Mapping of genome-wide copy number variations in the Iranian indigenous cattle using a dense SNP data set
K. Karimi A B F , A. Esmailizadeh A , D. D. Wu C D and C. Gondro E
+ Author Affiliations
- Author Affiliations
A Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran.
B Young Researchers Society, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran.
C State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
D Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China.
E School of Environmental and Rural Science, University of New England, Armidale, NSW Australia.
F Corresponding author. Email: karim.karimi81@gmail.com
Animal Production Science 58(7) 1192-1200 https://doi.org/10.1071/AN16384
Submitted: 14 June 2016 Accepted: 15 November 2016 Published: 30 January 2017
Abstract
The objective of this study was to present the first map of the copy number variations (CNVs) in Iranian indigenous cattle based on a high-density single nucleotide polymorphism (SNP) dataset. A total of 90 individuals were genotyped using the Illumina BovineHD BeadChip containing 777 962 SNPs. The QuantiSNP algorithm was used to perform a genome-wide CNV detection across autosomal genome. After merging the overlapping CNV, a total of 221 CNV regions were identified encompassing 36.4 Mb or 1.44% of the bovine autosomal genome. The length of the CNV regions ranged from 3.5 to 2252.8 Kb with an average of 163.8 Kb. These regions included 147 loss (66.52%) and 74 gain (33.48%) events containing a total of 637 annotated Ensembl genes. Gene ontology analysis revealed that most of genes in the CNV regions were involved in environmental responses, disease susceptibility and immune system functions. Furthermore, 543 of these genes corresponded to the human orthologous genes, which involved in a wide range of biological functions. Altogether, 73% of the 221 CNV regions overlapped either completely or partially with those previously reported in other cattle studies. Moreover, novel CNV regions involved several quantitative trait loci (QTL)-related to adaptative traits of Iranian indigenous cattle. These results provided a basis to conduct future studies on association between CNV regions and phenotypic variations in the Iranian indigenous cattle.
Additional keywords: bovine genome, CNV annotation, structural variations.
References
Alkan C, Coe BP, Eichler EE (2011) Genome structural variation discovery and genotyping. Nature Reviews Genetics 12, 363–376.| Genome structural variation discovery and genotyping.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXkslelu7g%3D&md5=ee816e088185ca486c5a1139b8e0095bCAS |
Bae JS, Cheong HS, Kim LH, NamGung S, Park TJ, Chun J-Y, Kim JY, Pasaje CFA, Lee JS, Shin HD (2010) Identification of copy number variations and common deletion polymorphisms in cattle. BMC Genomics 11, 232
| Identification of copy number variations and common deletion polymorphisms in cattle.Crossref | GoogleScholarGoogle Scholar |
Bickhart DM, Liu GE (2014) The challenges and importance of structural variation detection in livestock. Frontiers in Genetics 5, 37
| The challenges and importance of structural variation detection in livestock.Crossref | GoogleScholarGoogle Scholar |
Bickhart DM, Hou Y, Schroeder SG, Alkan C, Cardone MF, Matukumalli LK (2012) Copy number variation of individual cattle genomes using next-generation sequencing. Genome Research 22, 778–790.
Bickhart DM, Xu L, Hutchison JL, Cole JB, Null DJ, Schroeder SG, Liu GE (2016) Diversity and population-genetic properties of copy number variations and multicopy genes in cattle. DNA Research 23, 253–262.
| Diversity and population-genetic properties of copy number variations and multicopy genes in cattle.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC28XhsF2jsr3L&md5=56328616b69dd0f211d82b66db6c4837CAS |
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 (2015) Genome-wide study of structural variants in bovine Holstein, Montbéliarde and Normande dairy breeds. PLoS One 10, e0135931
| Genome-wide study of structural variants in bovine Holstein, Montbéliarde and Normande dairy breeds.Crossref | GoogleScholarGoogle Scholar |
Cissé M, Halabisky B, Harris J, Devidze N, Dubal DB, Sun B, Orr A, Lotz G, Kim DH, Hamto P, Ho K, Yu G-Q, Mucke L (2011) Reversing EphB2 depletion rescues cognitive functions in Alzheimer model. Nature 469, 47–52.
| Reversing EphB2 depletion rescues cognitive functions in Alzheimer model.Crossref | GoogleScholarGoogle Scholar |
Clop A, Vidal O, Amills M (2012) Copy number variation in the genomes of domestic animals. Animal Genetics 43, 503–517.
