Skip to main content
SpringerLink
Log in

Copy number variation and disease resistance in plants

  • Review
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

Plant genome diversity varies from single nucleotide polymorphisms to large-scale deletions, insertions, duplications, or re-arrangements. These re-arrangements of sequences resulting from duplication, gains or losses of DNA segments are termed copy number variations (CNVs). During the last decade, numerous studies have emphasized the importance of CNVs as a factor affecting human phenotype; in particular, CNVs have been associated with risks for several severe diseases. In plants, the exploration of the extent and role of CNVs in resistance against pathogens and pests is just beginning. Since CNVs are likely to be associated with disease resistance in plants, an understanding of the distribution of CNVs could assist in the identification of novel plant disease-resistance genes. In this paper, we review existing information about CNVs; their importance, role and function, as well as their association with disease resistance in plants.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  • Abel HJ, Duncavage EJ (2013) Detection of structural DNA variation from next generation sequencing data: a review of informatic approaches. Cancer Genet 206:432–440

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Alkan C, Coe BP, Eichler EE (2011) Genome structural variation discovery and genotyping. Nat Rev Genet 12:363–376

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Armour JA, Sismani C, Patsalis PC, Cross G (2000) Measurement of locus copy number by hybridisation with amplifiable probes. Nucleic Acids Res 28:605–609

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Armour JA, Palla R, Zeeuwen PL, den Heijer M, Schalkwijk J, Hollox EJ (2007) Accurate, high-throughput typing of copy number variation using paralogue ratios from dispersed repeats. Nucleic Acids Res 35:1–8

    Article  CAS  Google Scholar 

  • Bai H, Cao Y, Quan J et al (2013) Identifying the genome-wide sequence variations and developing new molecular markers for genetics research by re-sequencing a landrace cultivar of foxtail millet. PLoS One 8:e73514

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bai Z, Chen J, Liao Y, Wang M, Liu R, Ge S et al (2016) The impact and origin of copy number variations in the Oryza species. BMC Genom 17:261

    Article  CAS  Google Scholar 

  • Bayer PE, Ruperao P, Mason AS, Stiller J, Chan CKK, Hayashi S, Long Y, Meng J, Sutton T, Visendi P, Varshney RK, Batley J, Edwards D (2015) High resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus. Theor Appl Genet 128:1039–1047

    Article  PubMed  Google Scholar 

  • Belo A, Beatty MK, Hondred D et al (2010) Allelic genome structural variations in maize detected by array comparative genome hybridization. Theor Appl Genet 120:355–367

    Article  PubMed  CAS  Google Scholar 

  • Berglund J, Nevalainen EM, Molin A-M, Perloski M, The Lupa Consortium, Andre C, Zody MC, Sharpe T, Hitte C, Lindblad-Toh K, Lohi H, Webster MT (2012) Novel origins of copy number variation in the dog genome. Genome Biol 13:R73

    Article  PubMed  PubMed Central  Google Scholar 

  • Bertioli DJ, Leal-Bertioli SCM, Lion MB, Santos VL, Pappas G Jr, Cannon SB, Guimaraes PM (2003) A large scale analysis of resistance gene homologues in Arachis. Mol Gen Genom 270:34–45

    Article  CAS  Google Scholar 

  • Bickhart DM, Hou Y, Schroeder SG, Alkan C, Cardone MF, Matukumalli LK, Song J, Schnabel RD, Ventura M, Taylor JF et al (2012) Copy number variation of individual cattle genomes using next-generation sequencing. Genome Res 22:778–790

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bignell GR, Santarius T, Pole JCM et al (2007) Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution. Genome Res 17:1296–1303

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Boocock J, Chagné D, Merriman TR, Black MA (2015) The distribution and impact of common copy-number variation in the genome of the domesticated apple, Malus × domestica Borkh. BMC Genom 16:848

    Article  CAS  Google Scholar 

  • Bradeen JM, Iorizzo M, Mollov DS, Raasch J, Kramer LC, Millett BP, Austin-Phillips S, Jiang J, Carputo D (2009) Higher copy numbers of the potato RB transgene correspond to enhanced transcript and late blight resistance levels. Mol Plant Microbe Interact 22:437–446

    Article  PubMed  CAS  Google Scholar 

  • Campbell PC, Stephens PJ, Pleasance ED et al (2008) Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet 40:722–729

