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Zhang J, Nie C, Li X, Zhao X, Jia Y, Han J, Chen Y, Wang L, Lv X, Yang W, Li K, Zhang J, Ning Z, Bao H, Zhao C, Li J, Qu L. Comprehensive analysis of structural variants in chickens using PacBio sequencing. Front Genet 2022; 13:971588. [PMID: 36338955 PMCID: PMC9632285 DOI: 10.3389/fgene.2022.971588] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Structural variants (SVs) are one of the main sources of genetic variants and have a greater impact on phenotype evolution, disease susceptibility, and environmental adaptations than single nucleotide polymorphisms (SNPs). However, SVs remain challenging to accurately type, with several detection methods showing different limitations. Here, we explored SVs from 10 different chickens using PacBio technology and detected 49,501 high-confidence SVs. The results showed that the PacBio long-read detected more SVs than Illumina short-read technology genomes owing to some SV sites on chromosomes, which are related to chicken growth and development. During chicken domestication, some SVs beneficial to the breed or without any effect on the genomic function of the breed were retained, whereas deleterious SVs were generally eliminated. This study could facilitate the analysis of the genetic characteristics of different chickens and provide a better understanding of their phenotypic characteristics at the SV level, based on the long-read sequencing method. This study enriches our knowledge of SVs in chickens and improves our understanding of chicken genomic diversity.
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Affiliation(s)
- Jinxin Zhang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Changsheng Nie
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xinghua Li
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiurong Zhao
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yaxiong Jia
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianlin Han
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Chen
- Beijing Municipal General Station of Animal Science, Beijing, China
| | - Liang Wang
- Beijing Municipal General Station of Animal Science, Beijing, China
| | - Xueze Lv
- Beijing Municipal General Station of Animal Science, Beijing, China
| | - Weifang Yang
- Beijing Municipal General Station of Animal Science, Beijing, China
| | - Kaiyang Li
- Beijing Municipal General Station of Animal Science, Beijing, China
| | - Jianwei Zhang
- Beijing Municipal General Station of Animal Science, Beijing, China
| | - Zhonghua Ning
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Haigang Bao
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chunjiang Zhao
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Junying Li
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lujiang Qu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Lujiang Qu,
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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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Piégu B, Arensburger P, Beauclair L, Chabault M, Raynaud E, Coustham V, Brard S, Guizard S, Burlot T, Le Bihan-Duval E, Bigot Y. Variations in genome size between wild and domesticated lineages of fowls belonging to the Gallus gallus species. Genomics 2020; 112:1660-1673. [DOI: 10.1016/j.ygeno.2019.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 08/05/2019] [Accepted: 10/07/2019] [Indexed: 11/26/2022]
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Identification of Copy Number Variation in Domestic Chicken Using Whole-Genome Sequencing Reveals Evidence of Selection in the Genome. Animals (Basel) 2019; 9:ani9100809. [PMID: 31618984 PMCID: PMC6826909 DOI: 10.3390/ani9100809] [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: 08/27/2019] [Revised: 10/13/2019] [Accepted: 10/14/2019] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Chickens have been bred for meat and egg production as a source of animal protein. With the increase of productivity as the main purpose of domestication, factors such as metabolism and immunity were boosted, which are detectable signs of selection on the genome. This study focused on copy number variation (CNV) to find evidence of domestication on the genome. CNV was detected from whole-genome sequencing of 65 chickens including Red Jungle Fowl, broilers, and layers. After that, CNV region, the overlapping region of CNV between individuals, was made to identify which genomic regions showed copy number differentiation. The 663 domesticated-specific CNV regions were associated with various functions such as metabolism and organ development. Also, by performing population differentiation analyses such as clustering analysis and ANOVA test, we found that there are a lot of genomic regions with different copy number patterns between broilers and layers. This result indicates that different genetic variations can be found, depending on the purpose of artificial selection and provides considerations for future animal breeding. Abstract Copy number variation (CNV) has great significance both functionally and evolutionally. Various CNV studies are in progress to find the cause of human disease and to understand the population structure of livestock. Recent advances in next-generation sequencing (NGS) technology have made CNV detection more reliable and accurate at whole-genome level. However, there is a lack of CNV studies on chickens using NGS. Therefore, we obtained whole-genome sequencing data of 65 chickens including Red Jungle Fowl, Cornish (broiler), Rhode Island Red (hybrid), and White Leghorn (layer) from the public databases for CNV region (CNVR) detection. Using CNVnator, a read-depth based software, a total of 663 domesticated-specific CNVRs were identified across autosomes. Gene ontology analysis of genes annotated in CNVRs showed that mainly enriched terms involved in organ development, metabolism, and immune regulation. Population analysis revealed that CN and RIR are closer to each other than WL, and many genes (LOC772271, OR52R1, RD3, ADH6, TLR2B, PRSS2, TPK1, POPDC3, etc.) with different copy numbers between breeds found. In conclusion, this study has helped to understand the genetic characteristics of domestic chickens at CNV level, which may provide useful information for the development of breeding systems in chickens.
