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Panda S, Kumar A, Gaur GK, Ahmad SF, Chauhan A, Mehrotra A, Dutt T. Genome wide copy number variations using Porcine 60K SNP Beadchip in Landlly pigs. Anim Biotechnol 2023; 34:1891-1899. [PMID: 35369845 DOI: 10.1080/10495398.2022.2056047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
In the present study, Porcine 60K SNP genotype data from 69 Landlly pigs were used to explore Copy Number Variations (CNVs) across the autosomes. A total of 386 CNVs were identified using Hidden Markov Model (HMM) in PennCNV software, which were subsequently aggregated to 115 CNV regions (CNVRs). Among the total detected CNVRs, 58 gain, 49 were loss type while remaining 8 events were both gain and loss types. Identified CNVRs covered 12.5 Mb (0.55%) of Sus scrofa reference 11.1 genome. Comparison of our results with previous investigations on pigs revealed that approximately 75% CNVRs were novel, which may be due to differences in genetic background, environment and implementation of artificial selection in Landlly pigs. Functional annotation and pathway analysis showed the significant enrichment of 267 well-annotated Sus scrofa genes in CNVRs. These genes were involved in different biological functions like sensory perception, meat quality traits, back fat thickness and immunity. Additionally, KIT and FUT1 were two major genes detected on CNVR in our population. This investigation provided a comprehensive overview of CNV distribution in the Indian porcine genome for the first time, which may be useful for further investigating the association of important quantitative traits in Landlly pigs.Highlights115 CNVRs were identified in 69 Landlly pig population.Approximately 75% detected CNVRs were novel for Landlly population.Significant enrichment of 267 well-annotated Sus scrofa genes observed in these CNVRs.These genes were involved in different biological functions like sensory perception, meat quality traits, back fat thickness and immunity.Comprehensive CNV map in the Indian porcine genome developed for the first time.
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Affiliation(s)
- Snehasmita Panda
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, UP, India
| | - Amit Kumar
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, UP, India
| | - Gyanendra Kumar Gaur
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, UP, India
| | - Sheikh Firdous Ahmad
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, UP, India
| | - Anuj Chauhan
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, UP, India
| | - Arnav Mehrotra
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, UP, India
- Animal Genomics, ETH Zürich, Zürich, Switzerland
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, UP, India
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Zhang C, Yang H, Xu Q, Liu M, Chao X, Chen J, Zhou B, Liu Y. Comprehensive Genome and Transcriptome Analysis Identifies SLCO3A1 Associated with Aggressive Behavior in Pigs. Biomolecules 2023; 13:1381. [PMID: 37759782 PMCID: PMC10526945 DOI: 10.3390/biom13091381] [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: 08/16/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Copy number variation (CNV) represents a significant reservoir of genetic diversity within the genome and exhibits a strong association with economically valuable traits in livestock. The manifestation of aggressive behavior in pigs has detrimental effects on production efficiency, immune competency, and meat quality. Nevertheless, the impact of CNV on the aggressive behavior of pigs remains elusive. In this investigation, we employed an integrated analysis of genome and transcriptome data to investigate the interplay between CNV, gene expression changes, and indicators of aggressive behavior in weaned pigs. Specifically, a subset of pigs comprising the most aggressive pigs (MAP, n = 12) and the least aggressive pigs (LAP, n = 11) was purposefully selected from a herd of 500 weaned pigs following a mixing procedure based on their composite aggressive score (CAS). Subsequently, we thoroughly analyzed copy number variation regions (CNVRs) across the entire genome using next-generation sequencing techniques, ultimately revealing the presence of 6869 CNVRs. Using genome-wide association study (GWAS) analysis and evaluating variance-stabilizing transformation (VST) values, we successfully identified distinct CNVRs that distinguished the MAP and LAP counterparts. Among the prioritized CNVRs, CNVR-4962 (designated as the top-ranked p-value and VST value, No. 1) was located within the Solute Carrier Organic Anion Transporter Family Member 3A1 (SLCO3A1) gene. The results of our analyses indicated a significantly higher (p < 0.05) copy number of SLCO3A1 in the MAP compared to the LAP. Furthermore, this increased copy number exhibited a positive correlation with the CAS of the pigs (p < 0.05). Furthermore, we integrated genomic data with transcriptomic data from the temporal lobe to facilitate the examination of expression quantitative trait loci (eQTL). Importantly, these observations were consistent with the mRNA expression pattern of SLCO3A1 in the temporal lobe of both MAP and LAP (p < 0.05). Consequently, our findings strongly suggest that CNVs affecting SLCO3A1 may influence gene expression through a dosage effect. These results highlight the potential of SLCO3A1 as a candidate gene associated with aggressive traits in pig breeding programs.