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Cao J, Schneeberger K, Ossowski S, Gunther T, Bender S, Fitz J, Koenig D, Lanz C, Stegle O, Lippert C, Wang X, Ott F, Müller J, Alonso-Blanco C, Borgwardt K, Schmid KJ, Weigel D (2011) Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet 43:956–963

    Article  PubMed  CAS  Google Scholar 

  • Chalhoub B, Denoeud F, Liu S, Parkin IAP, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B et al (2014) Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 345:950–953

    Article  PubMed  CAS  Google Scholar 

  • Chen K, Wallis JW, Mclellan MD, Larson DE, Kalicki JM, Pohl CS et al (2009) Break dancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods 6:677–681

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chia JM, Song C, Bradbury PJ, Costich D, de Leon N, Doebley J, Elshire RJ, Gaut B, Geller L, Glaubitz JC, Gore M, Guill KE, Holland J, Hufford MB, Lai J, Li M, Liu X, Lu Y, McCombie R, Nelson R, Poland J, Prasanna BM, Pyhäjärvi T, Rong T, Sekhon RS, Sun Q, Tenaillon MI, Tian F, Wang J, Xu X, Zhang Z, Kaeppler SM, Ross-Ibarra J, McMullen MD, Buckler ES, Zhang G, Xu Y, Ware D (2012) Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet 44:803–807

    Article  PubMed  CAS  Google Scholar 

  • Cong B, Barrero LS, Tanksley SD (2008) Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication. Nat Genet 40:800–804

    Article  PubMed  CAS  Google Scholar 

  • Conrad DF, Andrews TD, Carter NP, Hurles ME, Pritchard JKA (2006) High-resolution survey of deletion polymorphism in the human genome. Nat Genet 38:75–81

    Article  PubMed  CAS  Google Scholar 

  • Cook DE, Lee TG, Guo X et al (2012) Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean. Science 338:1206–1209

    Article  PubMed  CAS  Google Scholar 

  • Dalton-Morgan J, Hayward A, Alamery S, Tollenaere R, Mason AS, Campbell E, Patel D, Lorenc MT, Yi B, Long Y, Meng J, Raman R, Raman H, Lawley C, Edwards D, Batley J (2014) A high-throughput SNP array in the amphidiploid species Brassica napus shows diversity in resistance genes. Funct Integr Genom 14:643–655

    Article  CAS  Google Scholar 

  • David P, Chen NWG, Pedrosa-Harand A, Thareau V, Sévignac M, Cannon SB, Debouck D, Langin T, Geffroy V (2009) A nomadic subtelomeric disease resistance gene cluster in common bean. Plant Physiol 151:1048–1065

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • DeBolt S (2010) Copy number variation shapes genome diversity in Arabidopsis over immediate family generational scales. Genome Biol Evol 2:441–453

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Diaz A, Zikhali M, Turner AS, Isaac P, Laurie DA (2012) Copy number variation affecting the photoperiod-B1 and vernalization-A1 genes is associated with altered flowering time in wheat (Triticum aestivum). PLoS One 7:e33234

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Dixon MS, Hatzixanthis K, Jones DA, Harrison K, Jones JDG (1998) The tomato Cf-5 disease resistance gene and six homologs show pronounced allelic variation in leucine-rich repeat copy number. Plant Cell 10:1915–1925

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Douchkov D, Lück S, Johrde A, Nowara D, Himmelbach A, Rajaraman J, Stein N, Sharma R, Kilian B, Schweizer P (2014) Discovery of genes affecting resistance of barley to adapted and non-adapted powdery mildew fungi. Genome Biol 15:518

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Fadista J, Thomsen B, Holm LE, Bendixen C (2010) Copy number variation in the bovine genome. BMC Genom 11:284

    Article  CAS  Google Scholar 

  • Feuk L, Marshall CR, Wintle RF et al (2006) Structural variants: changing the landscape of chromosomes and design of disease studies. Hum Mol Genet 15:R57–R66

    Article  PubMed  CAS  Google Scholar 

  • Flagel LE, Willis J, Vision TJ (2013) The standing pool of genomic structural variation in a natural population of Mimulus guttatus. Genome Biol Evol 6:53–64

