic technology available to study horses and describes the use of this technology in investigating R. equi. This review provides readers with a foundational understanding of candidate gene approaches, single nucleotide polymorphism‐based, and copy number variant‐based genome‐wide association studies, and next generation sequencing (both DNA and RNA).
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Affiliation(s)
- C M McQueen
- Department of Large Animal Clinical Sciences, Texas A&M University, College Station, TX
| | - S V Dindot
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX
| | - M J Foster
- Medical Sciences Library, Texas A&M University, College Station, TX
| | - N D Cohen
- Department of Large Animal Clinical Sciences, Texas A&M University, College Station, TX
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Hestand MS, Kalbfleisch TS, Coleman SJ, Zeng Z, Liu J, Orlando L, MacLeod JN. Annotation of the Protein Coding Regions of the Equine Genome. PLoS One 2015; 10:e0124375. [PMID: 26107351 PMCID: PMC4481266 DOI: 10.1371/journal.pone.0124375] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 03/01/2015] [Indexed: 12/30/2022] Open
Abstract
Current gene annotation of the horse genome is largely derived from in silico predictions and cross-species alignments. Only a small number of genes are annotated based on equine EST and mRNA sequences. To expand the number of equine genes annotated from equine experimental evidence, we sequenced mRNA from a pool of forty-three different tissues. From these, we derived the structures of 68,594 transcripts. In addition, we identified 301,829 positions with SNPs or small indels within these transcripts relative to EquCab2. Interestingly, 780 variants extend the open reading frame of the transcript and appear to be small errors in the equine reference genome, since they are also identified as homozygous variants by genomic DNA resequencing of the reference horse. Taken together, we provide a resource of equine mRNA structures and protein coding variants that will enhance equine and cross-species transcriptional and genomic comparisons.
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Affiliation(s)
- Matthew S. Hestand
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, United States of America
| | - Theodore S. Kalbfleisch
- Biochemistry and Molecular Biology Department, School of Medicine, University of Louisville, Louisville, Kentucky, United States of America
| | - Stephen J. Coleman
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, United States of America
| | - Zheng Zeng
- Department of Computer Science, University of Kentucky, Lexington, Kentucky, United States of America
| | - Jinze Liu
- Department of Computer Science, University of Kentucky, Lexington, Kentucky, United States of America
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - James N. MacLeod
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, United States of America
- * E-mail:
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35
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Finno CJ, Stevens C, Young A, Affolter V, Joshi NA, Ramsay S, Bannasch DL. SERPINB11 frameshift variant associated with novel hoof specific phenotype in Connemara ponies. PLoS Genet 2015; 11:e1005122. [PMID: 25875171 PMCID: PMC4395385 DOI: 10.1371/journal.pgen.1005122] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 03/03/2015] [Indexed: 01/01/2023] Open
Abstract
Horses belong to the order Perissodactyla and bear the majority of their weight on their third toe; therefore, tremendous force is applied to each hoof. An inherited disease characterized by a phenotype restricted to the dorsal hoof wall was identified in the Connemara pony. Hoof wall separation disease (HWSD) manifests clinically as separation of the dorsal hoof wall along the weight-bearing surface of the hoof during the first year of life. Parents of affected ponies appeared clinically normal, suggesting an autosomal recessive mode of inheritance. A case-control allelic genome wide association analysis was performed (ncases = 15, ncontrols = 24). Population stratification (λ = 1.48) was successfully improved by removing outliers (ncontrols = 7) identified on a multidimensional scaling plot. A genome-wide significant association was detected on chromosome 8 (praw = 1.37x10-10, pgenome = 1.92x10-5). A homozygous region identified in affected ponies spanned from 79,936,024-81,676,900 bp and contained a family of 13 annotated SERPINB genes. Whole genome next-generation sequencing at 6x coverage of two cases and two controls revealed 9,758 SNVs and 1,230 indels within the ~1.7-Mb haplotype, of which 17 and 5, respectively, segregated with the disease and were located within or adjacent to genes. Additional genotyping of these 22 putative functional variants in 369 Connemara ponies (ncases = 23, ncontrols = 346) and 169 horses of other breeds revealed segregation of three putative variants adjacent or within four SERPIN genes. Two of the variants were non-coding and one was an insertion within SERPINB11 that introduced a frameshift resulting in a premature stop codon. Evaluation of mRNA levels at the proximal hoof capsule (ncases = 4, ncontrols = 4) revealed that SERPINB11 expression was significantly reduced in affected ponies (p<0.001). Carrier frequency was estimated at 14.8%. This study describes the first genetic variant associated with a hoof wall specific phenotype and suggests a role of SERPINB11 in maintaining hoof wall structure.
