SRA

Two wild diploid wheat species, Triticum monococcum ssp. aegilopoides and T. urartu, are closely related, and respectively harbour the Am and A genomes. The A-genome donor of tetraploid and common wheat is T. urartu, and T. monococcum ssp. monococcum is the cultivated form derived from the wild einkorn wheat T. monococcum ssp. aegilopoides. Although T. monococcum ssp. aegilopoides has been a useful genetic resource for wheat breeding, genome-wide molecular markers have not been sufficiently developed in the subspecies aegilopoides. Here, we obtained the genome-wide polymorphisms such as single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) from the RNA sequencing (RNA-seq) data of leaf transcripts in 15 accessions of the two diploid wheat species. The detected SNPs and indels covered the entire chromosomes, discriminating between between T. monococcum ssp. aegilopoides and ssp. monococcum that had recently diverged. The polymorphism information contributed to compare the genetic diversity of einkorn wheat with those of two related diploid Aegilops species, Ae. tauschii and Ae. umbellulata. Cleaved amplified polymorphic sequence (CAPS) markers converted from the SNP data were efficiently developed to confirm the chromosome addition of the subspecies aegilopoides chromosomes to tetraploid wheat in nascent allohexaploid lines with AABBAmAm genome. In addition, the CAPS markers were available for linkage map construction in mapping population of the subspecies aegilopoides accessions. The SNP and indel data are applicable to further genetic studies in einkorn wheat.