| Copy number variation in the genomes of domestic animals.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38Xht1ymtr7P&md5=560d3fbf2f7304f9f33da10326fa0c31CAS |
Colella S, Yau C, Taylor JM, Mirza G, Butler H, Clouston P, Bassett AS, Seller A, Holmes CC, Ragoussis J (2007) QuantiSNP: an objective Bayes Hidden-Markov model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Research 35, 2013–2025.
| QuantiSNP: an objective Bayes Hidden-Markov model to detect and accurately map copy number variation using SNP genotyping data.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXlsV2ru7k%3D&md5=594c000e738164ed0a4390714e76f53aCAS |
Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P, Fitzgerald T, Hu M, Ihm CH, Kristiansson K, MacArthur DG, MacDonald JR, Onyiah I, Pang AWC, Robson S, Stirrups K, Valsesia A, Walter K, Wei J, Wellcome Trust Case Control C, Tyler-Smith C, Carter NP, Lee C, Scherer SW, Hurles ME (2010) Origins and functional impact of copy number variation in the human genome. Nature 464, 704–712.
| Origins and functional impact of copy number variation in the human genome.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1MXht1CisLrL&md5=937f159ab3f121388cfc3902b2a22b3aCAS |
Damaj L, Lupien-Meilleur A, Lortie A, Riou E, Ospina LH, Gagnon L, Rossignol E (2015) CACNA1A haploinsufficiency causes cognitive impairment, autism and epileptic encephalopathy with mild cerebellar symptoms. European Journal of Human Genetics 23, 1505–1512.
| CACNA1A haploinsufficiency causes cognitive impairment, autism and epileptic encephalopathy with mild cerebellar symptoms.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2MXjvFWktLg%3D&md5=aa5b624594db9dbd39a9c7e626adc003CAS |
Davarniya B, Hu H, Kahrizi K (2015) The role of a novel TRMT1 gene mutation and rare GRM1 gene defect in intellectual disability in two Azeri families. PLoS One 10, e0129631
| The role of a novel TRMT1 gene mutation and rare GRM1 gene defect in intellectual disability in two Azeri families.Crossref | GoogleScholarGoogle Scholar |
de Smith AJ, Walters RG, Froguel P, Blakemore AI (2009) Human genes involved in copy number variation: mechanisms of origin, functional effects and implications for disease. Cytogenetic and Genome Research 123, 17–26.
| Human genes involved in copy number variation: mechanisms of origin, functional effects and implications for disease.Crossref | GoogleScholarGoogle Scholar |
Dekkers JCM (2012) Application of genomics tools to animal breeding. Current Genomics 13, 207–212.
| Application of genomics tools to animal breeding.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38XnsVWjtbw%3D&md5=734534698934960778e0893c8b36a750CAS |
Driller K, Pagenstecher A, Uhl M, Omran H, Berlis A, Grunder A (2007) Nuclear factor I X deficiency causes brain malformation and severe skeletal defects. Molecular and Cellular Biology 27, 3855–3867.
| Nuclear factor I X deficiency causes brain malformation and severe skeletal defects.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXltlant7c%3D&md5=26437a7c55c847d788c54b440eb1cd37CAS |
Fadista J, Thomsen B, Holm L-E, Bendixen C (2010) Copy number variation in the bovine genome. BMC Genomics 11, 284
| Copy number variation in the bovine genome.Crossref | GoogleScholarGoogle Scholar |
FAO (2007) The state of the world’s animal genetic resources for food and agriculture. (Eds B Rischkowsky, D Pilling) (United Nations Food and Agriculture Organization (FAO): Rome, Italy)
Flisikowski K, Venhoranta H, Nowacka-Woszuk J, Mckay SD, Flyckt A, Taponen J (2010) A novel mutation in the maternally imprinted PEG3 domain results in a loss of MIMT1 expression and causes abortions and stillbirths in cattle (Bos taurus). PLoS One 5, e15116
| A novel mutation in the maternally imprinted PEG3 domain results in a loss of MIMT1 expression and causes abortions and stillbirths in cattle (Bos taurus).Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXhsFGjur%2FE&md5=66f49f9df44662f5bde97babb8fb1d0dCAS |
Fontanesi L, Martelli PL, Beretti F, Riggio V, Dall’Olio S, Colombo M, Casadio R, Russo V, Portolano B (2010) An initial comparative map of copy number variations in the goat (Capra hircus) genome. BMC Genomics 11, 639
| An initial comparative map of copy number variations in the goat (Capra hircus) genome.Crossref | GoogleScholarGoogle Scholar |
Fontanesi L, Beretti F, Martelli PL, Colombo M, Dall’Olio S, Occidente M, Portolano B, Casadio R, Matassino D, Russo V (2011) A first comparative map of copy number variations in the sheep genome. Genomics 97, 158–165.
