Skip to main content
SpringerLink
Log in

Polyploid and aneuploid detection in apple using a single nucleotide polymorphism array

  • Short Communication
  • Published:
Tree Genetics & Genomes Aims and scope Submit manuscript

Abstract

Polyploidisation is a common mechanism underlying genome evolution in plants. Both polyploid and aneuploid individuals occur naturally at low frequency in diploid species because of unbalanced or unreduced gamete formation during meiosis. We evaluated the Illumina Infinium® II FruitBreedomics 20K apple single nucleotide polymorphism (SNP) array for its ability to detect polyploid and aneuploid individuals in an apple germplasm collection comprising 663 genotypes. The set of SNPs employed to perform the analysis consisted of 6733 high-quality polymorphic markers spanning the entire apple genome at an average density of one SNP every 85.6 kb. The method we used to detect chromosomal aberrations is based on analysis of the B allele frequency (BAF) at each SNP position. We have demonstrated that this simple method can be used successfully to detect triploid, tetraploid and aneuploid accessions of apple and validated our findings using flow cytometry analysis.

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

References

  • Bianco L, Cestaro A, Sargent DJ, Banchi E, Derdak S, Di Guardo M, Salvi S, Viola R, Gut I, Laurens F, Chagné D, Velasco R, van de Weg E, Troggio M (2014) Development and validation of a 20K SNP whole genome genotyping array for apple (Malus × domestica Borkh). PLoS One

  • Chagné D, Crowhurst RN, Troggio M, Davey MW, Gilmore B, Lawley C, Vanderzande S, Hellens RP, Kumar S, Cestaro A, Velasco R, Main D, Rees JD, Iezzoni A, Mockler T, Wilhelm L, Van de Weg E, Gardiner SE, Bassil N, Peace C (2012) Genome-Wide SNP Detection, Validation, and Development of an 8K SNP Array for Apple. PLoS One 7. DOI 10.1371/journal.pone.0031745

  • Considine MJ, Wan YZ, D'Antuono MF, Zhou Q, Han MY, Gao H, Wang M (2012) Molecular genetic features of polyploidization and aneuploidization reveal unique patterns for genome duplication in diploid Malus. PLoS One 7:57–65. doi:10.1371/journal.pone.0029449

    Article  Google Scholar 

  • Dolezel J, Bartos J (2005) Plant DNA flow cytometry and estimation of nuclear genome size. Ann Bot 95:99–110. doi:10.1093/aob/mci005

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Druart P (2000) Aneuploids and variants of apple (Malus x domestica Borkh.) through in vitro culture techniques. In: VanderPlas LHW (ed) Proceedings of the Xxv International Horticultural Congress, Pt 10: Application of Biotechnology and Molecular Biology and Breeding in Vitro Culture. International Society Horticultural Science, Leuven 1, pp 301-307

  • Dunbar AJ, Gondek LP, O'Keefe CL, Makishima H, Rataul MS, Szpurka H, Sekeres MA, Wang XF, McDevitt MA, Maciejewski JP (2008) 250K Single nucleotide polymorphism array karyotyping identifies acquired uniparental disomy and homozygous mutations, including novel missense dubstitutions of c-Cbl, in myeloid malignancies. Cancer Res 68:10349–10357. doi:10.1158/0008-5472.can-08-2754

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Figueroa DM, Bass HW (2010) A historical and modern perspective on plant cytogenetics. Brief Funct Genomics 9:95–102. doi:10.1093/bfgp/elp058

    Article  PubMed  Google Scholar 

  • Gill KS, Lubbers EL, Gill BS, Raupp WJ, Cox TS (1991) A genetic-linkage map of Triticum tauschii (DD) and its relationship to the D-genome of bread wheat (AABBDD). Genome 34:362–374

    Article  Google Scholar 

  • Jaillon O, Aury J-M, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyere C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G, Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pe ME, Valle G, Morgante M, Caboche M, Adam-Blondon A-F, Weissenbach J, Quetier F, Wincker P, French-Italian P (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463–U465. doi:10.1038/nature06148

    Article  CAS  PubMed  Google Scholar 

  • Korban SS, Wannarat W, Rayburn CM, Tatum TC, Rayburn AL (2009) Genome size and nucleotypic variation in Malus germplasm. Genome 52:148–155

    Article  CAS  PubMed  Google Scholar 

  • Lathi RB, Loring M, Massie JAM, Demko ZP, Johnson D, Sigurjonsson S, Gemelos G, Rabinowitz M (2012) Informatics Enhanced SNP Microarray Analysis of 30 Miscarriage Samples Compared to Routine Cytogenetics. PLoS One 7. DOI 10.1371/journal.pone.0031282

  • Le Scouarnec S, Gribble SM (2012) Characterising chromosome rearrangements: recent technical advances in molecular cytogenetics. Heredity 108:75–85. doi:10.1038/hdy.2011.100

    Article  PubMed Central  PubMed  Google Scholar 

  • Midorikawa Y, Yamamoto S, Ishikawa S, Kamimura N, Igarashi H, Sugimura H, Makuuchi M, Aburatani H (2006) Molecular karyotyping of human hepatocellular carcinoma using single-nucleotide polymorphism arrays. Oncogene 25:5581–5590. doi:10.1038/sj.onc.1209537

