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Du L, Ma W, Peng W, Zhao H, Zhao J, Wang J, Wang W, Lyu S, Zhang Z, Qi X, Wang E, Lei C, Huang Y. Impact of STAT5A-CNVs on growth traits in Chinese beef cattle breeds. Gene 2024; 896:148073. [PMID: 38086453 DOI: 10.1016/j.gene.2023.148073] [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: 09/20/2023] [Revised: 11/30/2023] [Accepted: 12/08/2023] [Indexed: 12/18/2023]
Abstract
CNVs, which are a type of structural variation, make a substantial impact on diverse characteristics in multiple species. Q-PCR and data association analysis were used for STAT5A gene copy in this study. This study aimed to investigate the copy number variation (CNV) of the STAT5A gene in seven Chinese cattle breeds, namely Qinchuan cattle, Xianan cattle, Yunling cattle, Ji'an cattle, Jiaxian Red cattle, Qaidam cattle, and Guyuan yellow cattle. Blood samples were collected for CNV typing, and the correlation between CNV type and growth traits was analyzed using SPSS 23.0 software and ANOVA. The findings revealed variations in the distribution of different copy number types among the different cattle breeds. Furthermore, association analysis demonstrated a positive impact of CNV in the STAT5A gene on cattle growth: in the JX, individuals with duplication types exhibited superior performance in terms of rump length (P < 0.05). Conversely, normal GY cattle demonstrated better body height and abdomen circumference (P < 0.05), while QD cattle exhibited a significant correlation between weight and body length with normal individuals (P < 0.05). Moreover, QC bovine duplication individuals outperformed other types, with copy number variation significantly associated with chest depth, chest width, and body length (P < 0.05). The results validate the correlation between copy number variation (CNV) of the STAT5A gene and growth characteristics in five different cattle breeds, providing a reliable benchmark for the purpose of cattle breeding.
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Affiliation(s)
- Lei Du
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, People's Republic of China
| | - Weidong Ma
- Shaanxi Agricultural and Animal Husbandry Seed Farm, Shaanxi, Fufeng 722203, People's Republic of China
| | - Wei Peng
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, People's Republic of China
| | - Huangqing Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, People's Republic of China
| | - Jiahao Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, People's Republic of China
| | - Jiamei Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, People's Republic of China
| | - Wusheng Wang
- Shaanxi Agricultural and Animal Husbandry Seed Farm, Shaanxi, Fufeng 722203, People's Republic of China
| | - Shijie Lyu
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan 450008, People's Republic of China
| | - Zijing Zhang
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan 450008, People's Republic of China
| | - Xingshan Qi
- Biyang County Xiananniu Technology Development Co., Ltd, 463700, People's Republic of China
| | - Eryao Wang
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan 450008, People's Republic of China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, People's Republic of China
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, People's Republic of China
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Liu X, Chen W, Huang B, Wang X, Peng Y, Zhang X, Chai W, Khan MZ, Wang C. Advancements in copy number variation screening in herbivorous livestock genomes and their association with phenotypic traits. Front Vet Sci 2024; 10:1334434. [PMID: 38274664 PMCID: PMC10808162 DOI: 10.3389/fvets.2023.1334434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 12/27/2023] [Indexed: 01/27/2024] Open
Abstract
Copy number variations (CNVs) have garnered increasing attention within the realm of genetics due to their prevalence in human, animal, and plant genomes. These structural genetic variations have demonstrated associations with a broad spectrum of phenotypic diversity, economic traits, environmental adaptations, epidemics, and other essential aspects of both plants and animals. Furthermore, CNVs exhibit extensive sequence variability and encompass a wide array of genomes. The advancement and maturity of microarray and sequencing technologies have catalyzed a surge in research endeavors pertaining to CNVs. This is particularly prominent in the context of livestock breeding, where molecular markers have gained prominence as a valuable tool in comparison to traditional breeding methods. In light of these developments, a contemporary and comprehensive review of existing studies on CNVs becomes imperative. This review serves the purpose of providing a brief elucidation of the fundamental concepts underlying CNVs, their mutational mechanisms, and the diverse array of detection methods employed to identify these structural variations within genomes. Furthermore, it seeks to systematically analyze the recent advancements and findings within the field of CNV research, specifically within the genomes of herbivorous livestock species, including cattle, sheep, horses, and donkeys. The review also highlighted the role of CNVs in shaping various phenotypic traits including growth traits, reproductive traits, pigmentation and disease resistance etc., in herbivorous livestock. The main goal of this review is to furnish readers with an up-to-date compilation of knowledge regarding CNVs in herbivorous livestock genomes. By integrating the latest research findings and insights, it is anticipated that this review will not only offer pertinent information but also stimulate future investigations into the realm of CNVs in livestock. In doing so, it endeavors to contribute to the enhancement of breeding strategies, genomic selection, and the overall improvement of herbivorous livestock production and resistance to diseases.
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Affiliation(s)
| | | | | | | | | | | | | | - Muhammad Zahoor Khan
- Liaocheng Research Institute of Donkey High-Efficiency Breeding, Liaocheng University, Liaocheng, China
| | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding, Liaocheng University, Liaocheng, China
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Li L, Quan J, Liu H, Yu H, Chen H, Xia C, Zhao S, Gao C. Identification of the genetic characteristics of copy number variations in experimental specific pathogen-free ducks using whole-genome resequencing. BMC Genomics 2024; 25:17. [PMID: 38166615 PMCID: PMC10759622 DOI: 10.1186/s12864-023-09928-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Specific pathogen-free ducks are a valuable laboratory resource for waterfowl disease research and poultry vaccine development. High throughput sequencing allows the systematic identification of structural variants in genomes. Copy number variation (CNV) can explain the variation of important duck genetic traits. Herein, the genome-wide CNVs of the three experimental duck species in China (Jinding ducks (JD), Shaoxing ducks (SX), and Fujian Shanma ducks (SM)) were characterized using resequencing to determine their genetic characteristics and selection signatures. RESULTS We obtained 4,810 CNV regions (CNVRs) by merging 73,012 CNVs, covering 4.2% of the duck genome. Functional analysis revealed that the shared CNVR-harbored genes were significantly enriched for 31 gene ontology terms and 16 Kyoto Encyclopedia of Genes and Genomes pathways (e.g., olfactory transduction and immune system). Based on the genome-wide fixation index for each CNVR, growth (SPAG17 and PTH1R), disease resistance (CATHL3 and DMBT1), and thermoregulation (TRPC4 and SLIT3) candidate genes were identified in strongly selected signatures specific to JD, SM, and SX, respectively. CONCLUSIONS In conclusion, we investigated the genome-wide distribution of experimental duck CNVs, providing a reference to establish the genetic basis of different phenotypic traits, thus contributing to the management of experimental animal genetic resources.
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Affiliation(s)
- Lanlan Li
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, 730070, P.R. China
- College of Animal Science & Technology, Ningxia University, Yinchuan, 750021, P.R. China
| | - Jinqiang Quan
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, 730070, P.R. China.
| | - Hongyi Liu
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China
| | - Haibo Yu
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China
| | - Hongyan Chen
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China
| | - Changyou Xia
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China
| | - Shengguo Zhao
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, 730070, P.R. China
| | - Caixia Gao
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China.
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Zhu H, Lu X, Jiang H, Yang Z, Xu T. Descriptive Statistics and Genome-Wide Copy Number Analysis of Milk Production Traits of Jiangsu Chinese Holstein Cows. Animals (Basel) 2023; 14:17. [PMID: 38200748 PMCID: PMC10778490 DOI: 10.3390/ani14010017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/05/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Milk production traits are the most important quantitative economic traits in dairy cow production; improving the yield and quality of milk is an important way to ensure the production efficiency of the dairy industry. This study carried out a series of in-depth statistical genetics studies and molecular analyses on the Chinese Holstein cows in the Jiangsu Province, such as descriptive statistics and copy number variation analysis. A genetic correlation, phenotypic correlation, and descriptive statistical analysis of five milk production traits (milk yield, milk fat percentage, milk fat yield, milk protein percentage, and milk protein yield) of the dairy cows were analyzed using the SPSS and DMU software. Through quality control, 4173 cows and their genomes were used for genomic study. Then, SNPs were detected using DNA chips, and a copy number variation (CNV) analysis was carried out to locate the quantitative trait loci (QTL) of the milk production traits by Perl program software Penn CNV and hidden Markov model (HMM). The phenotypic means of the milk yield, milk fat percentage, milk fat mass, milk protein percentage, and milk protein mass at the first trimester were lower than those at the other trimesters by 8.821%, 1.031%, 0.930%, 0.003%, and 0.826%, respectively. The five milk production traits showed a significant phenotypic positive correlation (p < 0.01) and a high genetic positive correlation among the three parities. Based on the GGPBovine 100 K SNP data, QTL-detecting research on the fist-parity milk performance of dairy cows was carried out via the CNV. We identified 1731 CNVs and 236 CNVRs in the 29 autosomes of 984 Holstein dairy cows, and 19 CNVRs were significantly associated with the milk production traits (p < 0.05). These CNVRs were analyzed via a bioinformatics analysis; a total of 13 gene ontology (GO) terms and 20 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were significantly enriched (p < 0.05), and these terms and pathways are mainly related to lipid metabolism, amino acid metabolism, and cellular catabolic processes. This study provided a theoretical basis for the molecular-marker-assisted selection of dairy cows by developing descriptive statistics on the milk production traits of dairy cows and by locating the QTL and functional genes that affect the milk production traits of first-born dairy cows. The results describe the basic status of the milk production traits of the Chinese Holstein cows in Jiangsu and locate the QTL and functional genes that affect the milk production traits of the first-born cows, providing a theoretical basis for the molecular-marker-assisted selection of dairy cows.
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Affiliation(s)
- Hao Zhu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.Y.)
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China;
| | - Xubin Lu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China;
| | - Hui Jiang
- Center for Quantitative Genetics and Genomics, Aarhus University, 8000 Aarhus C, Denmark;
| | - Zhangping Yang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.Y.)
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China;
| | - Tianle Xu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.Y.)
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China;
- International Joint Research Laboratory, Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou 225009, China
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Yang Y, Tang J, Yang H, Yang S, Cai M, Qi A, Lan X, Huang B, Su C, Chen H. Copy number variation of bovine S100A7 as a positional candidate affected body measurements. Anim Biotechnol 2023; 34:2141-2149. [PMID: 35815693 DOI: 10.1080/10495398.2022.2077740] [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] [Indexed: 11/01/2022]
Abstract
Beef production is closely related to the national economy and the attention has been paid to the improvement of beef cattle by molecular markers associated. Copy number variations (CNVs) recently have been gained many researches and recognized as an important source of genetic variation. Extensive studies have indicated that CNVs have effects on a large range of economic traits by a wide range of gene copy number alteration. S100A7 is a member of S100 family which is a famous family of Ca2+-binding proteins. S100A7 plays a crucial role in many important phenotypes (progress) including inflammatory diseases, psoriasis, obesity, etc. The aim of our study was to explore the phenotypic effects of CNV located in the S100A7 gene of bovine chromosome 3. We detected S100A7 CNV by qPCR in different cattle breeds, including Qinchuan cattle, Yunling cattle, Xianan cattle and a crossbred group Pinan. The copy number was identified as gain, normal and loss type, our results showed that the gain type was the main type in three types of S100A7 CNV of the whole tested breeds. After CNV detection, association analysis between S100A7 CNV and growth traits was carried out in four cattle breeds. We found significant effects of the CNV on cattle growth traits with differently preferred CNV types such as gain type with better chest depth (p = 0.043) in QC, loss type with better body length (p = 0.008) and rump width (p = 0.014) in YL, normal with better chest girth (p = 0.001), gain with better waist width (p = 0.001) and rump width (p = 0.044) in PN. These results suggested that the S100A7 CNV could affect the phenotypic traits and be used as a promising genetic marker for cattle molecular breeding.
