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Paim TDP, Hay EHA, Wilson C, Thomas MG, Kuehn LA, Paiva SR, McManus C, Blackburn HD. Dynamics of genomic architecture during composite breed development in cattle. Anim Genet 2020; 51:224-234. [PMID: 31961956 PMCID: PMC7065137 DOI: 10.1111/age.12907] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 12/31/2022]
Abstract
Some livestock breeds face the challenge of reduced genetic variation, increased inbreeding depression owing to genetic drift and selection. Hybridization can reverse these processes and increase levels of productivity and adaptation to various environmental stressors. Samples from American Brangus were used to evaluate the indicine/taurine composition through nine generations (~45 years) after the hybridization process was completed. The purpose was to determine how hybridization alters allelic combinations of a breed over time when genetic factors such as selection and drift are operating. Furthermore, we explored genomic regions with deviations from the expected composition from the progenitor breeds and related these regions to traits under selection. The Brangus composition deviated from the theoretical expectation, defined by the breed association, of 62.5% taurine, showing taurine composition to be 70.4 ± 0.6%. Taurine and indicine proportion were not consistent across chromosomes. Furthermore, these non‐uniform areas were found to be associated with traits that were probably under selection such as intermuscular fat and average daily gain. Interestingly, the sex chromosomes were predominantly taurine, which could be due to the composite being formed particularly in the final cross that resulted in progeny designated as purebred Brangus. This work demonstrated the process of new breed formation on a genomic level. It suggests that factors like genetic drift, selection and complementarity shift the genetic architecture into a uniquely different population. These findings are important to better understand how hybridization and crossbreeding systems shape the genetic architecture of composite populations.
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Affiliation(s)
- T do P Paim
- Instituto Federal de Educação, Ciência e Tecnologia Goiano, Avenida Oeste n. 350, Iporá, 76.200-000, Brazil.,Universidade de Brasília, Asa Norte, Campus Darcy Ribeiro, ICC Sul, Brasília, 70.910-900, Brazil
| | - E H A Hay
- US Department of Agriculture, Fort Keogh Livestock and Range Research Laboratory, Agricultural Research Service, 243 Fort Keogh Road, Miles City, 59301, USA
| | - C Wilson
- US Department of Agriculture, National Laboratory for Genetic Resources Preservation, Agricultural Research Service, National Animal Germplasm Program, 1111 S Mason St., Fort Collins, 80521, USA
| | - M G Thomas
- Department of Animal Sciences, Colorado State University, 350 W. Pitkin St., Fort Collins, 80523-1171, USA
| | - L A Kuehn
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, 844 Rd 313, Clay Center, 68933, USA
| | - S R Paiva
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5 Norte (final) Caixa Postal 02372, Brasília, 70.770-917, Brazil
| | - C McManus
- Universidade de Brasília, Asa Norte, Campus Darcy Ribeiro, ICC Sul, Brasília, 70.910-900, Brazil
| | - H D Blackburn
- US Department of Agriculture, National Laboratory for Genetic Resources Preservation, Agricultural Research Service, National Animal Germplasm Program, 1111 S Mason St., Fort Collins, 80521, USA
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Zhou Y, Xu L, Bickhart DM, Abdel Hay EH, Schroeder SG, Connor EE, Alexander LJ, Sonstegard TS, Van Tassell CP, Chen H, Liu GE. Reduced representation bisulphite sequencing of ten bovine somatic tissues reveals DNA methylation patterns and their impacts on gene expression. BMC Genomics 2016; 17:779. [PMID: 27716143 PMCID: PMC5053184 DOI: 10.1186/s12864-016-3116-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 09/23/2016] [Indexed: 01/16/2023] Open
Abstract
Background As a major epigenetic component, DNA methylation plays important functions in individual development and various diseases. DNA methylation has been well studied in human and model organisms, but only limited data exist in economically important animals like cattle. Results Using reduced representation bisulphite sequencing (RRBS), we obtained single-base-resolution maps of bovine DNA methylation from ten somatic tissues. In total, we evaluated 1,868,049 cytosines in CG-enriched regions. While we found slightly low methylation levels (29.87 to 38.06 %) in cattle, the methylation contexts (CGs and non-CGs) of cattle showed similar methylation patterns to other species. Non-CG methylation was detected but methylation levels in somatic tissues were significantly lower than in pluripotent cells. To study the potential function of the methylation, we detected 10,794 differentially methylated cytosines (DMCs) and 836 differentially methylated CG islands (DMIs). Further analyses in the same tissues revealed many DMCs (including non-CGs) and DMIs, which were highly correlated with the expression of genes involved in tissue development. Conclusions In summary, our study provides a baseline dataset and essential information for DNA methylation profiles of cattle. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3116-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yang Zhou
- Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.,Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Building 306, Room 111, BARC-East, Beltsville, MD, 20705, USA
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, People's Republic of China
| | - Derek M Bickhart
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Building 306, Room 111, BARC-East, Beltsville, MD, 20705, USA
| | - El Hamidi Abdel Hay
- USDA Agricultural Research Service, Fort Keogh Livestock and Range Research Laboratory, Miles City, MT, 59301, USA
| | - Steven G Schroeder
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Building 306, Room 111, BARC-East, Beltsville, MD, 20705, USA
| | - Erin E Connor
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Building 306, Room 111, BARC-East, Beltsville, MD, 20705, USA
| | - Leeson J Alexander
- USDA Agricultural Research Service, Fort Keogh Livestock and Range Research Laboratory, Miles City, MT, 59301, USA
| | | | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Building 306, Room 111, BARC-East, Beltsville, MD, 20705, USA
| | - Hong Chen
- Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Building 306, Room 111, BARC-East, Beltsville, MD, 20705, USA.
