title: The occurrence of spring forms in tetraploid Timopheevi wheat is associated with variation in the first intron of the VRN-A1 gene.
abstract: BACKGROUND
  Triticum araraticum and Triticum timopheevii are tetraploid species of the Timopheevi group. The former includes both winter and spring forms with a predominance of winter forms, whereas T. timopheevii is considered a spring species. In order to clarify the origin of the spring growth habit in T. timopheevii, allelic variability of the VRN-1 gene was investigated in a set of accessions of both tetraploid species, together with the diploid species Ae. speltoides, presumed donor of the G genome to these tetraploids.
  
  
  RESULTS
  The promoter region of the VRN-A1 locus in all studied tetraploid accessions of both T. araraticum and T. timopheevii represents the previously described allele VRN-A1f with a 50 bp deletion near the start codon. Three additional alleles were identified namely, VRN-A1f-del, VRN-A1f-ins and VRN-A1f-del/ins, which contained large mutations in the first (1st) intron of VRN-A1. The first allele, carrying a deletion of 2.7 kb in a central part of intron 1, occurred in a few accessions of T. araraticum and no accessions of T. timopheevii. The VRN-A1f-ins allele, containing the insertion of a 0.4 kb MITE element about 0.4 kb upstream from the start of intron 1, and allele VRN-A1f-del/ins having this insertion coupled with a deletion of 2.7 kb are characteristic only for T. timopheevii. Allelic variation at the VRN-G1 locus includes the previously described allele VRN-G1a (with the insertion of a 0.2 kb MITE in the promoter) found in a few accessions of both tetraploid species. We showed that alleles VRN-A1f-del and VRN-G1a have no association with the spring growth habit, while in all accessions of T. timopheevii this habit was associated with the dominant VRN-A1f-ins and VRN-A1f-del/ins alleles. None of the Ae. speltoides accessions included in this study had changes in the promoter or 1stintron regions of VRN-1 which might confer a spring growth habit. The VRN-1 promoter sequences analyzed herein and downloaded from databases have been used to construct a phylogram to assess the time of divergence of Ae. speltoides in relation to other wheat species.
  
  
  CONCLUSIONS
  Among accessions of T. araraticum, the preferentially winter predecessor of T. timopheevii, two large mutations were found in both VRN-A1 and VRN-G1 loci (VRN-A1f-del and VRN-G1a) that were found to have no effect on vernalization requirements. Spring tetraploid T. timopheevii had one VRN-1 allele in common for two species (VRN-G1a), and two that were specific (VRN-A1f-ins, VRN-A1f-del/ins). The latter alleles include mutations in the 1stintron of VRN-A1 and also share a 0.4 kb MITE insertion near the start of intron 1. We suggested that this insertion resulted in a spring growth habit in a progenitor of T. timopheevii which has probably been selected during subsequent domestication. The phylogram constructed on the basis of the VRN-1 promoter sequences confirmed the early divergence (~3.5 MYA) of the ancestor(s) of the B/G genomes from Ae. speltoides.
authors.affiliation: The Federal Research Center "Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences", Lavrentiev ave. 10, Novosibirsk, 630090, Russia. atos@bionet.nsc.ru.
authors.forename: Andrey Borisovich
authors.initials: AB
authors.lastname: Shcherban
authors.affiliation: Institute of General Genetics of the Russian Academy of Sciences, Gubkina str., 3, Moscow, 119991, Russia.
authors.forename: Aleksandra Aleksandrovna
authors.initials: AA
authors.lastname: Schichkina
authors.affiliation: The Federal Research Center "Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences", Lavrentiev ave. 10, Novosibirsk, 630090, Russia.
authors.forename: Elena Artemovna
authors.initials: EA
authors.lastname: Salina
mesh_terms: D000483:Alleles; D014644:Genetic Variation; D007438:Introns / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D006109:Poaceae / Q000235:genetics / Q000254:growth & development; D011401:Promoter Regions, Genetic; D012621:Seasons; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D057891:Tetraploidy; D014908:Triticum / Q000235:genetics* / Q000254:growth & development*
chemical_list: D010940:Plant Proteins
keywords: Aegilops; Allelic variation; First intron; Promoter; Triticum; VRN-1 gene; Vernalization