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Affiliation(s)
- Yu Yang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, China
| | - Jia Tang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, China
| | - Haiyan Yang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, China
| | - Shuling Yang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, China
| | - Ming Cai
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Ao Qi
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, China
| | - Xianyong Lan
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Chao Su
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, China
| | - Hong Chen
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, China
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
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Singh VK, Singh S, Nandhini PB, Bhatia AK, Dixit SP, Ganguly I. Comparative genomic diversity analysis of copy number variations (CNV) in indicine and taurine cattle thriving in Europe and Indian subcontinent. Anim Biotechnol 2023; 34:3483-3494. [PMID: 36592947 DOI: 10.1080/10495398.2022.2162910] [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] [Indexed: 01/04/2023]
Abstract
Copy number variations (CNVs) include deletions, duplications, and insertions that are larger than 50 bp in size causing structural variation responsible for diversity, adaptation, and breed development. Indian cattle breeds are highly diverse from the taurine breeds. The pattern of CNVRs in 191 animals belonging to 39 cattle breeds (four Indicine and 35 Taurine) was studied based on Illumina 777K BovineHD chip data. The Indicine breeds revealed 2590 CNVs and 335 copy number variation regions (CNVRs) in autosomes. Out of the identified CNVs, 50 were found to be novel. Structure analysis revealed admixed nature of Siri. Neighbor joining tree from CNVR data showed that hot (Kankrej and Hallikar) and cold (Ladakhi and Siri) adapted cattle breeds clustered separately. CNVR of Indian and European breeds revealed that Balkan and Italian breeds of Podolian group are admixed with Indian cattle breeds corroborating indicine introgression (6.1-13.5%). CNVRs spanning the regions of olfactory receptors and immune system genes were identified. AMOVA revealed 9% variation among populations which is 2% greater than SNP based studies showing higher inclusion of variation by CNVR. Detailed analysis of CNVs/CNVRs in Indian cattle adapted to hot and cold climate, and their diversity among worldwide cattle is presented in this study.
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Affiliation(s)
- V K Singh
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - S Singh
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - P B Nandhini
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - A K Bhatia
- Animal Genetic Resources Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - S P Dixit
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - I Ganguly
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
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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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Steensma MJ, Lee YL, Bouwman AC, Pita Barros C, Derks MFL, Bink MCAM, Harlizius B, Huisman AE, Crooijmans RPMA, Groenen MAM, Mulder HA, Rochus CM. Identification and characterisation of de novo germline structural variants in two commercial pig lines using trio-based whole genome sequencing. BMC Genomics 2023; 24:208. [PMID: 37072725 PMCID: PMC10114323 DOI: 10.1186/s12864-023-09296-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/04/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND De novo mutations arising in the germline are a source of genetic variation and their discovery broadens our understanding of genetic disorders and evolutionary patterns. Although the number of de novo single nucleotide variants (dnSNVs) has been studied in a number of species, relatively little is known about the occurrence of de novo structural variants (dnSVs). In this study, we investigated 37 deeply sequenced pig trios from two commercial lines to identify dnSVs present in the offspring. The identified dnSVs were characterised by identifying their parent of origin, their functional annotations and characterizing sequence homology at the breakpoints. RESULTS We identified four swine germline dnSVs, all located in intronic regions of protein-coding genes. Our conservative, first estimate of the swine germline dnSV rate is 0.108 (95% CI 0.038-0.255) per generation (one dnSV per nine offspring), detected using short-read sequencing. Two detected dnSVs are clusters of mutations. Mutation cluster 1 contains a de novo duplication, a dnSNV and a de novo deletion. Mutation cluster 2 contains a de novo deletion and three de novo duplications, of which one is inverted. Mutation cluster 2 is 25 kb in size, whereas mutation cluster 1 (197 bp) and the other two individual dnSVs (64 and 573 bp) are smaller. Only mutation cluster 2 could be phased and is located on the paternal haplotype. Mutation cluster 2 originates from both micro-homology as well as non-homology mutation mechanisms, where mutation cluster 1 and the other two dnSVs are caused by mutation mechanisms lacking sequence homology. The 64 bp deletion and mutation cluster 1 were validated through PCR. Lastly, the 64 bp deletion and the 573 bp duplication were validated in sequenced offspring of probands with three generations of sequence data. CONCLUSIONS Our estimate of 0.108 dnSVs per generation in the swine germline is conservative, due to our small sample size and restricted possibilities of dnSV detection from short-read sequencing. The current study highlights the complexity of dnSVs and shows the potential of breeding programs for pigs and livestock species in general, to provide a suitable population structure for identification and characterisation of dnSVs.
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Affiliation(s)
- Marije J Steensma
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands.
| | - Y L Lee
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
| | - A C Bouwman
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
| | - C Pita Barros
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
| | - M F L Derks
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
- Topigs Norsvin Research Center, Schoenaker 6, Beuningen, 6641 SZ, the Netherlands
| | - M C A M Bink
- Hendrix Genetics, P.O. Box 114, Boxmeer, 5830 AC, the Netherlands
| | - B Harlizius
- Topigs Norsvin Research Center, Schoenaker 6, Beuningen, 6641 SZ, the Netherlands
| | - A E Huisman
- Hendrix Genetics, P.O. Box 114, Boxmeer, 5830 AC, the Netherlands
| | - R P M A Crooijmans
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
| | - M A M Groenen
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
| | - H A Mulder
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands
| | - C M Rochus
- University of Guelph, Centre for Genetic Improvement of Livestock, 50 Stone Rd E, Guelph, O N, N1G 2W1, Canada
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Braga LG, Chud TCS, Watanabe RN, Savegnago RP, Sena TM, do Carmo AS, Machado MA, Panetto JCDC, da Silva MVGB, Munari DP. Identification of copy number variations in the genome of Dairy Gir cattle. PLoS One 2023; 18:e0284085. [PMID: 37036840 PMCID: PMC10085049 DOI: 10.1371/journal.pone.0284085] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 03/23/2023] [Indexed: 04/11/2023] Open
Abstract
Studying structural variants that can control complex traits is relevant for dairy cattle production, especially for animals that are tolerant to breeding conditions in the tropics, such as the Dairy Gir cattle. This study identified and characterized high confidence copy number variation regions (CNVR) in the Gir breed genome. A total of 38 animals were whole-genome sequenced, and 566 individuals were genotyped with a high-density SNP panel, among which 36 animals had both sequencing and SNP genotyping data available. Two sets of high confidence CNVR were established: one based on common CNV identified in the studied population (CNVR_POP), and another with CNV identified in sires with both sequence and SNP genotyping data available (CNVR_ANI). We found 10 CNVR_POP and 45 CNVR_ANI, which covered 1.05 Mb and 4.4 Mb of the bovine genome, respectively. Merging these CNV sets for functional analysis resulted in 48 unique high confidence CNVR. The overlapping genes were previously related to embryonic mortality, environmental adaptation, evolutionary process, immune response, longevity, mammary gland, resistance to gastrointestinal parasites, and stimuli recognition, among others. Our results contribute to a better understanding of the Gir breed genome. Moreover, the CNV identified in this study can potentially affect genes related to complex traits, such as production, health, and reproduction.
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Affiliation(s)
- Larissa G Braga
- Departamento de Engenharia e Ciências Exatas, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brazil
| | - Tatiane C S Chud
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada
| | - Rafael N Watanabe
- Departamento de Engenharia e Ciências Exatas, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brazil
| | - Rodrigo P Savegnago
- Department of Animal Science, Michigan State University, East Lansing, Michigan, United States of America
| | - Thomaz M Sena
- Departamento de Engenharia e Ciências Exatas, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brazil
| | - Adriana S do Carmo
- Departamento de Zootecnia, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | | | | | | | - Danísio P Munari
- Departamento de Engenharia e Ciências Exatas, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brazil
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10
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Davoudi P, Do DN, Rathgeber B, Colombo SM, Sargolzaei M, Plastow G, Wang Z, Karimi K, Hu G, Valipour S, Miar Y. Genome-wide detection of copy number variation in American mink using whole-genome sequencing. BMC Genomics 2022; 23:649. [PMID: 36096727 PMCID: PMC9468235 DOI: 10.1186/s12864-022-08874-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/05/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Copy number variations (CNVs) represent a major source of genetic diversity and contribute to the phenotypic variation of economically important traits in livestock species. In this study, we report the first genome-wide CNV analysis of American mink using whole-genome sequence data from 100 individuals. The analyses were performed by three complementary software programs including CNVpytor, DELLY and Manta. RESULTS A total of 164,733 CNVs (144,517 deletions and 20,216 duplications) were identified representing 5378 CNV regions (CNVR) after merging overlapping CNVs, covering 47.3 Mb (1.9%) of the mink autosomal genome. Gene Ontology and KEGG pathway enrichment analyses of 1391 genes that overlapped CNVR revealed potential role of CNVs in a wide range of biological, molecular and cellular functions, e.g., pathways related to growth (regulation of actin cytoskeleton, and cAMP signaling pathways), behavior (axon guidance, circadian entrainment, and glutamatergic synapse), lipid metabolism (phospholipid binding, sphingolipid metabolism and regulation of lipolysis in adipocytes), and immune response (Wnt signaling, Fc receptor signaling, and GTPase regulator activity pathways). Furthermore, several CNVR-harbored genes associated with fur characteristics and development (MYO5A, RAB27B, FGF12, SLC7A11, EXOC2), and immune system processes (SWAP70, FYN, ORAI1, TRPM2, and FOXO3). CONCLUSIONS This study presents the first genome-wide CNV map of American mink. We identified 5378 CNVR in the mink genome and investigated genes that overlapped with CNVR. The results suggest potential links with mink behaviour as well as their possible impact on fur quality and immune response. Overall, the results provide new resources for mink genome analysis, serving as a guideline for future investigations in which genomic structural variations are present.
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Affiliation(s)
- Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Duy Ngoc Do
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Bruce Rathgeber
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Stefanie M Colombo
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
- Select Sires Inc., Plain City, OH, USA
| | - Graham Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Zhiquan Wang
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Karim Karimi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Guoyu Hu
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Shafagh Valipour
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada.
