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Cai H, Li X, Niu X, Li J, Lan X, Lei C, Huang Y, Xu H, Li M, Chen H. Copy number variations within fibroblast growth factor 13 gene influence growth traits and alternative splicing in cattle. Anim Biotechnol 2024; 35:2314104. [PMID: 38426908 DOI: 10.1080/10495398.2024.2314104] [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: 03/02/2024]
Abstract
Previous researches revealed a copy number variation (CNV) region in the bovine fibroblast growth factor 13 (FGF13) gene. However, its effects remain unknown. This study detected the various copy number types in seven Chinese cattle breeds and analysed their population genetic characteristics and effects on growth traits and transcription levels. Copy number Loss was more frequent in Caoyuan Red cattle and Xianan cattle than in the other breeds. Association analysis between CNV and growth traits of Qinchuan indicated that the CNV was significantly related to chest depth, hip width and hucklebone width (P < 0.05). Additionally, the growth traits of individuals with copy number Loss were significantly inferior to those with copy number Gain or Median (P < 0.05). Besides, we found two splicing isoforms, AS1 and AS2, in FGF13 gene, which resulted from alternative 5' splicing sites of intron 1. These isoforms showed varied expression levels in various tissues. Moreover, CNV was significantly and negatively associated with the mRNA expression of AS1 (r = -0.525, P < 0.05). The CNVs in bovine FGF13 gene negatively regulated growth traits and gene transcription. These observations provide new insights into bovine FGF13 gene, delivering potentially useful information for future Chinese cattle breeding programs.
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Affiliation(s)
- Hanfang Cai
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou, China
| | - Xin Li
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou, China
| | - Xinran Niu
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou, China
| | - Jing Li
- Animal Health Supervision Institute of Biyang, Biyang, Henan, 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, Shaanxi, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Huifen Xu
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou, China
| | - Ming Li
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou, China
| | - Hong Chen
- College of Animal Science, Xinjiang Agriculture University, Urumqi, China
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Wang W, Dong Y, Guo W, Zhang X, Degen AA, Bi S, Ding L, Chen X, Long R. Linkages between rumen microbiome, host, and environment in yaks, and their implications for understanding animal production and management. Front Microbiol 2024; 15:1301258. [PMID: 38348184 PMCID: PMC10860762 DOI: 10.3389/fmicb.2024.1301258] [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: 09/24/2023] [Accepted: 01/03/2024] [Indexed: 02/15/2024] Open
Abstract
Livestock on the Qinghai-Tibetan Plateau is of great importance for the livelihood of the local inhabitants and the ecosystem of the plateau. The natural, harsh environment has shaped the adaptations of local livestock while providing them with requisite eco-services. Over time, unique genes and metabolic mechanisms (nitrogen and energy) have evolved which enabled the yaks to adapt morphologically and physiologically to the Qinghai-Tibetan Plateau. The rumen microbiota has also co-evolved with the host and contributed to the host's adaptation to the environment. Understanding the complex linkages between the rumen microbiota, the host, and the environment is essential to optimizing the rumen function to meet the growing demands for animal products while minimizing the environmental impact of ruminant production. However, little is known about the mechanisms of host-rumen microbiome-environment linkages and how they ultimately benefit the animal in adapting to the environment. In this review, we pieced together the yak's adaptation to the Qinghai-Tibetan Plateau ecosystem by summarizing the natural selection and nutritional features of yaks and integrating the key aspects of its rumen microbiome with the host metabolic efficiency and homeostasis. We found that this homeostasis results in higher feed digestibility, higher rumen microbial protein production, higher short-chain fatty acid (SCFA) concentrations, and lower methane emissions in yaks when compared with other low-altitude ruminants. The rumen microbiome forms a multi-synergistic relationship among the rumen microbiota services, their communities, genes, and enzymes. The rumen microbial proteins and SCFAs act as precursors that directly impact the milk composition or adipose accumulation, improving the milk or meat quality, resulting in a higher protein and fat content in yak milk and a higher percentage of protein and abundant fatty acids in yak meat when compared to dairy cow or cattle. The hierarchical interactions between the climate, forage, rumen microorganisms, and host genes have reshaped the animal's survival and performance. In this review, an integrating and interactive understanding of the host-rumen microbiome environment was established. The understanding of these concepts is valuable for agriculture and our environment. It also contributes to a better understanding of microbial ecology and evolution in anaerobic ecosystems and the host-environment linkages to improve animal production.
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Affiliation(s)
- Weiwei Wang
- Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang, Guizhou, China
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Yuntao Dong
- Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang, Guizhou, China
| | - Wei Guo
- Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang, Guizhou, China
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiao Zhang
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - A. Allan Degen
- Desert Animal Adaptations and Husbandry, Wyler Department of Dryland Agriculture, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Sisi Bi
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Luming Ding
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiang Chen
- Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang, Guizhou, China
| | - Ruijun Long
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 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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Tian D, Sun D, Ren Q, Zhang P, Zhang Z, Zhang W, Luo H, Li X, Han B, Liu D, Zhao K. Genome-wide identification of candidate copy number polymorphism genes associated with complex traits of Tibetan-sheep. Sci Rep 2023; 13:17283. [PMID: 37828092 PMCID: PMC10570297 DOI: 10.1038/s41598-023-44402-1] [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: 03/28/2023] [Accepted: 10/07/2023] [Indexed: 10/14/2023] Open
Abstract
Copy number variation (CNV) is a genetic structural polymorphism important for phenotypic diversity and important economic traits of livestock breeds, and it plays an important role in the desired genetic variation. This study used whole genome sequencing to detect the CNV variation in the genome of 6 local Tibetan sheep groups. We detected 69,166 CNV events and 7230 copy number variable regions (CNVRs) after merging the overlapping CNVs, accounting for 2.72% of the reference genome. The CNVR length detected ranged from 1.1 to 1693.5 Kb, with a total length of 118.69 Mb and an average length of 16.42 Kb per CNVR. Functional GO cluster analysis showed that the CNVR genes were mainly involved in sensory perception systems, response to stimulus, and signal transduction. Through CNVR-based Vst analysis, we found that the CACNA2D3 and CTBP1 genes related to hypoxia adaptation, the HTR1A gene related to coat color, and the TRNAS-GGA and PIK3C3 genes related to body weight were all strongly selected. The findings of our study will contribute novel insights into the genetic structural variation underlying hypoxia adaptation and economically important traits in Tibetan sheep.
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Affiliation(s)
- Dehong Tian
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, Qinghai, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - De Sun
- Animal Husbandry and Veterinary Station of Huzhu County of Qinghai Province, Huzhu, 810500, Qinghai, China
| | - Qianben Ren
- Qinghai Sheep Breeding and Promotion Service Center, Gangcha, 812300, Qinghai, China
| | - Pei Zhang
- Qinghai Animal and Plant Quarantine Station, Xining, 810000, Qinghai, China
| | - Zian Zhang
- Qinghai Sheep Breeding and Promotion Service Center, Gangcha, 812300, Qinghai, China
| | - Wenkui Zhang
- Qinghai Sheep Breeding and Promotion Service Center, Gangcha, 812300, Qinghai, China
| | - Haizhou Luo
- Qinghai Sheep Breeding and Promotion Service Center, Gangcha, 812300, Qinghai, China
| | - Xue Li
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, Qinghai, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Buying Han
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, Qinghai, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dehui Liu
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, Qinghai, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kai Zhao
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, Qinghai, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Kooverjee BB, Soma P, van der Nest MA, Scholtz MM, Neser FWC. Copy Number Variation Discovery in South African Nguni-Sired and Bonsmara-Sired Crossbred Cattle. Animals (Basel) 2023; 13:2513. [PMID: 37570321 PMCID: PMC10417447 DOI: 10.3390/ani13152513] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/26/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
Crossbreeding forms part of Climate-Smart beef production and is one of the strategies to mitigate the effects of climate change. Two Nguni-sired and three Bonsmara-sired crossbred animals underwent whole genome sequencing. Following quality control and file preparation, the sequence data were investigated for genome-wide copy number variation (CNV) using the panelcn.MOPS tool. A total of 355 CNVs were identified in the crossbreds, of which 274 were unique in Bonsmara-sired crossbreds and 81 unique in the Nguni-sired crossbreds. Genes that differed in copy number in both crossbreds included genes related to growth (SCRN2, LOC109572916) and fertility-related factors (RPS28, LOC1098562432, LOC109570037). Genes that were present only in the Bonsmara-sired crossbreds included genes relating to lipid metabolism (MAF1), olfaction (LOC109569114), body size (HES7), immunity (LOC10957335, LOC109877039) and disease (DMBT1). Genes that were present only in the Nguni-sired crossbreds included genes relating to ketosis (HMBOX1) and amino acid transport (LOC109572916). Results of this study indicate that Nguni and Bonsmara cattle can be utilized in crossbreeding programs as they may enhance the presence of economically important traits associated with both breeds. This will produce crossbred animals that are good meat producers, grow faster, have high fertility, strong immunity and a better chance of producing in South Africa's harsh climate conditions. Ultimately, this study provides new genetic insights into the adaptability of Nguni and Bonsmara crossbred cattle.
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Affiliation(s)
| | - Pranisha Soma
- Animal Production, Agricultural Research Council, Pretoria 0062, South Africa;
| | - Magrieta A. van der Nest
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa;
| | - Michiel M. Scholtz
- Animal Production, Agricultural Research Council, Pretoria 0062, South Africa;
- Department of Animal Science, University of the Free State, Bloemfontein 9300, South Africa;
| | - Frederick W. C. Neser
- Department of Animal Science, University of the Free State, Bloemfontein 9300, South Africa;
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Molecular Cytogenetics in Domestic Bovids: A Review. Animals (Basel) 2023; 13:ani13050944. [PMID: 36899801 PMCID: PMC10000107 DOI: 10.3390/ani13050944] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
The discovery of the Robertsonian translocation (rob) involving cattle chromosomes 1 and 29 and the demonstration of its deleterious effects on fertility focused the interest of many scientific groups on using chromosome banding techniques to reveal chromosome abnormalities and verify their effects on fertility in domestic animals. At the same time, comparative banding studies among various species of domestic or wild animals were found useful for delineating chromosome evolution among species. The advent of molecular cytogenetics, particularly the use of fluorescence in situ hybridization (FISH), has allowed a deeper investigation of the chromosomes of domestic animals through: (a) the physical mapping of specific DNA sequences on chromosome regions; (b) the use of specific chromosome markers for the identification of the chromosomes or chromosome regions involved in chromosome abnormalities, especially when poor banding patterns are produced; (c) better anchoring of radiation hybrid and genetic maps to specific chromosome regions; (d) better comparisons of related and unrelated species by comparative FISH mapping and/or Zoo-FISH techniques; (e) the study of meiotic segregation, especially by sperm-FISH, in some chromosome abnormalities; (f) better demonstration of conserved or lost DNA sequences in chromosome abnormalities; (g) the use of informatic and genomic reconstructions, in addition to CGH arrays, to predict conserved or lost chromosome regions in related species; and (h) the study of some chromosome abnormalities and genomic stability using PCR applications. This review summarizes the most important applications of molecular cytogenetics in domestic bovids, with an emphasis on FISH mapping applications.