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Affiliation(s)
| | | | | | | | | | | | - Bo Zhou
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (H.Y.); (Q.X.); (M.L.); (X.C.); (J.C.)
| | - Yang Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (H.Y.); (Q.X.); (M.L.); (X.C.); (J.C.)
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3
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Jiang YF, Wang S, Wang CL, Xu RH, Wang WW, Jiang Y, Wang MS, Jiang L, Dai LH, Wang JR, Chu XH, Zeng YQ, Fang LZ, Wu DD, Zhang Q, Ding XD. Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs. iScience 2023; 26:106119. [PMID: 36852268 PMCID: PMC9958381 DOI: 10.1016/j.isci.2023.106119] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/21/2022] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Long-read sequencing (LRS) facilitates both the genome assembly and the discovery of structural variants (SVs). Here, we built a graph-based pig pangenome by incorporating 11 LRS genomes with an average of 94.01% BUSCO completeness score, revealing 206-Mb novel sequences. We discovered 183,352 nonredundant SVs (63% novel), representing 12.12% of the reference genome. By genotyping SVs in an additional 196 short-read sequencing samples, we identified thousands of population stratified SVs. Particularly, we detected 7,568 Tibetan specific SVs, some of which demonstrate significant population differentiation between Tibetan and low-altitude pigs, which might be associated with the high-altitude hypoxia adaptation in Tibetan pigs. Further integrating functional genomic data, the most promising candidate genes within the SVs that might contribute to the high-altitude hypoxia adaptation were discovered. Overall, our study generates a benchmark pangenome resource for illustrating the important roles of SVs in adaptive evolution, domestication, and genetic improvement of agronomic traits in pigs.
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Affiliation(s)
- Yi-Fan Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Chong-Long Wang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Ru-Hai Xu
- Key Laboratory of Animal Genetics and Breeding of Zhejiang Province, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wen-Wen Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian 271001, China
| | - Yao Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Li Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Li-He Dai
- Key Laboratory of Animal Genetics and Breeding of Zhejiang Province, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jie-Ru Wang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xiao-Hong Chu
- Key Laboratory of Animal Genetics and Breeding of Zhejiang Province, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yong-Qing Zeng
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian 271001, China
| | - Ling-Zhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, Denmark
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian 271001, China
| | - Xiang-Dong Ding
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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Davoudi P, Do DN, Rathgeber B, Colombo SM, Sargolzaei M, Plastow G, Wang Z, Karimi K, Hu G, Valipour S, Miar Y. Genome-wide detection of copy number variation in American mink using whole-genome sequencing. BMC Genomics 2022; 23:649. [PMID: 36096727 PMCID: PMC9468235 DOI: 10.1186/s12864-022-08874-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/05/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Copy number variations (CNVs) represent a major source of genetic diversity and contribute to the phenotypic variation of economically important traits in livestock species. In this study, we report the first genome-wide CNV analysis of American mink using whole-genome sequence data from 100 individuals. The analyses were performed by three complementary software programs including CNVpytor, DELLY and Manta. RESULTS A total of 164,733 CNVs (144,517 deletions and 20,216 duplications) were identified representing 5378 CNV regions (CNVR) after merging overlapping CNVs, covering 47.3 Mb (1.9%) of the mink autosomal genome. Gene Ontology and KEGG pathway enrichment analyses of 1391 genes that overlapped CNVR revealed potential role of CNVs in a wide range of biological, molecular and cellular functions, e.g., pathways related to growth (regulation of actin cytoskeleton, and cAMP signaling pathways), behavior (axon guidance, circadian entrainment, and glutamatergic synapse), lipid metabolism (phospholipid binding, sphingolipid metabolism and regulation of lipolysis in adipocytes), and immune response (Wnt signaling, Fc receptor signaling, and GTPase regulator activity pathways). Furthermore, several CNVR-harbored genes associated with fur characteristics and development (MYO5A, RAB27B, FGF12, SLC7A11, EXOC2), and immune system processes (SWAP70, FYN, ORAI1, TRPM2, and FOXO3). CONCLUSIONS This study presents the first genome-wide CNV map of American mink. We identified 5378 CNVR in the mink genome and investigated genes that overlapped with CNVR. The results suggest potential links with mink behaviour as well as their possible impact on fur quality and immune response. Overall, the results provide new resources for mink genome analysis, serving as a guideline for future investigations in which genomic structural variations are present.