    Article  PubMed Central  Google Scholar 

  • Freeman JL, Perry GH, Feuk L, Redon R, McCarroll SA, Altshuler DM, Aburatani H, Jones KW, Tyler-Smith C, Hurles ME, Carter NP, Scherer SW, Lee C (2006) Copy number variation: new insights in genome diversity. Genome Res 16:949–961

    Article  PubMed  CAS  Google Scholar 

  • Gaines TA, Zhang W, Wang D, Bukun B, Chisholm ST, Shaner DL, Nissen SJ, Patzoldt WL, Tranel PJ, Culpepper AS, Grey TL, Webster TM, Vencill WK, Sammons RD, Jiang J, Preston C, Leach JE, Westra P (2010) Gene amplification confers glyphosate resistance in Amaranthus palmeri. Proc Natl Acad Sci USA 107:1029–1034

    Article  PubMed  CAS  Google Scholar 

  • Gaines TA, Shaner DL, Ward SM, Leach JE, Preston C, Westra P (2011) Mechanism of resistance of evolved glyphosate-resistant Amaranthus palmeri. J Agric Food Chem 59:5886–5889

    Article  PubMed  CAS  Google Scholar 

  • Gazave E, Darré F, Morcillo-Suarez C, Petit-Marty N, Carreño A, Marigorta UM, Ryder OA, Blancher A, Rocchi M, Bosch E, Baker C, Marquès-Bonet T, Eichler EE, Navarro A (2011) Copy number variation analysis in the great apes reveals species-specific patterns of structural variation. Genome Res 21:1626–1639

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gillet-Markowska A, Richard H, Fischer G, Lafontaine I (2014) Ulysses: accurate detection of low-frequency structural variations in large insert-size sequencing libraries. Bioinformatics 31:801–808

    Article  PubMed  CAS  Google Scholar 

  • Girirajan S, Campbell CD, Eichler EE (2011) Human copy number variation and complex genetic disease. Annu Rev Genet 45:203–226

    Article  PubMed  CAS  Google Scholar 

  • Golicz AA, Schliep M, Lee HT, Larkum AWD, Dolferus R, Batley J, Chan CKK, Sablok G, Ralph PJ, Edwards D (2015) Genome-wide survey of the seagrass Zostera muelleri suggests modification of the ethylene signalling network. J Exp Bot 6:1–10

    Google Scholar 

  • Golicz AA, Batley J, Edwards D (2016a) Towards plant pangenomics. Plant Biotechnol J 14:1099–1105

    Article  PubMed  Google Scholar 

  • Golicz AA, Bayer PE, Barker GC, Edger PP, Kim HR, Martinez PA, Chan CKC, Severn-Ellis A, McCombie WR, Parkin IAP, Paterson AH, Pires JC, Sharpe AG, Tang H, Teakle GR, Town CD, Batley J, Edwards D (2016b) The pangenome of an agronomically important crop plant Brassica oleracea. Nat Commun 7:13390

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Guo YL, Fitz J, Schneeberger K, Ossowski S, Cao J, Weigel D et al (2011) Genome-wide comparison of nucleotide-binding site-leucine-rich repeat-encoding genes in Arabidopsis. Plant Physiol 157:757–769

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gururani MA, Venkatesh J, Upadhyaya CP, Nookaraju A, Pandey SK, Park SW (2012) Plant disease resistance genes: current status and future directions. Physiol Mol Plant Pathol 78:51–65

    Article  CAS  Google Scholar 

  • Hanikenne M, Talke IN, Haydon MJ, Lanz C, Nolte A, Motte P, Kroymann J, Weigel D, Krämer U (2008) Evolution of metal hyperaccumulation required cis-regulatory changes and triplication of HMA4. Nature 453:391–395

    Article  PubMed  CAS  Google Scholar 

  • Hanikenne M, Kroymann J, Trampczynska A, Bernal M, Motte P, Clemens S, Krämer U (2013) Hard selective sweep and ectopic gene conversion in a gene cluster affording environmental adaptation. PLoS Genet 9:e1003707

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hardigan MA, Crisovan E, Hamilton JP, Kim J, Laimbeer P, Leisner CP, Manrique-Carpintero NC, Newton L, Pham GM, Vaillancourt B, Xueming Y, Zeng Z, Douches DS, Jiang J, Veilleux RE, Buell CB (2016) Genome reduction uncovers a large dispensable genome and adaptive role for copy number variation in asexually propagated Solanum tuberosum. Plant Cell 28:388–405

