Genome-wide polymorphisms from RNA sequencing assembly of leaf transcripts facilitate phylogenetic analysis and molecular marker development in wild einkorn wheat

  • Asami Michikawa
  • Kentaro YoshidaEmail author
  • Moeko Okada
  • Kazuhiro Sato
  • Shigeo TakumiEmail author
Original Article


A survey of genome-wide polymorphisms between closely related species is required to understand the molecular basis of the evolutionary differentiation of their genomes. Two wild diploid wheat species, namely Triticum monococcum ssp. aegilopoides and T. urartu, are closely related and harbour the Am and A genomes, respectively. 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 subspecies aegilopoides. Although subspecies aegilopoides has been a useful genetic resource in wheat breeding, genome-wide molecular markers for this subspecies have not been sufficiently developed. Here, we describe the detection of genome-wide polymorphisms such as single-nucleotide polymorphisms (SNPs) and insertions/deletions (indels) from RNA sequencing (RNA-seq) data of leaf transcripts in 15 accessions of the two diploid wheat species. The SNPs and indels, detected using the A genome of common wheat as the reference genome, covered the entire chromosomes of these species. The polymorphism information facilitated a comparison of the genetic diversity of einkorn wheat with that of two related diploid Aegilops species, namely, Ae. tauschii and Ae. umbellulata. Cleaved amplified polymorphic sequence (CAPS) markers converted from the SNP data were efficiently developed to confirm the addition of aegilopoides subspecies chromosomes to tetraploid wheat in nascent allohexaploid lines with AABBAmAm genomes. In addition, the CAPS markers permitted linkage map construction in mapping populations of aegilopoides subspecies accessions. Therefore, these RNA-seq data provide information for further breeding of closely related species with no reference genome sequence data.


Allopolyploidization Chromosomal synteny Molecular marker Single-nucleotide polymorphism Wheat 



The authors thank Drs. N. Watanabe and K. Murai for providing seeds of two einkorn wheat accessions. Seeds of the other diploid wheat species used in this study were supplied by the National BioResource Project-Wheat, Japan ( Computations for RNA sequence assembly of reads were performed on the NIG supercomputer at the ROIS National Institute of Genetics, Japan.


This work was supported by Grant-in-Aid for Scientific Research (B) No. 16H04862 from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan to ST, by Grant-in-Aid for Scientific Research on Innovative Areas No. 17H05842 from the MEXT to ST, and by the MEXT as part of a Joint Research Program implemented at the Institute of Plant Science and Resources, Okayama University, Japan. KY was supported by JST, PRESTO (No. JPMJPR15QB).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest.

Ethical standards

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

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Supplementary material 1 (PDF 74 kb)
438_2019_1581_MOESM2_ESM.pdf (49 kb)
Supplementary material 2 (PDF 48 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Graduate School of Agricultural ScienceKobe UniversityKobeJapan
  2. 2.Institute of Plant Science and ResourcesOkayama UniversityKurashikiJapan

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