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Affiliation(s)
- Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Duy Ngoc Do
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Bruce Rathgeber
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Stefanie M Colombo
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
- Select Sires Inc., Plain City, OH, USA
| | - Graham Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Zhiquan Wang
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Karim Karimi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Guoyu Hu
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Shafagh Valipour
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada.
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5
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Zhou Z, Jiang T, Zhu Y, Ling Z, Yang B, Huang L. A comparative investigation on
H3K27ac
enhancer activities in the brain and liver tissues between wild boars and domesticated pigs. Evol Appl 2022; 15:1281-1290. [PMID: 36051459 PMCID: PMC9423090 DOI: 10.1111/eva.13461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/28/2022] [Accepted: 07/20/2022] [Indexed: 11/29/2022] Open
Abstract
Dramatic phenotypic differences between domestic pigs and wild boars (Sus scrofa) provide opportunities to investigate molecular mechanisms underlying the formation of complex traits, including morphology, physiology and behaviour. Most studies comparing domestic pigs and wild boars have focused on variations in DNA sequences and mRNA expression, but not on epigenetic changes. Here, we present a genome‐wide comparative study on H3K27ac enhancer activities and the corresponding mRNA profiling in the brain and liver tissues of adult Bama Xiang pigs (BMXs) and Chinese wild boars (CWBs). We identified a total of 1,29,487 potential regulatory elements, among which 11,241 H3K27ac peaks showed differential activity between CWBs and BMXs in at least one tissue. These peaks were overrepresented by binding motifs of FOXA1, JunB, ATF3 and BATF, and overlapped with differentially expressed genes that are involved in female mating behaviour, response to growth factors and hormones, and lipid metabolism. We also identified 4118 nonredundant super‐enhancers from ChIP‐Seq data on H3K27ac. Notably, we identified differentially active peaks located close to or within candidate genes, including TBX19, MSTN, AHR and P2RY1, which were identified in DNA sequence‐based population differentiation studies. This study generates a valuable dataset on H3K27ac profiles of the brain and liver from domestic pigs and wild boars, which helps gain insights into the changes in enhancer activities from wild boars to domestic pigs.
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Affiliation(s)
- Zhimin Zhou
- State Key Laboratory of Swine Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Tao Jiang
- State Key Laboratory of Swine Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Yaling Zhu
- State Key Laboratory of Swine Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Ziqi Ling
- State Key Laboratory of Swine Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Bin Yang
- State Key Laboratory of Swine Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Lusheng Huang
- State Key Laboratory of Swine Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
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6
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Zhang C, Zhao J, Guo Y, Xu Q, Liu M, Cheng M, Chao X, Schinckel AP, Zhou B. Genome-Wide Detection of Copy Number Variations and Evaluation of Candidate Copy Number Polymorphism Genes Associated With Complex Traits of Pigs. Front Vet Sci 2022; 9:909039. [PMID: 35847642 PMCID: PMC9280686 DOI: 10.3389/fvets.2022.909039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/09/2022] [Indexed: 12/12/2022] Open
Abstract
Copy number variation (CNV) has been considered to be an important source of genetic variation for important phenotypic traits of livestock. In this study, we performed whole-genome CNV detection on Suhuai (SH) (n = 23), Chinese Min Zhu (MZ) (n = 11), and Large White (LW) (n = 12) pigs based on next-generation sequencing data. The copy number variation regions (CNVRs) were annotated and analyzed, and 10,885, 10,836, and 10,917 CNVRs were detected in LW, MZ, and SH pigs, respectively. Some CNVRs have been randomly selected for verification of the variation type by real-time PCR. We found that SH and LW pigs are closely related, while MZ pigs are distantly related to the SH and LW pigs by CNVR-based genetic structure, PCA, VST, and QTL analyses. A total of 14 known genes annotated in CNVRs were unique for LW pigs. Among them, the cyclin T2 (CCNT2) is involved in cell proliferation and the cell cycle. The FA Complementation Group M (FANCM) is involved in defective DNA repair and reproductive cell development. Ten known genes annotated in 47 CNVRs were unique for MZ pigs. The genes included glycerol-3-phosphate acyltransferase 3 (GPAT3) is involved in fat synthesis and is essential to forming the glycerol triphosphate. Glutathione S-transferase mu 4 (GSTM4) gene plays an important role in detoxification. Eleven known genes annotated in 23 CNVRs were unique for SH pigs. Neuroligin 4 X-linked (NLGN4X) and Neuroligin 4 Y-linked (NLGN4Y) are involved with nerve disorders and nerve signal transmission. IgLON family member 5 (IGLON5) is related to autoimmunity and neural activities. The unique characteristics of LW, MZ, and SH pigs are related to these genes with CNV polymorphisms. These findings provide important information for the identification of candidate genes in the molecular breeding of pigs.