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Horiguchi G, Gonzalez N, Beemster GT, Inzé D, Tsukaya H (2009) Impact of segmental chromosomal duplications on leaf size in the grandifolia-D mutants of Arabidopsis thaliana. Plant J 60:122–133

    Article  PubMed  CAS  Google Scholar 

  • Hurgobin B, Edwards D (2017) SNP discovery using a pangenome: has the single reference approach become obsolete? Biology 6(1):21

    Article  PubMed Central  Google Scholar 

  • Iwakami S, Shimono Y, Manabe Y, Endo M, Shibaike H, Uchino A, Tominaga T (2017) Copy number variation in acetolactate synthase genes of thifensulfuron-methyl resistant Alopecurus aequalis (Short-awn Foxtail) accessions in Japan. Front Plant Sci 8:254

    Article  PubMed  PubMed Central  Google Scholar 

  • Jamann TM, Poland JA, Kolkman JM, Smith LG, Nelson RJ (2014) Unraveling genomic complexity at a quantitative disease resistance locus in maize. Genetics 198:333–344

    Article  PubMed  PubMed Central  Google Scholar 

  • Jiang Y, Wang Y, Brudno M (2012) PRISM: pair-read informed split- read mapping for base-pair level detection of insertion, deletion and structural variants. Bioinformatics 28:2576–2583

    Article  PubMed  CAS  Google Scholar 

  • Katoh H, Inoue H, Iwanami T (2015) Changes in variable number of tandem repeats in ‘Candidatus Liberibacter asiaticus’ through insect transmission. PLoS One 10(9):e0138699

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kidd JM, Cooper GM, Donahue WF et al (2008) Mapping and sequencing of structural variation from eight human genomes. Nature 453:56–64

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Klambauer G, Schwarzbauer K, Mayr A, Clevert DA, Mitterecker A, Bodenhofer U et al (2012) cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate. Nucleic Acids Res 40:e69

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kolomietz E, Meyn MS, Pandita A et al (2002) The role of Alu repeat clusters as mediators of recurrent chromosomal aberrations in tumours. Genes Chromosomes Cancer 35:97–112

    Article  PubMed  CAS  Google Scholar 

  • Kondrashov FA (2012) Gene duplication as a mechanism of genomic adaptation to a changing environment. Proc Biol Sci 279:5048–5057

    Article  PubMed  PubMed Central  Google Scholar 

  • Lam HY, Mu XJ, Stütz AM, Tanzer A, Cayting PD, Snyder M, Kim PM, Korbel JO, Gerstein MB (2009) Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nat Biotechnol 28:47–55

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lam HYK, Clark MJ, Chen R, Chen R, Natsoulis G, O’Huallachain M, Dewey FE, Habegger L, Ashley EA, Gerstein MB, Butte AJ, Ji HP, Snyder M (2012) Performance comparison of whole-genome sequencing platforms. Nat Biotechnol 30:78–82

    Article  CAS  Google Scholar 

  • Layer RM, Chiang C, Quinlan AR, Hall IM (2014) LUMPY: a probabilistic frame work for structural variant discovery. Genome Biol 15:R84

    Article  PubMed  PubMed Central  Google Scholar 

  • Lee OG, Kumar I, Diers BW, Hudson ME (2015) Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus. Mol Ecol 24:1774–1791

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Leister D, Kurth J, Laurie DA, Yano M, Sasaki T, Devos K, Graner A, Schulze-Lefert P (1998) Rapid reorganization of resistance gene homologues in cereal genomes. Proc Natl Acad Sci USA 95:370–375

    Article  PubMed  CAS  Google Scholar 

  • Li W, Olivier M (2013) Current analysis platforms and methods for detecting copy number variation. Physiol Genom 45:1–16

    Article  CAS  Google Scholar 

  • Li Y, Xiao J, Wu J, Duan J, Liu Y, Ye X, Zhang X, Guo X, Gu Y, Zhang L, Jia J, Kong X (2012) A tandem segmental duplication (TSD) in green revolution gene Rht-D1b region underlies plant height variation. New Phytol 196:282–291

