Identification of a new Vrn-B1 allele using two near-isogenic wheat lines with difference in heading time

We conducted a molecular analysis of the Vrn-B1 gene in two near-isogenic lines (NILs) carrying the dominant Vrn-B1 (S) and Vrn-B1 (Dm) alleles from the Saratovskaya 29 and Diamant 2 cultivars, respectively. These lines are characterized by different times of ear emergence. PCR analysis and subsequent sequencing of the regulatory regions of Vrn-B1 revealed the full identity of the promoter region in both alleles. Simultaneously, we found significant differences in the structure of the first intron of the Vrn-B1 (S) allele when compared to Vrn-B1 (Dm) ; specifically, the deletion of 0.8 kb coupled with the duplication of 0.4 kb. We suggest that these changes in intron 1 of Vrn-B1 (S) caused earlier ear emergence in the corresponding NIL. The unusual structure of intron 1 within the Vrn-B1 (S) allele was described for the first time in this study. The allele Vrn-B1 (Dm) was almost identical with the previously studied sequence of the Vrn-B1a allele of T. aestivum, Triple Dirk B. We designated the new Vrn-B1 (S) allele as Vrn-B1c. PCR analysis of the Vrn-B1 gene in 26 spring wheat cultivars of both Russian and foreign breeding revealed that 16 of them contain the Vrn-B1a allele and 6 contain the Vrn-B1c allele. Other cultivars studied contained the recessive vrn-B1 gene, except for Novosibirskaya 67. This study demonstrates that the traditional system of Vrn-1 markers does not fully encompass the allelic diversity of these genes because none of the cultivars containing the Vrn-B1c allele gave a PCR product using the previously developed set of primers for identification of the Vrn-B1 locus. We showed that the newly characterized Vrn-B1c allele is widely distributed among different genotypes of spring wheat. The findings indicate the impact of structural changes in the first intron of Vrn-1 on the vernalization response and heading time.