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Affiliation(s)
- Chunlei Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Jing Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yanli Guo
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Qinglei Xu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Mingzheng Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Meng Cheng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiaohuan Chao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Allan P. Schinckel
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Bo Zhou
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Bo Zhou
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7
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Suvakov M, Panda A, Diesh C, Holmes I, Abyzov A. CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing. Gigascience 2021; 10:giab074. [PMID: 34817058 PMCID: PMC8612020 DOI: 10.1093/gigascience/giab074] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 08/21/2021] [Accepted: 10/22/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Detecting copy number variations (CNVs) and copy number alterations (CNAs) based on whole-genome sequencing data is important for personalized genomics and treatment. CNVnator is one of the most popular tools for CNV/CNA discovery and analysis based on read depth. FINDINGS Herein, we present an extension of CNVnator developed in Python-CNVpytor. CNVpytor inherits the reimplemented core engine of its predecessor and extends visualization, modularization, performance, and functionality. Additionally, CNVpytor uses B-allele frequency likelihood information from single-nucleotide polymorphisms and small indels data as additional evidence for CNVs/CNAs and as primary information for copy number-neutral losses of heterozygosity. CONCLUSIONS CNVpytor is significantly faster than CNVnator-particularly for parsing alignment files (2-20 times faster)-and has (20-50 times) smaller intermediate files. CNV calls can be filtered using several criteria, annotated, and merged over multiple samples. Modular architecture allows it to be used in shared and cloud environments such as Google Colab and Jupyter notebook. Data can be exported into JBrowse, while a lightweight plugin version of CNVpytor for JBrowse enables nearly instant and GUI-assisted analysis of CNVs by any user. CNVpytor release and the source code are available on GitHub at https://github.com/abyzovlab/CNVpytor under the MIT license.
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Affiliation(s)
- Milovan Suvakov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Arijit Panda
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Colin Diesh
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
| | - Ian Holmes
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
| | - Alexej Abyzov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
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8
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Wang Z, Guo Y, Liu S, Meng Q. Genome-Wide Assessment Characteristics of Genes Overlapping Copy Number Variation Regions in Duroc Purebred Population. Front Genet 2021; 12:753748. [PMID: 34721540 PMCID: PMC8552909 DOI: 10.3389/fgene.2021.753748] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/23/2021] [Indexed: 11/13/2022] Open
Abstract
Copy number variations (CNVs) are important structural variations that can cause significant phenotypic diversity. Reliable CNVs mapping can be achieved by identification of CNVs from different genetic backgrounds. Investigations on the characteristics of overlapping between CNV regions (CNVRs) and protein-coding genes (CNV genes) or miRNAs (CNV-miRNAs) can reveal the potential mechanisms of their regulation. In this study, we used 50 K SNP arrays to detect CNVs in Duroc purebred pig. A total number of 211 CNVRs were detected with a total length of 118.48 Mb, accounting for 5.23% of the autosomal genome sequence. Of these CNVRs, 32 were gains, 175 losses, and four contained both types (loss and gain within the same region). The CNVRs we detected were non-randomly distributed in the swine genome and were significantly enriched in the segmental duplication and gene density region. Additionally, these CNVRs were overlapping with 1,096 protein-coding genes (CNV-genes), and 39 miRNAs (CNV-miRNAs), respectively. The CNV-genes were enriched in terms of dosage-sensitive gene list. The expression of the CNV genes was significantly higher than that of the non-CNV genes in the adult Duroc prostate. Of all detected CNV genes, 22.99% genes were tissue-specific (TSI > 0.9). Strong negative selection had been underway in the CNV-genes as the ones that were located entirely within the loss CNVRs appeared to be evolving rapidly as determined by the median dN plus dS values. Non-CNV genes tended to be miRNA target than CNV-genes. Furthermore, CNV-miRNAs tended to target more genes compared to non-CNV-miRNAs, and a combination of two CNV-miRNAs preferentially synergistically regulated the same target genes. We also focused our efforts on examining CNV genes and CNV-miRNAs functions, which were also involved in the lipid metabolism, including DGAT1, DGAT2, MOGAT2, miR143, miR335, and miRLET7. Further molecular experiments and independent large studies are needed to confirm our findings.