    Article  PubMed  CAS  Google Scholar 

  • Li Y, Zhou G, Ma J, Jiang W, Jin L, Zhang Z, Guo Y, Zhang J, Sui Y, Zheng L, Zhang S, Zuo Q, Shi X, Li Y, Zhang W, Hu Y, Kong G, Hong H, Tan B, Song J, Liu Z, Wang Y, Ruan H, Yeung CKL, Liu J, Wang H, Zhang L, Guan R, Wang K, Li W, Chen S, Chang R, Jiang Z, Jackson SA, Li R, Qiu L (2014) De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nat Biotechnol 32:1045–1054

    Article  PubMed  CAS  Google Scholar 

  • Lin X, Zhang Y, Kuang H, Chen J (2013) Frequent loss of lineages and deficient duplications accounted for low copy number of disease resistance genes in Cucurbitaceae. BMC Genom 14:335

    Article  CAS  Google Scholar 

  • Lin K, Zhang N, Severing EI, Nijveen H, Cheng F, Visser RGF, Wang X, de Ridder D, Bonnema G (2014) Beyond genomic variation—comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage. BMC Genom 15:250

    Article  Google Scholar 

  • Liu GE, Hou Y, Zhu B, Cardone MF, Jiang L, Cellamare A, Mitra A, Alexander LJ, Coutinho LL, Dell’Aquila ME, Gasbarre LC, Lacalandra G, Li RW, Matukumalli LK, Nonneman D, Regitano LCA, Smith TPL, Song J, Sonstegard TS, Van Tassell CP, Ventura M, Eichler EE, McDaneld TG, Keele JW (2010) Analysis of copy number variations among diverse cattle breeds. Genome Res 20:693–703

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lu P, Han X, Qi J et al (2012) Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by re-sequencing Landsberg erecta and all four products of a single meiosis. Genome Res 22:508–518

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Mace E, Tai S, Innes D, Godwin I, Hu W, Campbell B, Gilding E, Cruickshank A, Prentis P, Wang J, Jordan D (2014) The plasticity of NBS resistance genes in sorghum is driven by multiple evolutionary processes. Plant Biol 14:253

    Google Scholar 

  • Marcinkowska-Swojak M, Uszczynska B, Figlerowicz M, Kozlowski P (2013) An MLPA-based strategy for discrete CNV genotyping: CNV-miRNAs as an example. Hum Mutat 34:763–773

    Article  PubMed  CAS  Google Scholar 

  • Maron LG, Guimaraes CT, Kirst M, Albert PS, Birchler JA, Bradbury PJ, Buckler ES, Coluccio AE, Danilova TV, Kudrna D et al (2013) Aluminum tolerance in maize is associated with higher MATE1 gene copy number. Proc Natl Acad Sci 110:5241–5246

    Article  PubMed  Google Scholar 

  • Marschall T, Hajirasouliha I, Schonhuth A (2013) MATE-CLEVER: mendelian-inheritance-aware discovery and genotyping of midsize and long indels. Bioinformatics 29:3143–3150

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Mason AM, Zhang J, Tollenaere R, Vasquez Teuber P, Dalton-Morgan J, Hu L, Yan G, Edwards D, Redden R, Batley J (2015) High-throughput genotyping for species identification and diversity assessment in germplasm collections. Mol Ecol Resour 15:1091–1101

    Article  PubMed  CAS  Google Scholar 

  • McHale LK, Haun WJ, Xu WW, Bhaskar PB, Anderson JE, Hyten DL, Gerhardt DJ, Jeddeloh JA, Stupar RM (2012) Structural variants in the soybean genome localize to clusters of biotic stress response genes. Plant Physiol 159:1295–1308

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Muñoz-Amatriaín M, Eichten SR, Wicker T, Richmond TA, Mascher M, Steuernagel B, Scholz U, Ariyadasa R, Spannagl M, Nussbaumer T, Mayer KFX, Taudien S, Platzer M, Jeddeloh JA, Springer NM, Muehlbauer GJ, Stein N (2013) Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome. Genome Biol 14:R58

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Muñoz-Amatriaín M, Lonardi S, Luo MC et al (2015) Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. Plant J 84:216–227

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Nguyen HT, Merriman TR, Black MA (2014) The CNVrd2 package: measurement of copy number at complex loci using high-throughput sequencing data. Front Genet 5:248

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Nicholas TJ, Baker C, Eichler EE, Akey JM (2011) A high-resolution integrated map of copy number polymorphisms within and between breeds of the modern domesticated dog. BMC Genom 12:414

