Abstract
The VERNALIZATION1 (VRN1) 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 VRN1 homoeologs has been associated with large differences in flowering time. The aim of this study was to investigate the genetic variability of VRN1 homoeologs (VRN-A1, VRN-B1 and VRN-D1). We performed an in-depth sequence analysis of VRN1 homoeologs in a panel of 105 winter and spring varieties of hexaploid wheat. We describe the novel allele Vrn-B1f 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 Vrn-A1b allele, revealing a 177 bp insertion in intron 1, which is transcribed into an alternative splice variant. Copy number variation (CNV) analysis of VRN1 homoeologs showed that VRN-B1 and VRN-D1 are present in only one copy. The copy number of recessive vrn-A1 ranged from one to four, while that of dominant Vrn-A1 was one or two. Different numbers of Vrn-A1a 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 vrn-A1 copies.
Highlights
Bread wheat (Triticum aestivum L., 2n = 6x = 42) is one of the most important crops worldwide
Copy number variation (CNV) of VRN-A1, VRN-B1 and VRN-D1 was estimated in all 65 winter and 40 spring cultivars (Supplementary Table S1)
To estimate the CNV of VRN-B1 and VRN-D1, we developed a droplet digital PCR (ddPCR) assay, as described in the Materials and Methods section (Table 1)
Summary
Bread wheat (Triticum aestivum L., 2n = 6x = 42) is one of the most important crops worldwide. It originated in the Fertile Crescent via hybridization of tetraploid and diploid ancestors and was domesticated in this region. The VERNALIZATION1 (VRN1) gene encoding a MADS-box transcription factor (TF) expressed in leaves and the shoot apical meristem plays a significant role in the vernalization response [5,6]. Other vernalization genes, such as VRN2 and VRN3, are important members of the flowering pathway. VRN2 encodes a long-day dominant repressor of flowering while VRN3 encodes a mobile protein operating flowering activator [7,8,9]
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