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Affiliation(s)
- Zhipeng Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Yuanyuan Guo
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Shengwei Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Qingli Meng
- Beijing Breeding Swine Center, Beijing, China
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9
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Wu Q, Zhou Y, Wang Y, Zhang Y, Shen Y, Su Q, Gao G, Xu H, Zhou X, Liu B. Whole-genome sequencing reveals breed-differential CNVs between Tongcheng and Large White pigs. Anim Genet 2020; 51:940-944. [PMID: 32808316 DOI: 10.1111/age.12993] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2020] [Indexed: 01/26/2023]
Abstract
Large phenotypic differences have been observed between Tongcheng and Large White pigs. However, little is known about their genetic basis. This study performed a genome-wide comparison of CNVs between Tongcheng and Large White pigs using genome sequencing data. By combining the advantages of three different strategies (read depth, paired-end mapping and split read), we detected in total 18 687 CNVs that covered approximately 3.5% of the pig genome length for Tongcheng and Large White pigs. We identified 1864 breed-stratified CNVs (top 10%) by performing VST statistics. Functional enrichment analyses for genes located in breed-stratified CNVs were found to be involved in pigmentation, behavior, immune system and reproductive processes, which coincide with phenotypic differences between the two breeds. Using a systematic analysis of the genome and transcriptome data, we further identified four novel breed-differential CNVs on the functional genes (disease-resistant, DCUN1D2 and SPARCL1; lipid metabolism, PLEKHA2 and SLCO1A2). Subsequent PCR validation confirmed their accurate breakpoint positions in 33 Tongcheng pigs and 33 Large White pigs. This study provides essential information on differential CNVs for further research on the genetic basis of phenotypic differences between Tongcheng and Large White pigs.
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Affiliation(s)
- Q Wu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Y Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Y Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Y Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Y Shen
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Q Su
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - G Gao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - H Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - X Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - B Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
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10
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Bovo S, Ribani A, Muñoz M, Alves E, Araujo JP, Bozzi R, Charneca R, Di Palma F, Etherington G, Fernandez AI, García F, García-Casco J, Karolyi D, Gallo M, Gvozdanović K, Martins JM, Mercat MJ, Núñez Y, Quintanilla R, Radović Č, Razmaite V, Riquet J, Savić R, Schiavo G, Škrlep M, Usai G, Utzeri VJ, Zimmer C, Ovilo C, Fontanesi L. Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states. Anim Genet 2020; 51:541-556. [PMID: 32510676 DOI: 10.1111/age.12954] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2020] [Indexed: 02/06/2023]
Abstract
In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed-specific DNA pooling approach (30-35 animals per pool) obtaining an average depth per pool of 42×. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed-specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production systems.
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Affiliation(s)
- S Bovo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy
| | - A Ribani
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy
| | - M Muñoz
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, Madrid, 28040, Spain
| | - E Alves
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, Madrid, 28040, Spain
| | - J P Araujo
- Centro de Investigação de Montanha, Instituto Politécnico de Viana do Castelo, Escola Superior Agrária, Refóios do Lima, Ponte de Lima, 4990-706, Portugal
| | - R Bozzi
- DAGRI - Animal Science Section, Università di Firenze, Via delle Cascine 5, Firenze, 50144, Italy
| | - R Charneca
- MED - Mediterranean Institute for Agriculture, Environment and Development, Universidade de Évora, Pólo da Mitra, Apartado 94, Évora, 7006-554, Portugal
| | - F Di Palma
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR47UZ, UK