    Article  Google Scholar 

  • Nijkamp JF, Van Den Broek MA, Geertman JM, Reinders MJ, Daran JM, De Ridder D (2012) De novo detection of copy number variation by co-assembly. Bioinformatics 28:3195–3202

    Article  PubMed  CAS  Google Scholar 

  • Nishida H, Yoshida T, Kawakami K et al (2013) Structural variation in the 5′ upstream region of photoperiod-insensitive alleles Ppd-A1a and Ppd-B1a identified in hexaploid wheat (Triticum aestivum L.), and their effect on heading time. Mol Breed 31:27–37

    Article  CAS  Google Scholar 

  • O’Rawe J, Jiang T, Sun G, Wu Y, Wang W, Hu J, Bodily P, Tian L, Hakonarson H, Johnson WE, Wei Z, Wang Kai, Lyon GJ (2013) Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Med 5:28

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Orozco LD, Cokus SJ, Ghazalpour A, Ingram-Drake L, Wang S, Van Nas A, Che N, Araujo JA, Pellegrini M, Lusis AJ (2009) Copy number variation influences gene expression and metabolic traits in mice. Hum Mol Genet 18:4118–4129

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ortiz-Estevez M, De Las Rivas J, Fontanillo C, Rubio A (2011) Segmentation of genomic and transcriptomic microarrays data reveals major correlation between DNA copy number aberrations and gene-loci expression. Genomics 97:86–93

    Article  PubMed  CAS  Google Scholar 

  • Pinosio S, Giacomello S, Faivre-Rampant P, Taylor G, Jorge V, Le Paslier MC, Zaina G, Bastien C, Cattonaro F, Marroni F, Morgante M (2016) Characterization of the poplar pan-genome by genome-wide identification of structural variation. Mol Biol Evol 33:2706–2719

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Pirooznia M, Goes FS, Zandi PP (2015) Whole-genome CNV analysis: advances in computational approaches. Front Genet 6:138

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Redon R, Ishikawa S, Fitch KR et al (2006) Global variation in copy number in the human genome. Nature 444:444–454

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Samelak-Czajka A, Marszalek-Zenczak M, Marcinkowska-Swojak M, Kozlowski P, Figlerowicz M, Zmienko A (2017) MLPA-based analysis of copy number variation in plant populations. Front Plant Sci 8:222

    Article  PubMed  PubMed Central  Google Scholar 

  • Sammons RD, Gaines TA (2014) Glyphosate resistance: state of knowledge. Pest Manag Sci 70:1367–1377

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Saxena RK, Edwards D, Varshney RK (2014) Structural variations in plant genomes. Brief Funct Genom 13:296–307

    Article  Google Scholar 

  • Scherer SW, Lee C, Birney E, Altshuler DM, Eichler EE, Carter NP, Hurles ME, Feuk L (2007) Challenges and standards in integrating surveys of structural variation. Nat Genet 39:S7–S15

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Schiessl S, Huettel B, Kuehn D, Reinhardt R, Snowdon R (2017) Post-polyploidisation morphotype diversification associates with gene copy number variation. Nat/Sci Rep 7:41845

    CAS  Google Scholar 

  • Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner S, Massa H, Walker M, Chi M et al (2004) Large-scalecopy number polymorphism in the human genome. Science 305:525–528

    Article  PubMed  CAS  Google Scholar 

  • Sieber AN, Longin CFH, Leiser WL, Würschum T (2016) Copy number variation of CBF-A14 at the Fr-A2 locus determines frost tolerance in winter durum wheat. Theor Appl Genet 129:1087–1097

    Article  PubMed  CAS  Google Scholar 

  • Šķipars V, Krivmane B, Ruņģis D (2011) Thaumatin-like protein gene copy number variation in Scots pine (Pinus sylvestris). Environ Exp Biol 9:75–81

    Google Scholar 

  • Slabaugh MB, Yu JK, Tang S, Heesacker A, Hu X, Lu G, Han F, Bidney D, Knapp SJ (2003) Haplotyping and mapping a large cluster of resistance gene candidates in sunflower using multilocus intron fragment length polymorphisms. Plant Biotechnol J 1:167–185

    Article  PubMed  CAS  Google Scholar 

  • Springer NM, Ying K, Fu Y et al (2009) Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genet 5:e1000734