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Zhang Z, Chu M, Bao Q, Bao P, Guo X, Liang C, Yan P. Two Different Copy Number Variations of the SOX5 and SOX8 Genes in Yak and Their Association with Growth Traits. Animals (Basel) 2022; 12:ani12121587. [PMID: 35739923 PMCID: PMC9219506 DOI: 10.3390/ani12121587] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/16/2022] [Accepted: 06/16/2022] [Indexed: 11/16/2022] Open
Abstract
Copy number variation (CNV) is a structural variant with significant impact on genetic diversity. CNV has been widely used in breeding for growth traits, meat production or quality, and coat color. SRY-like box genes (SOXs) are a class of transcription factors that play a regulatory role in cell fate specification and differentiation. SOX5 and SOX8 belong to subgroups D and E of the SOXs, respectively. Previous studies have shown that SOX5 and SOX8 are essential in the development of bones. In this study, we explored the association between the growth traits and CNVs of SOX5 and SOX8 in 326 Ashidan yaks and detected mRNA expression levels in different tissues. Our results illustrated that CNVs of SOX5 and SOX8 were significantly associated with withers height at 18 months of age and chest girth at 30 months of age (p < 0.05). The CNV combination of SOX5 and SOX8 was significantly associated with withers height at 18 months of age (p < 0.01). SOX5 expression in the lung was significantly higher than in the heart, spleen, kidney, and muscle (p < 0.05). SOX8 expression in the lung was significantly higher than in the liver and muscle (p < 0.05). Our results provide evidence that the CNVs of SOX5 and SOX8 genes could be used as new markers for the selection of yak growth traits.
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Affiliation(s)
- Zhilong Zhang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (Z.Z.); (M.C.); (Q.B.); (P.B.); (X.G.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Min Chu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (Z.Z.); (M.C.); (Q.B.); (P.B.); (X.G.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Qi Bao
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (Z.Z.); (M.C.); (Q.B.); (P.B.); (X.G.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Pengjia Bao
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (Z.Z.); (M.C.); (Q.B.); (P.B.); (X.G.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xian Guo
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (Z.Z.); (M.C.); (Q.B.); (P.B.); (X.G.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Chunnian Liang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (Z.Z.); (M.C.); (Q.B.); (P.B.); (X.G.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Correspondence: (C.L.); (P.Y.)
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (Z.Z.); (M.C.); (Q.B.); (P.B.); (X.G.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Correspondence: (C.L.); (P.Y.)
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Guo X, Pei J, Wu X, Bao P, Ding X, Xiong L, Chu M, Lan X, Yan P. Detection of InDel and CNV of SPAG17 gene and their associations with bovine growth traits. Anim Biotechnol 2022; 33:440-447. [PMID: 32820682 DOI: 10.1080/10495398.2020.1803342] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Sperm-associated antigen 17 (SPAG17) gene encodes a central pair protein, which is involved in flagellar motility, male fertility and skeletal growth in ruminants. The insertions/deletions (indels) and copy number variations (CNVs) influence phenotypic traits by altering the sequences and copy numbers of functional genes, respectively. This study identified a novel 8-bp indel of SPAG17 gene in 1520 individuals from eight different cattle breeds, as well as a novel CNV region in 355 animals. The correlation analysis of indel showed that the individuals of ID genotype had superior performance traits such as body height (p = 0.038) and body slanting length (p = 0.041) as compared to other genotypes in Xianan cattle. For the CNV, different copy numbers were closely related to the body height in Qinchuan (p = 0.045) and body weight in Xianan (p = 0.036) breeds. Importantly, significant difference was observed between the 8-bp indel and the copy number loss in Xianan breed (p < 0.01). These findings indicated that the variations within the bovine SPAG17 gene can be considered as an effective DNA molecular marker for beef cattle breeding.
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Affiliation(s)
- Xian Guo
- Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, Gansu, China
| | - Jie Pei
- Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, Gansu, China
| | - Xiaoyun Wu
- Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, Gansu, China
| | - Pengjia Bao
- Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, Gansu, China
| | - Xuezhi Ding
- Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, Gansu, China
| | - Lin Xiong
- Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, Gansu, China
| | - Min Chu
- Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, Gansu, China
| | - Xianyong Lan
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Ping Yan
- Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, Gansu, China
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Yang P, Cai C, Niu M, Liu X, Wang H, Liang H, Cheng B, Zhang Z, Chen F, Xie J, Qi Z, Yang G, Shi Q, Wang E, Lei C, Chen H, Ru B, Huang Y. Effect of copy number variation of PLA2G2A gene to growth traits in Chinese cattle. Gene 2022; 809:146014. [PMID: 34655722 DOI: 10.1016/j.gene.2021.146014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 08/06/2021] [Accepted: 10/11/2021] [Indexed: 11/19/2022]
Abstract
SIMPLE SUMMARY As a member of genetic polymorphism, copy number variation has been a commonly used method in the world for investigating effect of genetic polymorphism on gene expression. Effect of genetic polymorphism made on livestock development has been more and more important in beef cattle molecular breeding. The characteristics of Chinese cattle are excellent meat quality, tolerant to rough feeding, good environmental adaptability and so on. But there are some obvious weaknesses still exist in the process of cattle growth and development, such as weak hindquarters and growth slowly. To improve the growth performance and market competitiveness of Chinese cattle, a lot of studies have been made about finding and investigating effective molecular marker. In this study, Q-PCR and data association analysis were used for PLA2G2A gene copy number variation detection and related effect analysis in Chinese cattle. Results showed that PLA2G2A gene has a significant effect on two breeds of Chinese cattle on growth traits, which could be a basic materials and effective information of cattle molecular markers breeding. PLA2G2A, member of secreted phospholipases A2 (sPLA2) in superfamily of phospholipase A2, could catalyze the process of glycerophospholipids hydrolysis from position of sn-2 acyl with the release of free fatty acids and lysophospholipids. Researches about PLA2G2A gene are mostly focus on disease, including tumors and diabetes, the number of study occurred on animal breeding is weak. In this study, blood samples were collected from five breeds of Chinese cattle (Qingchuan cattle, Xianan cattle, Yunling cattle, Pinan cattle and Guyuan cattle) for PLA2G2A gene CNV type detection. SPSS 20.0 software and method of ANOVA were used to analyzed the association between types of CNV and growth traits. Results reveal that the distribution of different copy number types in different cattle breeds is different. In QC, XN and GY cattle, the frequencies of Deletion and Duplication are about 40%; in YL cattle, the frequency of Deletion type exceeds 60%; in PN cattle, the frequency of Duplication is closed to 80%. Association analysis indicate that CNV of PLA2G2A gene showed a positive effect in cattle growth: in QC cattle, Chest depth with Normal type copy number possess a increased trend (P < 0.05); individuals with Deletion type copy number have better performance on Height at sacrum, Heart girth and Body height in GY cattle (P < 0.05). The functional role and molecular mechanism of PLA2G2A gene in animal growth and development are still unclear, and it is necessary for processing a further research. This research aims to provide basic materials for molecular breeding of Chinese cattle.
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Affiliation(s)
- Peng Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Cuicui Cai
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China; Guyuan Branch of Ningxia Academy of Agriculture and Forestry Sciences, Guyuan, Ningxia 756000, People's Republic of China
| | - Mengxiao Niu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Xian Liu
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan 450008, People's Republic of China
| | - Hongli Wang
- Jiaxian Animal Husbandry Bureau, Jiaxian, Henan 467100, People's Republic of China
| | - Huifeng Liang
- Jiaxian Animal Husbandry Bureau, Jiaxian, Henan 467100, People's Republic of China
| | - Baowei Cheng
- Jiaxian Animal Husbandry Bureau, Jiaxian, Henan 467100, 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
| | - Fuying Chen
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, People's Republic of China
| | - Jianliang Xie
- Guyuan Branch of Ningxia Academy of Agriculture and Forestry Sciences, Guyuan, Ningxia 756000, People's Republic of China
| | - Zengfang Qi
- 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
| | - Qiaoting Shi
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, 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
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Baorui Ru
- 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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10
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Wang X, Wang Y, Cao X, Huang Y, Li P, Lan X, Buren C, Hu L, Chen H. Copy number variations of the KAT6A gene are associated with body measurements of Chinese sheep breeds. Anim Biotechnol 2021:1-8. [PMID: 34842492 DOI: 10.1080/10495398.2021.2005616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Copy number variation (CNV) is one kind of genomic structure variations and presents as gains and losses of genomic fragments. More recently, we have made an atlas of CNV maps for livestock. In the future, it is a primary focus to determine the phenotypic effects of candidate CNVs. Lysine Acetyltransferase 6 A (KAT6A) is a protein coding gene and plays a critical role in many cellular processes. However, the effects of KAT6A CNVs on sheep body measurements remains unknown. In this study, we performed quantitative polymerase chain reaction (qPCR) to detect the presences and distributions of three CNV regions within KAT6A gene in 672 sheep from four Chinese breeds. Association analysis indicated that the three CNVs of KAT6A gene were significantly associated with body measurement(s) in Small-tailed Han sheep (STH) and Hu sheep (HU) (p < 0.05), while no effects on Large-tailed Han sheep (LTH) were observed (p > 0.05) were observed. Additionally, only one CNV was significantly associated with body measurement (body length) in Chaka sheep (CK) (p < 0.05). Our study provided evidence that the CNV(s) of KAT6A gene could be used as candidate marker(s) for molecular breedings of STH, HU, and CK breeds.
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Affiliation(s)
- Xiaogang Wang
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yiru Wang
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiukai Cao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Yongzhen Huang
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Pi Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 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, Shaanxi, China
| | - Chaogetu Buren
- Animal Disease Control Center of Haixi Mongolian and Tibetan Autonomous Prefecture, Delingha, Qinghai, China
| | - Linyong Hu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
| | - Hong Chen
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,College of Animal Science, Xinjiang Agricultural University, Urumqi, China
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11
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Guo S, Wu X, Pei J, Wang X, Bao P, Xiong L, Chu M, Liang C, Yan P, Guo X. Genome-wide CNV analysis reveals variants associated with high-altitude adaptation and meat traits in Qaidam cattle. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2021.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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12
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Copy number variation of the HPGDS gene in the Ashidan yak and its associations with growth traits. Gene 2020; 772:145382. [PMID: 33373661 DOI: 10.1016/j.gene.2020.145382] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/05/2020] [Accepted: 12/18/2020] [Indexed: 02/06/2023]
Abstract
Copy number variation (CNV) is a structural variation at the submicroscopic level of the genome, which can affect gene-related phenotypes by changing genes dosage and transcript structure. Hematopoietic prostaglandin D synthase (HPGDS) is a member whose functions are closely related to weight gain and inflammatory diseases of the glutathione S-transferase (GSTs) family. In this study, the growth characteristics (body weight, withers height, body length, and chest girth) of 336 Ashidan yaks were monitored at four stages (6 months, 12 months, 18 months, and 30 months). In addition, CNV of the HPGDS gene was detected, discovered relationships of CNV with growth traits, and explored the level of gene expression. Based on the statistical analysis by IBM SPSS software, significant correlations were observed between HPGDS-CNV and body weight in 12-month-old yak (P < 0.01), 18-month-old yak (P < 0.001) and 30-month-old yak (P < 0.001) and body length in 18-month-old yak (P < 0.05) and 30-month-old yak (P < 0.05), respectively. Additionally, the individuals with gain copy number type performed better in body weight and body length than those with normal or loss copy number type. To our best of knowledge, this is the first time to make efforts to probe into the role of HPGDS-CNV and its interaction with livestock growth traits. Our results suggested that the CNV of the HPGDS gene may be an active candidate gene for the marker-assisted selection (MAS) of yaks.
