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Jia C, Wang H, Li C, Wu X, Zan L, Ding X, Guo X, Bao P, Pei J, Chu M, Liang C, Yan P. Genome-wide detection of copy number variations in polled yak using the Illumina BovineHD BeadChip. BMC Genomics 2019; 20:376. [PMID: 31088363 PMCID: PMC6518677 DOI: 10.1186/s12864-019-5759-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/02/2019] [Indexed: 01/29/2023] Open
Abstract
Background Copy number variations (CNVs), which are genetic variations present throughout mammalian genomes, are a vital source of phenotypic variation that can lead to the development of unique traits. In this study we used the Illunima BovineHD BeadChip to conduct genome-wide detection of CNVs in 215 polled yaks. Results A total of 1066 CNV regions (CNVRs) were detected with a total length of 181.6 Mb, comprising ~ 7.2% of the bovine autosomal genome. The size of these CNVRs ranged from 5.53 kb to 1148.45 kb, with an average size of 170.31 kb. Eight out of nine randomly chosen CNVRs were successfully validated by qPCR. A functional enrichment analysis of the CNVR-associated genes indicated their relationship to a number of molecular adaptations that enable yaks to thrive at high altitudes. One third of the detected CNVRs were mapped to QTLs associated with six classes of economically important traits, indicating that these CNVRs may play an important role in variations of these traits. Conclusions Our genome-wide yak CNV map may thus provide valuable insights into both the molecular mechanisms of high altitude adaptation and the potential genomic basis of economically important traits in yak. Electronic supplementary material The online version of this article (10.1186/s12864-019-5759-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Congjun Jia
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.,College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Hongbo Wang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Chen Li
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Xiaoyun Wu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xuezhi Ding
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Xian Guo
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Pengjia Bao
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Jie Pei
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Min Chu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Chunnian Liang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.
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Yang L, Xu L, Zhu B, Niu H, Zhang W, Miao J, Shi X, Zhang M, Chen Y, Zhang L, Gao X, Gao H, Li L, Liu GE, Li J. Genome-wide analysis reveals differential selection involved with copy number variation in diverse Chinese Cattle. Sci Rep 2017; 7:14299. [PMID: 29085051 PMCID: PMC5662686 DOI: 10.1038/s41598-017-14768-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 10/12/2017] [Indexed: 12/20/2022] Open
Abstract
Copy number variations (CNVs) are defined as deletions, insertions, and duplications between two individuals of a species. To investigate the diversity and population-genetic properties of CNVs and their diverse selection patterns, we performed a genome-wide CNV analysis using high density SNP array in Chinese native cattle. In this study, we detected a total of 13,225 CNV events and 3,356 CNV regions (CNVRs), overlapping with 1,522 annotated genes. Among them, approximately 71.43 Mb of novel CNVRs were detected in the Chinese cattle population for the first time, representing the unique genomic resources in cattle. A new V i statistic was proposed to estimate the region-specific divergence in CNVR for each group based on unbiased estimates of pairwise V ST . We obtained 12 and 62 candidate CNVRs at the top 1% and top 5% of genome-wide V i value thresholds for each of four groups (North, Northwest, Southwest and South). Moreover, we identified many lineage-differentiated CNV genes across four groups, which were associated with several important molecular functions and biological processes, including metabolic process, response to stimulus, immune system, and others. Our findings provide some insights into understanding lineage-differentiated CNVs under divergent selection in the Chinese native cattle.
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Affiliation(s)
- Liu Yang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Lingyang Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Bo Zhu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Hong Niu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wengang Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jian Miao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Xinping Shi
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,College of Animal Science and Technology, Agricultural University of Hebei, Baoding, Hebei, 071001, China
| | - Ming Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yan Chen
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lupei Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xue Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Huijiang Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Li Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland, 20705, USA
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Lee D, Cho M, Hong WY, Lim D, Kim HC, Cho YM, Jeong JY, Choi BH, Ko Y, Kim J. Evolutionary Analyses of Hanwoo (Korean Cattle)-Specific Single-Nucleotide Polymorphisms and Genes Using Whole-Genome Resequencing Data of a Hanwoo Population. Mol Cells 2016; 39:692-8. [PMID: 27640093 PMCID: PMC5050534 DOI: 10.14348/molcells.2016.0148] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/10/2016] [Accepted: 08/16/2016] [Indexed: 01/08/2023] Open
Abstract
Advances in next generation sequencing (NGS) technologies have enabled population-level studies for many animals to unravel the relationships between genotypic differences and traits of specific populations. The objective of this study was to perform evolutionary analysis of single nucleotide polymorphisms (SNP) in genes of Korean native cattle Hanwoo in comparison to SNP data from four other cattle breeds (Jersey, Simmental, Angus, and Holstein) and four related species (pig, horse, human, and mouse) obtained from public databases through NGS-based resequencing. We analyzed population structures and differentiation levels for the five cattle breeds and estimated species-specific SNPs with their origins and phylogenetic relationships among species. In addition, we identified Hanwoo-specific genes and proteins, and determined distinct changes in protein-protein interactions among five species (cattle, pig, horse, human, mouse) in the STRING network database by additionally considering indirect protein interactions. We found that the Hanwoo population was clearly different from the other four cattle populations. There were Hanwoo-specific genes related to its meat trait. Protein interaction rewiring analysis also confirmed that there were Hanwoo-specific protein-protein interactions that might have contributed to its unique meat quality.