    Article  CAS  PubMed  Google Scholar 

  • Otto F (1990) DAPI staining of fixed cells for high-resolution flow cytometry of nuclear DNA. Methods Cell Biol 33:105–110

    Article  CAS  PubMed  Google Scholar 

  • Rauch A, Ruschendorf F, Huang J, Trautmann U, Becker C, Thiel C, Jones KW, Reis A, Nurnberg P (2004) Molecular karyotyping using an SNP array for genomewide genotyping. J Med Genet 41:916–922. doi:10.1136/jmg.2004.022855

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Sears ER (1954) The Aneuploids of common wheat. Research Bulletin / University of Missouri, College of Agriculture, Agricultural Experiment Station 572:1-59

  • Speicher MR, Carter NP (2005) The new cytogenetics: blurring the boundaries with molecular biology. Nat Rev Genet 6:782–792. doi:10.1038/nrg1692

    Article  CAS  PubMed  Google Scholar 

  • Vandepoele K, Simillion C, Van de Peer Y (2003) Evidence that rice and other cereals are ancient aneuploids. Plant Cell 15:2192–2202. doi:10.1105/tpc.014019

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Vanneste K, Maere S, Van de Peer Y (2014) Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution. Philos Trans R Soc B 369. DOI 10.1098/rstb.2013.0353

  • Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, Zini E, Eldredge G, Fitzgerald LM, Gutin N, Lanchbury J, Macalma T, Mitchell JT, Reid J, Wardell B, Kodira C, Chen Z, Desany B, Niazi F, Palmer M, Koepke T, Jiwan D, Schaeffer S, Krishnan V, Wu C, Chu VT, King ST, Vick J, Tao Q, Mraz A, Stormo A, Stormo K, Bogden R, Ederle D, Stella A, Vecchietti A, Kater MM, Masiero S, Lasserre P, Lespinasse Y, Allan AC, Bus V, Chagne D, Crowhurst RN, Gleave AP, Lavezzo E, Fawcett JA, Proost S, Rouze P, Sterck L, Toppo S, Lazzari B, Hellens RP, Durel C-E, Gutin A, Bumgarner RE, Gardiner SE, Skolnick M, Egholm M, Van de Peer Y, Salamini F, Viola R (2010) The genome of the domesticated apple (Malus x domestica Borkh.). Nat Gene 42:833. doi:10.1038/ng.654

    Article  CAS  Google Scholar 

  • Wapner RJ, Martin CL, Levy B, Ballif BC, Eng CM, Zachary JM, Savage M, Platt LD, Saltzman D, Grobman WA, Klugman S, Scholl T, Simpson JL, McCall K, Aggarwal VS, Bunke B, Nahum O, Patel A, Lamb AN, Thom EA, Beaudet AL, Ledbetter DH, Shaffer LG, Jackson L (2012) Chromosomal microarray versus karyotyping for prenatal diagnosis. N Engl J Med 367:2175–2184. doi:10.1056/NEJMoa1203382

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Zhang H, Bian Y, Gou X, Zhu B, Xu C, Qi B, Li N, Rustgi S, Zhou H, Han F, Jiang J, von Wettstein D, Liu B (2013) Persistent whole-chromosome aneuploidy is generally associated with nascent allohexaploid wheat. Proc Natl Acad Sci 110:3447–3452. doi:10.1073/pnas.1300153110

    Article  PubMed Central  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This research was supported by a New Zealand Ministry of Business, Innovation and Employment (MBIE) core funding programme (contract number 29749e, 29832e and 30096e) and the EU seventh Framework Programme FruitBreedomics project N°. 265582: Integrated Approach for increasing breeding efficiency in fruit tree crops. DC thanks Di Hyndmann from AgResearch Ltd for SNP array genotyping.

Author information

Authors and Affiliations

  1. Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand

    David Chagné & Chris Kirk

  2. Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via Mach 1, 38010, San Michele all’Adige, TN, Italy

    Daniel J. Sargent & Michela Troggio

  3. Plant & Food Research, Hawke’s Bay Research Centre, Havelock North, New Zealand

    Claire Whitworth & Satish Kumar

  4. Plant & Food Research, Lincoln Research Centre, Lincoln, New Zealand

    Sylvia Erasmuson & Ross Bicknell

Authors
  1. David Chagné
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Chris Kirk
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Claire Whitworth
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Sylvia Erasmuson
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ross Bicknell
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Daniel J. Sargent
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Satish Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Michela Troggio
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to David Chagné.

Additional information

Communicated by A. G. Abbott

This article is part of the Topical Collection on Germplasm Diversity

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1

(XLSX 1214 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Chagné, D., Kirk, C., Whitworth, C. et al. Polyploid and aneuploid detection in apple using a single nucleotide polymorphism array. Tree Genetics & Genomes 11, 94 (2015). https://doi.org/10.1007/s11295-015-0920-8

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s11295-015-0920-8

Keywords

Search

Navigation