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Stankiewicz P, Lupski JR (2010) Structural variation in the human genome and its role in disease. Annu Rev Med 61:437–455

    Article  PubMed  CAS  Google Scholar 

  • Sutton T, Baumann U, Hayes J, Collins NC, Shi BJ, Schnurbusch T, Hay A, Mayo G, Pallotta M, Tester M et al (2007) Boron-toxicity tolerance in barley arising from efflux transporter amplification. Science 318:1446–1449

    Article  PubMed  CAS  Google Scholar 

  • Swanson-Wagner RA, Eichten SR, Kumari S, Tiffin P, Stein JC, Ware D, Springer NM (2010) Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Res 20:1689–1699

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Teo SM, Pawitan Y, Ku CS, Chia KS, Salim A (2012) Statisticalchal lenges associated with detecting copy number variations with next-generation sequencing. Bioinformatics 28:2711–2718

    Article  PubMed  CAS  Google Scholar 

  • Trappe K, Emde AK, Ehrlich HC, Reinert K (2014) Gustaf: detecting and correctly classifying SVs in the NGS twilight zone. Bioinformatics 30:3484–3490

    Article  PubMed  CAS  Google Scholar 

  • Trębicki P, Nancarrow N, Cole E, Bosque-Pérez NA, Constable FE, Freeman AJ, Rodoni B, Yen AL, Luck JE, Fitzgerald GJ (2015) Virus disease in wheat predicted to increase with a changing climate. Glob Change Biol 21:3511–3519

    Article  Google Scholar 

  • Turner TL, Bourne EC, Von Wettberg EJ, Hu TT, Nuzhdin SV (2010) Population re-sequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils. Nat Genet 42:260–263

    Article  PubMed  CAS  Google Scholar 

  • Vallejos CE, Astua-Monge G, Jones V, Plyler TR, Sakiyama NS, Mackenzie SA (2006) Genetic and molecular characterization of the I locus of Phaseolus vulgaris. Genetics 172:1229–1242

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Veltman JA, Brunner HG (2012) De novo mutations in human genetic disease. Nat Rev Genet 18(13):565–575

    Article  CAS  Google Scholar 

  • Wang D, Amornsiripanitch N, Dong X (2006) A genomic approach to identify regulatory nodes in the transcriptional network of systemic acquired resistance in plants. PLoS Pathog 2:e123

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wang H, Nettleton D, Ying K (2014) Copy number variation detection using next generation sequencing read counts. BMC Bioinform 15:109

    Article  Google Scholar 

  • Wang Y, Xiong G, Hu J, Jiang L, Yu H, Xu J, Fang Y, Zeng L, Xu E, Xu J, Ye W, Meng X, Liu R, Chen H, Jing Y, Wang Y, Zhu X, Li J, Qian Q (2015) Copy number variation at the GL7 locus contributes to grain size diversity in rice. Nat Genet 47:944–949

    Article  PubMed  CAS  Google Scholar 

  • Weaver S, Dube S, Mir A, Qin J, Sun G, Ramakrishnan R, Jones RC, Li-vak KJ (2010) Taking qPCR to a higher level: analysis of CNV reveals the power of high throughput qPCR to enhance quantitative resolution. Methods 50:271–276

    Article  PubMed  CAS  Google Scholar 

  • Wei C, Chen J, Kuang H (2016) Dramatic number variation of R genes in Solanaceae species accounted for by a few R gene subfamilies. PLoS One 11:e0148708

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Würschum T, Boeven PHG, Langer SM, Longin CFH, Wl Leiser (2015) Multiply to conquer: copy number variations at Ppd-B1 and Vrn-A1 facilitate global adaptation in wheat. BMC Genet 16:96

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Würschum T, Longin CFH, Hahn V, Tucker MR, Leiser WL (2017) Copy number variations of CBF genes at the Fr-A2 locus are essential components of winter hardiness in wheat. Plant J 89:764–773

    Article  PubMed  CAS  Google Scholar 

  • Xi R, Lee S, Park PJ (2012) A survey of copy-number variation detection tools based on high-throughput sequencing data, chapter 7. Curr Protoc Hum Genet (Unit 7–19). doi:10.1002/0471142905.hg0719s75

  • Xiao H, Jiang N, Schaffner E, Stockinger EJ, Vander Knaap E (2008) Retro-transposon-mediated gene duplication under lies morphological variation of tomato fruit. Science 319:1527–1530