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13
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Cheng J, Cao X, Hanif Q, Pi L, Hu L, Huang Y, Lan X, Lei C, Chen H. Integrating Genome-Wide CNVs Into QTLs and High Confidence GWAScore Regions Identified Positional Candidates for Sheep Economic Traits. Front Genet 2020; 11:569. [PMID: 32655616 PMCID: PMC7325882 DOI: 10.3389/fgene.2020.00569] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/11/2020] [Indexed: 12/21/2022] Open
Abstract
Copy number variations (CNVs) are important source of genetic variation, which can affect diverse economic traits through a variety of mechanisms. In addition, genome scan can identify many quantitative trait loci (QTLs) for the economic traits, while genome-wide association studies (GWAS) can localize genetic variants associated with the phenotypic variations. Here, we developed a method called GWAScore which collected GWAS summary data to identify potential candidates, and integrated CNVs into QTLs and high confidence GWAScore regions to detect crucial CNV markers for sheep growth traits. We got 197 candidate genes which were overlapping with the candidate CNVs. Some crucial genes (MYLK3, TTC29, HERC6, ABCG2, RUNX1, etc.) showed significantly elevated GWAScore peaks than other candidate genes. In this study, we developed the GWAScore method to excavate the potential value of candidate genes as markers for the sheep molecular breeding.
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Affiliation(s)
- Jie Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiukai Cao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Quratulain Hanif
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.,Computational Biology Lab, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Li Pi
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Linyong Hu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 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, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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14
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Genomic Structural Diversity in Local Goats: Analysis of Copy-Number Variations. Animals (Basel) 2020; 10:ani10061040. [PMID: 32560248 PMCID: PMC7341319 DOI: 10.3390/ani10061040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/05/2020] [Accepted: 06/12/2020] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Copy-number variations (CNVs) are one of the widely dispersed forms of structural variations in mammalian genomes and are known to be present in genomic regions that regulate important physiological functions. In this study, CNV detection was performed starting from genotypic data of 120 individuals, belonging to four Sicilian dairy goat breeds, genotyped with the Illumina GoatSNP50 BeadChip array. Using PennCNV software, a total of 702 CNVs were identified in 107 individuals. These were merged in 75 CNV regions (CNVRs), i.e., regions containing CNVs overlapped by at least 1 base pair. Functional annotation of the CNVRs allowed the identification of 139 genes/loci within the most frequent CNVRs, which are involved in local adaptation, mild behaviour, immune response, reproduction, and olfactory receptors. This study provides insights into the genomic variations within these Italian goat breeds and should be of value for future studies to identify the relationships between this type of genetic variation and phenotypic traits. Abstract Copy-number variations (CNVs) are one of the widely dispersed forms of structural variations in mammalian genomes, and are present as deletions, insertions, or duplications. Only few studies have been conducted in goats on CNVs derived from SNP array data, and many local breeds still remain uncharacterized, e.g., the Sicilian goat dairy breeds. In this study, CNV detection was performed, starting from the genotypic data of 120 individuals, belonging to four local breeds (Argentata dell’Etna, Derivata di Siria, Girgentana, and Messinese), genotyped with the Illumina GoatSNP50 BeadChip array. Overall, 702 CNVs were identified in 107 individuals using PennCNV software based on the hidden Markov model algorithm. These were merged in 75 CNV regions (CNVRs), i.e., regions containing CNVs overlapped by at least 1 base pair, while 85 CNVs remained unique. The part of the genome covered by CNV events was 35.21 Mb (1.2% of the goat genome length). Functional annotation of the CNVRs allowed the identification of 139 genes/loci within the most frequent CNVRs that are involved in local adaptations, such as coat colour (ADAMTS20 and EDNRA), mild behaviour (NR3C2), immune response (EXOC3L4 and TNFAIP2), reproduction (GBP1 and GBP6), and olfactory receptors (OR7E24). This study provides insights into the genomic variations for these Sicilian dairy goat breeds and should be of value for future studies to identify the relationships between this type of genetic variation and phenotypic traits.
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15
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Zheng X, Zhao P, Yang K, Ning C, Wang H, Zhou L, Liu J. CNV analysis of Meishan pig by next-generation sequencing and effects of AHR gene CNV on pig reproductive traits. J Anim Sci Biotechnol 2020; 11:42. [PMID: 32337028 PMCID: PMC7171861 DOI: 10.1186/s40104-020-00442-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 02/27/2020] [Indexed: 12/17/2022] Open
Abstract
Background Reproductive performance of livestock is an economically important aspect of global food production. The Chinese Meishan pig is a prolific breed, with an average of three to five more piglets per litter than European breeds; however, the genetic basis for this difference is not well understood. Results In this study, we investigated copy number variations (CNVs) of 32 Meishan pigs and 29 Duroc pigs by next-generation sequencing. A genome-wide analysis of 61 pigs revealed 12,668 copy number variable regions (CNVRs) that were further divided into three categories based on copy number (CN) of the whole population, i.e., gain (n = 7,638), and loss (n = 5,030) CNVRs. We then compared Meishan and Duroc pigs and identified 17.17 Mb of 6,387 CNVRs that only existing in Meishan pigs CNVRs that overlapped the reproduction-related gene encoding the aryl hydrocarbon receptor (AHR) gene. We found that normal AHR CN was more frequent than CN loss in four different pig breeds. An association analysis showed that AHR CN had a positive effect on litter size (P < 0.05) and that a higher CN was associated with higher total number born (P < 0.05), number born alive (P < 0.05), number of weaned piglets, and birth weight. Conclusions The present study provides comprehensive CNVRs for Meishan and Duroc pigs through large-scale population resequencing. Our results provide a supplement for the high-resolution map of copy number variation in the porcine genome and valuable information for the investigation of genomic structural variation underlying traits of interest in pig. In addition, the association results provide evidence for AHR as a candidate gene associated with reproductive traits that can be used as a genetic marker in pig breeding programs.
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Affiliation(s)
- Xianrui Zheng
- 1National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Pengju Zhao
- 1National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Kaijie Yang
- 1National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Chao Ning
- 1National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Haifei Wang
- 1National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China.,2Department of Animal Genetics, Breeding and Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 China
| | - Lei Zhou
- 1National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Jianfeng Liu
- 1National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
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16
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Goshu HA, Xiaoyun W, Chu M, Pengjia B, Xue Zhi D, Yan P. Novel copy number variations of the CHRM3 gene associated with gene expression and growth traits in Chinese Datong yak (Bos grunniens). JOURNAL OF APPLIED ANIMAL RESEARCH 2020. [DOI: 10.1080/09712119.2020.1753750] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Habtamu Abera Goshu
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, People’s Republic of China
- Oromia Agricultural Research Institute, Bako Agricultural Research Center, Bako, Ethiopia
| | - Wu Xiaoyun
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, People’s Republic of China
| | - Min Chu
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, People’s Republic of China
| | - Bao Pengjia
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, People’s Republic of China
| | - Ding Xue Zhi
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, People’s Republic of China
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, People’s Republic of China
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17
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Hao D, Wang X, Thomsen B, Kadarmideen HN, Wang X, Lan X, Huang Y, Qi X, Chen H. Copy Number Variations and Expression Levels of Guanylate-Binding Protein 6 Gene Associated with Growth Traits of Chinese Cattle. Animals (Basel) 2020; 10:E566. [PMID: 32230930 PMCID: PMC7222342 DOI: 10.3390/ani10040566] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/18/2020] [Accepted: 03/22/2020] [Indexed: 11/16/2022] Open
Abstract
Association studies have indicated profound effects of copy number variations (CNVs) on various phenotypes in different species. In this study, we identified the CNV distributions and expression levels of guanylate-binding protein 6 (GBP6) associated with the growth traits of Chinese cattle. The results showed that the phenotypic values of body size and weight of Xianan (XN) cattle were higher than those of Nanyang (NY) cattle. The medium CNV types were mostly identified in the XN and NY breeds, but their CNV distributions were significantly different (adjusted p < 0.05). The association analysis revealed that the body weight, cannon circumference and chest circumference of XN cattle had significantly different values in different CNV types (p < 0.05), with CNV gain types (Log22-ΔΔCt > 0.5) displaying superior phenotypic values. We also found that transcription levels varied in different tissues (p < 0.001) and the CNV gain types showed the highest relative gene expression levels in the muscle tissue, consistent with the highest phenotypic values of body weight and cannon circumference among the three CNV types. Consequently, our results suggested that CNV gain types of GBP6 could be used as the candidate markers in the cattle-breeding program for growth traits.
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Affiliation(s)
- Dan Hao
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, Yangling 712100, Shaanxi, China; (D.H.); (X.W.); (X.L.); (Y.H.)
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark;
| | - Xiao Wang
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (X.W.); (H.N.K.)
| | - Bo Thomsen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark;
| | - Haja N. Kadarmideen
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (X.W.); (H.N.K.)
| | - Xiaogang Wang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, Yangling 712100, Shaanxi, China; (D.H.); (X.W.); (X.L.); (Y.H.)
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, Yangling 712100, Shaanxi, China; (D.H.); (X.W.); (X.L.); (Y.H.)
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, Yangling 712100, Shaanxi, China; (D.H.); (X.W.); (X.L.); (Y.H.)
| | - Xinglei Qi
- Bureau of Animal Husbandry of Biyang County, Biyang 463700, Henan, China;
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, Yangling 712100, Shaanxi, China; (D.H.); (X.W.); (X.L.); (Y.H.)