| A first comparative map of copy number variations in the sheep genome.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXitFentb8%3D&md5=4aeb132d484dfb8c6915193c65823b2fCAS |
Gel B, Díez-Villanueva A, Serra E, Buschbeck M, Peinado MA, Malinverni R (2015) regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests. Bioinformatics 32, 289–291.
Gill JL, Capper D, Vanbellinghen JF, Chung SK, Higgins RJ, Rees MI, Shelton GD, Harvey RJ (2011) Startle disease in Irish wolfhounds associated with a microdeletion in the glycine transporter GlyT2 gene. Neurobiology of Disease 43, 184–189.
| Startle disease in Irish wolfhounds associated with a microdeletion in the glycine transporter GlyT2 gene.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXmtFCkt7c%3D&md5=2b728c169c8749c56bd64eac339f5058CAS |
Ghosh S, Qu Z, Das PJ, Fang E, Juras R, Cothran EG, McDonell S, Kenney DG, Lear TL, Adelson DL, Chowdhary BP, Raudsepp T (2014) Copy number variation in the Horse genome. PLOS Genetics 10, e1004712
| Copy number variation in the Horse genome.Crossref | GoogleScholarGoogle Scholar |
Graubert TA, Cahan P, Edwin D, Selzer RR, Richmond TA, Eis PS, Ley TJ (2007) A high-resolution map of segmental DNA copy number variation in the Mouse genome. PLOS Genetics 3, e3
| A high-resolution map of segmental DNA copy number variation in the Mouse genome.Crossref | GoogleScholarGoogle Scholar |
Henrichsen CN, Chaignat E, Reymond A (2009) Copy number variants, diseases and gene expression. Human Molecular Genetics 18, R1–R8.
| Copy number variants, diseases and gene expression.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1MXjsFSnt70%3D&md5=184ed86382ec5b4454cae52848e92eb1CAS |
Herrero-Medrano JM, Megens HJ, Groenen MA, Ramis G, Bosse M, Perez-Enciso M, Crooijmans RP (2013) Conservation genomic analysis of domestic and wild pig populations from the Iberian Peninsula. BMC Genetics 14, 106
| Conservation genomic analysis of domestic and wild pig populations from the Iberian Peninsula.Crossref | GoogleScholarGoogle Scholar |
Hoffmann I (2010) Climate change and the characterization, breeding and conservation of animal genetic resources. Animal Genetics 41, 32–46.
| Climate change and the characterization, breeding and conservation of animal genetic resources.Crossref | GoogleScholarGoogle Scholar |
Hou Y, Liu GE, Bickhart DM, Cardone MF, Wang K, Kim E, Matukumalli LK, Ventura M, Song J, VanRaden PM, Sonstegard TS, Van Tassell CP (2011) Genomic characteristics of cattle copy number variations. BMC Genomics 12, 127
| Genomic characteristics of cattle copy number variations.Crossref | GoogleScholarGoogle Scholar |
Hou Y, Bickhart DM, Hvinden ML, Li C, Song J, Boichard DA, Fritz S, Eggen A, Denise S, Wiggans GR (2012a) Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array. BMC Genomics 13, 376
| Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXot1Wmt78%3D&md5=ee96c9a50bc9033cf7e1f61fa60fdaf3CAS |
Hou Y, Liu GE, Bickhart DM, Matukumalli LK, Li C, Song J, Gasberre LC, Van Tassell CP, Sonstegard TS (2012b) Genomic regions showing copy number variations associate with resistance or susceptibility to gastrointestinal nematodes in Angus cattle. Functional & Integrative Genomics 12, 81–92.
| Genomic regions showing copy number variations associate with resistance or susceptibility to gastrointestinal nematodes in Angus cattle.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38XjvVSktb8%3D&md5=5d47657a1976c62723e14f88d13b15e6CAS |
Jia X, Chen S, Zhou H, Li D, Liu W, Yang N (2013) Copy number variations identified in the chicken using a 60K SNP BeadChip. Animal Genetics 44, 276–284.
