In-Depth Sequence Analysis of Bread Wheat Genes.

The () gene encodes a MADS-box transcription factor and plays an important role in the cold-induced transition from the vegetative to reproductive stage. Allelic variability of homoeologs has been associated with large differences in flowering time. The aim of this study was to investigate the genetic variability of homoeologs (-, - and -). We performed an in-depth sequence analysis of homoeologs in a panel of 105 winter and spring varieties of hexaploid wheat. We describe the novel allele - with an 836 bp insertion within intron 1 and show its specific expression pattern associated with reduced heading time. We further provide the complete sequence of the - allele, revealing a 177 bp insertion in intron 1, which is transcribed into an alternative splice variant. Copy number variation (CNV) analysis of homoeologs showed that - and - are present in only one copy. The copy number of recessive - ranged from one to four, while that of dominant - was one or two. Different numbers of - copies in the spring cultivars Branisovicka IX/49 and Bastion did not significantly affect heading time. We also report on the deletion of secondary structures (G-quadruplex) in promoter sequences of cultivars with more - copies.