Conserved regulatory elements identified from a comparative puroindoline gene sequence survey of Triticum and Aegilops diploid taxa

Kernel texture (‘hardness’) is an important trait that determines end-use quality of wheat (Triticum aestivum L. and Triticum turgidum ssp. durum [Desf.] Husn.). Variation in texture is associated with the presence/absence or sequence polymorphism of two proteins, puroindoline a and puroindoline b. This work describes the flanking and coding region sequences of puroindoline genes from 25 accessions representing wild diploid taxa of the Triticeae related to the three genomes of T. aestivum. Analysis of variation at the nucleotide level included hard and soft T. aestivum wheat cultivars. Various degrees of insertions/deletions and point mutations were found, that did not affect the overall sequence structure identity. Nucleotide sequence comparisons and database searches facilitated the identification of the 5′ proximal regulating regions, revealing the presence of several putative control elements. An absolute conservation of some known regulatory elements for tissue specificity was observed, while different rates of conservation of reiterated motifs with possible enhancer functions, and the exclusive presence of some elements either in puroindoline a or puroindoline b were also found. A total of 24 new puroindoline alleles (unique sequences) were identified. Despite some primary structure variation, the main features of puroindolines, i.e. the signal peptide, the cysteine backbone, the tryptophan-rich domain, the hydrophobicity and basic identity of the proteins were all conserved.