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

Julio Cesar Masaru Iehisa, Akifumi Shimizu, Kazuhiro Sato, Ryo Nishijima, Kouhei Sakaguchi, Ryusuke Matsuda, Shuhei Nasuda, Shigeo Takumi

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

Key message 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.

Original languageEnglish
Pages (from-to)261-271
Number of pages11
JournalTheoretical And Applied Genetics
Volume127
Issue number2
DOIs
Publication statusPublished - 2014

Fingerprint

Aegilops tauschii
single nucleotide polymorphism
Triticum
Single Nucleotide Polymorphism
Genome
wheat
genome
hexaploidy
Transcriptome
Chromosomes
chromosomes
Diploidy
transcriptome
diploidy
genetic polymorphism
DNA Shuffling
High-Throughput Nucleotide Sequencing
cultivars
transcriptomics
Computer Simulation

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Genetics
  • Biotechnology
  • Medicine(all)

Cite this

Genome-wide marker development for the wheat D genome based on single nucleotide polymorphisms identified from transcripts in the wild wheat progenitor Aegilops tauschii. / Iehisa, Julio Cesar Masaru; Shimizu, Akifumi; Sato, Kazuhiro; Nishijima, Ryo; Sakaguchi, Kouhei; Matsuda, Ryusuke; Nasuda, Shuhei; Takumi, Shigeo.

In: Theoretical And Applied Genetics, Vol. 127, No. 2, 2014, p. 261-271.

Research output: Contribution to journalArticle

Iehisa, Julio Cesar Masaru ; Shimizu, Akifumi ; Sato, Kazuhiro ; Nishijima, Ryo ; Sakaguchi, Kouhei ; Matsuda, Ryusuke ; Nasuda, Shuhei ; Takumi, Shigeo. / Genome-wide marker development for the wheat D genome based on single nucleotide polymorphisms identified from transcripts in the wild wheat progenitor Aegilops tauschii. In: Theoretical And Applied Genetics. 2014 ; Vol. 127, No. 2. pp. 261-271.
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AU - Iehisa, Julio Cesar Masaru

AU - Shimizu, Akifumi

AU - Sato, Kazuhiro

AU - Nishijima, Ryo

AU - Sakaguchi, Kouhei

AU - Matsuda, Ryusuke

AU - Nasuda, Shuhei

AU - Takumi, Shigeo

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AB - Key message 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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