| | - G Etherington
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR47UZ, UK
| | - A I Fernandez
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, Madrid, 28040, Spain
| | - F García
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, Madrid, 28040, Spain
| | - J García-Casco
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, Madrid, 28040, Spain
| | - D Karolyi
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, Zagreb, 10000, Croatia
| | - M Gallo
- Associazione Nazionale Allevatori Suini, Via Nizza 53, Roma, 00198, Italy
| | - K Gvozdanović
- Faculty of Agrobiotechnical Sciences Osijek, University of Osijek, Vladimira Preloga 1, Osijek, 31000, Croatia
| | - J M Martins
- MED - Mediterranean Institute for Agriculture, Environment and Development, Universidade de Évora, Pólo da Mitra, Apartado 94, Évora, 7006-554, Portugal
| | - M J Mercat
- IFIP Institut Du Porc, La Motte au Vicomte, BP 35104, Le Rheu Cedex, 35651, France
| | - Y Núñez
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, Madrid, 28040, Spain
| | - R Quintanilla
- Programa de Genética y Mejora Animal, IRTA, Torre Marimon, Caldes de Montbui, Barcelona, 08140, Spain
| | - Č Radović
- Department of Pig Breeding and Genetics, Institute for Animal Husbandry, Belgrade-Zemun, 11080, Serbia
| | - V Razmaite
- Animal Science Institute, Lithuanian University of Health Sciences, R. Žebenkos 12, Baisogala, 82317, Lithuania
| | - J Riquet
- GenPhySE, INRA, Université de Toulouse, Chemin de Borde-Rouge 24, Auzeville Tolosane, Castanet Tolosan, 31326, France
| | - R Savić
- Faculty of Agriculture, University of Belgrade, Nemanjina 6, Belgrade-Zemun, 11080, Serbia
| | - G Schiavo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy
| | - M Škrlep
- Kmetijski Inštitut Slovenije, Hacquetova 17, Ljubljana, SI-1000, Slovenia
| | - G Usai
- AGRIS SARDEGNA, Loc. Bonassai, Sassari, 07100, Italy
| | - V J Utzeri
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy
| | - C Zimmer
- Bäuerliche Erzeugergemeinschaft Schwäbisch Hall, Haller Str. 20, Wolpertshausen, 74549, Germany
| | - C Ovilo
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, Madrid, 28040, Spain
| | - L Fontanesi
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy
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11
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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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12
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Keel BN, Nonneman DJ, Lindholm-Perry AK, Oliver WT, Rohrer GA. A Survey of Copy Number Variation in the Porcine Genome Detected From Whole-Genome Sequence. Front Genet 2019; 10:737. [PMID: 31475038 PMCID: PMC6707380 DOI: 10.3389/fgene.2019.00737] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 07/12/2019] [Indexed: 12/11/2022] Open
Abstract
Copy number variations (CNVs) are gains and losses of large regions of genomic sequence between individuals of a species. Although CNVs have been associated with various phenotypic traits in humans and other species, the extent to which CNVs impact phenotypic variation remains unclear. In swine, as well as many other species, relatively little is understood about the frequency of CNV in the genome, sizes, locations, and other chromosomal properties. In this work, we identified and characterized CNV by utilizing whole-genome sequence from 240 members of an intensely phenotyped experimental swine herd at the U.S. Meat Animal Research Center (USMARC). These animals included all 24 of the purebred founding boars (12 Duroc and 12 Landrace), 48 of the founding Yorkshire-Landrace composite sows, 109 composite animals from generations 4 through 9, 29 composite animals from generation 15, and 30 purebred industry boars (15 Landrace and 15 Yorkshire) used as sires in generations 10 through 15. Using a combination of split reads, paired-end mapping, and read depth approaches, we identified a total of 3,538 copy number variable regions (CNVRs), including 1,820 novel CNVRs not reported in previous studies. The CNVRs covered 0.94% of the porcine genome and overlapped 1,401 genes. Gene ontology analysis identified that CNV-overlapped genes were enriched for functions related to organism development. Additionally, CNVRs overlapped with many known quantitative trait loci (QTL). In particular, analysis of QTL previously identified in the USMARC herd showed that CNVRs were most overlapped with reproductive traits, such as age of puberty and ovulation rate, and CNVRs were significantly enriched for reproductive QTL.
