The Insertion of a Novel Retrotransposon in the Promoter of a Vernalization Gene Resulted in Early Flowering in Tetraploid Wheat

Previous reports showed allelic variation in wheat vernalization gene VRN1 was due to deletions either in the promoter or the first intron. Here, we identified a novel Vrn-B1 allele that has a retrotransposon in its promoter conferring spring growth habit. The VRN-B1 gene was mapped in a doubled haploid population that segregated for winter/spring growth habit but was derived from two spring tetraploid wheat genotypes, the durum wheat variety ‘Lebsock’ and Persian wheat accession PI 94749.  Genetic analysis revealed that Lebsock carried the dominant Vrn-A1 and recessive vrn-B1 alleles, whereas PI 94749 had the recessive vrn-A1 and dominant Vrn-B1 alleles. The Vrn-A1 allele in Lebsock was the same as the Vrn-A1c allele previously reported in hexaploid wheat. No differences existed between the vrn-B1 and Vrn-B1 alleles except that a 5,463-bp insertion was detected in the 5’-untranslated region of the Vrn-B1 allele. This insertion was a novel retrotransposon (designated as retrotrans_VRN), which was flanked by a 5-bp target site duplication and contained primer binding site and polypurine tract motifs, a 325-bp long terminal repeat, and an open reading frame encoding 1,231 amino acids. The insertion of retrotrans_VRN resulted in expression of Vrn-B1 without vernalization. Retrotrans_VRN is prevalent among Persian wheat accessions, less prevalent among Emmer wheat accessions, and rarely found in other tetraploid wheat sub-species.