    Article  PubMed  CAS  Google Scholar 

  • Xu X, Liu X, Ge S et al (2012) Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol 30:105–111

    Article  CAS  Google Scholar 

  • Yang S, Lia J, Zhanga X, Zhangb Q, Huanga J, Chena JQ, Hartlc DL, Tian D (2013) Rapidly evolving R genes in diverse grass species confer resistance to rice blast disease. Proc Natl Acad Sci 110:18572–18577

    Article  PubMed  CAS  Google Scholar 

  • Yao W, Li G, Zhao H, Wang G, Lian X, Xie W (2015) Exploring the rice dispensable genome using a metagenome-like assembly strategy. Genome Biol 16:1–20

    Article  CAS  Google Scholar 

  • Yu P, Wang C, Xu Q, Feng Y, Yuan X, Yu H, Wang Y, Tang S, Wei X (2011) Detection of copy number variations in rice using array-based comparative genomic hybridization. BMC Genom 12:372

    Article  CAS  Google Scholar 

  • Yu P, Wang CH, Xu Q, Feng Y, Yuan XP, Yu HY, Wang YP, Tang SX, Wei XH (2013) Genome-wide copy number variations in Oryza sativa L. BMC Genom 14:649

    Article  CAS  Google Scholar 

  • Zhai J, Jeong DH, De Paoli E, Park S, Rosen BD, Li Y, González AJ, Yan Z, Kitto SL, Grusak MA (2011) MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. Genes Dev 25:2540–2553

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhang F, Gu W, Hurles ME, Lupski JR (2009) Copy number variation in human health, disease, and evolution. Annu Rev Genom Hum Genet 10:451–481

    Article  CAS  Google Scholar 

  • Zhang R, Murat F, Pont C, Langin T, Salse J (2014) Paleo-evolutionary plasticity of plant disease resistance genes. BMC Genom 15:187

    Article  Google Scholar 

  • Zhao M, Wang Q, Wang Q, Jia P, Zhao Z (2013) Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. BMC Bioinform 14(Suppl 11):S1

    Article  Google Scholar 

  • Zheng LY, Guo XS, He B, Sun LJ, Peng Y, Dong SS, Liu TF, Jiang S, Ramachandran S, Liu CM, Jing HC (2011) Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor). Genome Biol 12:1–14

    Article  Google Scholar 

  • Zhou P, Silverstein KAT, Ramaraj T, Guhlin J, Denny R, Liu J, Farmer AD, Steele KP, Stupar RM, Miller JR, Tiffin P, Mudge J, Young ND (2017) Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes. BMC Genom 18:261

    Article  CAS  Google Scholar 

  • Zhu M, Need AC, Han Y, Ge D, Maia JM, Zhu Q et al (2012) Using ERDS to infer copy number variants in high-coverage genomes. Am J Hum Genet 91:408–421

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zmienko A, Samelak-Czajka A, Kozlowski P, Szymanska M, Figlerowicz M (2016) Arabidopsis thaliana population analysis reveals high plasticity of the genomic region spanning MSH2 AT3G18530 and AT3G18535 genes and provides evidence for NAHR-driven recurrent CNV events occurring in this location. BMC Genom 17:893

    Article  CAS  Google Scholar 

  • Żmieńko A, Samelak A, Kozłowski P, Figlerowicz M (2014) Copy number polymorphism in plant genomes. Theor Appl Genet 127:1–18

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgements

The authors thank the Australian Research Council Projects FT130100604, DP1601004497, LP140100537, LP160100030 and LP130100925.

Author information

Authors and Affiliations

  1. School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia

    Aria Dolatabadian, Dhwani Apurva Patel, David Edwards & Jacqueline Batley

Authors
  1. Aria Dolatabadian
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Dhwani Apurva Patel
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. David Edwards
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jacqueline Batley
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jacqueline Batley.

Ethics declarations

Conflict of interest

The authors declare no conflicts of interest.

Additional information

Communicated by Rajeev K. Varshney.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Dolatabadian, A., Patel, D.A., Edwards, D. et al. Copy number variation and disease resistance in plants. Theor Appl Genet 130, 2479–2490 (2017). https://doi.org/10.1007/s00122-017-2993-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-017-2993-2

Search

Navigation