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

Sayaka Tanaka, Kentaro Yoshida, Kazuhiro Sato, and Shigeo Takumi

BMC Genomics 21, 246 (2020).


Published:March 2020



Triticum and Aegilops diploid species have morphological and genetic diversity and are crucial genetic resources for wheat breeding. According to the chromosomal pairing-affinity of these species, their genome nomenclatures have been defined. However, evaluations of genome differentiation based on genome-wide nucleotide variations are still limited, especially in the 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 the genome differentiation of these diploid species, we first performed RNA-seq-based polymorphic analyses for C, M, and N genomes, and then expanded the analysis to include the 12 diploid species of Triticum and Aegilops.


Genetic divergence of the exon regions throughout 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 following Ae. speltoides, the putative B genome donor of common wheat. In the phylogenetic trees derived from the nuclear and chloroplast genome-wide polymorphism data, the C, D, M, N, U, and S genome species were connected with short internal branches, suggesting that these diploid species emerged during a relatively short period in the evolutionary process. The highly consistent nuclear and chloroplast phylogenetic topologies indicated that nuclear and chloroplast genomes of the diploid Triticum and Aegilops species coevolved after their diversification into each genome, accounting for most of the genome differentiation among the diploid species.

Identification of a hard kernel texture line of synthetic allohexaploid wheat reducing the puroindoline accumulation on the D genome from Aegilops tauschii

Yuka Miki, Tatsuya M. Ikeda, Kentaaro Yoshida, and Shigeo Takumi

Journal of Cereal Science,Volume 93:102964



Grain hardness is an important factor for wheat breeding. Generally, the grain hardness of hexaploid wheat is determined by two puroindoline (PIN) genes, Pina-D1 and Pinb-D1, at the Hardness locus on chromosome 5D. Here, the grain hardness of 55 synthetic wheat lines from crosses between a durum wheat cultivar and 55 Ae. tauschii accessions were examined, and nucleotide sequence variation in Pina-Dtau1 and Pinb-Dtau1 was analyzed using the Ae. tauschii accessions. Most synthetic wheat lines showed a soft texture with smoothly rounded starch granules, whereas one exceptional line exhibited a hard texture with starch granules that tightly adhered to the matrix proteins and reduced PINA and PINB protein accumulation. The parental Ae. tauschii accession of the hard-textured synthetic line has smoothly rounded starch granules and abundant PIN accumulation in the endosperm.

Any genetic change that occurred at the Pin loci was transmitted from the parental Ae. tauschii accession, but the Pina and Pinb transcription was decreased in the hard-textured synthetic line. Therefore, any genetic and/or epigenetic modification in the process of allopolyploidization might have affected the PIN accumulation in synthetic hexaploid wheat lines.

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