| Copy number variations identified in the chicken using a 60K SNP BeadChip.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXmsVWrtbc%3D&md5=610af260187e740334b97d0a6ccb04a0CAS |
Jiang Y, Liu H-B (2015) Myocyte enhancer factor-2A gene mutation and coronary artery disease. Chinese Medical Journal 128, 2688–2691.
| Myocyte enhancer factor-2A gene mutation and coronary artery disease.Crossref | GoogleScholarGoogle Scholar |
Jiang L, Jiang J, Yang J, Liu X, Wang J, Wang H (2013) Genome-wide detection of copy number variations using high-density SNP genotyping platforms in Holsteins. BMC Genomics 14, 131
| Genome-wide detection of copy number variations using high-density SNP genotyping platforms in Holsteins.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXosVSgur4%3D&md5=ed68652fb181ffee7bfa8b40adb3dda9CAS |
Jiang J, Wang J, Wang H, Zhang Y, Kang H, Feng X, Wang J, Yin Z, Bao W, Zhang Q, Liu J-F (2014) Global copy number analyses by next generation sequencing provide insight into pig genome variation. BMC Genomics 15, 593
| Global copy number analyses by next generation sequencing provide insight into pig genome variation.Crossref | GoogleScholarGoogle Scholar |
Karimi K, Esmailizadeh Koshkoiyeh A, Asadi Fozi M, Porto-Neto LR, Gondro C (2016) Prioritization for conservation of Iranian native cattle breeds based on genome-wide SNP data. Conservation Genetics 17, 77–89.
| Prioritization for conservation of Iranian native cattle breeds based on genome-wide SNP data.Crossref | GoogleScholarGoogle Scholar |
Kim JH, Hu HJ, Yim SH, Bae JS, Kim SY, Chung YJ (2012) CNVRuler: a copy number variation-based case-control association analysis tool. Bioinformatics 28, 1790–1792.
| CNVRuler: a copy number variation-based case-control association analysis tool.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38XptF2ht7s%3D&md5=2e026c3378e91240a627672cb45e7ec3CAS |
Kott E, Duquesnoy P, Copin B, Legendre M, Dastot-Le Moal F, Montantin G, Amselem S (2012) Loss-of-function mutations in LRRC6, a gene essential for proper axonemal assembly of inner and outer Dynein arms, cause primary ciliary Dyskinesia. American Journal of Human Genetics 91, 958–964.
| Loss-of-function mutations in LRRC6, a gene essential for proper axonemal assembly of inner and outer Dynein arms, cause primary ciliary Dyskinesia.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38Xhs1ajsLnM&md5=820279bcc6d84b490aa9bc99aa1d2c50CAS |
Lichter-Peled A, Polani S, Stanyon R, Rocchi M, Kahila Bar-Gal G (2013) Role of KCNQ2 and KCNQ3 genes in juvenile idiopathic epilepsy in Arabian foals. Veterinary Journal (London, England) 196, 57–63.
| Role of KCNQ2 and KCNQ3 genes in juvenile idiopathic epilepsy in Arabian foals.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38XhslGjsb7M&md5=d000b468676182824a9d5c74f1228337CAS |
Liu GE, Hou Y, Zhu B, Cardone MF, Jiang L, Cellamare A, Mitra A, Alexander LJ, Coutinho LL, Dell’Aquila ME (2010) Analysis of copy number variations among diverse cattle breeds. Genome Research 20, 693–703.
| Analysis of copy number variations among diverse cattle breeds.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXlslyisL0%3D&md5=d0bfe5ac6503c730502bdb64208a5fe4CAS |
Liu J, Zhang L, Xu L, Ren H, Lu J, Zhang X, Zhang S, Zhou X, Wei C, Zhao F, Du L (2013) Analysis of copy number variations in the sheep genome using 50K SNP BeadChip array. BMC Genomics 14, 229
| Analysis of copy number variations in the sheep genome using 50K SNP BeadChip array.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXot1yhsL8%3D&md5=c7621651bf98e230a2d1fc8b14193e08CAS |
Lupski JR, Belmont JW, Boerwinkle E, Gibbs RA (2011) Clan genomics and the complex architecture of human disease. Cell 147, 32–43.
| Clan genomics and the complex architecture of human disease.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXht1GrsLnK&md5=170f28ad8bf7ee468d41b1e59d83d969CAS |
Marenne G, Rodriguez-Santiago B, Closas MG, Perez-Jurado L, Rothman N, Rico D, Pita G, Pisano DG, Kogevinas M, Silverman DT, Valencia A, Real FX, Chanock SJ, Genin E, Malats N (2011) Assessment of copy number variation using the Illumina Infinium 1M SNP-array: a comparison of methodological approaches in the Spanish Bladder Cancer/EPICURO study. Human Mutation 32, 240–248.