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Affiliation(s)
- Carrie J. Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Carlynn Stevens
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Amy Young
- Department of Animal Science, University of California Davis, Davis, California, United States of America
| | - Verena Affolter
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Nikhil A. Joshi
- Genome Center Bioinformatics Core, University of California Davis, Davis, California United States of America
| | - Sheila Ramsay
- Institute of Veterinary, Animal and Biomedical Sciences (IVABS) Massey University, Palmerston North, New Zealand
| | - Danika L. Bannasch
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
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Jun J, Cho YS, Hu H, Kim HM, Jho S, Gadhvi P, Park KM, Lim J, Paek WK, Han K, Manica A, Edwards JS, Bhak J. Whole genome sequence and analysis of the Marwari horse breed and its genetic origin. BMC Genomics 2014; 15 Suppl 9:S4. [PMID: 25521865 PMCID: PMC4290615 DOI: 10.1186/1471-2164-15-s9-s4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Background The horse (Equus ferus caballus) is one of the earliest domesticated species and has played an important role in the development of human societies over the past 5,000 years. In this study, we characterized the genome of the Marwari horse, a rare breed with unique phenotypic characteristics, including inwardly turned ear tips. It is thought to have originated from the crossbreeding of local Indian ponies with Arabian horses beginning in the 12th century. Results We generated 101 Gb (~30 × coverage) of whole genome sequences from a Marwari horse using the Illumina HiSeq2000 sequencer. The sequences were mapped to the horse reference genome at a mapping rate of ~98% and with ~95% of the genome having at least 10 × coverage. A total of 5.9 million single nucleotide variations, 0.6 million small insertions or deletions, and 2,569 copy number variation blocks were identified. We confirmed a strong Arabian and Mongolian component in the Marwari genome. Novel variants from the Marwari sequences were annotated, and were found to be enriched in olfactory functions. Additionally, we suggest a potential functional genetic variant in the TSHZ1 gene (p.Ala344>Val) associated with the inward-turning ear tip shape of the Marwari horses. Conclusions Here, we present an analysis of the Marwari horse genome. This is the first genomic data for an Asian breed, and is an invaluable resource for future studies of genetic variation associated with phenotypes and diseases in horses.
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Abstract
We constructed a 400K WG tiling oligoarray for the horse and applied it for the discovery of copy number variations (CNVs) in 38 normal horses of 16 diverse breeds, and the Przewalski horse. Probes on the array represented 18,763 autosomal and X-linked genes, and intergenic, sub-telomeric and chrY sequences. We identified 258 CNV regions (CNVRs) across all autosomes, chrX and chrUn, but not in chrY. CNVs comprised 1.3% of the horse genome with chr12 being most enriched. American Miniature horses had the highest and American Quarter Horses the lowest number of CNVs in relation to Thoroughbred reference. The Przewalski horse was similar to native ponies and draft breeds. The majority of CNVRs involved genes, while 20% were located in intergenic regions. Similar to previous studies in horses and other mammals, molecular functions of CNV-associated genes were predominantly in sensory perception, immunity and reproduction. The findings were integrated with previous studies to generate a composite genome-wide dataset of 1476 CNVRs. Of these, 301 CNVRs were shared between studies, while 1174 were novel and require further validation. Integrated data revealed that to date, 41 out of over 400 breeds of the domestic horse have been analyzed for CNVs, of which 11 new breeds were added in this study. Finally, the composite CNV dataset was applied in a pilot study for the discovery of CNVs in 6 horses with XY disorders of sexual development. A homozygous deletion involving AKR1C gene cluster in chr29 in two affected horses was considered possibly causative because of the known role of AKR1C genes in testicular androgen synthesis and sexual development. While the findings improve and integrate the knowledge of CNVs in horses, they also show that for effective discovery of variants of biomedical importance, more breeds and individuals need to be analyzed using comparable methodological approaches. Genomes of individuals in a species vary in many ways, one of which is DNA copy number variation (CNV). This includes deletions, duplications, and complex rearrangements typically larger than 50 base-pairs. CNVs are part of normal genetic variation contributing to phenotypic diversity but can also be pathogenic and associated with diseases and disorders. In order to distinguish between the two, detailed knowledge about CNVs in the species of interest is needed. Here we studied the genomes of 38 normal horses of 16 diverse breeds, and identified 258 CNV regions. We integrated our findings with previously published horse CNVs and generated a composite dataset of ∼1400 CNVRs. Despite this large number, our analysis shows that CNV research in horses needs further improvement because the current data are based on 10% of horse breeds and that most CNVRs are study-specific and require validation. Finally, we analyzed CNVs in horses with disorders of sexual development and found in two male pseudo-hermaphrodites a large deletion disrupting a group of genes involved in sex hormone metabolism and sexual differentiation. The findings underline the possible role of CNVs in complex disorders such as development and reproduction.
