Journal Article

Maize genetic diversity and association mapping using transposable element insertion polymorphisms

Charcosset, Alain, Rousselet, Agnès, Grandbastien, Marie-Angèle, Madur, Delphine, Tenaillon, Maud I, Mhiri, Corinne, Zerjal, Tatiana, Combes, Valérie

2012

Overview

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.

• Publisher: Springer Verlag,HAL CCSD,Springer-Verlag,Springer
• Subject: Agricultural sciences / Agriculture / Alleles / Analysis / Bayes Theorem / Biochemistry / Biomedical and Life Sciences / Biotechnology / chromosomes / Corn / Crosses, Genetic / Cytochrome P-450 Enzyme System / Cytochrome P-450 Enzyme System - genetics / DNA Transposable Elements / Europe / exons / flowering / genes / Genetic aspects / Genetic Markers / Genetic polymorphisms / Genetic Variation / genetics / Genotype / heat sums / Heterozygote / landraces / Life Sciences / linkage disequilibrium / methods / microsatellite repeats / miniature inverted repeat transposable elements / Models, Genetic / Models, Statistical / nucleotides / Original Paper / Phenotype / phenotypic variation / Phylogeny / Physiological aspects / Plant Biochemistry / Plant Breeding/Biotechnology / Plant Genetics and Genomics / Polymerase Chain Reaction / Polymerase Chain Reaction - methods / Polymorphism, Genetic / Polymorphism, Genetic - genetics / quantitative trait loci / sequence homology / single nucleotide polymorphism / small interfering RNA / surveys / Transposons / United States / variance / Zea mays / Zea mays - genetics
• ISBN: 0003034348, 9780003034349