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11
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Igoshin AV, Romashov GA, Chernyaeva EN, Elatkin NP, Yudin NS, Larkin DM. Comparative analysis of allele frequencies for DNA polymorphisms associated with disease and economically important traits in the genomes of Russian and foreign cattle breeds. Vavilovskii Zhurnal Genet Selektsii 2022; 26:298-307. [PMID: 35774360 PMCID: PMC9167823 DOI: 10.18699/vjgb-22-28] [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: 11/30/2021] [Revised: 12/20/2021] [Accepted: 12/30/2021] [Indexed: 11/19/2022] Open
Abstract
The genetic makeup of a breed including its genetic differences from other breeds determines its appearance and characteristics, including economically important traits and resistance to pathologies. To date, many loci controlling significant phenotypes have been identified, which is successfully used in the world practice of marker-assisted selection to improve breed properties. The aim of this study was a comparative analysis of frequencies for known causative nucleotide substitutions, insertions and deletions associated with disease and economically important traits in Russian and foreign cattle breeds. As a result, we identified frequencies of these DNA polymorphisms in the populations of Russian cattle breeds, compared them with those of foreign populations of the same breed, as well as other foreign breeds. Our results indicate similarities in frequencies for most of such alleles within breeds (populations of Russian and foreign breeding), as well as the relationship between the causative allele prevalence and the presence of phenotypic traits under the effect. We also found an excess of some undesirable alleles in the Russian cattle populations, which should be paid attention to when designing breeding programs. We found that the alleles increasing fertility in the Hereford breed have a higher frequency in the Russian Hereford population compared to the foreign counterpart. Interestingly, unlike for the European breeds, for Asian Turano-Mongolian Wagyu and Yakut cattle, there was a less clear link between phenotypic traits and frequencies of known causative alleles. Our work points to specific genetic variants that could be used to improve and/or maintain the performance of certain cattle breeds bred in the Russian Federation.
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Affiliation(s)
- A. V. Igoshin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - G. A. Romashov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | | | | | - N. S. Yudin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
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12
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The copy number variation of DMBT1 gene effects body traits in two Chinese cattle breeds. 3 Biotech 2022; 12:93. [PMID: 35342679 PMCID: PMC8921421 DOI: 10.1007/s13205-022-03124-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 01/23/2022] [Indexed: 11/01/2022] Open
Abstract
Copy number variations (CNVs) belong to mutations in the genome level with loci in the region of genic or intergenic. It is through different effects (such as position effect and dose effect) that influence complex traits and diseases. Deleted in Malignant Brain Tumors 1 (DMBT1) gene is a member of the scavenger receptor cysteine-rich super family. In cattle, this gene has been associated with the susceptibility to bovine tuberculosis. In this study, a new CNV was found in DMBT1 gene of Chinese cattle breeds and tested in two different Chinese cattle breeds (Jiaxian red and Pinan) for frequency distribution analysis. Besides, the body size data such as body length, body height, chest girth, chest width, rump length, and rump girth for Jiaxian (JX) and Pinan (PN) cattle were collected and associated with the newly identified CNV. The CNV was significantly associated with the body length and chest girth of JX cattle, and the rump length of PN cattle (P < 0.05). Furthermore, the expression profile of the DMBT1 gene was tested in calves' tissues and the myoblasts differentiation. It was found that the DMBT1 gene expression was high in tuberculosis susceptible tissues (liver and lungs) at the calf stage and high in myoblast early differentiation. These tests were done using the qPCR method. As the result, the CNV of DMBT1 gene could be used as a candidate marker for bovine growth and health in marker-assisted selection (MAS) breeding.
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13
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Yao Z, Li J, Zhang Z, Chai Y, Liu X, Li J, Huang Y, Li L, Huang W, Yang G, Chen F, Shi Q, Ru B, Lei C, Wang E, Huang Y. The relationship between MFN1 copy number variation and growth traits of beef cattle. Gene 2022; 811:146071. [PMID: 34864096 DOI: 10.1016/j.gene.2021.146071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/22/2021] [Accepted: 11/16/2021] [Indexed: 02/05/2023]
Abstract
Copy number variation, as a kind of genetic submicroscopic structural variation, refers to the deletion or repetition of a large segment of genomic DNA, involving a segment size ranging from 50 bp to several MB. Mitochondrial fusion protein (MFN1) gene regulates the fusion of mitochondrial outer membrane in cells and maintains the dynamic needs of reticular mitochondria in cells. In this study, we conducted to tested the dstribution characteristics of MFN1-CNV in 522 cattles across Xianan cattle (XN), Pinan cattle (PN), Qinchuan cattle (QC), Jiaxian cattle (JX), Yunling cattle (YL), and correlated it with phenotypic traits. Then we observed the expression of MFN1 in various tissues of QC cattle (n = 3), and the expression levels were higher in lung and muscle. The results showed that there was significant correlation between MFN1 gene CNV and hucklebone width of QC cattle, hip width and height at sacrum of JX red cattle, chest width and rump length of YL cattle (P < 0.05). Individuals with duplication type were better than the type of normal or deletion in phenotypic traits. In conclusion, our data showed the correlation between MFN1 gene and growth traits of Chinese cattle. MFN1 gene can be used as a molecular marker for cattle selection and breeding, and accelerate the improvement of Chinese cattle.
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Affiliation(s)
- Zhi Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling Shanxi, 712100, People's Republic of China
| | - Jiaxiao Li
- College of Animal Science and Technology, Northwest A&F University, Yangling Shanxi, 712100, People's Republic of China
| | - Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, People's Republic of China
| | - Yanan Chai
- College of Animal Science and Technology, Northwest A&F University, Yangling Shanxi, 712100, People's Republic of China
| | - Xian Liu
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan 450008, People's Republic of China
| | - Jungang Li
- Jiaxian Animal Husbandry Bureau, Jiaxian Henan 467100, People's Republic of China
| | - Yajun Huang
- Jiaxian Animal Husbandry Bureau, Jiaxian Henan 467100, People's Republic of China
| | - Lijuan Li
- Jiaxian Animal Husbandry Bureau, Jiaxian Henan 467100, People's Republic of China
| | - Weihong Huang
- Jiaxian Animal Husbandry Bureau, Jiaxian Henan 467100, People's Republic of China
| | - Guojie Yang
- Jiaxian Animal Husbandry Bureau, Jiaxian Henan 467100, People's Republic of China
| | - Fuying Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling Shanxi, 712100, People's Republic of China
| | - Qiaoting Shi
- College of Animal Science and Technology, Northwest A&F University, Yangling Shanxi, 712100, People's Republic of China
| | - Baorui Ru
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan 450008, People's Republic of China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling Shanxi, 712100, People's Republic of China
| | - Eryao Wang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, People's Republic of China.
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling Shanxi, 712100, People's Republic of China.
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14
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Yang H, Yue B, Yang Y, Tang J, Yang S, Qi A, Qu K, Lan X, Lei C, Wei Z, Huang B, Chen H. Distribution of Copy Number Variation in SYT11 Gene and Its Association with Growth Conformation Traits in Chinese Cattle. BIOLOGY 2022; 11:biology11020223. [PMID: 35205089 PMCID: PMC8869484 DOI: 10.3390/biology11020223] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 12/01/2022]
Abstract
Simple Summary It is known that many different breeds of cattle are widely distributed in China. However, due to a lengthy selection of draught direction, there are obvious shortcomings in Chinese cattle, such as less meat production, slow weight gain, poor meat quality, and a lack of specialized beef cattle breeds. Animal breeding heavily benefits from molecular technologies, among which molecular genetic markers were widely used to improve the economic traits of beef cattle. Because the copy number variation (CNV) involves a longer DNA sequence or even the entire functional gene, it may have a greater impact on the phenotype. Recent studies have indicated that CNVs are widespread in the Chinese cattle genome. By investigating the effects of CNVs on gene expression and cattle traits, we aim to find those genomic variations which could significantly affect cattle traits, and which could provide a basis for genetic selection and molecular breeding of local Chinese cattle. Abstract Currently, studies of the SYT11 gene mainly focus on neurological diseases such as schizophrenia and Parkinson’s disease. However, some studies have shown that the C2B domain of SYT11 can interact with RISC components and affect the gene regulation of miRNA, which is important for cell differentiation, proliferation, and apoptosis, and therefore has an impact on muscle growth and development in animals. The whole-genome resequencing data detected a CNV in the SYT11 gene, and this may affect cattle growth traits. In this study, CNV distribution of 672 individuals from four cattle breeds, Yunling, Pinan, Xianan, and Qinchuan, were detected by qPCR. The relationship between CNV, gene expression and growth traits was further investigated. The results showed that the proportion of multiple copy types was the largest in all cattle breeds, but there were some differences among different breeds. The normal type had higher gene expression than the abnormal copy type. The CNVs of the SYT11 gene were significantly correlated with body length, cannon circumference, chest depth, rump length, and forehead size of Yunling cattle, and was significantly correlated with the bodyweight of Xianan cattle, respectively. These data improve our understanding of the effects of CNV on cattle growth traits. Our results suggest that the CNV of SYT11 gene is a protentional molecular marker, which may be used to improve growth traits in Chinese cattle.
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Affiliation(s)
- Haiyan Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China; (H.Y.); (B.Y.); (Y.Y.); (J.T.); (S.Y.); (A.Q.); (X.L.); (C.L.)
| | - Binglin Yue
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China; (H.Y.); (B.Y.); (Y.Y.); (J.T.); (S.Y.); (A.Q.); (X.L.); (C.L.)
| | - Yu Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China; (H.Y.); (B.Y.); (Y.Y.); (J.T.); (S.Y.); (A.Q.); (X.L.); (C.L.)
| | - Jia Tang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China; (H.Y.); (B.Y.); (Y.Y.); (J.T.); (S.Y.); (A.Q.); (X.L.); (C.L.)
| | - Shuling Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China; (H.Y.); (B.Y.); (Y.Y.); (J.T.); (S.Y.); (A.Q.); (X.L.); (C.L.)
| | - Ao Qi
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China; (H.Y.); (B.Y.); (Y.Y.); (J.T.); (S.Y.); (A.Q.); (X.L.); (C.L.)
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong 675000, China;
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China; (H.Y.); (B.Y.); (Y.Y.); (J.T.); (S.Y.); (A.Q.); (X.L.); (C.L.)
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China; (H.Y.); (B.Y.); (Y.Y.); (J.T.); (S.Y.); (A.Q.); (X.L.); (C.L.)
| | - Zehui Wei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China; (H.Y.); (B.Y.); (Y.Y.); (J.T.); (S.Y.); (A.Q.); (X.L.); (C.L.)
- Correspondence: (Z.W.); (B.H.); (H.C.)
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming 650212, China
- Correspondence: (Z.W.); (B.H.); (H.C.)
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China; (H.Y.); (B.Y.); (Y.Y.); (J.T.); (S.Y.); (A.Q.); (X.L.); (C.L.)
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
- Correspondence: (Z.W.); (B.H.); (H.C.)