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Zhang RQ, Wang JJ, Zhang T, Zhai HL, Shen W. Copy-number variation in goat genome sequence: A comparative analysis of the different litter size trait groups. Gene 2019; 696:40-46. [DOI: 10.1016/j.gene.2019.02.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/17/2019] [Accepted: 02/01/2019] [Indexed: 02/04/2023]
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Drobik-Czwarno W, Wolc A, Fulton JE, Dekkers JCM. Detection of copy number variations in brown and white layers based on genotyping panels with different densities. Genet Sel Evol 2018; 50:54. [PMID: 30400769 PMCID: PMC6219011 DOI: 10.1186/s12711-018-0428-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 10/23/2018] [Indexed: 11/13/2022] Open
Abstract
Background Copy number variations (CNV) are an important source of genetic variation that has gained increasing attention over the last couple of years. In this study, we performed CNV detection and functional analysis for 18,719 individuals from four pure lines and one commercial cross of layer chickens. Samples were genotyped on four single nucleotide polymorphism (SNP) genotyping platforms, i.e. the Illumina 42K, Affymetrix 600K, and two different customized Affymetrix 50K chips. CNV recovered from the Affymetrix chips were identified by using the Axiom® CNV Summary Tools and PennCNV software and those from the Illumina chip were identified by using the cnvPartition in the Genome Studio software. Results The mean number of CNV per individual varied from 0.50 to 4.87 according to line or cross and size of the SNP genotyping set. The length of the detected CNV across all datasets ranged from 1.2 kb to 3.2 Mb. The number of duplications exceeded the number of deletions for most lines. Between the lines, there were considerable differences in the number of detected CNV and their distribution. Most of the detected CNV had a low frequency, but 19 CNV were identified with a frequency higher than 5% in birds that were genotyped on the 600K panel, with the most common CNV being detected in 734 birds from three lines. Conclusions Commonly used SNP genotyping platforms can be used to detect segregating CNV in chicken layer lines. The sample sizes for this study enabled a detailed characterization of the CNV landscape within commercially relevant lines. The size of the SNP panel used affected detection efficiency, with more CNV detected per individual on the higher density 600K panel. In spite of the high level of inter-individual diversity and a large number of CNV observed within individuals, we were able to detect 19 frequent CNV, of which, 57.9% overlapped with annotated genes and 89% overlapped with known quantitative trait loci. Electronic supplementary material The online version of this article (10.1186/s12711-018-0428-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wioleta Drobik-Czwarno
- Department of Animal Science, Iowa State University, 806 Stange Road, 239E Kildee Hall, Ames, IA, 50010, USA. .,Department of Animal Genetics and Breeding, Faculty of Animal Science, Warsaw University of Life Sciences, Ciszewskiego 8, 02-786, Warsaw, Poland.
