Single nucleotide polymorphisms in Pina gene sequences of some diploid species of the genus Aegilops

Species of the genus Aegilops L. are a genetic resource for transferring new genes, in particular new alleles of puroindoline genes, into common wheat. Puroindolines a and b are low molecular weight proteins that determine the grain endosperm texture in Triticum aestivum and related species. The aim of the study was to analyze frequencies of single nucleotide polymorphisms (SNPs) in the coding sequences of the Pina gene in diploid Aegilops species in comparison with the reference sequence of the T. aestivum variety Chinese Spring (CS) among sequences available in the NCBI database.Sequences of the Pina gene of diploid Aegilops species were selected from the NCBI database, comprising 32 sequences of Ae. speltoides, 8 sequences of Ae. bicornis, 5 sequences of Ae. sharonensis, 6 sequences of Ae. searsii, 8 sequences of Ae. caudata, 10 sequences of Ae. comosa, and 14 sequences of Ae. umbellulata. The sequence of the puroindoline a gene (the Pina-D1a allele) DQ363911.1 of CS was used as a reference. The sequences were aligned using the MEGA11 software.Among the sequences of the Pina gene of Ae. speltoides, Ae. bicornis, Ae. sharonensis, Ae. searsii, Ae. caudata, Ae. comosa, and Ae. umbellulata, a total of 61 SNPs were detected in the coding sequence. Different species showed between 11 and 30 SNPs. The Aegilops species were characterized with respect to the frequencies of nucleotide substitutions. In the majority of Aegilops species, nonsynonymous substitutions predominate. SNPs at two positions occur in all the diploid Aegilops species, and seven SNPs are characteristic of only the species from the section Sitopsis. Among the Aegilops species, only in Ae. searsii there are species-specific SNPs that are fixed in all its sequences presented in the database.