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15
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Yudin NS, Yurchenko AA, Larkin DM. [Signatures of selection and candidate genes for adaptation to extreme environmental factors in the genomes of Turano-Mongolian cattle breeds]. Vavilovskii Zhurnal Genet Selektsii 2021; 25:190-201. [PMID: 34901717 PMCID: PMC8627871 DOI: 10.18699/vj21.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/18/2020] [Accepted: 10/20/2020] [Indexed: 11/19/2022] Open
Abstract
Changes in the environment force populations of organisms to adapt to new conditions, either through phenotypic plasticity or through genetic or epigenetic changes. Signatures of selection, such as specific changes in the frequency of alleles and haplotypes, as well as the reduction or increase in genetic diversity, help to identify changes in the cattle genome in response to natural and artificial selection, as well as loci and genetic variants directly affecting adaptive and economically important traits. Advances in genetics and biotechnology enable a rapid transfer of unique genetic variants that have originated in local cattle breeds in the process of adaptation to local environments into the genomes of cosmopolitan high-performance breeds, in order to preserve their outstanding performance in new environments. It is also possible to use genomic selection approach to increase the frequency of already present adaptive alleles in cosmopolitan breeds. The review examines recent work on the origin and evolution of Turano-Mongolian cattle breeds, adaptation of Turano-Mongolian cattle to extreme environments, and summarizes available information on potential candidate genes for climate adaptation of Turano-Mongolian breeds, including cold resistance genes, immune response genes, and high-altitude adaptation genes. The authors conclude that the current literature data do not provide preference to one of the two possible scenarios of Turano-Mongolian breed origins: as a result of the domestication of a wild aurochs at East Asia or as a result of the migration of taurine proto-population from the Middle East. Turano-Mongolian breeds show a high degree of adaptation to extreme climatic conditions (cold, heat, lack of oxygen in the highlands) and parasites (mosquitoes, ticks, bacterial and viral infections). As a result of high-density genotyping and sequencing of genomes and transcriptomes, prospective candidate genes and genetic variants involved in adaptation to environmental factors have recently been identified.
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Affiliation(s)
- N S Yudin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Yurchenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - D M Larkin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia The Royal Veterinary College, University of London, London, United Kingdom
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16
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Jang J, Kim K, Lee YH, Kim H. Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids. BMC Genomics 2021; 22:531. [PMID: 34253178 PMCID: PMC8276479 DOI: 10.1186/s12864-021-07808-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/10/2021] [Indexed: 01/10/2023] Open
Abstract
Background CNV comprises a large proportion in cattle genome and is associated with various traits. However, there were few population-scale comparison studies on cattle CNV. Results Here, autosome-wide CNVs were called by read depth of NGS alignment result and copy number variation regions (CNVRs) defined from 102 Eurasian taurine (EAT) of 14 breeds, 28 Asian indicine (ASI) of 6 breeds, 22 African taurine (AFT) of 2 breeds, and 184 African humped cattle (AFH) of 17 breeds. The copy number of every CNVRs were compared between populations and CNVRs with population differentiated copy numbers were sorted out using the pairwise statistics VST and Kruskal-Wallis test. Three hundred sixty-two of CNVRs were significantly differentiated in both statistics and 313 genes were located on the population differentiated CNVRs. Conclusion For some of these genes, the averages of copy numbers were also different between populations and these may be candidate genes under selection. These include olfactory receptors, pathogen-resistance, parasite-resistance, heat tolerance and productivity related genes. Furthermore, breed- and individual-level comparison was performed using the presence or copy number of the autosomal CNVRs. Our findings were based on identification of CNVs from short Illumina reads of 336 individuals and 39 breeds, which to our knowledge is the largest dataset for this type of analysis and revealed important CNVs that may play a role in cattle adaption to various environments. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07808-7.
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Affiliation(s)
- Jisung Jang
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Kwondo Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Young Ho Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Heebal Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea. .,Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea. .,eGnome, Inc, Seoul, South Korea.
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17
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Nandolo W, Mészáros G, Wurzinger M, Banda LJ, Gondwe TN, Mulindwa HA, Nakimbugwe HN, Clark EL, Woodward-Greene MJ, Liu M, Liu GE, Van Tassell CP, Rosen BD, Sölkner J. Detection of copy number variants in African goats using whole genome sequence data. BMC Genomics 2021; 22:398. [PMID: 34051743 PMCID: PMC8164248 DOI: 10.1186/s12864-021-07703-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/11/2021] [Indexed: 12/21/2022] Open
Abstract
Background Copy number variations (CNV) are a significant source of variation in the genome and are therefore essential to the understanding of genetic characterization. The aim of this study was to develop a fine-scaled copy number variation map for African goats. We used sequence data from multiple breeds and from multiple African countries. Results A total of 253,553 CNV (244,876 deletions and 8677 duplications) were identified, corresponding to an overall average of 1393 CNV per animal. The mean CNV length was 3.3 kb, with a median of 1.3 kb. There was substantial differentiation between the populations for some CNV, suggestive of the effect of population-specific selective pressures. A total of 6231 global CNV regions (CNVR) were found across all animals, representing 59.2 Mb (2.4%) of the goat genome. About 1.6% of the CNVR were present in all 34 breeds and 28.7% were present in all 5 geographical areas across Africa, where animals had been sampled. The CNVR had genes that were highly enriched in important biological functions, molecular functions, and cellular components including retrograde endocannabinoid signaling, glutamatergic synapse and circadian entrainment. Conclusions This study presents the first fine CNV map of African goat based on WGS data and adds to the growing body of knowledge on the genetic characterization of goats. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07703-1.
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Affiliation(s)
- Wilson Nandolo
- University of Natural Resources and Life Sciences, Vienna, Austria.,Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
| | - Gábor Mészáros
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Maria Wurzinger
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Liveness J Banda
- Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
| | - Timothy N Gondwe
- Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
| | | | | | - Emily L Clark
- The Roslin Institute, University of Edinburgh, Edinburgh, Scotland, UK
| | - M Jennifer Woodward-Greene
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, USA.,National Agricultural Library, USDA-ARS, Beltsville, MD, USA
| | - Mei Liu
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, USA
| | | | - George E Liu
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, USA
| | | | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, USA.
| | - Johann Sölkner
- University of Natural Resources and Life Sciences, Vienna, Austria
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18
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Mei C, Gui L, Hong J, Raza SHA, Aorigele C, Tian W, Garcia M, Xin Y, Yang W, Zhang S, Zan L. Insights into adaption and growth evolution: a comparative genomics study on two distinct cattle breeds from Northern and Southern China. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 23:959-967. [PMID: 33614243 PMCID: PMC7868925 DOI: 10.1016/j.omtn.2020.12.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/31/2020] [Indexed: 11/29/2022]
Abstract
Mongolian cattle (MG, Bos taurus) and Minnan cattle (MN, Bos indicus) are two different breeds of Chinese indigenous cattle, representing North type and South type, respectively. However, their value and potential have not yet been discovered at the genomic level. In this study, 26 individuals of MN and MG were sequenced for the first time at an average of 13.9- and 12.8-fold, respectively. Large numbers of different variations were identified. In addition, the analyses of phylogenetic and population structure showed that these two cattle breeds are distinct from each other, and results of linkage disequilibrium analysis revealed that these two cattle breeds have undergone various degrees of intense natural or artificial selection. Subsequently, 496 and 306 potential selected genes (PSRs) were obtained in MN and MG, containing 1,096 and 529 potential selected genes (PSGs), respectively. These PSGs, together with the analyzed copy number variation (CNV)-related genes, showed potential relations with their phenotypic characteristics, including environmental adaptability (e.g., DVL2, HSPA4, CDHR4), feed efficiency (e.g., R3HDM1, PLAG1, XKR4), and meat/milk production (e.g., PDHB, LEMD3, APOF). The results of this study help to gain new insights into the genetic characteristics of two distinct cattle breeds and will contribute to future cattle breeding.
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Affiliation(s)
- Chugang Mei
- Northwest A&F University, Yangling 712100, Shaanxi, China.,National Beef Cattle Improvement Center, Yangling 712100, China
| | - Linsheng Gui
- Northwest A&F University, Yangling 712100, Shaanxi, China.,Qinghai University, Xining 810008, China
| | - Jieyun Hong
- Northwest A&F University, Yangling 712100, Shaanxi, China.,Yunnan Agricultural University, Kunming 650031, China
| | | | - Chen Aorigele
- Inner Mongolia Agricultural University, Hohhot 010000, China
| | - Wanqiang Tian
- Yangling Vocational & Technical College, Yangling 712100, China
| | | | - Yaping Xin
- Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wucai Yang
- Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Song Zhang
- Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Linsen Zan
- Northwest A&F University, Yangling 712100, Shaanxi, China.,National Beef Cattle Improvement Center, Yangling 712100, China
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19
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Xu Z, Wang X, Zhang Z, An Q, Wen Y, Wang D, Liu X, Li Z, Lyu S, Li L, Wang E, Ru B, Xu Z, Huang Y. Copy number variation of CADM2 gene revealed its association with growth traits across Chinese Capra hircus (goat) populations. Gene 2020; 741:144519. [PMID: 32126252 DOI: 10.1016/j.gene.2020.144519] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/26/2020] [Accepted: 02/28/2020] [Indexed: 12/15/2022]
Abstract
Copy number variations (CNVs) are the wide structural variations ranging from 50 bp to several Mb at genome which can affect gene expression and further impacting growth and development traits of livestock. Comparing with single nucleotide polymorphisms (SNPs), CNVs can better explain the genetic and phenotypic diversity, are increasingly important in biological research. As a member of immunoglobulin super-family, cell adhesion molecule 2 (CADM2) plays a vital role in cancer development and metabolic regulation. Here, we tested the CNV of CADM2 gene in 443 goats across five breeds (Guizhou white goat, GZW; Guizhou black goat, GZB; Africa Nubian goat, AN; Boer goat × Huai goat, BH; Boer goat, BG) and detected its association with phenotypic traits. Subsequently, we analyzed the CADM2 gene expression level in different tissues of NB goats (n = 3, Nubian × Black) and the transcriptional expression in lung is much higher than others. The results showed that the CNV of CADM2 has a significant association with withers height and body length in GZB goat (P < 0.01), in which individuals with type of deletion were superior to those with duplication or normal type in term of body hight and body length (P < 0.01). In summary, this study confirmed the association between CNV of CADM2 gene and growth traits, and our research data indicated the CADM2-CNV may considered as a prospective candidate for the molecular marker-assisted selection breeding of goat growth traits, which conducived to accelerating the genetic amelioration in Chinese goats.
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Affiliation(s)
- Zijie Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China.
| | - Xianwei Wang
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan 450008, People's Republic of China
| | - Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, People's Republic of China
| | - Qingming An
- College of Agriculture and Forestry Engineering, Tongren University, Tongren, Guizhou 554300, People's Republic of China
| | - Yifan Wen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Dahui Wang
- College of Agriculture and Forestry Engineering, Tongren University, Tongren, Guizhou 554300, People's Republic of China
| | - Xian Liu
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan 450008, People's Republic of China
| | - Zhiming Li
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan 450008, People's Republic of China
| | - Shijie Lyu
- College of Agriculture and Forestry Engineering, Tongren University, Tongren, Guizhou 554300, People's Republic of China
| | - Lijuan Li
- Guizhou University of Engineering Science, Institute of Bijie Test Area, Bijie, Guizhou 551700, People's Republic of China
| | - Eryao Wang
- College of Agriculture and Forestry Engineering, Tongren University, Tongren, Guizhou 554300, People's Republic of China
| | - Baorui Ru
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan 450008, People's Republic of China
| | - Zejun Xu
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan 450008, People's Republic of China
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China.
