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Maize genetic diversity and association mapping using transposable element insertion polymorphisms

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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.

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Abbreviations

TE:

Transposable element

TD:

Transposon display

MITE:

Miniature inverted repeat transposable element

siRNA:

Small interfering RNA

MAF:

Minor allele frequency

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Acknowledgments

We are very grateful to Domenica Manicacci for her advice on the association analysis and insightful discussions, to Brandon Gaut and Domenica Manicacci for providing comments on the manuscript. We thank Jean-Baptiste Veyrieras for helping in choosing maize landraces, Celine Mir who shared unpublished data, Pauline Garnier-Géré who brought valuable insights and help with Fdist2, Fabrice Dumas and Xavier Raffoux who provided technical assistance. This work was funded by the Agence Nationale de la Recherche (ANR-05-JCJC-0067-01 to MIT) and by Promaïs members: Caussade Semences, Euralis semences, Limagrain Verneuil holding, Maïsadour Semences, Monsanto France SAS, Syngenta seeds SAS, RAGT 2n and KWS France. We are particularly thankful to Jean Beigbeder for stimulating coordination of Genetic Diversity programs within Promaïs.

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Authors and Affiliations

  1. CNRS, UMR 0320/UMR 8120 Génétique Végétale, Ferme Du Moulon, 91190, Gif sur Yvette, France

    Tatiana Zerjal & Maud I. Tenaillon

  2. Institut Jean-Pierre Bourgin, UMR 1318 INRA-AgroParisTech, 78026, Versailles Cedex, France

    Corinne Mhiri & Marie-Angèle Grandbastien

  3. UMR1313 Génétique Animale et Biologie Intégrative INRA-AgroParisTech, Domaine de Vilvert, 78352, Jouy en Josas, France

    Tatiana Zerjal

  4. INRA, UMR 0320/UMR 8120 Génétique Végétale, Ferme Du Moulon, 91190, Gif sur Yvette, France

    Agnès Rousselet, Valérie Combes, Delphine Madur & Alain Charcosset

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  1. Tatiana Zerjal
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  2. Agnès Rousselet
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Correspondence to Tatiana Zerjal.

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Communicated by A. Schulman.

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122_2012_1807_MOESM1_ESM.pdf

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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Zerjal, T., Rousselet, A., Mhiri, C. et al. Maize genetic diversity and association mapping using transposable element insertion polymorphisms. Theor Appl Genet 124, 1521–1537 (2012). https://doi.org/10.1007/s00122-012-1807-9

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