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18
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Zhang Y, Hu Y, Wang X, Jiang Q, Zhao H, Wang J, Ju Z, Yang L, Gao Y, Wei X, Bai J, Zhou Y, Huang J. Population Structure, and Selection Signatures Underlying High-Altitude Adaptation Inferred From Genome-Wide Copy Number Variations in Chinese Indigenous Cattle. Front Genet 2020; 10:1404. [PMID: 32117428 PMCID: PMC7033542 DOI: 10.3389/fgene.2019.01404] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 12/23/2019] [Indexed: 12/12/2022] Open
Abstract
Copy number variations (CNVs) have been demonstrated as crucial substrates for evolution, adaptation and breed formation. Chinese indigenous cattle breeds exhibit a broad geographical distribution and diverse environmental adaptability. Here, we analyzed the population structure and adaptation to high altitude of Chinese indigenous cattle based on genome-wide CNVs derived from the high-density BovineHD SNP array. We successfully detected the genome-wide CNVs of 318 individuals from 24 Chinese indigenous cattle breeds and 37 yaks as outgroups. A total of 5,818 autosomal CNV regions (683 bp-4,477,860 bp in size), covering ~14.34% of the bovine genome (UMD3.1), were identified, showing abundant CNV resources. Neighbor-joining clustering, principal component analysis (PCA), and population admixture analysis based on these CNVs support that most Chinese cattle breeds are hybrids of Bos taurus taurus (hereinafter to be referred as Bos taurus) and Bos taurus indicus (Bos indicus). The distribution patterns of the CNVs could to some extent be related to the geographical backgrounds of the habitat of the breeds, and admixture among cattle breeds from different districts. We analyzed the selective signatures of CNVs positively involved in high-altitude adaptation using pairwise Fst analysis within breeds with a strong Bos taurus background (taurine-type breeds) and within Bos taurus×Bos indicus hybrids, respectively. CNV-overlapping genes with strong selection signatures (at top 0.5% of Fst value), including LETM1 (Fst = 0.490), TXNRD2 (Fst = 0.440), and STUB1 (Fst = 0.420) within taurine-type breeds, and NOXA1 (Fst = 0.233), RUVBL1 (Fst = 0.222), and SLC4A3 (Fst=0.154) within hybrids, were potentially involved in the adaptation to hypoxia. Thus, we provide a new profile of population structure from the CNV aspects of Chinese indigenous cattle and new insights into high-altitude adaptation in cattle.
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Affiliation(s)
- Yaran Zhang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yan Hu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiuge Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Qiang Jiang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Han Zhao
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jinpeng Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Zhihua Ju
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yaping Gao
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xiaochao Wei
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jiachen Bai
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jinming Huang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, China.,Engineering Center of Animal Breeding and Reproduction, Jinan, China
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19
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Jia C, Wang H, Li C, Wu X, Zan L, Ding X, Guo X, Bao P, Pei J, Chu M, Liang C, Yan P. Genome-wide detection of copy number variations in polled yak using the Illumina BovineHD BeadChip. BMC Genomics 2019; 20:376. [PMID: 31088363 PMCID: PMC6518677 DOI: 10.1186/s12864-019-5759-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/02/2019] [Indexed: 01/29/2023] Open
Abstract
Background Copy number variations (CNVs), which are genetic variations present throughout mammalian genomes, are a vital source of phenotypic variation that can lead to the development of unique traits. In this study we used the Illunima BovineHD BeadChip to conduct genome-wide detection of CNVs in 215 polled yaks. Results A total of 1066 CNV regions (CNVRs) were detected with a total length of 181.6 Mb, comprising ~ 7.2% of the bovine autosomal genome. The size of these CNVRs ranged from 5.53 kb to 1148.45 kb, with an average size of 170.31 kb. Eight out of nine randomly chosen CNVRs were successfully validated by qPCR. A functional enrichment analysis of the CNVR-associated genes indicated their relationship to a number of molecular adaptations that enable yaks to thrive at high altitudes. One third of the detected CNVRs were mapped to QTLs associated with six classes of economically important traits, indicating that these CNVRs may play an important role in variations of these traits. Conclusions Our genome-wide yak CNV map may thus provide valuable insights into both the molecular mechanisms of high altitude adaptation and the potential genomic basis of economically important traits in yak. Electronic supplementary material The online version of this article (10.1186/s12864-019-5759-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Congjun Jia
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.,College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Hongbo Wang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Chen Li
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Xiaoyun Wu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xuezhi Ding
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Xian Guo
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Pengjia Bao
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Jie Pei
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Min Chu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Chunnian Liang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.
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Copy number variation of bovine SHH gene is associated with body conformation traits in Chinese beef cattle. J Appl Genet 2019; 60:199-207. [PMID: 30997664 DOI: 10.1007/s13353-019-00496-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 10/27/2022]
Abstract
Sonic Hedgehog (Shh) regulates many key developmental processes during vertebrate limb development, fat formation, and skeletal tissue regeneration. Current whole genome sequencing data have identified a copy number variation mapping to bovine Sonic Hedgehog gene (SHH-CNV). The object of this study was to characterize the SHH-CNV distributions in 648 individuals from 11 Chinese cattle populations and further to investigate the associations of the copy number changes with gene expression and cattle growth traits. The SHH-CNV showed a high variance within Chinese indigenous yellow cattle. Compared to yak and dairy cattle, the beef cattle like Luxi and Xianan breed had significantly higher median copy numbers, suggesting the diversity of SHH-CNV in beef cattle selections. The negative correlation of SHH-CNV with SHH transcriptional level in adult adipose tissue (P < 0.01) indicated the dosage effects of SHH-CNV related to bovine fat formation. Association analysis of SHH-CNV and body size traits was conducted in five breeds. The results revealed that the copy number gain type of SHH-CNV exhibited significantly better chest depth in 24 months old Qinchuan cattle, and better body weight, body length, and chest girth in 18 months old Nanyang cattle, whereas the normal copy number had superior chest girth and body weight in adult Jinnan cattle (P < 0.05 or P < 0.01). In summary, this research uncovered meaningful effects of SHH-CNV on gene expression and cattle phenotypic traits, indicating its potential applications for genetic improvement of beef cattle.
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21
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Liu M, Fang L, Liu S, Pan MG, Seroussi E, Cole JB, Ma L, Chen H, Liu GE. Array CGH-based detection of CNV regions and their potential association with reproduction and other economic traits in Holsteins. BMC Genomics 2019; 20:181. [PMID: 30845913 PMCID: PMC6407259 DOI: 10.1186/s12864-019-5552-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 02/21/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Copy number variations (CNVs) are structural variants consisting of large-scale insertions and deletions of genomic fragments. Exploring CNVs and estimating their effects on phenotypes are useful for genome selection but remain challenging in the livestock. RESULTS We identified 1043 CNV regions (CNVRs) from array comparative genomic hybridization (CGH) data of 47 Holstein bulls. Using a probe-based CNV association approach, we detected 87 CNVRs significantly (Bonferroni-corrected P value < 0.05) associated with at least one out of 41 complex traits. Within them, 39 CNVRs were simultaneously associated with at least 2 complex traits. Notably, 24 CNVRs were markedly related to daughter pregnancy rate (DPR). For example, CNVR661 containing CYP4A11 and CNVR213 containing CTR9, respectively, were associated with DPR and other traits related to reproduction, production, and body conformation. CNVR758 was also significantly related to DPR, with a nearby gene CAPZA3, encoding one of F-actin-capping proteins which play a role in determining sperm architecture and male fertility. We corroborated these CNVRs by examining their overlapped quantitative trait loci and comparing with previously published CNV results. CONCLUSION To our knowledge, this is one of the first genome-wide association studies based on CNVs called by array CGH in Holstein cattle. Our results contribute substantial information about the potential CNV impacts on reproduction, health, production, and body conformation traits, which lay the foundation for incorporating CNV into the future dairy cattle breeding program.
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Affiliation(s)
- Mei Liu
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, 712100 Shaanxi China
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Lingzhao Fang
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD USA
| | - Shuli Liu
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Michael G. Pan
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Eyal Seroussi
- Agricultural Research Organization (ARO), Volcani Center, Institute of Animal Science, Department of Quantitative and Molecular Genetics, HaMaccabim Road, P.O.B 15159, 7528809 Rishon LeTsiyon, Israel
| | - John B. Cole
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD USA
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, 712100 Shaanxi China
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
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22
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Liu S, Kang X, Catacchio CR, Liu M, Fang L, Schroeder SG, Li W, Rosen BD, Iamartino D, Iannuzzi L, Sonstegard TS, Van Tassell CP, Ventura M, Low WY, Williams JL, Bickhart DM, Liu GE. Computational detection and experimental validation of segmental duplications and associated copy number variations in water buffalo ( Bubalus bubalis ). Funct Integr Genomics 2019; 19:409-419. [PMID: 30734132 DOI: 10.1007/s10142-019-00657-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 12/13/2018] [Accepted: 01/09/2019] [Indexed: 01/25/2023]
Abstract
Duplicated sequences are an important source of gene evolution and structural variation within mammalian genomes. Using a read depth approach based on next-generation sequencing, we performed a genome-wide analysis of segmental duplications (SDs) and associated copy number variations (CNVs) in the water buffalo (Bubalus bubalis). By aligning short reads of Olimpia (the reference water buffalo) to the UMD3.1 cattle genome, we identified 1,038 segmental duplications comprising 44.6 Mb (equivalent to ~1.73% of the cattle genome) of the autosomal and X chromosomal sequence in the buffalo genome. We experimentally validated 70.3% (71/101) of these duplications using fluorescent in situ hybridization. We also detected a total of 1,344 CNV regions across 14 additional water buffaloes, amounting to 59.8 Mb of variable sequence or the equivalent of 2.2% of the cattle genome. The CNV regions overlap 1,245 genes that are significantly enriched for specific biological functions including immune response, oxygen transport, sensory system and signal transduction. Additionally, we performed array Comparative Genomic Hybridization (aCGH) experiments using the 14 water buffaloes as test samples and Olimpia as the reference. Using a linear regression model, a high Pearson correlation (r = 0.781) was observed between the log2 ratios between copy number estimates and the log2 ratios of aCGH probes. We further designed Quantitative PCR assays to confirm CNV regions within or near annotated genes and found 74.2% agreement with our CNV predictions. These results confirm sub-chromosome-scale structural rearrangements present in the cattle and water buffalo. The information on genome variation that will be of value for evolutionary and phenotypic studies, and may be useful for selective breeding of both species.
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Affiliation(s)
- Shuli Liu
- USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, Maryland, 20705, USA
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xiaolong Kang
- USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, Maryland, 20705, USA
- College of Agriculture, Ningxia University, Yinchuan, 750021, China
| | | | - Mei Liu
- USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, Maryland, 20705, USA
- College of Animal Science and Technology, Shaanxi Key Laboratory of Agricultural Molecular Biology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Lingzhao Fang
- USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, Maryland, 20705, USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, 20742, USA
| | - Steven G Schroeder
- USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, Maryland, 20705, USA
| | - Wenli Li
- The Cell Wall Utilization and Biology Laboratory, US Dairy Forage Research Center, USDA, ARS, Madison, WI 53706, USA
| | - Benjamin D Rosen
- USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, Maryland, 20705, USA
| | - Daniela Iamartino
- AIA-LGS, Associazione Italiana Allevatori - Laboratorio Genetica e Servizi, Via Bergamo 292, 26100 (CR), Cremona, Italy
- Parco Tecnologico Padano, Via Einstein, Polo Universitario, 26900, Lodi, Italy
| | - Leopoldo Iannuzzi
- Laboratory of Animal Cytogenetics and Gene Mapping, Nationa Research Council (CNR), ISPAAM, Via Argine 1085, 80147, Naples, Italy
| | | | - Curtis P Van Tassell
- USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, Maryland, 20705, USA
| | - Mario Ventura
- Department of Biology, University of Bari, 70126, Bari, Italy
| | - Wai Yee Low
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia
| | - John L Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia
| | - Derek M Bickhart
- The Cell Wall Utilization and Biology Laboratory, US Dairy Forage Research Center, USDA, ARS, Madison, WI 53706, USA.
| | - George E Liu
- USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, Maryland, 20705, USA.