| Assessment of copy number variation using the Illumina Infinium 1M SNP-array: a comparison of methodological approaches in the Spanish Bladder Cancer/EPICURO study.Crossref | GoogleScholarGoogle Scholar |
Mi H, Muruganujan A, Casagrande JT, Thomas PD (2013) Large-scale gene function analysis with the PANTHER classification system. Nature Protocols 8, 1551–1566.
| Large-scale gene function analysis with the PANTHER classification system.Crossref | GoogleScholarGoogle Scholar |
Molin A-M, Berglund J, Webster MT, Lindblad-Toh K (2014) Genome-wide copy number variant discovery in dogs using the CanineHD genotyping array. BMC Genomics 15, 210
| Genome-wide copy number variant discovery in dogs using the CanineHD genotyping array.Crossref | GoogleScholarGoogle Scholar |
Nakayama K, Nakayama N, Davidson B, Sheu JJ, Jinawath N, Santillan A (2006) A BTB/POZ protein, NAC-1, is related to tumor recurrence and is essential for tumor growth and survival. Proceedings of the National Academy of Sciences of the United States of America 103, 18739–18744.
| A BTB/POZ protein, NAC-1, is related to tumor recurrence and is essential for tumor growth and survival.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28XhtlahtLrL&md5=377b6732289963e3ffe99362436b68a3CAS |
Pinto D, Darvishi K, Shi X, Rajan D, Rigler D, Fitzgerald T, Feuk L (2011) Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants. Nature Biotechnology 29, 512–520.
| Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXlslyku7g%3D&md5=15dbe262a351968300edb8971db0bf50CAS |
Polyak A, Rosenfeld JA, Girirajan S (2015) An assessment of sex bias in neurodevelopmental disorders. Genome Medicine 7, 94
| An assessment of sex bias in neurodevelopmental disorders.Crossref | GoogleScholarGoogle Scholar |
Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842.
| BEDTools: a flexible suite of utilities for comparing genomic features.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXivFGkurc%3D&md5=ebb01f44e49d2bc61ec889b752ca867aCAS |
Reimand J, Arak T, Vilo J (2011) g:Profiler- a web server for functional interpretation of gene lists (2011 update). Nucleic Acids Research 39, W307–W315.
| g:Profiler- a web server for functional interpretation of gene lists (2011 update).Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXosVOntbs%3D&md5=6da87c2fc97d4986c4bbc2e63f4683c7CAS |
Salomón-Torres R, Gonzalez-Vizcarra VM, Medina-Basulto GE, Montano-Gomez MF, Mahadevan P, Yaurima-Basaldua VH, Villa-Angulo C, Villa-Angulo R (2015) Genome-wide identification of copy number variations in Holstein cattle from Baja California, Mexico, using high-density SNP genotyping arrays. Genetics and Molecular Research 14, 11848–11859.
| Genome-wide identification of copy number variations in Holstein cattle from Baja California, Mexico, using high-density SNP genotyping arrays.Crossref | GoogleScholarGoogle Scholar |
Samarakoon U, Gonzales JM, Patel JJ, Tan A, Checkley L, Ferdig MT (2011) The landscape of inherited and de novo copy number variants in a plasmodium falciparum genetic cross. BMC Genomics 12, 457
| The landscape of inherited and de novo copy number variants in a plasmodium falciparum genetic cross.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXhtlWjs7fJ&md5=f65ae5ff7241fae467c173cc1b3c0016CAS |
Seroussi E, Glick G, Shirak A, Yakobson E, Weller JI, Ezra E, Zeron Y (2010) Analysis of copy loss and gain variations in Holstein cattle autosomes using BeadChip SNPs. BMC Genomics 11, 673
| Analysis of copy loss and gain variations in Holstein cattle autosomes using BeadChip SNPs.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXhsFCgs77L&md5=fb340dad6834ca5784f3130d9c6e49aaCAS |
Shin D-H, Lee H-J, Cho S, Kim HJ, Hwang JY, Lee C-K, Jeong J, Yoon D, Kim H (2014) Deleted copy number variation of Hanwoo and Holstein using next generation sequencing at the population level. BMC Genomics 15, 240
| Deleted copy number variation of Hanwoo and Holstein using next generation sequencing at the population level.Crossref | GoogleScholarGoogle Scholar |
Silva VHd, Regitano LCdA, Geistlinger L, Pértille F, Giachetto PF, Brassaloti RA, Morosini NS, Zimmer R, Coutinho LL (2016) Genome-wide detection of CNVs and their association with meat tenderness in Nelore cattle. PLoS One 11, e0157711
| Genome-wide detection of CNVs and their association with meat tenderness in Nelore cattle.Crossref | GoogleScholarGoogle Scholar |
Stinchcombe JR, Hoekstra HE (2008) Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits. Heredity 100, 158–170.
| Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXovFKltQ%3D%3D&md5=73202fdf9b33e58c25ba9443803d8dbdCAS |
Stothard P, Choi JW, Basu U, Sumner-Thomson JM, Meng Y, Liao X, Moore SS (2011) Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery. BMC Genomics 12, 559
| Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38XpvVWqtg%3D%3D&md5=541d6b4e1696aa29e3cfb1f4134b4f11CAS |
Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J, Eichler EE (2010) Diversity of human copy number variation and multicopy genes. Science 330, 641–646.
| Diversity of human copy number variation and multicopy genes.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXhtlaqt7bL&md5=686b799257fb0a19d37df57091704f54CAS |
Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM, Haugen E, Hayden H, Albertson D, Pinkel D, Olson MV, Eichler EE (2005) Fine-scale structural variation of the human genome. Nature Genetics 37, 727–732.
| Fine-scale structural variation of the human genome.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2MXlslWhsrk%3D&md5=662144e267f7efe6cd52f86131dbe0e1CAS |
Wang Y, Tang Z, Sun Y, Wang H, Wang C, Yu S, Liu J, Zhang Y, Fan B, Li K, Liu B (2014) Analysis of genome-wide copy number variations in Chinese indigenous and western pig breeds by 60 K SNP genotyping arrays. PLoS One 9, e106780
| Analysis of genome-wide copy number variations in Chinese indigenous and western pig breeds by 60 K SNP genotyping arrays.Crossref | GoogleScholarGoogle Scholar |
Wang MD, Dzama K, Hefer CA, Muchadeyi FC (2015) Genomic population structure and prevalence of copy number variations in South African Nguni cattle. BMC Genomics 16, 894
| Genomic population structure and prevalence of copy number variations in South African Nguni cattle.Crossref | GoogleScholarGoogle Scholar |
Weischenfeldt J, Symmons O, Spitz F, Korbel JO (2013) Phenotypic impact of genomic structural variation: insights from and for human disease. Nature Reviews. Genetics 14, 125–138.
| Phenotypic impact of genomic structural variation: insights from and for human disease.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXptlOgsw%3D%3D&md5=1e4423b5cb3b2cf9114724a562df9266CAS |
Xu L, Hou Y, Bickhart D, Song J, Liu G (2013) Comparative analysis of CNV calling algorithms: literature survey and a case study using Bovine high-density SNP data. Microarrays (Basel, Switzerland) 2, 171–185.
| Comparative analysis of CNV calling algorithms: literature survey and a case study using Bovine high-density SNP data.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXhtFGqsrnE&md5=85dd10916137b0cd347dfe4dab15aa72CAS |
Yang Y, Zhao W, Xu Q-W, Wang X-S, Zhang Y, Zhang J (2014) IQGAP3 promotes EGFR-ERK signaling and the growth and metastasis of lung cancer cells. PLoS One 9, e97578
| IQGAP3 promotes EGFR-ERK signaling and the growth and metastasis of lung cancer cells.Crossref | GoogleScholarGoogle Scholar |
Zhang Q, Ma Y, Wang X, Zhang Y, Zhao X (2015) Identification of copy number variations in Qinchuan cattle using BovineHD Genotyping Beadchip array. Molecular Genetics and Genomics 290, 319–327.
| Identification of copy number variations in Qinchuan cattle using BovineHD Genotyping Beadchip array.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2cXhsFyqsbrN&md5=601dad832fe6d080e36d7a222a84ee00CAS |
Zhou J, Lemos B, Dopman EB, Hartl DL (2011) Copy-number variation: the balance between gene dosage and expression in Drosophila melanogaster. Genome Biology and Evolution 3, 1014–1024.
| Copy-number variation: the balance between gene dosage and expression in Drosophila melanogaster.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXhtl2mt7%2FO&md5=6152bdf3b718d9c861b130e1566652e0CAS |