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20
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Yang P, Zhang Z, Xu J, Qu K, Lyv S, Wang X, Cai C, Li Z, Wang E, Xie J, Ru B, Xu Z, Lei C, Chen H, Huang B, Huang Y. The Association of the Copy Number Variation of the MLLT10 Gene with Growth Traits of Chinese Cattle. Animals (Basel) 2020; 10:ani10020250. [PMID: 32033330 PMCID: PMC7070264 DOI: 10.3390/ani10020250] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/10/2020] [Accepted: 02/01/2020] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Copy number variation is a common genetic polymorphism, mainly represented by submicroscopic levels of deletion and duplication, caused by rearrangement of the genome. It is well-known that the copy number variation of a gene is associated with growth traits of livestock. In this study, we detected the correlation between the copy number variation of the the MLLT10 gene and the growth traits of Chinese yellow cattle. We found that the copy number variation of the MLLT10 gene has a significant influence on hip width, rump length, hucklebone width, and cannon bone circumference of some Chinese yellow cattle breeds. The results provide preliminary suggestions for Chinese yellow cattle breeding and new insights about the future of copy number variation (CNV) as a new promising molecular marker in animal breeding. Abstract Copy number variation is a part of genomic structural variation and has caused widespread concern. According to the results of high-throughput screening of the MLLT10 gene, we found that the copy number variation region of the MLLT10 gene was correlated with bovine growth traits. We aimed to detect the MLLT10 gene copy number variation and provide materials for the Chinese yellow cattle breed. In this study, the SPSS software was used to analyze the correlation among the copy number type of six different cattle breeds (i.e., Qinchuan, Xianan, Jiaxian, Yanbian, Sinan, Yunling) and the corresponding growth traits. The results showed the following: In Qinchuan cattle, the copy number duplication type was greater than the deletion and normal types; in Xianan cattle, the copy number duplication and normal types were less as compared with the deletion type; and in Yunling cattle, the frequency of the duplication type was dominant among the three types of copy number variants. The correlation analysis result showed that there is a significant correlation between the copy number variation (CNV) of the MLLT10 gene and the growth traits of three cattle breeds. Furthermore, correlation analysis showed that MLLT10 CNV had positive effects on growth traits such as hip width, rump length, hucklebone width, and cannon bone circumference (p < 0.05). This study provides a basis for the molecular-assisted marker breeding of cattle and contributes to the breeding of cattle.
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Affiliation(s)
- Peng Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (P.Y.); (J.X.); (C.L.); (H.C.)
| | - Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 45002, China; (Z.Z.); (S.L.); (E.W.)
| | - Jiawei Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (P.Y.); (J.X.); (C.L.); (H.C.)
| | - Kaixing Qu
- Yunnan Academy of Grassland Animal Science, Kunming 650212, China;
| | - Shijie Lyv
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 45002, China; (Z.Z.); (S.L.); (E.W.)
| | - Xianwei Wang
- Henan Provincial Animal Husbandry General Station, Zhengzhou 450008, China; (X.W.); (Z.L.); (B.R.); (Z.X.)
| | - Cuicui Cai
- Guyuan Branch of Ningxia Academy of Agriculture and Forestry Sciences, Guyuan 756000, China; (C.C.); (J.X.)
| | - Zhiming Li
- Henan Provincial Animal Husbandry General Station, Zhengzhou 450008, China; (X.W.); (Z.L.); (B.R.); (Z.X.)
| | - Eryao Wang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 45002, China; (Z.Z.); (S.L.); (E.W.)
| | - Jianliang Xie
- Guyuan Branch of Ningxia Academy of Agriculture and Forestry Sciences, Guyuan 756000, China; (C.C.); (J.X.)
| | - Baorui Ru
- Henan Provincial Animal Husbandry General Station, Zhengzhou 450008, China; (X.W.); (Z.L.); (B.R.); (Z.X.)
| | - Zejun Xu
- Henan Provincial Animal Husbandry General Station, Zhengzhou 450008, China; (X.W.); (Z.L.); (B.R.); (Z.X.)
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (P.Y.); (J.X.); (C.L.); (H.C.)
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (P.Y.); (J.X.); (C.L.); (H.C.)
| | - Bizhi Huang
- Yunnan Academy of Grassland Animal Science, Kunming 650212, China;
- Correspondence: (B.H.); (Y.H.)
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (P.Y.); (J.X.); (C.L.); (H.C.)
- Correspondence: (B.H.); (Y.H.)
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21
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Mei C, Junjvlieke Z, Raza SHA, Wang H, Cheng G, Zhao C, Zhu W, Zan L. Copy number variation detection in Chinese indigenous cattle by whole genome sequencing. Genomics 2019; 112:831-836. [PMID: 31145994 DOI: 10.1016/j.ygeno.2019.05.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/30/2019] [Accepted: 05/25/2019] [Indexed: 12/15/2022]
Abstract
Copy number variation (CNV) refers to a kind of structural variation, having functional and evolutionary effects on phenotypes. Thus far, further elucidation of the CNVs in different Chinese indigenous cattle breeds by whole genome sequencing have yet not been done. In this study, a comprehensive genomic analysis was performed on 75 cattle individuals including six Chinese indigenous cattle breeds and two non-native specialized beef cattle breeds. Based on the 11,486 CNVRs discovered, population analysis was performed, showed that all the cattle breeds clustered in to three clades, consistent with their lineages Bos taurus, Bos taurus × Bos indicus and Bos indicus. Importantly, a set of CNVRs related genes were found to be associated with the traits of interest, which include meat production or quality (CAST, ACTC1, etc.), adaption (BLA-DQB, EGLN2, etc.) and coat color (KIT, MITF, etc.). These results provide valuable full genome variation resources for Chinese bovine genome research and would be helpful for cattle breeding and selection programs in the future.
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Affiliation(s)
- Chugang Mei
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Zainaguli Junjvlieke
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | | | - Hongbao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Gong Cheng
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Chuping Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Wenjuan Zhu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
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22
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Stafuzza NB, Silva RMDO, Fragomeni BDO, Masuda Y, Huang Y, Gray K, Lourenco DAL. A genome-wide single nucleotide polymorphism and copy number variation analysis for number of piglets born alive. BMC Genomics 2019; 20:321. [PMID: 31029102 PMCID: PMC6487013 DOI: 10.1186/s12864-019-5687-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 04/11/2019] [Indexed: 12/19/2022] Open
Abstract
Background In this study we integrated the CNV (copy number variation) and WssGWAS (weighted single-step approach for genome-wide association) analyses to increase the knowledge about number of piglets born alive, an economically important reproductive trait with significant impact on production efficiency of pigs. Results A total of 3892 samples were genotyped with the Porcine SNP80 BeadChip. After quality control, a total of 57,962 high-quality SNPs from 3520 Duroc pigs were retained. The PennCNV algorithm identified 46,118 CNVs, which were aggregated by overlapping in 425 CNV regions (CNVRs) ranging from 2.5 Kb to 9718.4 Kb and covering 197 Mb (~ 7.01%) of the pig autosomal genome. The WssGWAS identified 16 genomic regions explaining more than 1% of the additive genetic variance for number of piglets born alive. The overlap between CNVR and WssGWAS analyses identified common regions on SSC2 (4.2–5.2 Mb), SSC3 (3.9–4.9 Mb), SSC12 (56.6–57.6 Mb), and SSC17 (17.3–18.3 Mb). Those regions are known for harboring important causative variants for pig reproductive traits based on their crucial functions in fertilization, development of gametes and embryos. Functional analysis by the Panther software identified 13 gene ontology biological processes significantly represented in this study such as reproduction, developmental process, cellular component organization or biogenesis, and immune system process, which plays relevant roles in swine reproductive traits. Conclusion Our research helps to improve the understanding of the genetic architecture of number of piglets born alive, given that the combination of GWAS and CNV analyses allows for a more efficient identification of the genomic regions and biological processes associated with this trait in Duroc pigs. Pig breeding programs could potentially benefit from a more accurate discovery of important genomic regions. Electronic supplementary material The online version of this article (10.1186/s12864-019-5687-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nedenia Bonvino Stafuzza
- Department of Exact Science, School of Agricultural and Veterinarian Sciences (FCAV), Sao Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil. .,Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA.
