Characterization of the waxy gene in diploid Triticum L. and Aegilops L. species and its geographic distribution

Waxy gene plays a key role for amylose synthesis in wheat seeds. The study evaluated the Waxy gene variability in 59 accessions of six diploid Triticum and Aegilops species. The percentages of variable sites, singleton variable sites, and parsimony informative sites were 16.38, 5.59, and 10.79 %, respectively. A total of 22 amino acid changes in the transit peptide and the remaining in the mature protein were observed. Moreover, 17 amino acid changes between Triticum and Aegilops species were also detected. Specially, Gla 14 and Phe 153 was observed in diploid Triticum, compared with Thr 14 and Tyr 153 in diploid Aegilops. Two types of amino acids, Gla 5/Val 5 and Ile 140/Val 140, were identified in T. urartu, as well as Val 22/Phe 22, Thr 52/Lys 52, and Gln 54/delete in A. tauschii. The insertion/deletions (InDels) had high frequency in intron region, but very low in transit peptide and exon region. Neighbour-joining tree showed that 146 sequences from 23 species could be clustered into eight groups with the species characterizations. The Wx-B1 of polyploid Triticum were grouped with A. sharonensis, A. longissima, A. searsii, A. speltoides, while Wx-D1 of T. aestivum and T. spelta together with A. umbellulata, A. markgrafii, A. comosa, and A. tauschii. The Wx-A1 of polyploid Triticum were separated clearly with the diploid species. The Wx-B1 could be divided into two subgroups and maybe had two phylogenetic origins, but most of them were related to A. speltoides. Waxy gene of A. tauschii also had two subgroups, and the sequences from southern Caspian (Mazandaran, Iran) were more closed with Wx-D1. The variability of 5′ Un-Translation Region (UTR) of waxy was stronger than intron and exon region based on genetic distance. Phylogeography analysis showed that geography affected strongly the distribution of all accessions along the north–south axis based on the partial open reading fragment (ORF) of waxy gene, A. speltoides and A. longissima along the west–east axis and north–south axis based on exon, and A. tauschii along the west–east axis based on 5′ UTR, respectively. Our results suggest that diploid Triticum and Aegilops have new waxy gene resources; waxy gene could play a more important role in genetic exploitation, genetic relationship evaluation and phylogeography investigation.