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Wang H, Chai Z, Hu D, Ji Q, Xin J, Zhang C, Zhong J. A global analysis of CNVs in diverse yak populations using whole-genome resequencing. BMC Genomics 2019; 20:61. [PMID: 30658572 PMCID: PMC6339343 DOI: 10.1186/s12864-019-5451-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 01/11/2019] [Indexed: 12/01/2022] Open
Abstract
Background Genomic structural variation represents a source for genetic and phenotypic variation, which may be subject to selection during the environmental adaptation and population differentiation. Here, we described a genome-wide analysis of copy number variations (CNVs) in 16 populations of yak based on genome resequencing data and CNV-based cluster analyses of these populations. Results In total, we identified 51,461 CNV events and defined 3174 copy number variation regions (CNVRs) that covered 163.8 Mb (6.2%) of yak genome with more “loss” events than both “gain” and “both” events, and we confirmed 31 CNVRs in 36 selected yaks using quantitative PCR. Of the total 163.8 Mb CNVR coverage, a 10.8 Mb region of high-confidence CNVRs directly overlapped with the 52.9 Mb of segmental duplications, and we confirmed their uneven distributions across chromosomes. Furthermore, functional annotation indicated that the CNVR-harbored genes have a considerable variety of molecular functions, including immune response, glucose metabolism, and sensory perception. Notably, some of the identified CNVR-harbored genes associated with adaptation to hypoxia (e.g., DCC, MRPS28, GSTCD, MOGAT2, DEXI, CIITA, and SMYD1). Additionally, cluster analysis, based on either individuals or populations, showed that the CNV clustering was divided into two origins, indicating that some yak CNVs are likely to arisen independently in different populations and contribute to population difference. Conclusions Collectively, the results of the present study advanced our understanding of CNV as an important type of genomic structural variation in yak, and provide a useful genomic resource to facilitate further research on yak evolution and breeding. Electronic supplementary material The online version of this article (10.1186/s12864-019-5451-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hui Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Southwest Minzu University), Ministry of Education, Chengdu, 610000, People's Republic of China
| | - Zhixin Chai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Southwest Minzu University), Ministry of Education, Chengdu, 610000, People's Republic of China
| | - Dan Hu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Southwest Minzu University), Ministry of Education, Chengdu, 610000, People's Republic of China
| | - Qiumei Ji
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850000, People's Republic of China
| | - Jinwei Xin
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850000, People's Republic of China
| | - Chengfu Zhang
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850000, People's Republic of China
| | - Jincheng Zhong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Southwest Minzu University), Ministry of Education, Chengdu, 610000, People's Republic of China.
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24
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Goshu HA, Chu M, Xiaoyun W, Pengjia B, Zhi DX, Yan P. Genomic copy number variation of the CHKB gene alters gene expression and affects growth traits of Chinese domestic yak (Bos grunniens) breeds. Mol Genet Genomics 2019; 294:549-561. [DOI: 10.1007/s00438-018-01530-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 12/29/2018] [Indexed: 12/22/2022]
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25
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Goshu HA, Chu M, Wu X, Pengjia B, Ding XZ, Yan P. Association study and expression analysis of GPC1 gene copy number variation in Chinese Datong yak ( Bos grunniens) breed. ITALIAN JOURNAL OF ANIMAL SCIENCE 2019. [DOI: 10.1080/1828051x.2019.1586456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Habtamu Abera Goshu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, Gansu, China
- Animal Science Department, Oromia Agricultural Research Institute, Bako Agricultural Research Center, Bako, Ethiopia
| | - Min Chu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, Gansu, China
| | - Xiaoyun Wu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, Gansu, China
| | - Bao Pengjia
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, Gansu, China
| | - Xue Zhi Ding
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, Gansu, China
| | - Ping Yan
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, Gansu, China
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26
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Wang GD, Shao XJ, Bai B, Wang J, Wang X, Cao X, Liu YH, Wang X, Yin TT, Zhang SJ, Lu Y, Wang Z, Wang L, Zhao W, Zhang B, Ruan J, Zhang YP. Structural variation during dog domestication: insights from gray wolf and dhole genomes. Natl Sci Rev 2019; 6:110-122. [PMID: 34694297 PMCID: PMC8291444 DOI: 10.1093/nsr/nwy076] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 06/27/2018] [Accepted: 07/17/2018] [Indexed: 12/11/2022] Open
Abstract
Several processes like phenotypic evolution, disease susceptibility and environmental adaptations, which fashion the domestication of animals, are largely attributable to structural variations (SVs) in the genome. Here, we present high-quality draft genomes of the gray wolf (Canis lupus) and dhole (Cuon alpinus) with scaffold N50 of 6.04 Mb and 3.96 Mb, respectively. Sequence alignment comprising genomes of three canid species reveals SVs specific to the dog, particularly 16 315 insertions, 2565 deletions, 443 repeats, 16 inversions and 15 translocations. Functional annotation of the dog SVs associated with genes indicates their enrichments in energy metabolisms, neurological processes and immune systems. Interestingly, we identify and verify at population level an insertion fully covering a copy of the AKR1B1 (Aldo-Keto Reductase Family 1 Member B) transcript. Transcriptome analysis reveals a high level of expression of the new AKR1B1 copy in the small intestine and liver, implying an increase in de novo fatty acid synthesis and antioxidant ability in dog compared to gray wolf, likely in response to dietary shifts during the agricultural revolution. For the first time, we report a comprehensive analysis of the evolutionary dynamics of SVs during the domestication step of dogs. Our findings demonstrate that retroposition can birth new genes to facilitate domestication, and affirm the importance of large-scale genomic variants in domestication studies.
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Affiliation(s)
- Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Xiu-Juan Shao
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Bing Bai
- Medical Faculty, Kunming University of Science and Technology, Kunming 650504, China
- Department of Pediatrics, the First People's Hospital of Yunnan Province, Kunming 650032, China
| | - Junlong Wang
- College of Pharmacology, Soochow University, Suzhou 215123, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xiaobo Wang
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xue Cao
- Department of Laboratory Animal Science, Kunming Medical University, Kunming 650500, China
| | - Yan-Hu Liu
- Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Xuan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Shao-Jie Zhang
- Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Yan Lu
- Beijing Zoo, Beijing 100044, China
| | | | - Lu Wang
- Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Wenming Zhao
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bing Zhang
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jue Ruan
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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27
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Zheng L, Xu JW, Li JC, Wang DH, An QM, Xu LN, Ma YL, Wang J, Peng SJ, Lei CZ, Lan XY, Chen H, Huo LJ, Huang YZ. Distribution and association study in copy number variation of KCNJ12 gene across four Chinese cattle populations. Gene 2018; 689:90-96. [PMID: 30572095 DOI: 10.1016/j.gene.2018.12.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 11/29/2018] [Accepted: 12/06/2018] [Indexed: 10/27/2022]
Abstract
Copy number variation is a large genome variation which usually happens in the noncoding-region, and it may occur at the locus associated with the functional gene to further influence the phenotype. Potassium inwardly-rectifying channel, subfamily J 12 (KCNJ12) gene expressed widely in cardiomyocytes and neurons, plays an important role in tumor therapy and muscle movement regulation. In this study, we detected the distribution of CNVs for KCNJ12 gene in 404 individuals belonging to four Chinese cattle breeds (NY, JX, JA and GF). We also investigated the KCNJ12 gene expression in different tissues of JX cattle. Additionally, we examined the association of two CNV regions (CNV1: 1,600 bp, intron 1; CNV2: 4,800 bp, intergenic) with growth traits. The statistical analyses indicated that the CNV1 is associated with the body length, rump length and weight in JX cattle population (P < 0.05); and there has a significant association with the body length, chest circumference, and body weight in GF cattle (P < 0.05).The CNV2 had a significant effect on the body length and body weight in JX cattle (P < 0.05); the body length, chest circumference, rump length and body weight in GF cattle (P < 0.01 or P < 0.05). The copy numbers of KCNJ12 gene presented the negative correlations with the transcript level of gene in skeletal muscles (P < 0.05). Our results provide evidence that CNV1 and CNV 2 in KCNJ12 are associated with growth traits in two cattle populations and may be used as candidates for marker-assisted selection and breeding management in cattle.
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Affiliation(s)
- Li Zheng
- Henan University of Animal Husbandry and Economy, Zhengzhou, Henan 450046, People's Republic of China; Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Jia-Wei Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Ji-Chao Li
- Henan University of Animal Husbandry and Economy, Zhengzhou, Henan 450046, People's Republic of China
| | - Da-Hui Wang
- College of Agriculture and Forestry Engineering, Tongren Unviersity, Tongren, Guizhou 554300, People's Republic of China
| | - Qing-Ming An
- College of Agriculture and Forestry Engineering, Tongren Unviersity, Tongren, Guizhou 554300, People's Republic of China
| | - Lin-Na Xu
- Gansu Animal Husbandry Industry Administration, Lanzhou, Gansu 730000, People's Republic of China
| | - Yi-Lei Ma
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Jian Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Shu-Jun Peng
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Chu-Zhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Xian-Yong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Li-Jun Huo
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
| | - Yong-Zhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China.
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28
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Copy Number Variations of KLF6 Modulate Gene Transcription and Growth Traits in Chinese Datong Yak (Bos Grunniens). Animals (Basel) 2018; 8:ani8090145. [PMID: 30134528 PMCID: PMC6162419 DOI: 10.3390/ani8090145] [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: 07/13/2018] [Revised: 08/06/2018] [Accepted: 08/18/2018] [Indexed: 02/08/2023] Open
Abstract
Copy number variation (CNV) is a significant marker of the genetic and phenotypic diversity among individuals that accounts for complex quantitative traits of phenotype and diseases via modulating gene dosage and disrupting coding regions in the genome. Biochemically, Kruppel-like factor 6 (KLF6) genes plays a significant role in the regulation of cell differentiation and proliferation and muscle development. The aim of this study was to detect the distributions of KLF6 copy number variations (CNVs) in five breeds of domestic yak and to explore their effect on growth traits and gene expression. The data were analyzed by real-time quantitative PCR (qPCR). Our results elucidated that a decreased CNV in the KLF6 gene is more highly associated (p < 0.05) with various growth traits than increased or normal CNVs in six-month-old and five-year-old Datong yak. Nevertheless, negative correlations between the DNA copy number and KLF6 gene expression were observed in the skeletal muscle of adult Datong yak. These results suggest that CNVs of the KLF6 gene could be crucial genomic markers for growth phenotypes of Chinese Datong yak breeds and this finding constitutes the first evidence of the biological role of KLF6 CNVs in Chinese Datong yak breeds.
