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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.
Theor Appl Genet. 2014 Feb; 127(2):261-71.TA

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. 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.

Authors+Show Affiliations

Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe, 657-8501, Japan.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

24158251

Citation

Iehisa, Julio Cesar Masaru, 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." TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik, vol. 127, no. 2, 2014, pp. 261-71.
Iehisa JC, 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. 2014;127(2):261-71.
Iehisa, J. C., Shimizu, A., Sato, K., Nishijima, R., Sakaguchi, K., Matsuda, R., Nasuda, S., & Takumi, S. (2014). Genome-wide marker development for the wheat D genome based on single nucleotide polymorphisms identified from transcripts in the wild wheat progenitor Aegilops tauschii. TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik, 127(2), 261-71. https://doi.org/10.1007/s00122-013-2215-5
Iehisa JC, 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. 2014;127(2):261-71. PubMed PMID: 24158251.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide marker development for the wheat D genome based on single nucleotide polymorphisms identified from transcripts in the wild wheat progenitor Aegilops tauschii. 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, Y1 - 2013/10/25/ PY - 2013/07/20/received PY - 2013/10/14/accepted PY - 2013/10/26/entrez PY - 2013/10/26/pubmed PY - 2014/9/23/medline SP - 261 EP - 71 JF - TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik JO - Theor Appl Genet VL - 127 IS - 2 N2 - 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. 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. SN - 1432-2242 UR - https://www.unboundmedicine.com/medline/citation/24158251/Genome_wide_marker_development_for_the_wheat_D_genome_based_on_single_nucleotide_polymorphisms_identified_from_transcripts_in_the_wild_wheat_progenitor_Aegilops_tauschii_ L2 - https://dx.doi.org/10.1007/s00122-013-2215-5 DB - PRIME DP - Unbound Medicine ER -