Allelic genome structural variations in maize detected by array comparative genome hybridization

  • André Beló
  • Mary K. Beatty
  • David Hondred
  • Kevin A. Fengler
  • Bailin Li
  • Antoni Rafalski
Original Paper


DNA polymorphisms such as insertion/deletions and duplications affecting genome segments larger than 1 kb are known as copy-number variations (CNVs) or structural variations (SVs). They have been recently studied in animals and humans by using array-comparative genome hybridization (aCGH), and have been associated with several human diseases. Their presence and phenotypic effects in plants have not been investigated on a genomic scale, although individual structural variations affecting traits have been described. We used aCGH to investigate the presence of CNVs in maize by comparing the genome of 13 maize inbred lines to B73. Analysis of hybridization signal ratios of 60,472 60-mer oligonucleotide probes between inbreds in relation to their location in the reference genome (B73) allowed us to identify clusters of probes that deviated from the ratio expected for equal copy-numbers. We found CNVs distributed along the maize genome in all chromosome arms. They occur with appreciable frequency in different germplasm subgroups, suggesting ancient origin. Validation of several CNV regions showed both insertion/deletions and copy-number differences. The nature of CNVs detected suggests CNVs might have a considerable impact on plant phenotypes, including disease response and heterosis.


Maize Genome Maize Inbred Line Heterotic Group Microarray Probe Genome Structural Variation 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



We are thankful to Scott Tingey for frequent challenging discussions and to DuPont Crop Genetics for providing financial support.

Supplementary material

122_2009_1128_MOESM1_ESM.pdf (67 kb)
List of PCR primers used for CNV validation. The primers are listed in the 5′ to 3′ direction. (PDF 66 kb)
122_2009_1128_MOESM2_ESM.pdf (2.5 mb)
Result of aCGH between Mo17 and B73. Probes highlighted in green and red are those detecting a CNV region with more copies or presence in Mo17 and B73, respectively. Solid and dashed horizontal red lines correspond to one and two standard-deviations, respectively, calculated for all probes in the experiment. The blue curve is a loess function (R Development Core Team 2009) based on the aCGH ratio. Coordinates along the chromosomes are given as bands in a maize physical map (Fengler et al. 2007). (PDF 2,581 kb)
122_2009_1128_MOESM3_ESM.pdf (2.4 mb)
Result of aCGH experiment between two independent preparations of the inbred line PHP38. Solid and dashed horizontal red lines correspond to one and two standard-deviations, respectively, calculated for all probes in the experiment. The blue curve is a loess function (R Development Core Team 2009) based on the aCGH ratio. Coordinates along the chromosomes are given as bands in a maize physical map (Fengler et al. 2007). (PDF 2,497 kb)
122_2009_1128_MOESM4_ESM.png (308 kb)
PCR of a CNV region on chromosome five at 530 cM. A. aCGH results. B. Detailed view of CNV regions showing B73 BACs, microarray probes (number of matches to B73 genome in parentheses), and PCR results. Left lane: PCR from B73; right lane: PCR from Mo17. C. PCR of probe regions in other maize inbreds. (PNG 308 kb)
122_2009_1128_MOESM5_ESM.png (193 kb)
PCR of two CNV regions on chromosomes eight (206 cM) and nine (300.2 cM). A. aCGH results. B. Detailed view of CNV regions showing B73 BACs, microarray probes (number of matches to B73 genome in parentheses) and PCR results. Left lane: PCR from B73; right lane: PCR from Mo17. C. PCR of probe regions in other maize inbreds. (PNG 193 kb)


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Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • André Beló
    • 1
    • 2
  • Mary K. Beatty
    • 3
  • David Hondred
    • 3
  • Kevin A. Fengler
    • 1
  • Bailin Li
    • 1
  • Antoni Rafalski
    • 1
    • 2
  1. 1.DuPont Crop GeneticsWilmingtonUSA
  2. 2.Department of Plant and Soil SciencesUniversity of DelawareNewarkUSA
  3. 3.Pioneer Hi-Bred InternationalJohnstonUSA

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