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Zhou Y, Utsunomiya YT, Xu L, Hay EHA, Bickhart DM, Alexandre PA, Rosen BD, Schroeder SG, Carvalheiro R, de Rezende Neves HH, Sonstegard TS, Van Tassell CP, Ferraz JBS, Fukumasu H, Garcia JF, Liu GE. Genome-wide CNV analysis reveals variants associated with growth traits in Bos indicus. BMC Genomics 2016; 17:419. [PMID: 27245577 PMCID: PMC4888316 DOI: 10.1186/s12864-016-2461-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 02/11/2016] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Apart from single nucleotide polymorphism (SNP), copy number variation (CNV) is another important type of genetic variation, which may affect growth traits and play key roles for the production of beef cattle. To date, no genome-wide association study (GWAS) for CNV and body traits in beef cattle has been reported, so the present study aimed to investigate this type of association in one of the most important cattle subspecies: Bos indicus (Nellore breed). RESULTS We have used intensity data from over 700,000 SNP probes across the bovine genome to detect common CNVs in a sample of 2230 Nellore cattle, and performed GWAS between the detected CNVs and nine growth traits. After filtering for frequency and length, a total of 231 CNVs ranging from 894 bp to 4,855,088 bp were kept and tested as predictors for each growth trait using linear regression analysis with principal components correction. There were 49 significant associations identified among 17 CNVs and seven body traits after false discovery rate correction (P < 0.05). Among the 17 CNVs, three were significant or marginally significant for all the traits. We have compared the locations of associated CNVs with quantitative trait locus and the RefGene database, and found two sets of 9 CNVs overlapping with either known QTLs or genes, respectively. The gene overlapping with CNV100, KCNJ12, is a functional candidate for muscle development and plays critical roles in muscling traits. CONCLUSION This study presents the first CNV-based GWAS of growth traits using high density SNP microarray data in cattle. We detected 17 CNVs significantly associated with seven growth traits and one of them (CNV100) may be involved in growth traits through KCNJ12.
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Affiliation(s)
- Yang Zhou
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA.,College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi, 712100, China
| | - Yuri T Utsunomiya
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, 14884-900, Brazil
| | - Lingyang Xu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA.,Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China
| | - El Hamidi Abdel Hay
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA
| | - Derek M Bickhart
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA
| | - Pamela Almeida Alexandre
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, 13635, Brazil
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA
| | - Steven G Schroeder
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA
| | - Roberto Carvalheiro
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, 14884-900, Brazil
| | - Haroldo Henrique de Rezende Neves
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, 14884-900, Brazil
| | - Tad S Sonstegard
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA.,Present address: Recombinetics, Inc., St Paul, MN, 55104, USA
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA
| | - José Bento Sterman Ferraz
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, 13635, Brazil
| | - Heidge Fukumasu
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, 13635, Brazil
| | - Jose Fernando Garcia
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, 14884-900, Brazil. .,Departamento de Apoio, Produção e Saúde Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP - Univ Estadual Paulista, Araçatuba, São Paulo, 16050-680, Brazil. .,International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil.
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA.
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Xu L, Hou Y, Bickhart DM, Zhou Y, Hay EHA, Song J, Sonstegard TS, Van Tassell CP, Liu GE. Population-genetic properties of differentiated copy number variations in cattle. Sci Rep 2016; 6:23161. [PMID: 27005566 PMCID: PMC4804293 DOI: 10.1038/srep23161] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 02/25/2016] [Indexed: 01/24/2023] Open
Abstract
While single nucleotide polymorphism (SNP) is typically the variant of choice for population genetics, copy number variation (CNV) which comprises insertion, deletion and duplication of genomic sequence, is an informative type of genetic variation. CNVs have been shown to be both common in mammals and important for understanding the relationship between genotype and phenotype. However, CNV differentiation, selection and its population genetic properties are not well understood across diverse populations. We performed a population genetics survey based on CNVs derived from the BovineHD SNP array data of eight distinct cattle breeds. We generated high resolution results that show geographical patterns of variations and genome-wide admixture proportions within and among breeds. Similar to the previous SNP-based studies, our CNV-based results displayed a strong correlation of population structure and geographical location. By conducting three pairwise comparisons among European taurine, African taurine, and indicine groups, we further identified 78 unique CNV regions that were highly differentiated, some of which might be due to selection. These CNV regions overlapped with genes involved in traits related to parasite resistance, immunity response, body size, fertility, and milk production. Our results characterize CNV diversity among cattle populations and provide a list of lineage-differentiated CNVs.
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Affiliation(s)
- Lingyang Xu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA.,Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742, USA
| | - Yali Hou
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Derek M Bickhart
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
| | - Yang Zhou
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA.,College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi, 712100, China
| | - El Hamidi Abdel Hay
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
| | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742, USA
| | - Tad S Sonstegard
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA
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