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Review
. 2014 Jan;127(1):1-18.
doi: 10.1007/s00122-013-2177-7. Epub 2013 Aug 29.

Copy number polymorphism in plant genomes

Agnieszka Żmieńko  1 , Anna Samelak, Piotr Kozłowski, Marek Figlerowicz
Affiliations
Review

Copy number polymorphism in plant genomes

Agnieszka Żmieńko et al. Theor Appl Genet. 2014 Jan.

Abstract

Copy number variants (CNVs) are genomic rearrangements resulting from gains or losses of DNA segments. Typically, the term refers to rearrangements of sequences larger than 1 kb. This type of polymorphism has recently been shown to be a key contributor to intra-species genetic variation, along with single-nucleotide polymorphisms and short insertion-deletion polymorphisms. Over the last decade, a growing number of studies have highlighted the importance of copy number variation (CNV) as a factor affecting human phenotype and individual CNVs have been linked to risks for severe diseases. In plants, the exploration of the extent and role of CNV is still just beginning. Initial genomic analyses indicate that CNVs are prevalent in plants and have greatly affected plant genome evolution. Many CNV events have been observed in outcrossing and autogamous species. CNVs are usually found on all chromosomes, with CNV hotspots interspersed with regions of very low genetic variation. Although CNV is mainly associated with intergenic regions, many CNVs encompass protein-coding genes. The collected data suggest that CNV mainly affects the members of large families of functionally redundant genes. Thus, the effects of individual CNV events on phenotype are usually modest. Nevertheless, there are many cases in which CNVs for specific genes have been linked to important traits such as flowering time, plant height and resistance to biotic and abiotic stress. Recent reports suggest that CNVs may form rapidly in response to stress.

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Figures

Fig. 1
Fig. 1
Potential effects of CNV on gene expression. a–c Examples of CNVs that result in an elevated transcript level; d–f Examples of CNVs that result in a decreased level of the full length transcript. Gene CNV (complete duplication or deletion) may change an effective gene dosage (a, b, d). CNV affecting an enhancer sequence may alter transcription level without change in gene copy number (c). Partial gene deletion (e) or insertion of a duplicated sequence (f) may disrupt gene structure and functionality. P promoter, G gene, R enhancer sequence
Fig. 2
Fig. 2
Gene CNV contributes to wheat phenotypic diversity. a CNV of Vrn-A1 gene controls flowering time by affecting vernalization requirement; b CNV of Ppd-B1 controls flowering time by affecting photoperiod sensitivity; c CNV of Rht-D1b gene (a truncated version of Rht-D1a) determines severity of plant dwarfism phenotype. In all three cases, the impact of gene copy number on observed phenotype has been verified experimentally. Source data: a, b Díaz et al. (2012); c Li et al. (2012)
Fig. 3
Fig. 3
Glyphosate resistance in Palmer amaranth mediated by CNV of EPSPS gene. a Graphical representation of the shikimate pathway. Step 7 is catalyzed by EPSPS enzyme; b–d mechanism of EPSPS inhibition by glyphosate and its overcoming by increased number of EPSPS gene copies. In absence of glyphosate, PEP and S3P bind to EPSPS (b). When glyphosate is present, it competitively binds to EPSPS, mimicking an intermediate state of the ternary enzyme–substrates complex and inhibiting EPSPS (c). Amplification of EPSPS gene leads to production of additional protein molecules and PEP binding, even in presence of glyphosate (d). e Differences in EPSPS gene copy number between glyphosate susceptible and glyphosate-resistant Palmer amaranth individuals. EPSPS 5-enolpyruvylshikimate-3-phosphate synthase, PEP phosphoenol pyruvate, S3P shikimate-3-phosphate, EPSP 5-enolpyruvylshikimate 3-phosphate, G glyphosate
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References

    1. Alkan C, Coe BP, Eichler EE. Genome structural variation discovery and genotyping. Nat Rev Genet. 2011;12(5):363–376. doi: 10.1038/nrg2958. - DOI - PMC - PubMed
    1. Armour JA, Sismani C, Patsalis PC, Cross G. Measurement of locus copy number by hybridisation with amplifiable probes. Nucleic Acids Res. 2000;28:605–609. doi: 10.1093/nar/28.2.605. - DOI - PMC - PubMed
    1. Armour JA, Palla R, Zeeuwen PL, den Heijer M, Schalkwijk J, Hollox EJ. Accurate, high-throughput typing of copy number variation using paralogue ratios from dispersed repeats. Nucleic Acids Res. 2007;35:e19. doi: 10.1093/nar/gkl1089. - DOI - PMC - PubMed
    1. Ashfield T, Egan AN, Pfeil BE, Chen NW, Podicheti R, Ratnaparkhe MB, Ameline-Torregrosa C, Denny R, Cannon S, Doyle JJ, Geffroy V, Roe BA, Saghai Maroof MA, Young ND, Innes RW. Evolution of a complex disease resistance gene cluster in diploid Phaseolus and tetraploid Glycine. Plant Physiol. 2012;159:336–354. doi: 10.1104/pp.112.195040. - DOI - PMC - PubMed
    1. Atwell S, Huang YS, Vilhjálmsson BJ, Willems G, Horton M, Li Y, Meng D, Platt A, Tarone AM, Hu TT, Jiang R, Muliyati NW, Zhang X, Amer MA, Baxter I, Brachi B, Chory J, Dean C, Debieu M, de Meaux J, Ecker JR, Faure N, Kniskern JM, Jones JD, Michael T, Nemri A, Roux F, Salt DE, Tang C, Todesco M, Traw MB, Weigel D, Marjoram P, Borevitz JO, Bergelson J, Nordborg M. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature. 2010;465:627–631. doi: 10.1038/nature08800. - DOI - PMC - PubMed

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