Allelic Variation in the Perennial Ryegrass FLOWERING LOCUS T Gene is Associated with Changes in Flowering Time across a Range of Populations

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  • Leif Skøt, Aberystwyth University, United Kingdom
  • Ruth Sanderson, Aberystwyth University, United Kingdom
  • Ann Thomas, Aberystwyth University, United Kingdom
  • Kirsten Skøt, Aberystwyth University, United Kingdom
  • Danny Thorogood, Aberystwyth University, United Kingdom
  • Galina Latypova, Aberystwyth University, United Kingdom
  • Torben Asp
  • Ian Armstead, Aberystwyth University, United Kingdom
The Arabidopsis (Arabidopsis thaliana) FLOWERING LOCUS T (FT) gene and its orthologs in other plant species (e.g. rice [Oryza sativa] OsFTL2/Hd3a) have an established role in the photoperiodic induction of flowering response. The genomic and phenotypic variations associated with the perennial ryegrass (Lolium perenne) ortholog of FT, designated LpFT3, was assessed in a diverse collection of nine European germplasm populations, which together constituted an association panel of 864 plants. Sequencing and genotyping of a series of amplicons derived from the nine populations, containing the complete exon and intron sequences as well as 5' and 3' noncoding sequences of LpFT3, identified a total of seven haplotypes. Genotyping assays designed to detect the genomic variation showed that three haplotypes were present in approximately equal proportions and represented 84% of the total, with a fourth representing a further 11%. Of the three major haplotypes, two were predicted to code for identical protein products and the third contained two amino acid substitutions. Association analysis using either a mixed model with a relationship matrix to correct for population structure and relatedness or structured association with further correction using genomic control indicated significant associations between LpFT3 and variation in flowering time. These associations were corroborated in a validation population segregating for the same major alleles. The most "diagnostic" region of genomic variation was situated 5' of the coding sequence. Analysis of this region identified that the interhaplotype variation was closely associated with sequence motifs that were apparently conserved in the 5' region of orthologs of LpFT3 from other plant species. These may represent cis-regulatory elements involved in influencing the expression of this gene
Original languageEnglish
JournalPlant Physiology
Volume155
Pages (from-to)1013-1022
Number of pages9
ISSN0032-0889
DOIs
Publication statusPublished - 2011

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