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Affiliation(s)
- Brittney N Keel
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Dan J Nonneman
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States
| | | | - William T Oliver
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Gary A Rohrer
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States
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13
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Stafuzza NB, Silva RMDO, Fragomeni BDO, Masuda Y, Huang Y, Gray K, Lourenco DAL. A genome-wide single nucleotide polymorphism and copy number variation analysis for number of piglets born alive. BMC Genomics 2019; 20:321. [PMID: 31029102 PMCID: PMC6487013 DOI: 10.1186/s12864-019-5687-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 04/11/2019] [Indexed: 12/19/2022] Open
Abstract
Background In this study we integrated the CNV (copy number variation) and WssGWAS (weighted single-step approach for genome-wide association) analyses to increase the knowledge about number of piglets born alive, an economically important reproductive trait with significant impact on production efficiency of pigs. Results A total of 3892 samples were genotyped with the Porcine SNP80 BeadChip. After quality control, a total of 57,962 high-quality SNPs from 3520 Duroc pigs were retained. The PennCNV algorithm identified 46,118 CNVs, which were aggregated by overlapping in 425 CNV regions (CNVRs) ranging from 2.5 Kb to 9718.4 Kb and covering 197 Mb (~ 7.01%) of the pig autosomal genome. The WssGWAS identified 16 genomic regions explaining more than 1% of the additive genetic variance for number of piglets born alive. The overlap between CNVR and WssGWAS analyses identified common regions on SSC2 (4.2–5.2 Mb), SSC3 (3.9–4.9 Mb), SSC12 (56.6–57.6 Mb), and SSC17 (17.3–18.3 Mb). Those regions are known for harboring important causative variants for pig reproductive traits based on their crucial functions in fertilization, development of gametes and embryos. Functional analysis by the Panther software identified 13 gene ontology biological processes significantly represented in this study such as reproduction, developmental process, cellular component organization or biogenesis, and immune system process, which plays relevant roles in swine reproductive traits. Conclusion Our research helps to improve the understanding of the genetic architecture of number of piglets born alive, given that the combination of GWAS and CNV analyses allows for a more efficient identification of the genomic regions and biological processes associated with this trait in Duroc pigs. Pig breeding programs could potentially benefit from a more accurate discovery of important genomic regions. Electronic supplementary material The online version of this article (10.1186/s12864-019-5687-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nedenia Bonvino Stafuzza
- Department of Exact Science, School of Agricultural and Veterinarian Sciences (FCAV), Sao Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil. .,Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA.
| | - Rafael Medeiros de Oliveira Silva
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA.,National Center for Cool and Cold Water Aquaculture (NCCCWA), Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, USA
| | | | - Yutaka Masuda
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Yijian Huang
- Smithfield Premium Genetics Group, Rose Hill, NC, USA
| | - Kent Gray
- Smithfield Premium Genetics Group, Rose Hill, NC, USA
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14
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Wang C, Chen H, Wang X, Wu Z, Liu W, Guo Y, Ren J, Ding N. Identification of copy number variations using high density whole-genome SNP markers in Chinese Dongxiang spotted pigs. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2019; 32:1809-1815. [PMID: 30744341 PMCID: PMC6819687 DOI: 10.5713/ajas.18.0696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/08/2019] [Indexed: 01/13/2023]
Abstract
Objective Copy number variations (CNVs) are a major source of genetic diversity complementary to single nucleotide polymorphism (SNP) in animals. The aim of the study was to perform a comprehensive genomic analysis of CNVs based on high density whole-genome SNP markers in Chinese Dongxiang spotted pigs. Methods We used customized Affymetrix Axiom Pig1.4M array plates containing 1.4 million SNPs and the PennCNV algorithm to identify porcine CNVs on autosomes in Chinese Dongxiang spotted pigs. Then, the next generation sequence data was used to confirm the detected CNVs. Next, functional analysis was performed for gene contents in copy number variation regions (CNVRs). In addition, we compared the identified CNVRs with those reported ones and quantitative trait loci (QTL) in the pig QTL database. Results We identified 871 putative CNVs belonging to 2,221 CNVRs on 17 autosomes. We further discarded CNVRs that were detected only in one individual, leaving us 166 CNVRs in total. The 166 CNVRs ranged from 2.89 kb to 617.53 kb with a mean value of 93.65 kb and a genome coverage of 15.55 Mb, corresponding to 0.58% of the pig genome. A total of 119 (71.69%) of the identified CNVRs were confirmed by next generation sequence data. Moreover, functional annotation showed that these CNVRs are involved in a variety of molecular functions. More than half (56.63%) of the CNVRs (n = 94) have been reported in previous studies, while 72 CNVRs are reported for the first time. In addition, 162 (97.59%) CNVRs were found to overlap with 2,765 previously reported QTLs affecting 378 phenotypic traits. Conclusion The findings improve the catalog of pig CNVs and provide insights and novel molecular markers for further genetic analyses of Chinese indigenous pigs.
