Diploid genome differentiation conferred by RNA sequencing-based survey of genome-wide polymorphisms throughout homoeologous loci in Triticum and Aegilops

Wheat relatives of Triticum and Aegilops diploid species have morphological and genetic diversity, being crucial genetic resources of wheat breeding. According to the chromosomal pairing-affinity of these species, their genome nomenclatures have been defined. However, studies for evaluation of genome differentiation based on genome-wide nucleotide variations are still limited, especially in three genomes of the genus Aegilops, Ae. caudata L. (CC genome), Ae. comosa Sibth. et Sm. (MM genome) and Ae. uniaristata Vis. (NN genome). To reveal genome differentiation of these diploid species, we first performed RNA-seq based polymorphic analyses for C, M, and N genomes, and then expanded into the analyses of the 12 diploid species of Triticum and Aegilops. Genetic divergence of the exon regions through the entire chromosomes in the M and N genomes was larger than that between A- and Am-genomes. Ae. caudata had the second highest genetic diversity in the tested Triticum and Aegilops diploid species.