Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat

Abstract

The broad adaptability of wheat and barley is in part attributable to their flexible growth habit, in that spring forms have recurrently evolved from the ancestral winter growth habit. In diploid wheat and barley growth habit is determined by allelic variation at the VRN-1 and/or VRN-2 loci, whereas in the polyploid wheat species it is determined primarily by allelic variation at VRN-1. Dominant Vrn-A1 alleles for spring growth habit are frequently associated with mutations in the promoter region in diploid wheat and in the A genome of common wheat. However, several dominant Vrn-A1, Vrn-B1, Vrn-D1 (common wheat) and Vrn-H1 (barley) alleles show no polymorphisms in the promoter region relative to their respective recessive alleles. In this study, we sequenced the complete VRN-1 gene from these accessions and found that all of them have large deletions within the first intron, which overlap in a 4-kb region. Furthermore, a 2.8-kb segment within the 4-kb region showed high sequence conservation among the different recessive alleles. PCR markers for these deletions showed that similar deletions were present in all the accessions with known Vrn-B1 and Vrn-D1 alleles, and in 51 hexaploid spring wheat accessions previously shown to have no polymorphisms in the VRN-A1 promoter region. Twenty-four tetraploid wheat accessions had a similar deletion in VRN-A1 intron 1. We hypothesize that the 2.8-kb conserved region includes regulatory elements important for the vernalization requirement. Epistatic interactions between VRN-H2 and the VRN-H1 allele with the intron 1 deletion suggest that the deleted region may include a recognition site for the flowering repression mediated by the product of the VRN-H2 gene of barley.

Identification of the VERNALIZATION 4 gene reveals the origin of spring growth habit in ancient wheats from South Asia

“…TaGRP2 binding to the VRN1 pre-mRNA is required for the inhibition of VRN1 expression (21), so the disruption of this interaction can explain the earlier expression of VRN-D4. This mechanism is also consistent with the spring growth habit associated with large deletions in the first intron of VRN1, including the RIP-3 region (20,68).…”

“…None of the polymorphisms previously known to be associated with spring growth habit in VRN1 regulatory regions (17)(18)(19)(20) were found in VRN-D4. Therefore, alternative mechanisms are required to explain the dominant spring growth habit associated with the Vrn-D4 allele.…”

“…Although VRN-D4 is expressed early in development in the absence of vernalization, its sequence lacks previously known mutations associated with spring growth habit (7,(17)(18)(19)(20). Instead, VRN-D4 has three close SNPs in the RIP-3 region of the first intron (SI Appendix, Fig.…”

“…Wheat varieties carrying the ancestral VRN1 allele have a strong vernalization requirement and are classified as "winter wheats." Mutation in the VRN1 promoter (17)(18)(19) or large deletions in the first intron (20) greatly reduce or eliminate the vernalization requirement, and wheat varieties carrying these alleles are classified as "spring wheats." A critical regulatory region in the VRN1 first intron is transcribed and contains binding sites for the RNA-binding protein TaGRP2 (21).…”

Short Vegetative Phase-Like MADS-Box Genes Inhibit Floral Meristem Identity in Barley

“…This is not consistent with the suggestion that derepression of HvVRT2 is required for cold induction of HvVRN1. Another mechanism proposed to account for induction of HvVRN1 by cold involves the HvVRN2 floral repressor locus (Yan et al, 2004;Fu et al, 2005). We found that HvVRN1 is induced by cold in the spring barley Golden Promise, which lacks HvVRN2, suggesting that cold induction of HvVRN1 can occur independently of HvVRN2.…”