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Transcriptional expression changes of glucose metabolism genes after exercise in thoroughbred horses. Gene 2014; 547:152-8. [DOI: 10.1016/j.gene.2014.06.051] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 05/15/2014] [Accepted: 06/23/2014] [Indexed: 11/22/2022]
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Metzger J, Tonda R, Beltran S, Agueda L, Gut M, Distl O. Next generation sequencing gives an insight into the characteristics of highly selected breeds versus non-breed horses in the course of domestication. BMC Genomics 2014; 15:562. [PMID: 24996778 PMCID: PMC4097168 DOI: 10.1186/1471-2164-15-562] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 06/24/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Domestication has shaped the horse and lead to a group of many different types. Some have been under strong human selection while others developed in close relationship with nature. The aim of our study was to perform next generation sequencing of breed and non-breed horses to provide an insight into genetic influences on selective forces. RESULTS Whole genome sequencing of five horses of four different populations revealed 10,193,421 single nucleotide polymorphisms (SNPs) and 1,361,948 insertion/deletion polymorphisms (indels). In comparison to horse variant databases and previous reports, we were able to identify 3,394,883 novel SNPs and 868,525 novel indels. We analyzed the distribution of individual variants and found significant enrichment of private mutations in coding regions of genes involved in primary metabolic processes, anatomical structures, morphogenesis and cellular components in non-breed horses and in contrast to that private mutations in genes affecting cell communication, lipid metabolic process, neurological system process, muscle contraction, ion transport, developmental processes of the nervous system and ectoderm in breed horses. CONCLUSIONS Our next generation sequencing data constitute an important first step for the characterization of non-breed in comparison to breed horses and provide a large number of novel variants for future analyses. Functional annotations suggest specific variants that could play a role for the characterization of breed or non-breed horses.
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Affiliation(s)
| | | | | | | | | | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559 Hannover, Germany.
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Finno CJ, Bannasch DL. Applied equine genetics. Equine Vet J 2014; 46:538-44. [PMID: 24802051 DOI: 10.1111/evj.12294] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 04/27/2014] [Indexed: 01/13/2023]
Abstract
Genome sequencing of the domestic horse and subsequent advancements in the field of equine genomics have led to an explosion in the development of tools for mapping traits and diseases and evaluating gene expression. The objective of this review is to discuss the current progress in the field of equine genomics, with specific emphasis on assembly and analysis of the reference sequence and subsequent sequencing of a Quarter Horse mare; the genomic tools currently available to researchers and their implications in genomic investigations in the horse; the genomics of Mendelian and non-Mendelian traits; the genomics of performance traits and considerations regarding genetic testing in the horse. The whole-genome sequencing of a Quarter Horse mare has provided additional variants within the equine genome that extend past single nucleotide polymorphisms to include insertions/deletions and copy number variants. Equine single nucleotide polymorphism arrays have allowed for the investigation of both simple and complex genetic traits while DNA microarrays have provided a tool for examining gene expression across various tissues and with certain disease conditions. Recently, next-generation sequencing has become more affordable and both whole-genome DNA sequencing and transcriptome-wide RNA sequencing are methodologies that are being applied to equine genomic research. Research in the field of equine genomics continues to expand rapidly as the cost of genotyping and sequencing decreases, resulting in a need for quality bioinformatics software and expertise to appropriately handle both the size and complexity of these data.