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29
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Gong J, Cheng T, Wu Y, Yang X, Feng Q, Mita K. Genome-wide patterns of copy number variations in Spodoptera litura. Genomics 2018; 111:1231-1238. [PMID: 30114452 DOI: 10.1016/j.ygeno.2018.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/26/2018] [Accepted: 08/04/2018] [Indexed: 01/06/2023]
Abstract
Spodoptera litura is a polyphagous pest and can feed on more than 100 species of plants, causing great damage to agricultural production. The SNP results showed that there were gene exchanges between different regions. To explore the variations of larger segments in S. litura genome, we used genome resequencing samples from 14 regions of China, India, and Japan to study the copy number variations (CNVs). We identified 3976 CNV events and 1581 unique copy number variation regions (CNVRs) occupying the 108.5 Mb genome of S. litura. A total of 5527 genes that overlapped with CNVRs were detected. Selection signal analysis identified 19 shared CNVRs and 105 group-specific CNVRs, whose related genes were involved in various biological processes in S. litura. We constructed the first CNVs map in S. litura genome, and our findings will be valuable for understanding the genomic variations and population differences of S. litura.
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Affiliation(s)
- Jiao Gong
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Tingcai Cheng
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, 2, Tiansheng Road, Beibei, Chongqing 400715, China.
| | - Yuqian Wu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Xi Yang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Qili Feng
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, South China Normal University, Guangzhou 510631, China
| | - Kazuei Mita
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
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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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Bhanuprakash V, Chhotaray S, Pruthviraj DR, Rawat C, Karthikeyan A, Panigrahi M. Copy number variation in livestock: A mini review. Vet World 2018; 11:535-541. [PMID: 29805222 PMCID: PMC5960796 DOI: 10.14202/vetworld.2018.535-541] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 03/31/2018] [Indexed: 01/22/2023] Open
Abstract
Copy number variation (CNV) is a phenomenon in which sections of the genome, ranging from one kilo base pair (Kb) to several million base pairs (Mb), are repeated and the number of repeats vary between the individuals in a population. It is an important source of genetic variation in an individual which is now being utilized rather than single nucleotide polymorphisms (SNPs), as it covers the more genomic region. CNVs alter the gene expression and change the phenotype of an individual due to deletion and duplication of genes in the copy number variation regions (CNVRs). Earlier, researchers extensively utilized SNPs as the main source of genetic variation. But now, the focus is on identification of CNVs associated with complex traits. With the recent advances and reduction in the cost of sequencing, arrays are developed for genotyping which cover the maximum number of SNPs at a time that can be used for detection of CNVRs and underlying quantitative trait loci (QTL) for the complex traits to accelerate genetic improvement. CNV studies are also being carried out to understand the evolutionary mechanism in the domestication of livestock and their adaptation to the different environmental conditions. The main aim of the study is to review the available data on CNV and its role in genetic variation among the livestock.
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Affiliation(s)
- V Bhanuprakash
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly - 243122, Uttar Pradesh, India
| | - Supriya Chhotaray
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly - 243122, Uttar Pradesh, India
| | - D R Pruthviraj
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly - 243122, Uttar Pradesh, India
| | - Chandrakanta Rawat
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly - 243122, Uttar Pradesh, India
| | - A Karthikeyan
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly - 243122, Uttar Pradesh, India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly - 243122, Uttar Pradesh, India
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Zhang GM, Zheng L, He H, Song CC, Zhang ZJ, Cao XK, Lei CZ, Lan XY, Qi XL, Chen H, Huang YZ. Associations of GBP2 gene copy number variations with growth traits and transcriptional expression in Chinese cattle. Gene 2018; 647:101-106. [PMID: 29325733 DOI: 10.1016/j.gene.2018.01.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 12/16/2017] [Accepted: 01/02/2018] [Indexed: 12/19/2022]
Abstract
Copy number variations (CNVs) recently have been recognized as another important genetic variability followed single nucleotide polymorphisms (SNPs). The guanylate binding protein 2 (GBP2) gene plays an important role in cell proliferation. This study was performed to determine the presence of GBP2 CNV (relative to Angus cattle) in 466 individuals representing six main cattle breeds from China, identify its relationship with growth, and explore the biological effects of gene expression. There were two CNV regions in the GBP2 gene, for three types, CNV1 loss type (relative to Angus cattle) was more frequent in XN than other breeds, and CNV2 loss type (relative to Angus cattle) was more frequent in XN and CDM than other breeds. Though the GBP2 gene copy number presented no correlation with the transcriptional expression of JX (P > .05), but the transcriptional expression in heart is higher than other tissues, and the copy number in muscles and fat of JX is higher than others breeds. Statistical analysis revealed that the GBP2 gene CNV1 and CNV2 were significantly associated with growth traits (P < .05). In conclusion, this research established the correlations between CNVs of GBP2 gene and growth traits in different cattle breeds, and our results suggested that the CNVs in GBP2 gene may be considered markers for the molecular breeding of Chinese beef cattle.
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Affiliation(s)
- Gui-Min Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Li Zheng
- Henan University of Animal Husbandry and Economy, Zhengzhou, Henan 450046, PR China
| | - Hua He
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China; College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Cheng-Chuang Song
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Zi-Jing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, PR China
| | - Xiu-Kai Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Chu-Zhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Xian-Yong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Xing-Lei Qi
- Bureau of Animal Husbandry of Biyang County, Biyang, Henan 463700, PR China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Yong-Zhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
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Antunes de Lemos MV, Berton MP, Ferreira de Camargo GM, Peripolli E, de Oliveira Silva RM, Ferreira Olivieri B, Cesar AS, Pereira ASC, de Albuquerque LG, de Oliveira HN, Tonhati H, Baldi F. Copy number variation regions in Nellore cattle: Evidences of environment adaptation. Livest Sci 2018. [DOI: 10.1016/j.livsci.2017.11.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Yang L, Xu L, Zhu B, Niu H, Zhang W, Miao J, Shi X, Zhang M, Chen Y, Zhang L, Gao X, Gao H, Li L, Liu GE, Li J. Genome-wide analysis reveals differential selection involved with copy number variation in diverse Chinese Cattle. Sci Rep 2017; 7:14299. [PMID: 29085051 PMCID: PMC5662686 DOI: 10.1038/s41598-017-14768-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 10/12/2017] [Indexed: 12/20/2022] Open
Abstract
Copy number variations (CNVs) are defined as deletions, insertions, and duplications between two individuals of a species. To investigate the diversity and population-genetic properties of CNVs and their diverse selection patterns, we performed a genome-wide CNV analysis using high density SNP array in Chinese native cattle. In this study, we detected a total of 13,225 CNV events and 3,356 CNV regions (CNVRs), overlapping with 1,522 annotated genes. Among them, approximately 71.43 Mb of novel CNVRs were detected in the Chinese cattle population for the first time, representing the unique genomic resources in cattle. A new V i statistic was proposed to estimate the region-specific divergence in CNVR for each group based on unbiased estimates of pairwise V ST . We obtained 12 and 62 candidate CNVRs at the top 1% and top 5% of genome-wide V i value thresholds for each of four groups (North, Northwest, Southwest and South). Moreover, we identified many lineage-differentiated CNV genes across four groups, which were associated with several important molecular functions and biological processes, including metabolic process, response to stimulus, immune system, and others. Our findings provide some insights into understanding lineage-differentiated CNVs under divergent selection in the Chinese native cattle.
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Affiliation(s)
- Liu Yang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Lingyang Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Bo Zhu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Hong Niu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wengang Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jian Miao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Xinping Shi
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,College of Animal Science and Technology, Agricultural University of Hebei, Baoding, Hebei, 071001, China
| | - Ming Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yan Chen
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lupei Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xue Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Huijiang Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Li Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland, 20705, USA
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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35
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Huang J, Li R, Zhang X, Huang Y, Dang R, Lan X, Chen H, Lei C. Copy number veriation regions detection in Qinchuan cattle. Livest Sci 2017. [DOI: 10.1016/j.livsci.2017.08.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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36
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Upadhyay M, da Silva VH, Megens HJ, Visker MHPW, Ajmone-Marsan P, Bâlteanu VA, Dunner S, Garcia JF, Ginja C, Kantanen J, Groenen MAM, Crooijmans RPMA. Distribution and Functionality of Copy Number Variation across European Cattle Populations. Front Genet 2017; 8:108. [PMID: 28878807 PMCID: PMC5572341 DOI: 10.3389/fgene.2017.00108] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 08/02/2017] [Indexed: 12/27/2022] Open
Abstract
Copy number variation (CNV), which is characterized by large-scale losses or gains of DNA fragments, contributes significantly to genetic and phenotypic variation. Assessing CNV across different European cattle populations might reveal genetic changes responsible for phenotypic differences, which have accumulated throughout the domestication history of cattle as consequences of evolutionary forces that act upon them. To explore pattern of CNVs across European cattle, we genotyped 149 individuals, that represent different European regions, using the Illumina Bovine HD Genotyping array. A total of 9,944 autosomal CNVs were identified in 149 samples using a Hidden Markov Model (HMM) as employed in PennCNV. Animals originating from several breeds of British Isles, and Balkan and Italian regions, on average, displayed higher abundance of CNV counts than Dutch or Alpine animals. A total of 923 CNV regions (CNVRs) were identified by aggregating CNVs overlapping in at least two animals. The hierarchical clustering of CNVRs indicated low differentiation and sharing of high-frequency CNVRs between European cattle populations. Various CNVRs identified in the present study overlapped with olfactory receptor genes and genes related to immune system. In addition, we also detected a CNV overlapping the Kit gene in English longhorn cattle which has previously been associated with color-sidedness. To conclude, we provide a comprehensive overview of CNV distribution in genome of European cattle. Our results indicate an important role of purifying selection and genomic drift in shaping CNV diversity that exists between different European cattle populations.