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Affiliation(s)
- Chengbin Wang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Hao Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xiaopeng Wang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zhongping Wu
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Weiwei Liu
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yuanmei Guo
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jun Ren
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Nengshui Ding
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
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15
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Fu Y, Yu Z, Liu S, Chen B, Zhu L, Li Z, Chou SH, He J. c-di-GMP Regulates Various Phenotypes and Insecticidal Activity of Gram-Positive Bacillus thuringiensis. Front Microbiol 2018; 9:45. [PMID: 29487570 PMCID: PMC5816809 DOI: 10.3389/fmicb.2018.00045] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 01/09/2018] [Indexed: 12/26/2022] Open
Abstract
C-di-GMP has been well investigated to play significant roles in the physiology of many Gram-negative bacteria. However, its effect on Gram-positive bacteria is less known. In order to more understand the c-di-GMP functions in Gram-positive bacteria, we have carried out a detailed study on the c-di-GMP-metabolizing enzymes and their physiological functions in Bacillus thuringiensis, a Gram-positive entomopathogenic bacterium that has been applied as an insecticide successfully. We performed a systematic study on the ten putative c-di-GMP-synthesizing enzyme diguanylate cyclases (DGCs) and c-di-GMP-degrading enzyme phosphodiesterases (PDEs) in B. thuringiensis BMB171, and artificially elevated the intracellular c-di-GMP level in BMB171 by deleting one or more pde genes. We found increasing level of intracellular c-di-GMP exhibits similar activities as those in Gram-negative bacteria, including altered activities in cell motility, biofilm formation, and cell-cell aggregation. Unexpectedly, we additionally found a novel function exhibited by the increasing level of c-di-GMP to promote the insecticidal activity of this bacterium against Helicoverpa armigera. Through whole-genome transcriptome profile analyses, we found that 4.3% of the B. thuringiensis genes were differentially transcribed when c-di-GMP level was increased, and 77.3% of such gene products are involved in some regulatory pathways not reported in other bacteria to date. In summary, our study represents the first comprehensive report on the c-di-GMP-metabolizing enzymes, their effects on phenotypes, and the transcriptome mediated by c-di-GMP in an important Gram-positive bacterium.
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Affiliation(s)
- Yang Fu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhaoqing Yu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shu Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Bo Chen
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Li Zhu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhou Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shan-Ho Chou
- NCHU Agricultural Biotechnology Center, Institute of Biochemistry, National Chung Hsing University, Taichung, Taiwan
| | - Jin He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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16
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Zhang J, Chen JH, Liu XD, Wang HY, Liu XL, Li XY, Wu ZF, Zhu MJ, Zhao SH. Genomewide association studies for hematological traits and T lymphocyte subpopulations in a Duroc × Erhualian F resource population. J Anim Sci 2017; 94:5028-5041. [PMID: 28046140 DOI: 10.2527/jas.2016-0924] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
It has been shown that hematological traits can act as important indicators of immune function in both humans and livestock. T lymphocytes are key components of the adaptive immune system, playing a critical role in immune response. To identify genomic regions affecting hematological traits and T lymphocyte subpopulations, we performed both a SNP-based genomewide association study (GWAS) and a haplotype analysis for 20 hematological traits and 8 T cell subpopulations at 3 different time points (d 20, 33, and 35) in a Duroc × Erhualian F intercross population. Bonferroni correction was used to calculate the threshold -values for suggestive and 5% genomewide significance levels. In total, for SNP-based GWAS, we detected 96 significant SNP, including 15 genomewide-significant SNP, associated with 23 hematological traits and 234 significant SNP, including 27 genomewide-significant SNP, associated with 8 T cell subpopulations. Meanwhile, we identified 563 significant SNP, including 7 genomewide-significant SNP, associated with 5 hematological traits and 2,407 significant SNP, including 1,261 genomewide-significant SNP, associated with 8 T cell subpopulations by haplotype analysis. Among the significant regions detected, we propose both the () gene and the () gene on SSC3 as plausible candidate genes associated with CD/CD T lymphocytes at d 20. The findings provide insights into the basis of molecular mechanisms that are involved with immune response in the domestic pig and would aid further identification of causative mutations.
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17
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Keel BN, Keele JW, Snelling WM. Genome-wide copy number variation in the bovine genome detected using low coverage sequence of popular beef breeds,. Anim Genet 2016; 48:141-150. [DOI: 10.1111/age.12519] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2016] [Indexed: 12/19/2022]
Affiliation(s)
- B. N. Keel
- USDA; ARS; U.S. Meat Animal Research Center; Clay Center NE 68933 USA
| | - J. W. Keele
- USDA; ARS; U.S. Meat Animal Research Center; Clay Center NE 68933 USA
| | - W. M. Snelling
- USDA; ARS; U.S. Meat Animal Research Center; Clay Center NE 68933 USA
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