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Affiliation(s)
- C J Finno
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, USA
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Affiliation(s)
- E Bailey
- MH Gluck Equine Research Center, University of Kentucky - Veterinary Science, Lexington, USA
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Identification of genomic loci associated with Rhodococcus equi susceptibility in foals. PLoS One 2014; 9:e98710. [PMID: 24892408 PMCID: PMC4043894 DOI: 10.1371/journal.pone.0098710] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 05/04/2014] [Indexed: 11/30/2022] Open
Abstract
Pneumonia caused by Rhodococcus equi is a common cause of disease and death in foals. Although agent and environmental factors contribute to the incidence of this disease, the genetic factors influencing the clinical outcomes of R. equi pneumonia are ill-defined. Here, we performed independent single nucleotide polymorphism (SNP)- and copy number variant (CNV)-based genome-wide association studies to identify genomic loci associated with R. equi pneumonia in foals. Foals at a large Quarter Horse breeding farm were categorized into 3 groups: 1) foals with R. equi pneumonia (clinical group [N = 43]); 2) foals with ultrasonographic evidence of pulmonary lesions that never developed clinical signs of pneumonia (subclinical group [N = 156]); and, 3) foals without clinical signs or ultrasonographic evidence of pneumonia (unaffected group [N = 49]). From each group, 24 foals were randomly selected and used for independent SNP- and CNV-based genome-wide association studies (GWAS). The SNP-based GWAS identified a region on chromosome 26 that had moderate evidence of association with R. equi pneumonia when comparing clinical and subclinical foals. A joint analysis including all study foals revealed a 3- to 4-fold increase in odds of disease for a homozygous SNP within the associated region when comparing the clinical group with either of the other 2 groups of foals or their combination. The region contains the transient receptor potential cation channel, subfamily M, member 2 (TRPM2) gene, which is involved in neutrophil function. No associations were identified in the CNV-based GWAS. Collectively, these data identify a region on chromosome 26 associated with R. equi pneumonia in foals, providing evidence that genetic factors may indeed contribute to this important disease of foals.
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Decourt C, Caraty A, Briant C, Guillaume D, Lomet D, Chesneau D, Lardic L, Duchamp G, Reigner F, Monget P, Dufourny L, Beltramo M, Dardente H. Acute Injection and Chronic Perfusion of Kisspeptin Elicit Gonadotropins Release but Fail to Trigger Ovulation in the Mare1. Biol Reprod 2014; 90:36. [DOI: 10.1095/biolreprod.113.114157] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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Sugiura M, Kasama Y, Araki R, Hoki Y, Sunayama M, Uda M, Nakamura M, Ando S, Abe M. Induced pluripotent stem cell generation-associated point mutations arise during the initial stages of the conversion of these cells. Stem Cell Reports 2014; 2:52-63. [PMID: 24511470 PMCID: PMC3916761 DOI: 10.1016/j.stemcr.2013.11.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 11/07/2013] [Accepted: 11/08/2013] [Indexed: 01/26/2023] Open
Abstract
A large number of point mutations have been identified in induced pluripotent stem cell (iPSC) genomes to date. Whether these mutations are associated with iPSC generation is an important and controversial issue. In this study, we approached this critical issue in different ways, including an assessment of iPSCs versus embryonic stem cells (ESCs), and an investigation of variant allele frequencies and the heterogeneity of point mutations within a single iPSC clone. Through these analyses, we obtained strong evidence that iPSC-generation-associated point mutations occur frequently in a transversion-predominant manner just after the onset of cell lineage conversion. The heterogeneity of the point mutation profiles within an iPSC clone was also revealed and reflects the history of the emergence of each mutation. Further, our results suggest a possible approach for establishing iPSCs with fewer point mutations. iPSCs versus ESCs—an obvious difference in the frequency and mode of point mutations A large number of iPSC generation-associated, not preexisting, point mutations Heterogeneity of point mutation profiles in an iPSC clone No common point mutations among iPSC clones
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Affiliation(s)
- Mayumi Sugiura
- Transcriptome Research Group, National Institute of Radiological Sciences, Chiba 263-8555, Japan
| | - Yasuji Kasama
- Transcriptome Research Group, National Institute of Radiological Sciences, Chiba 263-8555, Japan
| | - Ryoko Araki