| | - Rafael Medeiros de Oliveira Silva
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA.,National Center for Cool and Cold Water Aquaculture (NCCCWA), Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, USA
| | | | - Yutaka Masuda
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Yijian Huang
- Smithfield Premium Genetics Group, Rose Hill, NC, USA
| | - Kent Gray
- Smithfield Premium Genetics Group, Rose Hill, NC, USA
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23
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Mielczarek M, Frąszczak M, Nicolazzi E, Williams JL, Szyda J. Landscape of copy number variations in Bos taurus: individual - and inter-breed variability. BMC Genomics 2018; 19:410. [PMID: 29843606 PMCID: PMC5975385 DOI: 10.1186/s12864-018-4815-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 05/22/2018] [Indexed: 11/24/2022] Open
Abstract
Background The number of studies of Copy Number Variation in cattle has increased in recent years. This has been prompted by the increased availability of data on polymorphisms and their relationship with phenotypes. In addition, livestock species are good models for some human phenotypes. In the present study, we described the landscape of CNV driven genetic variation in a large population of 146 individuals representing 13 cattle breeds, using whole genome DNA sequence. Results A highly significant variation among all individuals and within each breed was observed in the number of duplications (P < 10−15) and in the number of deletions (P < 10−15). We also observed significant differences between breeds for duplication (P = 0.01932) and deletion (P = 0.01006) counts. The same variation CNV length - inter-individual and inter-breed differences were significant for duplications (P < 10−15) and deletions (P < 10−15). Moreover, breed-specific variants were identified, with the largest proportion of breed-specific duplications (9.57%) found for Fleckvieh and breed-specific deletions found for Brown Swiss (5.00%). Such breed-specific CNVs were predominantly located in intragenic regions, however in Simmental, one deletion present in five individuals was found in the coding sequence of a novel gene ENSBTAG00000000688 on chromosome 18. In Brown Swiss, Norwegian Red and Simmental breed-specific deletions were located within KIT and MC1R genes, which are responsible for a coat colour. The functional annotation of coding regions underlying the breed-specific CNVs showed that in Norwegian Red, Guernsey, and Simmental significantly under- and overrepresented GO terms were related to chemical stimulus involved in sensory perception of smell and the KEGG pathways for olfactory transduction. In addition, specifically for the Norwegian Red breed, the dopaminergic synapse KEGG pathway was significantly enriched within deleted parts of the genome. Conclusions The CNV landscape in Bos taurus genome revealed by this study was highly complex, with inter-breed differences, but also a significant variation within breeds. The former, may explain some of the phenotypic differences among analysed breeds, and the latter contributes to within-breed variation available for selection. Electronic supplementary material The online version of this article (10.1186/s12864-018-4815-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- M Mielczarek
- Biostatistics group, Department of Genetics, Wroclaw University of Environmental and Life Sciences, Kozuchowska 7, 51-631, Wroclaw, Poland. .,National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - M Frąszczak
- Biostatistics group, Department of Genetics, Wroclaw University of Environmental and Life Sciences, Kozuchowska 7, 51-631, Wroclaw, Poland
| | - E Nicolazzi
- Council on Dairy Cattle Breeding (CDCB), 4201 Northview Dr, Bowie, MD, 20716, USA
| | - J L Williams
- Davies Research Centre, University of Adelaide, School of Animal and Veterinary Sciences, Roseworthy, SA, 5371, Australia
| | - J Szyda
- Biostatistics group, Department of Genetics, Wroclaw University of Environmental and Life Sciences, Kozuchowska 7, 51-631, Wroclaw, Poland.,National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland
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24
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Pierce MD, Dzama K, Muchadeyi FC. Genetic Diversity of Seven Cattle Breeds Inferred Using Copy Number Variations. Front Genet 2018; 9:163. [PMID: 29868114 PMCID: PMC5962699 DOI: 10.3389/fgene.2018.00163] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/23/2018] [Indexed: 11/25/2022] Open
Abstract
Copy number variations (CNVs) comprise deletions, duplications, and insertions found within the genome larger than 50 bp in size. CNVs are thought to be primary role-players in breed formation and adaptation. South Africa boasts a diverse ecology with harsh environmental conditions and a broad spectrum of parasites and diseases that pose challenges to livestock production. This has led to the development of composite cattle breeds which combine the hardiness of Sanga breeds and the production potential of the Taurine breeds. The prevalence of CNVs within these respective breeds of cattle and the prevalence of CNV regions (CNVRs) in their diversity, adaptation and production is however not understood. This study therefore aimed to ascertain the prevalence, diversity, and correlations of CNVRs within cattle breeds used in South Africa. Illumina Bovine SNP50 data and PennCNV were utilized to identify CNVRs within the genome of 287 animals from seven cattle breeds representing Sanga, Taurine, Composite, and cross breeds. Three hundred and fifty six CNVRs of between 36 kb to 4.1 Mb in size were identified. The null hypothesis that one CNVR loci is independent of another was tested using the GENEPOP software. One hunded and two and seven of the CNVRs in the Taurine and Sanga/Composite cattle breeds demonstrated a significant (p ≤ 0.05) association. PANTHER overrepresentation analyses of correlated CNVRs demonstrated significant enrichment of a number of biological processes, molecular functions, cellular components, and protein classes. CNVR genetic variation between and within breed group was measured using phiPT which allows intra-individual variation to be suppressed and hence proved suitable for measuring binary CNVR presence/absence data. Estimate PhiPT within and between breed variance was 2.722 and 0.518 respectively. Pairwise population PhiPT values corresponded with breed type, with Taurine Holstein and Angus breeds demonstrating no between breed CNVR variation. Phylogenetic trees were drawn. CNVRs primarily clustered animals of the same breed type together. This study successfully identified, characterized, and analyzed 356 CNVRs within seven cattle breeds. CNVR correlations were evident, with many more correlations being present among the exotic Taurine breeds. CNVR genetic diversity of Sanga, Taurine and Composite breeds was ascertained with breed types exposed to similar selection pressures demonstrating analogous incidences of CNVRs.
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Affiliation(s)
- Magretha D Pierce
- Animal Production, Agricultural Research Council, Pretoria, South Africa
| | - Kennedy Dzama
- Department of Animal Sciences, University of Stellenbosch, Stellenbosch, South Africa
| | - Farai C Muchadeyi
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
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25
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Integrating CNVs into meta-QTL identified GBP4 as positional candidate for adult cattle stature. Funct Integr Genomics 2018; 18:559-567. [PMID: 29737453 DOI: 10.1007/s10142-018-0613-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/21/2018] [Accepted: 04/24/2018] [Indexed: 02/03/2023]
Abstract
Copy number variation (CNV) of DNA sequences, functionally significant but yet fully ascertained, is believed to confer considerable increments in unexplained heritability of quantitative traits. Identification of phenotype-associated CNVs (paCNVs) therefore is a pressing need in CNV studies to speed up their exploitation in cattle breeding programs. Here, we provided a new avenue to achieve this goal that is to project the published CNV data onto meta-quantitative trait loci (meta-QTL) map which connects causal genes with phenotypes. Any CNVs overlapping meta-QTL therefore will be potential paCNVs. This study reported potential paCNVs in Bos taurus autosome 3 (BTA3). Notably, overview indexes and CNVs both highlighted a narrower region (BTA3 54,500,000-55,000,000 bp, named BTA3_INQTL_6) within one constructed meta-QTL. Then, we ascertained guanylate-binding protein 4 (GBP4) among the nine positional candidate genes was significantly associated with adult cattle stature, including body weight (BW, P < 0.05) and withers height (WHT, P < 0.05), fitting GBP4 CNV either with three levels or with six levels in the model. Although higher copy number downregulated the mRNA levels of GBP2 (P < 0.05) and GBP4 (P < 0.05) in 1-Mb window (54.0-55.0 Mb) in muscle and adipose, additional analyses will be needed to clarify the causality behind the ascertained association.
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26
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Sohrabi SS, Mohammadabadi M, Wu DD, Esmailizadeh A. Detection of breed-specific copy number variations in domestic chicken genome. Genome 2017; 61:7-14. [PMID: 28961404 DOI: 10.1139/gen-2017-0016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Copy number variations (CNVs) are important large-scale variants. They are widespread in the genome and may contribute to phenotypic variation. Detection and characterization of CNVs can provide new insights into the genetic basis of important traits. Here, we perform whole-genome short read sequence analysis to identify CNVs in two indigenous and commercial chicken breeds to evaluate the impact of the identified CNVs on breed-specific traits. After filtration, a total of 12 955 CNVs spanning (on average) about 9.42% of the chicken genome were found that made up 5467 CNV regions (CNVRs). Chicken quantitative trait loci (QTL) datasets and Ensembl gene annotations were used as resources for the estimation of potential phenotypic effects of our CNVRs on breed-specific traits. In total, 34% of our detected CNVRs were also detected in earlier CNV studies. These CNVRs partly overlap several previously reported QTL and gene ontology terms associated with some important traits, including shank length QTL in Creeper-specific CNVRs and body weight and egg production characteristics, as well as muscle and body organ growth, in the Arian commercial breed. Our findings provide new insights into the genomic structure of the chicken genome for an improved understanding of the potential roles of CNVRs in differentiating between breeds or lines.
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Affiliation(s)
- Saeed S Sohrabi
- a Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran.,b Young Researchers Society, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
| | - Mohammadreza Mohammadabadi
- a Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
| | - Dong-Dong Wu
- c State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,d Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Ali Esmailizadeh
- a Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran.,c State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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Mielczarek M, Frąszczak M, Giannico R, Minozzi G, Williams JL, Wojdak-Maksymiec K, Szyda J. Analysis of copy number variations in Holstein-Friesian cow genomes based on whole-genome sequence data. J Dairy Sci 2017; 100:5515-5525. [DOI: 10.3168/jds.2016-11987] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 03/25/2017] [Indexed: 01/02/2023]
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Characterization of Copy Number Variation's Potential Role in Marek's Disease. Int J Mol Sci 2017; 18:ijms18051020. [PMID: 28486430 PMCID: PMC5454933 DOI: 10.3390/ijms18051020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 04/22/2017] [Accepted: 05/04/2017] [Indexed: 02/07/2023] Open
Abstract
Marek’s Disease (MD) is a highly contagious pathogenic and oncogenic disease primarily affecting chickens. Chicken Lines 63 and 72, as well as their recombinant congenic strains (RCS) with varied susceptibility to MD, are ideal models to study the complex mechanisms of genetic resistance to MD. In this study, we investigated copy number variation (CNV) in these inbred chicken lines using the Affymetrix Axiom HD 600 K SNP genotyping array. We detected 393 CNV segments across all ten chicken lines, of which 12 CNVs were specifically identified in Line 72. We then assessed genetic structure based on CNV and observed markedly different patterns. Finally, we validated two deletion events in Line 72 and correlated them with genes expression using qPCR and RNA-seq, respectively. Our combined results indicated that these two CNV deletions were likely to contribute to MD susceptibility.
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Li BJ, Li HL, Meng Z, Zhang Y, Lin H, Yue GH, Xia JH. Copy Number Variations in Tilapia Genomes. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:11-21. [PMID: 28168542 DOI: 10.1007/s10126-017-9733-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/23/2016] [Indexed: 06/06/2023]
Abstract
Discovering the nature and pattern of genome variation is fundamental in understanding phenotypic diversity among populations. Although several millions of single nucleotide polymorphisms (SNPs) have been discovered in tilapia, the genome-wide characterization of larger structural variants, such as copy number variation (CNV) regions has not been carried out yet. We conducted a genome-wide scan for CNVs in 47 individuals from three tilapia populations. Based on 254 Gb of high-quality paired-end sequencing reads, we identified 4642 distinct high-confidence CNVs. These CNVs account for 1.9% (12.411 Mb) of the used Nile tilapia reference genome. A total of 1100 predicted CNVs were found overlapping with exon regions of protein genes. Further association analysis based on linear model regression found 85 CNVs ranging between 300 and 27,000 base pairs significantly associated to population types (R 2 > 0.9 and P > 0.001). Our study sheds first insights on genome-wide CNVs in tilapia. These CNVs among and within tilapia populations may have functional effects on phenotypes and specific adaptation to particular environments.
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Affiliation(s)
- Bi Jun Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Hong Lian Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zining Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yong Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Haoran Lin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Gen Hua Yue
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| | - Jun Hong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
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DNA copy number profiling in microsatellite-stable and microsatellite-unstable hereditary non-polyposis colorectal cancers by targeted CNV array. Funct Integr Genomics 2016; 17:85-96. [DOI: 10.1007/s10142-016-0532-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/08/2016] [Accepted: 04/18/2016] [Indexed: 01/19/2023]
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da Silva VH, Regitano LCDA, Geistlinger L, Pértille F, Giachetto PF, Brassaloti RA, Morosini NS, Zimmer R, Coutinho LL. Genome-Wide Detection of CNVs and Their Association with Meat Tenderness in Nelore Cattle. PLoS One 2016; 11:e0157711. [PMID: 27348523 PMCID: PMC4922624 DOI: 10.1371/journal.pone.0157711] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 06/03/2016] [Indexed: 12/20/2022] Open
Abstract
Brazil is one of the largest beef producers and exporters in the world with the Nelore breed representing the vast majority of Brazilian cattle (Bos taurus indicus). Despite the great adaptability of the Nelore breed to tropical climate, meat tenderness (MT) remains to be improved. Several factors including genetic composition can influence MT. In this article, we report a genome-wide analysis of copy number variation (CNV) inferred from Illumina® High Density SNP-chip data for a Nelore population of 723 males. We detected >2,600 CNV regions (CNVRs) representing ≈6.5% of the genome. Comparing our results with previous studies revealed an overlap in ≈1400 CNVRs (>50%). A total of 1,155 CNVRs (43.6%) overlapped 2,750 genes. They were enriched for processes involving guanosine triphosphate (GTP), previously reported to influence skeletal muscle physiology and morphology. Nelore CNVRs also overlapped QTLs for MT reported in other breeds (8.9%, 236 CNVRs) and from a previous study with this population (4.1%, 109 CNVRs). Two CNVRs were also proximal to glutathione metabolism genes that were previously associated with MT. Genome-wide association study of CN state with estimated breeding values derived from meat shear force identified 6 regions, including a region on BTA3 that contains genes of the cAMP and cGMP pathway. Ten CNVRs that overlapped regions associated with MT were successfully validated by qPCR. Our results represent the first comprehensive CNV study in Bos taurus indicus cattle and identify regions in which copy number changes are potentially of importance for the MT phenotype.
