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Genome-wide marker development for the wheat D genome based on single nucleotide polymorphisms identified from transcripts in the wild wheat progenitor Aegilops tauschii

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13,347 high-confidence SNPs were discovered through transcriptome sequencing of Aegilops tauschii, which are useful for genomic analysis and molecular breeding of hexaploid wheat.

Abstract

In organisms with large and complex genomes, such as wheat, RNA-seq analysis is cost-effective for discovery of genome-wide single nucleotide polymorphisms (SNPs). In this study, deep sequencing of the spike transcriptome from two Aegilops tauschii accessions representing two major lineages led to the discovery of 13,347 high-confidence (HC) SNPs in 4,872 contigs. After removing redundant SNPs detected in the leaf transcriptome from the same accessions in an earlier study, 10,589 new SNPs were discovered. In total, 5,642 out of 5,808 contigs with HC SNPs were assigned to the Ae. tauschii draft genome sequence. On average, 732 HC polymorphic contigs were mapped in silico to each Ae. tauschii chromosome. Based on the polymorphic data, we developed markers to target the short arm of chromosome 2D and validated the polymorphisms using 20 Ae. tauschii accessions. Of the 29 polymorphic markers, 28 were successfully mapped to 2DS in the diploid F2 population of Ae. tauschii. Among ten hexaploid wheat lines, which included wheat synthetics and common wheat cultivars, 25 of the 43 markers were polymorphic. In the hexaploid F2 population between a common wheat cultivar and a synthetic wheat line, 23 of the 25 polymorphic markers between the parents were available for genotyping of the F2 plants and 22 markers mapped to chromosome 2DS. These results indicate that molecular markers that developed from polymorphisms between two distinct lineages of Ae. tauschii might be useful for analysis not only of the diploid, but also of the hexaploid wheat genome.

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Acknowledgments

The authors would like to thank Ms. Yuka Motoi at Okayama University for technical assistance. This work was supported by a grant from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan (Grant-in-Aid for Scientific Research (B) No. 25292008) to ST, and by MEXT as part of the Joint Research Program implemented at the Institute of Plant Science and Resources, Okayama University in Japan.

Conflict of interest

The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe, 657-8501, Japan

    Julio Cesar Masaru Iehisa, Ryo Nishijima, Kouhei Sakaguchi, Ryusuke Matsuda & Shigeo Takumi

  2. Department of Biological Resources Management, School of Environmental Science, University of Shiga Prefecture, Hikone, 522-8533, Japan

    Akifumi Shimizu

  3. Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan

    Kazuhiro Sato

  4. Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan

    Shuhei Nasuda

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  1. Julio Cesar Masaru Iehisa
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  2. Akifumi Shimizu
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  3. Kazuhiro Sato
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Correspondence to Shigeo Takumi.

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Communicated by X. Xia.

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Iehisa, J.C.M., Shimizu, A., Sato, K. et al. Genome-wide marker development for the wheat D genome based on single nucleotide polymorphisms identified from transcripts in the wild wheat progenitor Aegilops tauschii . Theor Appl Genet 127, 261–271 (2014). https://doi.org/10.1007/s00122-013-2215-5

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