- Transcriptome Research Group, National Institute of Radiological Sciences, Chiba 263-8555, Japan
| | - Yuko Hoki
- Transcriptome Research Group, National Institute of Radiological Sciences, Chiba 263-8555, Japan
| | - Misato Sunayama
- Transcriptome Research Group, National Institute of Radiological Sciences, Chiba 263-8555, Japan
| | - Masahiro Uda
- Transcriptome Research Group, National Institute of Radiological Sciences, Chiba 263-8555, Japan
| | - Miki Nakamura
- Transcriptome Research Group, National Institute of Radiological Sciences, Chiba 263-8555, Japan
| | - Shunsuke Ando
- Transcriptome Research Group, National Institute of Radiological Sciences, Chiba 263-8555, Japan
| | - Masumi Abe
- Transcriptome Research Group, National Institute of Radiological Sciences, Chiba 263-8555, Japan
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Xiong H, Barker SC, Burger TD, Raoult D, Shao R. Heteroplasmy in the mitochondrial genomes of human lice and ticks revealed by high throughput sequencing. PLoS One 2013; 8:e73329. [PMID: 24058467 PMCID: PMC3772822 DOI: 10.1371/journal.pone.0073329] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 07/10/2013] [Indexed: 01/03/2023] Open
Abstract
The typical mitochondrial (mt) genomes of bilateral animals consist of 37 genes on a single circular chromosome. The mt genomes of the human body louse, Pediculus humanus, and the human head louse, Pediculus capitis, however, are extensively fragmented and contain 20 minichromosomes, with one to three genes on each minichromosome. Heteroplasmy, i.e. nucleotide polymorphisms in the mt genome within individuals, has been shown to be significantly higher in the mt cox1 gene of human lice than in humans and other animals that have the typical mt genomes. To understand whether the extent of heteroplasmy in human lice is associated with mt genome fragmentation, we sequenced the entire coding regions of all of the mt minichromosomes of six human body lice and six human head lice from Ethiopia, China and France with an Illumina HiSeq platform. For comparison, we also sequenced the entire coding regions of the mt genomes of seven species of ticks, which have the typical mitochondrial genome organization of bilateral animals. We found that the level of heteroplasmy varies significantly both among the human lice and among the ticks. The human lice from Ethiopia have significantly higher level of heteroplasmy than those from China and France (Pt<0.05). The tick, Amblyomma cajennense, has significantly higher level of heteroplasmy than other ticks (Pt<0.05). Our results indicate that heteroplasmy level can be substantially variable within a species and among closely related species, and does not appear to be determined by single factors such as genome fragmentation.
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Affiliation(s)
- Haoyu Xiong
- Parasitology Section, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Stephen C. Barker
- Parasitology Section, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Thomas D. Burger
- Parasitology Section, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UMR CNRS 6236 IRD 198, Faculté de Mé decine, Mé diterranée Infection, Aix-Marseille Université, Marseille, France
| | - Renfu Shao
- GeneCology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
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Metzger J, Philipp U, Lopes MS, da Camara Machado A, Felicetti M, Silvestrelli M, Distl O. Analysis of copy number variants by three detection algorithms and their association with body size in horses. BMC Genomics 2013; 14:487. [PMID: 23865711 PMCID: PMC3720552 DOI: 10.1186/1471-2164-14-487] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Accepted: 07/15/2013] [Indexed: 12/14/2022] Open
Abstract
Background Copy number variants (CNVs) have been shown to play an important role in genetic diversity of mammals and in the development of many complex phenotypic traits. The aim of this study was to perform a standard comparative evaluation of CNVs in horses using three different CNV detection programs and to identify genomic regions associated with body size in horses. Results Analysis was performed using the Illumina Equine SNP50 genotyping beadchip for 854 horses. CNVs were detected by three different algorithms, CNVPartition, PennCNV and QuantiSNP. Comparative analysis revealed 50 CNVs that affected 153 different genes mainly involved in sensory perception, signal transduction and cellular components. Genome-wide association analysis for body size showed highly significant deleted regions on ECA1, ECA8 and ECA9. Homologous regions to the detected CNVs on ECA1 and ECA9 have also been shown to be correlated with human height. Conclusions Comparative analysis of CNV detection algorithms was useful to increase the specificity of CNV detection but had certain limitations dependent on the detection tool. GWAS revealed genome-wide associated CNVs for body size in horses.
