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

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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.

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Acknowledgments

The work was supported by the Russian Foundation for Basic Research (project no. 11-04-00-178) and the “Biodiversity and Dynamics of Gene Pools” program (project no 23.28).

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  1. Institute of Cytology and Genetics, Lavrentiev ave. 10, Novosibirsk, 630090, Russia

    A. B. Shcherban, T. T. Efremova & E. A. Salina

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  1. A. B. Shcherban
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  2. T. T. Efremova
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  3. E. A. Salina
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Correspondence to A. B. Shcherban.

Electronic supplementary material

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11032_2011_9581_MOESM1_ESM.ppt

Supplementary Fig. 1 Alignment of the promoter sequences of the Vrn-1 genes from T. aestivum genomes. The consensus forms of Vrn-A1, Vrn- B1, Vrn-D1 were constructed based on the following sequences: AY616461, AY616462, AY747601, AY616452, AY747600, AY747598, AY747599 (Vrn-A1); AY616456, AY747602, AY747603, AY747604,AY616453 (Vrn-B1); AY616454, AY616457, AY747606, AY747597, AY747605 (Vrn-D1). The base differences specific to Vrn-B1 are shown by asterisks. Pr1 and Pr2, shown by arrows, were the primers used for PCR. Numbers 1,968 indicate the first and last nucleotides in the sequence Vrn-B1 (PPT 760 kb)

11032_2011_9581_MOESM2_ESM.ppt

Supplementary Fig. 2 Hypothetical model used to explain the origin of the Vrn-B1 S (Vrn-B1c) allele from the Vrn-B1a allele during DNA replication (according Wessler et al. 1990). The region of deletion is marked by lowercase letters. The numerical positions of the deletion endpoints and the region of duplication (F) relative to the start of the first intron are shown. The F-region is boldface and underlined along with the flanking dinucleotides (A, B) and the corresponding dinucleotides at the deletion endpoints (A’, B’). Dotted lines represent newly a replicated DNA strand (PPT 148 kb)

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Shcherban, A.B., Efremova, T.T. & Salina, E.A. Identification of a new Vrn-B1 allele using two near-isogenic wheat lines with difference in heading time. Mol Breeding 29, 675–685 (2012). https://doi.org/10.1007/s11032-011-9581-y

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