| | - Anna Wolc
- Department of Animal Science, Iowa State University, 806 Stange Road, 239E Kildee Hall, Ames, IA, 50010, USA.,Hy-Line International, 2583 240th Street, Dallas Center, IA, 50063, USA
| | - Janet E Fulton
- Hy-Line International, 2583 240th Street, Dallas Center, IA, 50063, USA
| | - Jack C M Dekkers
- Department of Animal Science, Iowa State University, 806 Stange Road, 239E Kildee Hall, Ames, IA, 50010, USA
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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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Gorla E, Cozzi MC, Román-Ponce SI, Ruiz López FJ, Vega-Murillo VE, Cerolini S, Bagnato A, Strillacci MG. Genomic variability in Mexican chicken population using copy number variants. BMC Genet 2017; 18:61. [PMID: 28673234 PMCID: PMC5496433 DOI: 10.1186/s12863-017-0524-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/12/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Copy number variations are genome polymorphism that influence phenotypic variation and are an important source of genetic variation in populations. The aim of this study was to investigate genetic variability in the Mexican Creole chicken population using CNVs. RESULTS The Hidden Markov Model of the PennCNV software detected a total of 1924 CNVs in the genome of the 256 samples processed with Axiom® Genome-Wide Chicken Genotyping Array (Affymetrix). The mapped CNVs comprised 1538 gains and 386 losses, resulting at population level in 1216 CNV regions (CNVRs), of which 959 gains, 226 losses and 31 complex (i.e. containing both losses and gains). The CNVRs covered a total of 47 Mb of the whole genome sequence length, corresponding to 5.12% of the chicken galGal4 autosome assembly. CONCLUSIONS This study allowed a deep insight into the structural variation in the genome of unselected Mexican chicken population, which up to now has not been genetically characterized. The genomic study disclosed that the population, even if presenting extreme morphological variation, cannot be organized in differentiated genetic subpopulations. Finally this study provides a chicken CNV map based on the 600 K SNP chip array jointly with a genome-wide gene copy number estimates in a native unselected for more than 500 years chicken population.
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Affiliation(s)
- E. Gorla
- Department of Veterinary Medicine, Universitá degli Studi di Milano, Via Celoria 10, 20133 Milan, Italy
| | - M. C. Cozzi
- Department of Veterinary Medicine, Universitá degli Studi di Milano, Via Celoria 10, 20133 Milan, Italy
| | - S. I. Román-Ponce
- Centro Nacional de Investigación en Fisiología y Mejoramiento Animal, Instituto Nacional de Investigaciones Forestales, Agricola y Pecuarias (INIFAP), Km.1 Carretera a Colón, Auchitlán, 76280 Querétaro, CP Mexico
| | - F. J. Ruiz López
- Centro Nacional de Investigación en Fisiología y Mejoramiento Animal, Instituto Nacional de Investigaciones Forestales, Agricola y Pecuarias (INIFAP), Km.1 Carretera a Colón, Auchitlán, 76280 Querétaro, CP Mexico
| | - V. E. Vega-Murillo
- Centro Nacional de Investigación en Fisiología y Mejoramiento Animal, Instituto Nacional de Investigaciones Forestales, Agricola y Pecuarias (INIFAP), Melchor Ocampo # 234 Desp. 313, Col. Centro Veracruz, C.P. 91700 Veracruz, Mexico
| | - S. Cerolini
- Department of Veterinary Medicine, Universitá degli Studi di Milano, Via Celoria 10, 20133 Milan, Italy
| | - A. Bagnato
- Department of Veterinary Medicine, Universitá degli Studi di Milano, Via Celoria 10, 20133 Milan, Italy
| | - M. G. Strillacci
- Department of Veterinary Medicine, Universitá degli Studi di Milano, Via Celoria 10, 20133 Milan, Italy
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Characterization of Copy Number Variation's Potential Role in Marek's Disease. Int J Mol Sci 2017; 18:ijms18051020. [PMID: 28486430 PMCID: PMC5454933 DOI: 10.3390/ijms18051020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 04/22/2017] [Accepted: 05/04/2017] [Indexed: 02/07/2023] Open
Abstract
Marek’s Disease (MD) is a highly contagious pathogenic and oncogenic disease primarily affecting chickens. Chicken Lines 63 and 72, as well as their recombinant congenic strains (RCS) with varied susceptibility to MD, are ideal models to study the complex mechanisms of genetic resistance to MD. In this study, we investigated copy number variation (CNV) in these inbred chicken lines using the Affymetrix Axiom HD 600 K SNP genotyping array. We detected 393 CNV segments across all ten chicken lines, of which 12 CNVs were specifically identified in Line 72. We then assessed genetic structure based on CNV and observed markedly different patterns. Finally, we validated two deletion events in Line 72 and correlated them with genes expression using qPCR and RNA-seq, respectively. Our combined results indicated that these two CNV deletions were likely to contribute to MD susceptibility.