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Affiliation(s)
- Vinicius Henrique da Silva
- Animal Biotechnology Laboratory, Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
- * E-mail: (LLC); (VHS)
| | | | - Ludwig Geistlinger
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München (LMU), Amalienstrasse 17, 80333, München, Germany
| | - Fábio Pértille
- Animal Biotechnology Laboratory, Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | | | - Ricardo Augusto Brassaloti
- Animal Biotechnology Laboratory, Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - Natália Silva Morosini
- Animal Biotechnology Laboratory, Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - Ralf Zimmer
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München (LMU), Amalienstrasse 17, 80333, München, Germany
| | - Luiz Lehmann Coutinho
- Animal Biotechnology Laboratory, Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
- * E-mail: (LLC); (VHS)
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da Silva JM, Giachetto PF, da Silva LO, Cintra LC, Paiva SR, Yamagishi MEB, Caetano AR. Genome-wide copy number variation (CNV) detection in Nelore cattle reveals highly frequent variants in genome regions harboring QTLs affecting production traits. BMC Genomics 2016; 17:454. [PMID: 27297173 PMCID: PMC4907077 DOI: 10.1186/s12864-016-2752-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 05/19/2016] [Indexed: 11/10/2022] Open
Abstract
Background Copy number variations (CNVs) have been shown to account for substantial portions of observed genomic variation and have been associated with qualitative and quantitative traits and the onset of disease in a number of species. Information from high-resolution studies to detect, characterize and estimate population-specific variant frequencies will facilitate the incorporation of CNVs in genomic studies to identify genes affecting traits of importance. Results Genome-wide CNVs were detected in high-density single nucleotide polymorphism (SNP) genotyping data from 1,717 Nelore (Bos indicus) cattle, and in NGS data from eight key ancestral bulls. A total of 68,007 and 12,786 distinct CNVs were observed, respectively. Cross-comparisons of results obtained for the eight resequenced animals revealed that 92 % of the CNVs were observed in both datasets, while 62 % of all detected CNVs were observed to overlap with previously validated cattle copy number variant regions (CNVRs). Observed CNVs were used for obtaining breed-specific CNV frequencies and identification of CNVRs, which were subsequently used for gene annotation. A total of 688 of the detected CNVRs were observed to overlap with 286 non-redundant QTLs associated with important production traits in cattle. All of 34 CNVs previously reported to be associated with milk production traits in Holsteins were also observed in Nelore cattle. Comparisons of estimated frequencies of these CNVs in the two breeds revealed 14, 13, 6 and 14 regions in high (>20 %), low (<20 %) and divergent (NEL > HOL, NEL < HOL) frequencies, respectively. Conclusions Obtained results significantly enriched the bovine CNV map and enabled the identification of variants that are potentially associated with traits under selection in Nelore cattle, particularly in genome regions harboring QTLs affecting production traits. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2752-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joaquim Manoel da Silva
- Faculdade de Ciências Agrárias, Biológicas e Sociais Aplicadas, Universidade do Estado de Mato Grosso (UNEMAT), Av. Prof Dr. Renato Figueiro Varella, CEP 78.690-000, Nova Xavantina, Mato Grosso, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular-Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Poliana Fernanda Giachetto
- Embrapa Informática Agropecuária - Laboratório Multiusuário de Bioinformática (LMB), Campinas, São Paulo, Brazil
| | | | - Leandro Carrijo Cintra
- Embrapa Informática Agropecuária - Laboratório Multiusuário de Bioinformática (LMB), Campinas, São Paulo, Brazil
| | - Samuel Rezende Paiva
- Embrapa - Secretaria de Relações Internacionais, Brasília, Distrito Federal, Brazil.,Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil.,CNPq Fellow, ᅟ, ᅟ
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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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Wang MD, Dzama K, Rees DJG, Muchadeyi FC. Tropically adapted cattle of Africa: perspectives on potential role of copy number variations. Anim Genet 2015; 47:154-64. [DOI: 10.1111/age.12391] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2015] [Indexed: 12/12/2022]
Affiliation(s)
- M. D. Wang
- Department of Animal Sciences; University of Stellenbosch; Private Bag X1 Matieland 7602 South Africa
- Biotechnology Platform; Agricultural Research Council; Private Bag X5 Onderstepoort 0110 South Africa
| | - K. Dzama
- Department of Animal Sciences; University of Stellenbosch; Private Bag X1 Matieland 7602 South Africa
| | - D. J. G. Rees
- Biotechnology Platform; Agricultural Research Council; Private Bag X5 Onderstepoort 0110 South Africa
| | - F. C. Muchadeyi
- Biotechnology Platform; Agricultural Research Council; Private Bag X5 Onderstepoort 0110 South Africa
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35
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Wang MD, Dzama K, Hefer CA, Muchadeyi FC. Genomic population structure and prevalence of copy number variations in South African Nguni cattle. BMC Genomics 2015; 16:894. [PMID: 26531252 PMCID: PMC4632335 DOI: 10.1186/s12864-015-2122-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 10/22/2015] [Indexed: 12/21/2022] Open
Abstract
Background Copy number variations (CNVs) are modifications in DNA structure comprising of deletions, duplications, insertions and complex multi-site variants. Although CNVs are proven to be involved in a variety of phenotypic discrepancies, the full extent and consequence of CNVs is yet to be understood. To date, no such genomic characterization has been performed in indigenous South African Nguni cattle. Nguni cattle are recognized for their ability to sustain harsh environmental conditions while exhibiting enhanced resistance to disease and parasites and are thought to comprise of up to nine different ecotypes. Methods Illumina BovineSNP50 Beadchip data was utilized to investigate genomic population structure and the prevalence of CNVs in 492 South African Nguni cattle. PLINK, ADMIXTURE, R, gPLINK and Haploview software was utilized for quality control, population structure and haplotype block determination. PennCNV hidden Markov model identified CNVs and genes contained within and 10 Mb downstream from reported CNVs. PANTHER and Ensembl databases were subsequently utilized for gene annotation analyses. Results Population structure analyses on Nguni cattle revealed 5 sub-populations with a possible sub-structure evident at K equal to 8. Four hundred and thirty three CNVs that formed 334 CNVRs ranging from 30 kb to 1 Mb in size are reported. Only 231 of the 492 animals demonstrated CNVRs. Two hundred and eighty nine genes were observed within CNVRs identified. Of these 149, 28, 44, 2 and 14 genes were unique to sub-populations A, B, C, D and E respectively. Gene ontology analyses demonstrated a number of pathways to be represented by respective genes, including immune response, response to abiotic stress and biological regulation processess. Conclusions CNVs may explain part of the phenotypic diversity and the enhanced adaptation evident in Nguni cattle. Genes involved in a number of cellular components, biological processes and molecular functions are reported within CNVRs identified. The significance of such CNVRs and the possible effect thereof needs to be ascertained and may hold interesting insight into the functional and adaptive consequence of CNVs in cattle. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2122-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Magretha Diane Wang
- Department of Animal Sciences, University of Stellenbosch, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa. .,Biotechnology Platform, Agricultural Research Council, Private Bag X5, Onderstepoort, 0110, South Africa.
| | - Kennedy Dzama
- Department of Animal Sciences, University of Stellenbosch, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa.
| | - Charles A Hefer
- Biotechnology Platform, Agricultural Research Council, Private Bag X5, Onderstepoort, 0110, South Africa.
| | - Farai C Muchadeyi
- Biotechnology Platform, Agricultural Research Council, Private Bag X5, Onderstepoort, 0110, South Africa.
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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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Yi G, Qu L, Chen S, Xu G, Yang N. Genome-wide copy number profiling using high-density SNP array in chickens. Anim Genet 2015; 46:148-57. [PMID: 25662183 DOI: 10.1111/age.12267] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2014] [Indexed: 01/04/2023]
Abstract
Phenotypic diversity is a direct consequence resulting mainly from the impact of underlying genetic variation, and recent studies have shown that copy number variation (CNV) is emerging as an important contributor to both phenotypic variability and disease susceptibility. Herein, we performed a genome-wide CNV scan in 96 chickens from 12 diversified breeds, benefiting from the high-density Affymetrix 600 K SNP arrays. We identified a total of 231 autosomal CNV regions (CNVRs) encompassing 5.41 Mb of the chicken genome and corresponding to 0.59% of the autosomal sequence. The length of these CNVRs ranged from 2.6 to 586.2 kb with an average of 23.4 kb, including 130 gain, 93 loss and eight both gain and loss events. These CNVRs, especially deletions, had lower GC content and were located particularly in gene deserts. In particular, 102 CNVRs harbored 128 chicken genes, most of which were enriched in immune responses. We obtained 221 autosomal CNVRs after converting probe coordinates to Galgal3, and comparative analysis with previous studies illustrated that 153 of these CNVRs were regarded as novel events. Furthermore, qPCR assays were designed for 11 novel CNVRs, and eight (72.73%) were validated successfully. In this study, we demonstrated that the high-density 600 K SNP array can capture CNVs with higher efficiency and accuracy and highlighted the necessity of integrating multiple technologies and algorithms. Our findings provide a pioneering exploration of chicken CNVs based on a high-density SNP array, which contributes to a more comprehensive understanding of genetic variation in the chicken genome and is beneficial to unearthing potential CNVs underlying important traits of chickens.
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Affiliation(s)
- G Yi
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
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Invited review: Improving feed efficiency in dairy production: challenges and possibilities. Animal 2015; 9:395-408. [DOI: 10.1017/s1751731114002997] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Yi G, Qu L, Liu J, Yan Y, Xu G, Yang N. Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing. BMC Genomics 2014; 15:962. [PMID: 25378104 PMCID: PMC4239369 DOI: 10.1186/1471-2164-15-962] [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: 03/04/2014] [Accepted: 10/13/2014] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Copy number variation (CNV) is important and widespread in the genome, and is a major cause of disease and phenotypic diversity. Herein, we performed a genome-wide CNV analysis in 12 diversified chicken genomes based on whole genome sequencing. RESULTS A total of 8,840 CNV regions (CNVRs) covering 98.2 Mb and representing 9.4% of the chicken genome were identified, ranging in size from 1.1 to 268.8 kb with an average of 11.1 kb. Sequencing-based predictions were confirmed at a high validation rate by two independent approaches, including array comparative genomic hybridization (aCGH) and quantitative PCR (qPCR). The Pearson's correlation coefficients between sequencing and aCGH results ranged from 0.435 to 0.755, and qPCR experiments revealed a positive validation rate of 91.71% and a false negative rate of 22.43%. In total, 2,214 (25.0%) predicted CNVRs span 2,216 (36.4%) RefSeq genes associated with specific biological functions. Besides two previously reported copy number variable genes EDN3 and PRLR, we also found some promising genes with potential in phenotypic variation. Two genes, FZD6 and LIMS1, related to disease susceptibility/resistance are covered by CNVRs. The highly duplicated SOCS2 may lead to higher bone mineral density. Entire or partial duplication of some genes like POPDC3 may have great economic importance in poultry breeding. CONCLUSIONS Our results based on extensive genetic diversity provide a more refined chicken CNV map and genome-wide gene copy number estimates, and warrant future CNV association studies for important traits in chickens.
