Novel haplotype description and structural background of the eventual functional significance of the barley beta-amylase gene intron III rearrangements.

To extend the knowledge on the haplotype variability of the Bmy1 gene, region of the intron III was sequenced in a set of 20 Latvian accessions and Danish variety Maja, the data were compared to the previously reported allelic variants of the structural gene. Taking into account the polymorphisms of 59 loci and the microsatellite (MS) motif, 11 Latvian varieties turned out to have haplotype similar to cultivar Adorra, 1 - to Haruna Nijo, and 8 - to the newly described Abava Bmy1 intron III haplotype. High level of polymorphisms of (TG)(m) as well as (G)(n) component of MS was revealed for all the haplotypes studied. We conclude that the MS motif rather than the MS size length polymorphism correlates with mutations in the coding region of the beta-amylase gene. Five graphical haplotype-specific intron III structures were constructed on the basis of the co-localization of the transcription factor binding sites (TFBSs), remnants of the transposable elements, and intron III polymorphic loci. Inter- and intrahaplotype variability was analyzed on the eventual functional significance of the Bmy1 intron III rearrangements. Novel data on the intron III nucleotide sequences of the Bmy1 gene were deposited in the GenBank (http://www.ncbi.nlm.nih.gov/) under accession numbers DQ316895-DQ316905.