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Genomic and genetic variability of six chicken populations using single nucleotide polymorphism and copy number variants as markers. Animal 2016; 11:737-745. [PMID: 27819220 DOI: 10.1017/s1751731116002135] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Genomic and genetic variation among six Italian chicken native breeds (Livornese, Mericanel della Brianza, Milanino, Bionda Piemontese, Bianca di Saluzzo and Siciliana) were studied using single nucleotide polymorphism (SNP) and copy number variants (CNV) as markers. A total of 94 DNA samples genotyped with Axiom® Genome-Wide Chicken Genotyping Array (Affymetrix) were used in the analyses. The results showed the genetic and genomic variability occurring among the six Italian chicken breeds. The genetic relationship among animals was established with a principal component analysis. The genetic diversity within breeds was calculated using heterozygosity values (expected and observed) and with Wright's F-statistics. The individual-based CNV calling, based on log R ratio and B-allele frequency values, was done by the Hidden-Markov Model (HMM) of PennCNV software on autosomes. A hierarchical agglomerative clustering was applied in each population according to the absence or presence of definite CNV regions (CNV were grouped by overlapping of at least 1 bp). The CNV map was built on a total of 1003 CNV found in individual samples, after grouping by overlaps, resulting in 564 unique CNV regions (344 gains, 213 losses and 7 complex), for a total of 9.43 Mb of sequence and 1.03% of the chicken assembly autosome. All the approaches using SNP data showed that the Siciliana breed clearly differentiate from other populations, the Livornese breed separates into two distinct groups according to the feather colour (i.e. white and black) and the Bionda Piemontese and Bianca di Saluzzo breeds are closely related. The genetic variability found using SNP is comparable with that found by other authors in the same breeds using microsatellite markers. The CNV markers analysis clearly confirmed the SNP results.
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Copy number variation-based genome wide association study reveals additional variants contributing to meat quality in Swine. Sci Rep 2015; 5:12535. [PMID: 26234186 PMCID: PMC4522650 DOI: 10.1038/srep12535] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/02/2015] [Indexed: 01/26/2023] Open
Abstract
Pork quality is important both to the meat processing industry and consumers' purchasing attitude. Copy number variation (CNV) is a burgeoning kind of variants that may influence meat quality. In this study, a genome-wide association study (GWAS) was performed between CNVs and meat quality traits in swine. After false discovery rate (FDR) correction, a total of 8 CNVs on 6 chromosomes were identified to be significantly associated with at least one meat quality trait. All of the 8 CNVs were verified by next generation sequencing and six of them were verified by qPCR. Only the haplotype block containing CNV12 is adjacent to significant SNPs associated with meat quality, suggesting the effects of those CNVs were not likely captured by tag SNPs. The DNA dosage and EST expression of CNV12, which overlap with an obesity related gene Netrin-1 (Ntn1), were consistent with Ntn1 RNA expression, suggesting the CNV12 might be involved in the expression regulation of Ntn1 and finally influence meat quality. We concluded that CNVs may contribute to the genetic variations of meat quality beyond SNPs, and several candidate CNVs were worth further exploration.
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Zhou W, Liu R, Zhang J, Zheng M, Li P, Chang G, Wen J, Zhao G. A genome-wide detection of copy number variation using SNP genotyping arrays in Beijing-You chickens. Genetica 2014; 142:441-50. [PMID: 25214021 DOI: 10.1007/s10709-014-9788-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 08/18/2014] [Indexed: 12/28/2022]
Abstract
Copy number variation (CNV) has been recently examined in many species and is recognized as being a source of genetic variability, especially for disease-related phenotypes. In this study, the PennCNV software, a genome-wide CNV detection system based on the 60 K SNP BeadChip was used on a total sample size of 1,310 Beijing-You chickens (a Chinese local breed). After quality control, 137 high confidence CNVRs covering 27.31 Mb of the chicken genome and corresponding to 2.61 % of the whole chicken genome. Within these regions, 131 known genes or coding sequences were involved. Q-PCR was applied to verify some of the genes related to disease development. Results showed that copy number of genes such as, phosphatidylinositol-5-phosphate 4-kinase II alpha, PHD finger protein 14, RHACD8 (a CD8α- like messenger RNA), MHC B-G, zinc finger protein, sarcosine dehydrogenase and ficolin 2 varied between individual chickens, which also supports the reliability of chip-detection of the CNVs. As one source of genomic variation, CNVs may provide new insight into the relationship between the genome and phenotypic characteristics.
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Affiliation(s)
- Wei Zhou
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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