Flowering time in maize: linkage and epistasis at a major effect locus.
In a previous study, we identified a candidate fragment length polymorphism associated with flowering time variation after seven generations of selection for flowering time, starting from the maize inbred line F252. Here, we characterized the candidate region and identified underlying polymorphisms. Then, we combined QTL mapping, association mapping, and developmental characterization to dissect the genetic mechanisms responsible for the phenotypic variation. The candidate region contained the Eukaryotic Initiation Factor (eIF-4A) and revealed a high level of sequence and structural variation beyond the 3'-UTR of eIF-4A, including several insertions of truncated transposable elements. Using a biallelic single-nucleotide polymorphism (SNP) (C/T) in the candidate region, we confirmed its association with flowering time variation in a panel of 317 maize inbred lines. However, while the T allele was correlated with late flowering time within the F252 genetic background, it was correlated with early flowering time in the association panel with pervasive interactions between allelic variation and the genetic background, pointing to underlying epistasis. We also detected pleiotropic effects of the candidate polymorphism on various traits including flowering time, plant height, and leaf number. Finally, we were able to break down the correlation between flowering time and leaf number in the progeny of a heterozygote (C/T) within the F252 background consistent with causal loci in linkage disequilibrium. We therefore propose that both a cluster of tightly linked genes and epistasis contribute to the phenotypic variation for flowering time.
Université Paris-Sud, Gif sur Yvette, France.
Eléonore
E
Durand
Sophie
S
Bouchet
Pascal
P
Bertin
Adrienne
A
Ressayre
Philippe
P
Jamin
Alain
A
Charcosset
Christine
C
Dillmann
Maud I
MI
Tenaillon
D000483:Alleles; D002874:Chromosome Mapping; D004843:Epistasis, Genetic; D039601:Eukaryotic Initiation Factor-4A / Q000235:genetics; D035264:Flowers / Q000235:genetics / Q000502:physiology*; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D005819:Genetic Markers; D060005:Genotyping Techniques; D006579:Heterozygote; D007178:Inbreeding; D015810:Linkage Disequilibrium; D058977:Molecular Sequence Annotation; D010641:Phenotype; D018515:Plant Leaves / Q000235:genetics / Q000502:physiology; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D013997:Time Factors; D003313:Zea mays / Q000235:genetics* / Q000502:physiology
D005819:Genetic Markers; D039601:Eukaryotic Initiation Factor-4A