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Affiliation(s)
- Maulik Upadhyay
- Animal Breeding and Genomics, Wageningen University and ResearchWageningen, Netherlands.,Department of Animal Breeding and Genetics, Swedish University of Agricultural SciencesUppsala, Sweden
| | - Vinicus H da Silva
- Animal Breeding and Genomics, Wageningen University and ResearchWageningen, Netherlands.,Department of Animal Breeding and Genetics, Swedish University of Agricultural SciencesUppsala, Sweden
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics, Wageningen University and ResearchWageningen, Netherlands
| | - Marleen H P W Visker
- Animal Breeding and Genomics, Wageningen University and ResearchWageningen, Netherlands
| | - Paolo Ajmone-Marsan
- Institute of Zootechnics and Nutrigenomics and Proteomics Research Center, Università Cattolica del Sacro CuorePiacenza, Italy
| | - Valentin A Bâlteanu
- Institute of Life Sciences, Faculty of Animal Science and Biotechnologies, University of Agricultural Sciences and Veterinary Medicine of Cluj-NapocaCluj-Napoca, Romania
| | - Susana Dunner
- Department of Animal Production, Veterinary Faculty, Universidad Complutense de MadridMadrid, Spain
| | - Jose F Garcia
- Departamento de Apoio, Produção e Saúde Animal, Faculdade de Medicina Veterinária de Araçatuba, Universidade Estadual PaulistaAraçatuba, Brazil.,IAEA Collaborating Centre on Animal Genomics and BioinformaticsAraçatuba, Brazil
| | - Catarina Ginja
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-InBIO), Universidade do PortoVairao, Portugal
| | - Juha Kantanen
- Green Technology, Natural Resources Institute FinlandJokioinen, Finland.,Department of Environmental and Biological Sciences, University of Eastern FinlandKuopio, Finland
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University and ResearchWageningen, Netherlands
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Association study and expression analysis of CYP4A11 gene copy number variation in Chinese cattle. Sci Rep 2017; 7:46599. [PMID: 28492277 PMCID: PMC5425913 DOI: 10.1038/srep46599] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 03/22/2017] [Indexed: 11/09/2022] Open
Abstract
The identification of copy number variations (CNVs) allow us to explore genomic polymorphisms. In recent years, significant progress in understanding CNVs has been made in studies of human and animals, however, association and expression studies of CNVs are still in the early stage. It was previously reported that the Cytochrome P-450 4A11 (CYP4A11) gene is located within a copy number variable region (CNVR) that encompasses quantitative trait loci (QTLs) for economic traits like meat quality and milk production. So, this study was performed to determine the presence of CYP4A11 CNV in six distinct cattle breeds, identify its relationship with growth, and explore the biological effects of gene expression. For three CYP4A11 CNV types, Normal was more frequent than Gain or Loss. Association analysis revealed a positive effect of CYP4A11 copy number on growth traits (P < 0.05). One-way analysis of variance (ANOVA) analysis revealed that more CYP4A11 copies increased the gene expression level. Moreover, overexpression of CYP4A11 in vitro revealed its effect on lipid deposit. The data provide evidence for the functional role of CYP4A11 CNV and provide the basis for future applications in cattle breeding.
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Gao Y, Jiang J, Yang S, Hou Y, Liu GE, Zhang S, Zhang Q, Sun D. CNV discovery for milk composition traits in dairy cattle using whole genome resequencing. BMC Genomics 2017; 18:265. [PMID: 28356085 PMCID: PMC5371188 DOI: 10.1186/s12864-017-3636-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 03/17/2017] [Indexed: 01/08/2023] Open
Abstract
Background Copy number variations (CNVs) are important and widely distributed in the genome. CNV detection opens a new avenue for exploring genes associated with complex traits in humans, animals and plants. Herein, we present a genome-wide assessment of CNVs that are potentially associated with milk composition traits in dairy cattle. Results In this study, CNVs were detected based on whole genome re-sequencing data of eight Holstein bulls from four half- and/or full-sib families, with extremely high and low estimated breeding values (EBVs) of milk protein percentage and fat percentage. The range of coverage depth per individual was 8.2–11.9×. Using CNVnator, we identified a total of 14,821 CNVs, including 5025 duplications and 9796 deletions. Among them, 487 differential CNV regions (CNVRs) comprising ~8.23 Mb of the cattle genome were observed between the high and low groups. Annotation of these differential CNVRs were performed based on the cattle genome reference assembly (UMD3.1) and totally 235 functional genes were found within the CNVRs. By Gene Ontology and KEGG pathway analyses, we found that genes were significantly enriched for specific biological functions related to protein and lipid metabolism, insulin/IGF pathway-protein kinase B signaling cascade, prolactin signaling pathway and AMPK signaling pathways. These genes included INS, IGF2, FOXO3, TH, SCD5, GALNT18, GALNT16, ART3, SNCA and WNT7A, implying their potential association with milk protein and fat traits. In addition, 95 CNVRs were overlapped with 75 known QTLs that are associated with milk protein and fat traits of dairy cattle (Cattle QTLdb). Conclusions In conclusion, based on NGS of 8 Holstein bulls with extremely high and low EBVs for milk PP and FP, we identified a total of 14,821 CNVs, 487 differential CNVRs between groups, and 10 genes, which were suggested as promising candidate genes for milk protein and fat traits. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3636-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yahui Gao
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jianping Jiang
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Shaohua Yang
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yali Hou
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, Md, 20705, USA
| | - Shengli Zhang
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Qin Zhang
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Dongxiao Sun
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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39
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Copy number variation of bovine MAPK10 modulates the transcriptional activity and affects growth traits. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.09.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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40
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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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41
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Zhou Y, Utsunomiya YT, Xu L, Hay EHA, Bickhart DM, Alexandre PA, Rosen BD, Schroeder SG, Carvalheiro R, de Rezende Neves HH, Sonstegard TS, Van Tassell CP, Ferraz JBS, Fukumasu H, Garcia JF, Liu GE. Genome-wide CNV analysis reveals variants associated with growth traits in Bos indicus. BMC Genomics 2016; 17:419. [PMID: 27245577 PMCID: PMC4888316 DOI: 10.1186/s12864-016-2461-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 02/11/2016] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Apart from single nucleotide polymorphism (SNP), copy number variation (CNV) is another important type of genetic variation, which may affect growth traits and play key roles for the production of beef cattle. To date, no genome-wide association study (GWAS) for CNV and body traits in beef cattle has been reported, so the present study aimed to investigate this type of association in one of the most important cattle subspecies: Bos indicus (Nellore breed). RESULTS We have used intensity data from over 700,000 SNP probes across the bovine genome to detect common CNVs in a sample of 2230 Nellore cattle, and performed GWAS between the detected CNVs and nine growth traits. After filtering for frequency and length, a total of 231 CNVs ranging from 894 bp to 4,855,088 bp were kept and tested as predictors for each growth trait using linear regression analysis with principal components correction. There were 49 significant associations identified among 17 CNVs and seven body traits after false discovery rate correction (P < 0.05). Among the 17 CNVs, three were significant or marginally significant for all the traits. We have compared the locations of associated CNVs with quantitative trait locus and the RefGene database, and found two sets of 9 CNVs overlapping with either known QTLs or genes, respectively. The gene overlapping with CNV100, KCNJ12, is a functional candidate for muscle development and plays critical roles in muscling traits. CONCLUSION This study presents the first CNV-based GWAS of growth traits using high density SNP microarray data in cattle. We detected 17 CNVs significantly associated with seven growth traits and one of them (CNV100) may be involved in growth traits through KCNJ12.
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Affiliation(s)
- Yang Zhou
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA.,College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi, 712100, China
| | - Yuri T Utsunomiya
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, 14884-900, Brazil
| | - Lingyang Xu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA.,Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China
| | - El Hamidi Abdel Hay
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA
| | - Derek M Bickhart
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA
| | - Pamela Almeida Alexandre
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, 13635, Brazil
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA
| | - Steven G Schroeder
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA
| | - Roberto Carvalheiro
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, 14884-900, Brazil
| | - Haroldo Henrique de Rezende Neves
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, 14884-900, Brazil
| | - Tad S Sonstegard
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA.,Present address: Recombinetics, Inc., St Paul, MN, 55104, USA
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA
| | - José Bento Sterman Ferraz
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, 13635, Brazil
| | - Heidge Fukumasu
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, 13635, Brazil
| | - Jose Fernando Garcia
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, 14884-900, Brazil. .,Departamento de Apoio, Produção e Saúde Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP - Univ Estadual Paulista, Araçatuba, São Paulo, 16050-680, Brazil. .,International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil.
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Room 111, BARC-East, Beltsville, Maryland, 20705, USA.
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42
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Zhang X, Wang K, Wang L, Yang Y, Ni Z, Xie X, Shao X, Han J, Wan D, Qiu Q. Genome-wide patterns of copy number variation in the Chinese yak genome. BMC Genomics 2016; 17:379. [PMID: 27206476 PMCID: PMC4875690 DOI: 10.1186/s12864-016-2702-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 05/06/2016] [Indexed: 12/02/2022] Open
Abstract
Background Copy number variation (CNV) represents an important source of genetic divergence that can produce drastic phenotypic differences and may therefore be subject to selection during domestication and environmental adaptation. To investigate the evolutionary dynamics of CNV in the yak genome, we used a read depth approach to detect CNV based on genome resequencing data from 14 wild and 65 domestic yaks and determined CNV regions related to domestication and adaptations to high-altitude. Results We identified 2,634 CNV regions (CNVRs) comprising a total of 153 megabases (5.7 % of the yak genome) and 3,879 overlapping annotated genes. Comparison between domestic and wild yak populations identified 121 potentially selected CNVRs, harboring genes related to neuronal development, reproduction, nutrition and energy metabolism. In addition, we found 85 CNVRs that are significantly different between domestic yak living in high- and low-altitude areas, including three genes related to hypoxia response and six related to immune defense. This analysis shows that genic CNVs may play an important role in phenotypic changes during yak domestication and adaptation to life at high-altitude. Conclusions We present the first refined CNV map for yak along with comprehensive genomic analysis of yak CNV. Our results provide new insights into the genetic basis of yak domestication and adaptation to living in a high-altitude environment, as well as a valuable genetic resource that will facilitate future CNV association studies of important traits in yak and other bovid species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2702-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiao Zhang
- State Key Laboratory of Grassland Agroecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Kun Wang
- State Key Laboratory of Grassland Agroecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Lizhong Wang
- State Key Laboratory of Grassland Agroecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agroecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Zhengqiang Ni
- State Key Laboratory of Grassland Agroecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Xiuyue Xie
- State Key Laboratory of Grassland Agroecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Xuemin Shao
- State Key Laboratory of Grassland Agroecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Jin Han
- State Key Laboratory of Grassland Agroecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Dongshi Wan
- State Key Laboratory of Grassland Agroecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China.
| | - Qiang Qiu
- State Key Laboratory of Grassland Agroecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China.
