Theoretical and Applied Genetics

, Volume 124, Issue 8, pp 1521–1537 | Cite as

Maize genetic diversity and association mapping using transposable element insertion polymorphisms

  • Tatiana Zerjal
  • Agnès Rousselet
  • Corinne Mhiri
  • Valérie Combes
  • Delphine Madur
  • Marie-Angèle Grandbastien
  • Alain Charcosset
  • Maud I. Tenaillon
Original Paper

Abstract

Transposable elements are the major component of the maize genome and presumably highly polymorphic yet they have not been used in population genetics and association analyses. Using the Transposon Display method, we isolated and converted into PCR-based markers 33 Miniature Inverted Repeat Transposable Elements (MITE) polymorphic insertions. These polymorphisms were genotyped on a population-based sample of 26 American landraces for a total of 322 plants. Genetic diversity was high and partitioned within and among landraces. The genetic groups identified using Bayesian clustering were in agreement with published data based on SNPs and SSRs, indicating that MITE polymorphisms reflect maize genetic history. To explore the contribution of MITEs to phenotypic variation, we undertook an association mapping approach in a panel of 367 maize lines phenotyped for 26 traits. We found a highly significant association between the marker ZmV1-9, on chromosome 1, and male flowering time. The variance explained by this association is consistent with a flowering delay of +123 degree-days. This MITE insertion is located at only 289 nucleotides from the 3′ end of a Cytochrome P450-like gene, a region that was never identified in previous association mapping or QTL surveys. Interestingly, we found (i) a non-synonymous mutation located in the exon 2 of the gene in strong linkage disequilibrium with the MITE polymorphism, and (ii) a perfect sequence homology between the MITE sequence and a maize siRNA that could therefore potentially interfere with the expression of the Cytochrome P450-like gene. Those two observations among others offer exciting perspectives to validate functionally the role of this region on phenotypic variation.

Abbreviations

TE

Transposable element

TD

Transposon display

MITE

Miniature inverted repeat transposable element

siRNA

Small interfering RNA

MAF

Minor allele frequency

Supplementary material

122_2012_1807_MOESM1_ESM.pdf (166 kb)
Online Resource 1: Maize landraces geographical location. Online Resource 2: List of PCR primers Online Resource 3: Example of the Transposon Display gel for the Ins2 MITE family. Online Resource 4: Plot of Log likelihood values from the Structure analysis (PDF 165 kb)

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Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Tatiana Zerjal
    • 1
    • 3
  • Agnès Rousselet
    • 4
  • Corinne Mhiri
    • 2
  • Valérie Combes
    • 4
  • Delphine Madur
    • 4
  • Marie-Angèle Grandbastien
    • 2
  • Alain Charcosset
    • 4
  • Maud I. Tenaillon
    • 1
  1. 1.CNRS, UMR 0320/UMR 8120 Génétique Végétale, Ferme Du MoulonGif sur YvetteFrance
  2. 2.Institut Jean-Pierre Bourgin, UMR 1318 INRA-AgroParisTechVersailles CedexFrance
  3. 3.UMR1313 Génétique Animale et Biologie Intégrative INRA-AgroParisTechJouy en JosasFrance
  4. 4.INRA, UMR 0320/UMR 8120 Génétique Végétale, Ferme Du MoulonGif sur YvetteFrance

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