In-Depth Sequence Analysis of Bread Wheat VRN1 Genes

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.

The Czech Plant Nucleus Workshop 2021

“…Interestingly, the mechanism of vernalization response differs in monocot grasses including crops, where the release of transcriptional repression of the flowering MADS-box activator VERNALIZATION 1 (VRN1) is required for the induction of flowering. Analysis of over 100 hexaploid bread wheat cultivars by B. Strejčková (IEB) revealed several known as well as new vernalization insensitive VRN1 alleles, supporting earlier evidence that VRN1 is the major breeding locus in cereals (Strejčková et al 2021). J. Šafář (IEB) showed that genetic and epigenetic regulation of VRN1, including a putative role of the recently identified bread wheat PRC2 components (Strejčková et al 2020), remains unknown.…”

Long-Amplicon Single-Molecule Sequencing Reveals Novel, Trait-Associated Variants of VERNALIZATION1 Homoeologs in Hexaploid Wheat

“…We found nine cultivars harboring a recently described allele, Vrn-B1f ( Strejčková et al, 2021 ) in four spring and five winter type cultivars released in different geographic regions (Germany, Chile, Mexico, and Australia). Like the dominant Vrn-A1a and Vrn-B1a alleles, this allele is associated with a reduction in many agronomic traits (e.g., grain yield, kernels per m 2 , protein yield, NUE).…”

“…The same duplication was also observed in the reference genome of LongReach Lancer (see Supplementary Figure 3 ). Recently, this duplication was detected in three spring wheat genotypes and referred to as Vrn-B1f by Strejčková et al (2021) . In VRN-D1 , a novel allele with a 163 bp insertion in the first intron was identified in two cultivars, Mex.…”

“…Comparison of the number of VRN-A1 copies estimated by Würschum et al (2015) by TaqMan assay qPCR with the number of haplotypes extracted from long reads in this study, revealed in contradiction that most cultivars with three copies contained two haplotypes, while the vast majority of cultivars with two copies contained four haplotypes ( Table 4 ). Díaz et al (2012) and other authors including ( Zhu et al, 2014 ; Kippes et al, 2015 ; Würschum et al, 2015 ; Guedira et al, 2016 ; Dixon et al, 2019 ; Muterko and Salina, 2019 ; Dreisigacker et al, 2021 ; Strejčková et al, 2021 ) measured average fold-change ratio between the target gene VRN-A1 relative to the internal positive control gene CONSTANS2 (probes and primers binding to three homoeologous genes on 6A, 6B, and 6D). Thus, a ratio of 0.33 would represent one copy, 0.66 would represent two copies, 1.0 would represent 3 copies, and 1.3 would represent four copies.…”

“…This gene is considered to be a copy of the Vrn-A1 gene on chromosome 5A. Recently, copy numbers for the dominant alleles of VRN-A1 and recessive allele of VRN-B1 have been detected in different species of wheat by Muterko and Salina, 2018 , 2019 , 2021 and Strejčková et al (2021) .…”