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Affiliation(s)
- Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559, Hannover, Germany
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DeWoody JA, Abts KC, Fahey AL, Ji Y, Kimble SJA, Marra NJ, Wijayawardena BK, Willoughby JR. Of contigs and quagmires: next‐generation sequencing pitfalls associated with transcriptomic studies. Mol Ecol Resour 2013; 13:551-8. [PMID: 23615313 DOI: 10.1111/1755-0998.12107] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 03/13/2013] [Accepted: 03/14/2013] [Indexed: 12/15/2022]
Affiliation(s)
- J. Andrew DeWoody
- Department of Biological Sciences Purdue University West Lafayette IN 47907 USA
- Department of Forestry & Natural Resources Purdue University West Lafayette IN 47907 USA
| | - Kendra C. Abts
- Department of Forestry & Natural Resources Purdue University West Lafayette IN 47907 USA
| | - Anna L. Fahey
- Department of Forestry & Natural Resources Purdue University West Lafayette IN 47907 USA
| | - Yanzhu Ji
- Department of Forestry & Natural Resources Purdue University West Lafayette IN 47907 USA
| | - Steven J. A. Kimble
- Department of Forestry & Natural Resources Purdue University West Lafayette IN 47907 USA
| | - Nicholas J. Marra
- Department of Forestry & Natural Resources Purdue University West Lafayette IN 47907 USA
| | | | - Janna R. Willoughby
- Department of Forestry & Natural Resources Purdue University West Lafayette IN 47907 USA
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Meira CT, Curi RA, Vasconcelos Silva JAII, Monteiro Corrêa MJ, Nunes de Oliveira H, Silveira da Mota MD. Morphological and Genomic Differences Between Cutting and Racing Lines of Quarter Horses. J Equine Vet Sci 2013. [DOI: 10.1016/j.jevs.2012.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Côté O, Lillie BN, Hayes MA, Clark ME, van den Bosch L, Katavolos P, Viel L, Bienzle D. Multiple secretoglobin 1A1 genes are differentially expressed in horses. BMC Genomics 2012; 13:712. [PMID: 23253434 PMCID: PMC3556144 DOI: 10.1186/1471-2164-13-712] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 12/18/2012] [Indexed: 11/19/2022] Open
Abstract
Background Secretoglobin 1A1 (SCGB 1A1), also called Clara cell secretory protein, is the most abundantly secreted protein of the airway. The SCGB1A1 gene has been characterized in mammals as a single copy in the genome. However, analysis of the equine genome suggested that horses might have multiple SCGB1A1 gene copies. Non-ciliated lung epithelial cells produce SCGB 1A1 during inhalation of noxious substances to counter airway inflammation. Airway fluid and lung tissue of horses with recurrent airway obstruction (RAO), a chronic inflammatory lung disease affecting mature horses similar to environmentally induced asthma of humans, have reduced total SCGB 1A1 concentration. Herein, we investigated whether horses have distinct expressed SCGB1A1 genes; whether the transcripts are differentially expressed in tissues and in inflammatory lung disease; and whether there is cell specific protein expression in tissues. Results We identified three SCGB1A1 gene copies on equine chromosome 12, contained within a 512-kilobase region. Bioinformatic analysis showed that SCGB1A1 genes differ from each other by 8 to 10 nucleotides, and that they code for different proteins. Transcripts were detected for SCGB1A1 and SCGB1A1A, but not for SCGB1A1P. The SCGB1A1P gene had most inter-individual variability and contained a non-sense mutation in many animals, suggesting that SCGB1A1P has evolved into a pseudogene. Analysis of SCGB1A1 and SCGB1A1A sequences by endpoint-limiting dilution PCR identified a consistent difference affecting 3 bp within exon 2, which served as a gene-specific “signature”. Assessment of gene- and organ-specific expression by semiquantitative RT-PCR of 33 tissues showed strong expression of SCGB1A1 and SCGB1A1A in lung, uterus, Fallopian tube and mammary gland, which correlated with detection of SCGB 1A1 protein by immunohistochemistry. Significantly altered expression of the ratio of SCGB1A1A to SCGB1A1 was detected in RAO-affected animals compared to controls, suggesting different roles for SCGB 1A1 and SCGB 1A1A in this inflammatory condition. Conclusions This is the first report of three SCGB1A1 genes in a mammal. The two expressed genes code for proteins predicted to differ in function. Alterations in the gene expression ratio in RAO suggest cell and tissue specific regulation and functions. These findings may be important for understanding of lung and reproductive conditions.
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Affiliation(s)
- Olivier Côté
- Department of Pathobiology, University of Guelph, Stone Road, Guelph, ON, Canada
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