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Affiliation(s)
- Daehwan Lee
- Department of Stem Cell and Regenerative Biology, Konkuk University, Seoul 05029,
Korea
| | - Minah Cho
- Department of Stem Cell and Regenerative Biology, Konkuk University, Seoul 05029,
Korea
| | - Woon-young Hong
- Department of Stem Cell and Regenerative Biology, Konkuk University, Seoul 05029,
Korea
| | - Dajeong Lim
- National Institute of Animal Science, Wanju 55365,
Korea
| | - Hyung-Chul Kim
- National Institute of Animal Science, Wanju 55365,
Korea
| | - Yong-Min Cho
- National Institute of Animal Science, Wanju 55365,
Korea
| | | | - Bong-Hwan Choi
- National Institute of Animal Science, Wanju 55365,
Korea
| | - Younhee Ko
- Department of Clinical Genetics, Department of Pediatrics, Yonsei University College of Medicine, Seoul 03722,
Korea
| | - Jaebum Kim
- Department of Stem Cell and Regenerative Biology, Konkuk University, Seoul 05029,
Korea
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Durán Aguilar M, Román Ponce SI, Ruiz López FJ, González Padilla E, Vásquez Peláez CG, Bagnato A, Strillacci MG. Genome-wide association study for milk somatic cell score in holstein cattle using copy number variation as markers. J Anim Breed Genet 2016; 134:49-59. [PMID: 27578198 DOI: 10.1111/jbg.12238] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 08/03/2016] [Indexed: 12/21/2022]
Abstract
Mastitis, the most common and expensive disease in dairy cows, implies significant losses in the dairy industry worldwide. Many efforts have been made to improve genetic mastitis resistance in dairy populations, but low heritability of this trait made this process not as effective as desired. The purpose of this study was to identify genomic regions explaining genetic variation of somatic cell count using copy number variations (CNVs) as markers in the Holstein population, genotyped with the Illumina BovineHD BeadChip. We found 24 and 47 copy number variation regions significantly associated with estimated breeding values for somatic cell score (SCS_EBVs) using SVS 8.3.1 and PennCNV-CNVRuler software, respectively. The association analysis performed with these two software allowed the identification of 18 candidate genes (TERT, NOTCH1, SLC6A3, CLPTM1L, PPARα, BCL-2, ABO, VAV2, CACNA1S, TRAF2, RELA, ELF3, DBH, CDK5, NF2, FASN, EWSR1 and MAP3K11) that result classified in the same functional cluster. These genes are also part of two gene networks, whose genes share the 'stress', 'cell death', 'inflammation' and 'immune response' GO terms. Combining CNV detection/association analysis based on two different algorithms helps towards a more complete identification of genes linked to phenotypic variation of the somatic cell count.
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Affiliation(s)
- M Durán Aguilar
- Facultad de Estudios Superiores Cuautitlán, UNAM, Cuautitlán Izcalli, México
| | - S I Román Ponce
- Centro Nacional de Investigación en Fisiología y Mejoramiento Animal, INIFAP, Auchitlán, Querétaro, México
| | - F J Ruiz López
- Centro Nacional de Investigación en Fisiología y Mejoramiento Animal, INIFAP, Auchitlán, Querétaro, México
| | - E González Padilla
- Departamento de Genética y Bioestadística, Facultad Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, México DF, México
| | - C G Vásquez Peláez
- Departamento de Genética y Bioestadística, Facultad Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, México DF, México
| | - A Bagnato
- Department of Veterinary Medicine (DiMeVet), University of Milan, Milan, Italy
| | - M G Strillacci
- Department of Veterinary Medicine (DiMeVet), University of Milan, Milan, Italy
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