A recessive allele for delayed flowering at the soybean maturity locus E9 is a leaky allele of FT2a, a FLOWERING LOCUS T ortholog. Issue 1 (December 2016) - Zhao, Chen
Abstract Background Understanding the molecular mechanisms of flowering and maturity is important for improving the adaptability and yield of seed crops in different environments. In soybean, a facultative short-day plant, genetic variation at four maturity genes, E1 toE4, plays an important role in adaptation to environments with different photoperiods. However, the molecular basis of natural variation in time to flowering and maturity is poorly understood. Using a cross between early-maturing soybean cultivars, we performed a genetic and molecular study of flowering genes. The progeny of this cross segregated for two maturity loci, E1 andE9 . The latter locus was subjected to detailed molecular analysis to identify the responsible gene. Results Fine mapping, sequencing, and expression analysis revealed thatE9 isFT2a, an ortholog ofArabidopsis FLOWERING LOCUS T . Regardless of daylength conditions, thee9 allele was transcribed at a very low level in comparison with theE9 allele and delayed flowering. Despite identical coding sequences, a number of single nucleotide polymorphisms and insertions/deletions were detected in the promoter, untranslated regions, and introns between the two cultivars. Furthermore, thee9 allele had aTy1/copia –like retrotransposon, SORE-1, inserted in the first intron. Comparison of the expression levels of different alleles among near-isogenic lines and photoperiod-insensitive cultivars indicated that theSORE-1 insertion attenuatedFT2a expression by its allele-specific transcriptional repression.SORE-1 was highly methylated, and did not appear to disruptFT2a RNA processing. Conclusions The soybean maturity geneE9 isFT2a, and its recessive allele delays flowering because of lower transcript abundance that is caused by allele-specific transcriptional repression due to the insertion ofSORE-1 . TheFT2a transcript abundance is thus directly associated with the variation in flowering time in soybean. Thee9 allele may maintain vegetative growth in early-flowering genetic backgrounds, and also be useful as a long-juvenile allele, which causes late flowering under short-daylength conditions, in low-latitude regions.