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Affiliation(s)
| | | | | | | | | | - Ning Yang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
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40
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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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Zhang H, Du ZQ, Dong JQ, Wang HX, Shi HY, Wang N, Wang SZ, Li H. Detection of genome-wide copy number variations in two chicken lines divergently selected for abdominal fat content. BMC Genomics 2014; 15:517. [PMID: 24962627 PMCID: PMC4092215 DOI: 10.1186/1471-2164-15-517] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 06/19/2014] [Indexed: 12/13/2022] Open
Abstract
Background The chicken (Gallus gallus) is an important model organism that bridges the evolutionary gap between mammals and other vertebrates. Copy number variations (CNVs) are a form of genomic structural variation widely distributed in the genome. CNV analysis has recently gained greater attention and momentum, as the identification of CNVs can contribute to a better understanding of traits important to both humans and other animals. To detect chicken CNVs, we genotyped 475 animals derived from two broiler chicken lines divergently selected for abdominal fat content using chicken 60 K SNP array, which is a high-throughput method widely used in chicken genomics studies. Results Using PennCNV algorithm, we detected 438 and 291 CNVs in the lean and fat lines, respectively, corresponding to 271 and 188 CNV regions (CNVRs), which were obtained by merging overlapping CNVs. Out of these CNVRs, 99% were confirmed also by the CNVPartition program. These CNVRs covered 40.26 and 30.60 Mb of the chicken genome in the lean and fat lines, respectively. Moreover, CNVRs included 176 loss, 68 gain and 27 both (i.e. loss and gain within the same region) events in the lean line, and 143 loss, 25 gain and 20 both events in the fat line. Ten CNVRs were chosen for the validation experiment using qPCR method, and all of them were confirmed in at least one qPCR assay. We found a total of 886 genes located within these CNVRs, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed they could play various roles in a number of biological processes. Integrating the results of CNVRs, known quantitative trait loci (QTL) and selective sweeps for abdominal fat content suggested that some genes (including SLC9A3, GNAL, SPOCK3, ANXA10, HELIOS, MYLK, CCDC14, SPAG9, SOX5, VSNL1, SMC6, GEN1, MSGN1 and ZPAX) may be important for abdominal fat deposition in the chicken. Conclusions Our study provided a genome-wide CNVR map of the chicken genome, thereby contributing to our understanding of genomic structural variations and their potential roles in abdominal fat content in the chicken. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-517) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin 150030, P,R China.
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Abernathy J, Li X, Jia X, Chou W, Lamont SJ, Crooijmans R, Zhou H. Copy number variation in Fayoumi and Leghorn chickens analyzed using array comparative genomic hybridization. Anim Genet 2014; 45:400-11. [DOI: 10.1111/age.12141] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2014] [Indexed: 12/25/2022]
Affiliation(s)
- J. Abernathy
- Department of Animal Science; University of California; Davis CA 95616 USA
| | - X. Li
- College of Animal Science and Technology; Shandong Agricultural University; Taian Shandong 271018 China
- Department of Poultry Science; Texas A&M University; College Station TX 77843 USA
| | - X. Jia
- Department of Animal Science; University of California; Davis CA 95616 USA
- College of Animal Science and Technology; China Agricultural University; Beijing 100193 China
| | - W. Chou
- Department of Poultry Science; Texas A&M University; College Station TX 77843 USA
| | - S. J. Lamont
- Department of Animal Science; Iowa State University; Ames IA 50011 USA
| | - R. Crooijmans
- Animal Breeding and Genomics Centre; Wageningen University; Wageningen the Netherlands
| | - H. Zhou
- Department of Animal Science; University of California; Davis CA 95616 USA
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Wang J, Jiang J, Wang H, Kang H, Zhang Q, Liu JF. Enhancing genome-wide copy number variation identification by high density array CGH using diverse resources of pig breeds. PLoS One 2014; 9:e87571. [PMID: 24475311 PMCID: PMC3903766 DOI: 10.1371/journal.pone.0087571] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 12/20/2013] [Indexed: 11/18/2022] Open
Abstract
Copy number variations (CNVs) are important forms of genomic variation, and have attracted extensive attentions in humans as well as domestic animals. In the study, using a custom-designed 2.1 M array comparative genomic hybridization (aCGH), genome-wide CNVs were identified among 12 individuals from diverse pig breeds, including one Asian wild population, six Chinese indigenous breeds and two modern commercial breeds (Yorkshire and Landrace), with one individual of the other modern commercial breed, Duroc, as the reference. A total of 1,344 CNV regions (CNVRs) were identified, covering 47.79 Mb (∼1.70%) of the pig genome. The length of these CNVRs ranged from 3.37 Kb to 1,319.0 Kb with a mean of 35.56 Kb and a median of 11.11 Kb. Compared with similar studies reported, most of the CNVRs (74.18%) were firstly identified in present study. In order to confirm these CNVRs, 21 CNVRs were randomly chosen to be validated by quantitative real time PCR (qPCR) and a high rate (85.71%) of confirmation was obtained. Functional annotation of CNVRs suggested that the identified CNVRs have important function, and may play an important role in phenotypic and production traits difference among various breeds. Our results are essential complementary to the CNV map in the pig genome, which will provide abundant genetic markers to investigate association studies between various phenotypes and CNVs in pigs.
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Affiliation(s)
- Jiying Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jicai Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Haifei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Huimin Kang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qin Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jian-Feng Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- * E-mail:
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Koch CT, Bruggmann R, Tetens J, Drögemüller C. A non-coding genomic duplication at the HMX1 locus is associated with crop ears in highland cattle. PLoS One 2013; 8:e77841. [PMID: 24194898 PMCID: PMC3806818 DOI: 10.1371/journal.pone.0077841] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 09/05/2013] [Indexed: 11/18/2022] Open
Abstract
Highland cattle with congenital crop ears have notches of variable size on the tips of both ears. In some cases, cartilage deformation can be seen and occasionally the external ears are shortened. We collected 40 cases and 80 controls across Switzerland. Pedigree data analysis confirmed a monogenic autosomal dominant mode of inheritance with variable expressivity. All affected animals could be traced back to a single common ancestor. A genome-wide association study was performed and the causative mutation was mapped to a 4 Mb interval on bovine chromosome 6. The H6 family homeobox 1 (HMX1) gene was selected as a positional and functional candidate gene. By whole genome re-sequencing of an affected Highland cattle, we detected 6 non-synonymous coding sequence variants and two variants in an ultra-conserved element at the HMX1 locus with respect to the reference genome. Of these 8 variants, only a non-coding 76 bp genomic duplication (g.106720058_106720133dup) located in the conserved region was perfectly associated with crop ears. The identified copy number variation probably results in HMX1 misregulation and possible gain-of-function. Our findings confirm the role of HMX1 during the development of the external ear. As it is sometimes difficult to phenotypically diagnose Highland cattle with slight ear notches, genetic testing can now be used to improve selection against this undesired trait.
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Affiliation(s)
- Caroline Tina Koch
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland
| | - Jens Tetens
- Institute for Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- * E-mail:
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Kõks S, Lilleoja R, Reimann E, Salumets A, Reemann P, Jaakma Ü. Sequencing and annotated analysis of the Holstein cow genome. Mamm Genome 2013; 24:309-21. [PMID: 23893136 DOI: 10.1007/s00335-013-9464-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Accepted: 06/17/2013] [Indexed: 11/26/2022]
Abstract
The aim of our study was to create a high-quality Holstein cow genome reference sequence and describe the different types of variations in this genome compared to the reference Hereford breed. We generated one fragment and three mate-paired libraries from genomic DNA. Raw files were mapped and paired to the reference cow (Bos taurus) genome assemblies bosTau6/UMD_3.1. BioScope (v1.3) software was used for mapping and variant analysis. Initial sequencing resulted in 2,842,744,008 of 50-bp reads. Average mapping efficiency was 78.4 % and altogether 2,168,425,497 reads and 98,022,357,422 bp were successfully mapped, resulting in 36.7X coverage. Tertiary analysis found 5,923,230 SNPs in the bovine genome, of which 3,833,249 were heterozygous and 2,089,981 were homozygous variants. Annotation revealed that 4,241,000 of all discovered SNPs were annotated in the dbSNP database and 1,682,230 SNPs were considered as novel. Large indel variations accounted for 48,537,190 bp of the entire genome and there were 138,504 of them. The largest deletion was 18,594 bp and the largest insertion was 13,498 bp. Another group of variants, small indels (n = 458,061), accounted for the total variation of 1,839,872 nucleotides in the genome. Only 92,115 small indels were listed in the dbSNP and therefore 365,946 small indels were novel. Finally, we identified 1,876 inversions in the bovine genome. In conclusion, this is another description of the Holstein cow genome and, similar to previous studies, we found a large amount of novel variations. Better knowledge of these variations could explain significant phenotypic differences (e.g., health, production, reproduction) between different breeds.
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Affiliation(s)
- Sulev Kõks
- Department of Physiology, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia.
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Wang J, Wang H, Jiang J, Kang H, Feng X, Zhang Q, Liu JF. Identification of genome-wide copy number variations among diverse pig breeds using SNP genotyping arrays. PLoS One 2013; 8:e68683. [PMID: 23935880 PMCID: PMC3720780 DOI: 10.1371/journal.pone.0068683] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 06/03/2013] [Indexed: 11/25/2022] Open
Abstract
Copy number variations (CNVs) are important forms of genetic variation complementary to SNPs, and can be considered as promising markers for some phenotypic and economically important traits or diseases susceptibility in domestic animals. In the present study, we performed a genome-wide CNV identification in 14 individuals selected from diverse populations, including six types of Chinese indigenous breeds, one Asian wild boar population, as well as three modern commercial foreign breeds. We identified 63 CNVRs in total, which covered 9.98 Mb of polymorphic sequence and corresponded to 0.36% of the genome sequence. The length of these CNVRs ranged from 3.20 to 827.21 kb, with an average of 158.37 kb and a median of 97.85 kb. Functional annotation revealed these identified CNVR have important molecular function, and may play an important role in exploring the genetic basis of phenotypic variability and disease susceptibility among pigs. Additionally, to confirm these potential CNVRs, we performed qPCR for 12 randomly selected CNVRs and 8 of them (66.67%) were confirmed successfully. CNVs detected in diverse populations herein are essential complementary to the CNV map in the pig genome, which provide an important resource for studies of genomic variation and the association between various economically important traits and CNVs.
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Affiliation(s)
- Jiying Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Haifei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jicai Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Huimin Kang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiaotian Feng
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qin Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jian-Feng Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- * E-mail:
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