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43
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Shi T, Xu Y, Yang M, Huang Y, Lan X, Lei C, Qi X, Yang X, Chen H. Copy number variations atLEPRgene locus associated with gene expression and phenotypic traits in Chinese cattle. Anim Sci J 2015; 87:336-43. [DOI: 10.1111/asj.12531] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 07/11/2015] [Accepted: 07/29/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Tao Shi
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture; Northwest A&F University; Yangling China
| | - Yao Xu
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture; Northwest A&F University; Yangling China
| | - Mingjuan Yang
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture; Northwest A&F University; Yangling China
| | - Yongzhen Huang
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture; Northwest A&F University; Yangling China
| | - Xianyong Lan
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture; Northwest A&F University; Yangling China
| | - Chuzhao Lei
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture; Northwest A&F University; Yangling China
| | - Xinglei Qi
- Biyang Bureau of Animal Husbandry of Biyang County; Biyang Henan China
| | - Xiaoming Yang
- Institute of Animal Husbandry and Veterinary; Shanxi Academy of Agricultural Sciences; Taiyuan Shanxi China
| | - Hong Chen
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture; Northwest A&F University; Yangling China
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44
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Boussaha M, Esquerré D, Barbieri J, Djari A, Pinton A, Letaief R, Salin G, Escudié F, Roulet A, Fritz S, Samson F, Grohs C, Bernard M, Klopp C, Boichard D, Rocha D. Genome-Wide Study of Structural Variants in Bovine Holstein, Montbéliarde and Normande Dairy Breeds. PLoS One 2015; 10:e0135931. [PMID: 26317361 PMCID: PMC4552564 DOI: 10.1371/journal.pone.0135931] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 07/28/2015] [Indexed: 11/26/2022] Open
Abstract
High-throughput sequencing technologies have offered in recent years new opportunities to study genome variations. These studies have mostly focused on single nucleotide polymorphisms, small insertions or deletions and on copy number variants. Other structural variants, such as large insertions or deletions, tandem duplications, translocations, and inversions are less well-studied, despite that some have an important impact on phenotypes. In the present study, we performed a large-scale survey of structural variants in cattle. We report the identification of 6,426 putative structural variants in cattle extracted from whole-genome sequence data of 62 bulls representing the three major French dairy breeds. These genomic variants affect DNA segments greater than 50 base pairs and correspond to deletions, inversions and tandem duplications. Out of these, we identified a total of 547 deletions and 410 tandem duplications which could potentially code for CNVs. Experimental validation was carried out on 331 structural variants using a novel high-throughput genotyping method. Out of these, 255 structural variants (77%) generated good quality genotypes and 191 (75%) of them were validated. Gene content analyses in structural variant regions revealed 941 large deletions removing completely one or several genes, including 10 single-copy genes. In addition, some of the structural variants are located within quantitative trait loci for dairy traits. This study is a pan-genome assessment of genomic variations in cattle and may provide a new glimpse into the bovine genome architecture. Our results may also help to study the effects of structural variants on gene expression and consequently their effect on certain phenotypes of interest.
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Affiliation(s)
- Mekki Boussaha
- INRA, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
- AgroParisTech, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
- * E-mail:
| | - Diane Esquerré
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Johanna Barbieri
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Anis Djari
- INRA, SIGENAE, UR 875, INRA Auzeville, BP 52627, Castanet-Tolosan, France
| | - Alain Pinton
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Rabia Letaief
- INRA, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
- AgroParisTech, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
| | - Gérald Salin
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Frédéric Escudié
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Alain Roulet
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Sébastien Fritz
- INRA, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
- AgroParisTech, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
- Union Nationale des Coopératives Agricoles d’Elevage et d’Insémination Animale, Paris, France
| | - Franck Samson
- INRA, UR1077, Mathématique Informatique et Génome, Domaine de Vilvert, Jouy-en-Josas, France
| | - Cécile Grohs
- INRA, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
- AgroParisTech, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
| | - Maria Bernard
- INRA, SIGENAE, UR 875, INRA Auzeville, BP 52627, Castanet-Tolosan, France
| | - Christophe Klopp
- INRA, SIGENAE, UR 875, INRA Auzeville, BP 52627, Castanet-Tolosan, France
| | - Didier Boichard
- INRA, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
- AgroParisTech, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
| | - Dominique Rocha
- INRA, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
- AgroParisTech, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
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Zhang L, Jia S, Plath M, Huang Y, Li C, Lei C, Zhao X, Chen H. Impact of Parental Bos taurus and Bos indicus Origins on Copy Number Variation in Traditional Chinese Cattle Breeds. Genome Biol Evol 2015; 7:2352-61. [PMID: 26260653 PMCID: PMC4558867 DOI: 10.1093/gbe/evv151] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Copy number variation (CNV) is an important component of genomic structural variation and plays a role not only in evolutionary diversification but also in domestication. Chinese cattle were derived from Bos taurus and Bos indicus, and several breeds presumably are of hybrid origin, but the evolution of CNV regions (CNVRs) has not yet been examined in this context. Here, we of CNVRs, mtDNA D-loop sequence variation, and Y-chromosomal single nucleotide polymorphisms to assess the impact of maternal and paternal B. taurus and B. indicus origins on the distribution of CNVRs in 24 Chinese domesticated bulls. We discovered 470 genome-wide CNVRs, only 72 of which were shared by all three Y-lineages (B. taurus: Y1, Y2; B. indicus: Y3), whereas 265 were shared by inferred taurine or indicine paternal lineages, and 228 when considering their maternal taurine or indicine origins. Phylogenetic analysis uncovered eight taurine/indicine hybrids, and principal component analysis on CNVs corroborated genomic exchange during hybridization. The distribution patterns of CNVRs tended to be lineage-specific, and correlation analysis revealed significant positive or negative co-occurrences of CNVRs across lineages. Our study suggests that CNVs in Chinese cattle partly result from selective breeding during domestication, but also from hybridization and introgression.
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Affiliation(s)
- Liangzhi Zhang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China Key laboratory of adaptation and evolution of plateau biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences
| | - Shangang Jia
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China
| | - Martin Plath
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China
| | - Yongzhen Huang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China
| | - Congjun Li
- United States Department of Agriculture-Agricultural Research Service, Bovine Functional Genomics Laboratory, Beltsville, Maryland
| | - Chuzhao Lei
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China
| | - Xin Zhao
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China
| | - Hong Chen
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China
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46
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Ma Y, Zhang Q, Lu Z, Zhao X, Zhang Y. Analysis of copy number variations by SNP50 BeadChip array in Chinese sheep. Genomics 2015; 106:295-300. [PMID: 26244906 DOI: 10.1016/j.ygeno.2015.08.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/28/2015] [Accepted: 08/01/2015] [Indexed: 12/18/2022]
Abstract
The sheep (Ovis aries) plays a major socio-economic role in the world. Copy number variations (CNVs) are increasingly recognized as a key and potent source of genetic variation and phenotypic diversity, but little is known about the extent to which CNVs contribute to genetic variation in Chinese sheep breeds. Analyses of CNVs in the genomes of eight sheep breeds were performed using the sheep SNP50 BeadChip genotyping array. A total of 111 CNV regions (CNVRs) were obtained from 160 Chinese sheep breeds. These CNVRs covered 13.75Mb of the sheep genome sequence. A total of 22 Go terms and 17 candidate genes were obtained from the functional analysis. Ten CNVRs were selected for validation, of which 7 CNVRs were further experimentally confirmed by quantitative PCR. Four candidate genes were selected to confirm the results of the functional analysis. These results provide a resource for furthering understanding of ruminant biology, and for further improving the genetic quality of sheep breeds.
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Affiliation(s)
- Youji Ma
- College of Animal Science and Technology, Gansu Agriculture University, Lanzhou 730070, China.
| | - Quanwei Zhang
- College of Veterinary Medicine, Gansu Agriculture University, Lanzhou 730070, China
| | - Zengkui Lu
- College of Animal Science and Technology, Gansu Agriculture University, Lanzhou 730070, China
| | - Xingxu Zhao
- College of Veterinary Medicine, Gansu Agriculture University, Lanzhou 730070, China
| | - Yong Zhang
- College of Veterinary Medicine, Gansu Agriculture University, Lanzhou 730070, China
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47
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Yudin NS, Voevoda MI. Molecular genetic markers of economically important traits in dairy cattle. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415050087] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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48
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Bickhart DM, Hutchison JL, Xu L, Schnabel RD, Taylor JF, Reecy JM, Schroeder S, Van Tassell CP, Sonstegard TS, Liu GE. RAPTR-SV: a hybrid method for the detection of structural variants. Bioinformatics 2015; 31:2084-90. [PMID: 25686638 DOI: 10.1093/bioinformatics/btv086] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 02/09/2015] [Indexed: 12/30/2022] Open
Abstract
MOTIVATION Identification of structural variants (SVs) in sequence data results in a large number of false positive calls using existing software, which overburdens subsequent validation. RESULTS Simulations using RAPTR-SV and other, similar algorithms for SV detection revealed that RAPTR-SV had superior sensitivity and precision, as it recovered 66.4% of simulated tandem duplications with a precision of 99.2%. When compared with calls made by Delly and LUMPY on available datasets from the 1000 genomes project, RAPTR-SV showed superior sensitivity for tandem duplications, as it identified 2-fold more duplications than Delly, while making ∼85% fewer duplication predictions. AVAILABILITY AND IMPLEMENTATION RAPTR-SV is written in Java and uses new features in the collections framework in the latest release of the Java version 8 language specifications. A compiled version of the software, instructions for usage and test results files are available on the GitHub repository page: https://github.com/njdbickhart/RAPTR-SV. CONTACT derek.bickhart@ars.usda.gov.
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Affiliation(s)
- Derek M Bickhart
- Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD 20705, USA, Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20705, USA, Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA and Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Jana L Hutchison
- Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD 20705, USA, Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20705, USA, Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA and Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Lingyang Xu
- Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD 20705, USA, Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20705, USA, Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA and Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Robert D Schnabel
- Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD 20705, USA, Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20705, USA, Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA and Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Jeremy F Taylor
- Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD 20705, USA, Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20705, USA, Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA and Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - James M Reecy
- Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD 20705, USA, Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20705, USA, Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA and Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Steven Schroeder
- Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD 20705, USA, Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20705, USA, Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA and Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Curt P Van Tassell
- Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD 20705, USA, Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20705, USA, Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA and Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Tad S Sonstegard
- Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD 20705, USA, Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20705, USA, Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA and Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - George E Liu
- Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD 20705, USA, Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20705, USA, Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA and Department of Animal Science, Iowa State University, Ames, IA 50011, USA
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Xu L, Cole JB, Bickhart DM, Hou Y, Song J, VanRaden PM, Sonstegard TS, Van Tassell CP, Liu GE. Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins. BMC Genomics 2014; 15:683. [PMID: 25128478 PMCID: PMC4152564 DOI: 10.1186/1471-2164-15-683] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 07/31/2014] [Indexed: 12/21/2022] Open
Abstract
Background Milk production is an economically important sector of global agriculture. Much attention has been paid to the identification of quantitative trait loci (QTL) associated with milk, fat, and protein yield and the genetic and molecular mechanisms underlying them. Copy number variation (CNV) is an emerging class of variants which may be associated with complex traits. Results In this study, we performed a genome-wide association between CNVs and milk production traits in 26,362 Holstein bulls and cows. A total of 99 candidate CNVs were identified using Illumina BovineSNP50 array data, and association tests for each production trait were performed using a linear regression analysis with PCA correlation. A total of 34 CNVs on 22 chromosomes were significantly associated with at least one milk production trait after false discovery rate (FDR) correction. Some of those CNVs were located within or near known QTL for milk production traits. We further investigated the relationship between associated CNVs with neighboring SNPs. For all 82 combinations of traits and CNVs (less than 400 kb in length), we found 17 cases where CNVs directly overlapped with tag SNPs and 40 cases where CNVs were adjacent to tag SNPs. In 5 cases, CNVs located were in strong linkage disequilibrium with tag SNPs, either within or adjacent to the same haplotype block. There were an additional 20 cases where CNVs did not have a significant association with SNPs, suggesting that the effects of those CNVs were probably not captured by tag SNPs. Conclusion We conclude that combining CNV with SNP analyses reveals more genetic variations underlying milk production traits than those revealed by SNPs alone. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-683) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, Maryland 20705, USA.
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