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Discovery of high-confidence single nucleotide polymorphisms from large-scale de novo analysis of leaf transcripts of Aegilops tauschii, a wild wheat progenitor.
DNA Res. 2012 Dec; 19(6):487-97.DR

Abstract

Construction of high-resolution genetic maps is important for genetic and genomic research, as well as for molecular breeding. Single nucleotide polymorphisms (SNPs) are the predominant class of genetic variation and can be used as molecular markers. Aegilops tauschii, the D-genome donor of common wheat, is considered a valuable genetic resource for wheat improvement. Our previous study implied that Ae. tauschii accessions can be genealogically divided into two major lineages. In this study, the transcriptome of two Ae. tauschii accessions from each lineage, lineage 1 (L1) and 2 (L2), was sequenced, yielding 9435 SNPs and 739 insertion/deletion polymorphisms (indels) after de novo assembly of the reads. Based on 36 contig sequences, 31 SNPs and six indels were validated on 20 diverse Ae. tauschii accessions. Because almost all of the SNP markers were polymorphic between L1 and L2, and the D-genome donor of common wheat is presumed to belong to L2, these markers are available for D-genome typing in crosses between common wheat varieties and L1-derived synthetic wheat. Due to the conserved synteny between wheat and barley chromosomes, the high-density expressed sequence tag barley map and the hypothetical gene order in barley can be applied to develop markers on target chromosomal regions in wheat.

Authors+Show Affiliations

Laboratory of Plant Genetics, 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 available

Pub Type(s)

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

Language

eng

PubMed ID

23125207

Citation

Iehisa, Julio Cesar Masaru, et al. "Discovery of High-confidence Single Nucleotide Polymorphisms From Large-scale De Novo Analysis of Leaf Transcripts of Aegilops Tauschii, a Wild Wheat Progenitor." DNA Research : an International Journal for Rapid Publication of Reports On Genes and Genomes, vol. 19, no. 6, 2012, pp. 487-97.
Iehisa JC, Shimizu A, Sato K, et al. Discovery of high-confidence single nucleotide polymorphisms from large-scale de novo analysis of leaf transcripts of Aegilops tauschii, a wild wheat progenitor. DNA Res. 2012;19(6):487-97.
Iehisa, J. C., Shimizu, A., Sato, K., Nasuda, S., & Takumi, S. (2012). Discovery of high-confidence single nucleotide polymorphisms from large-scale de novo analysis of leaf transcripts of Aegilops tauschii, a wild wheat progenitor. DNA Research : an International Journal for Rapid Publication of Reports On Genes and Genomes, 19(6), 487-97. https://doi.org/10.1093/dnares/dss028
Iehisa JC, et al. Discovery of High-confidence Single Nucleotide Polymorphisms From Large-scale De Novo Analysis of Leaf Transcripts of Aegilops Tauschii, a Wild Wheat Progenitor. DNA Res. 2012;19(6):487-97. PubMed PMID: 23125207.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Discovery of high-confidence single nucleotide polymorphisms from large-scale de novo analysis of leaf transcripts of Aegilops tauschii, a wild wheat progenitor. AU - Iehisa,Julio Cesar Masaru, AU - Shimizu,Akifumi, AU - Sato,Kazuhiro, AU - Nasuda,Shuhei, AU - Takumi,Shigeo, Y1 - 2012/11/02/ PY - 2012/11/6/entrez PY - 2012/11/6/pubmed PY - 2013/8/22/medline SP - 487 EP - 97 JF - DNA research : an international journal for rapid publication of reports on genes and genomes JO - DNA Res VL - 19 IS - 6 N2 - Construction of high-resolution genetic maps is important for genetic and genomic research, as well as for molecular breeding. Single nucleotide polymorphisms (SNPs) are the predominant class of genetic variation and can be used as molecular markers. Aegilops tauschii, the D-genome donor of common wheat, is considered a valuable genetic resource for wheat improvement. Our previous study implied that Ae. tauschii accessions can be genealogically divided into two major lineages. In this study, the transcriptome of two Ae. tauschii accessions from each lineage, lineage 1 (L1) and 2 (L2), was sequenced, yielding 9435 SNPs and 739 insertion/deletion polymorphisms (indels) after de novo assembly of the reads. Based on 36 contig sequences, 31 SNPs and six indels were validated on 20 diverse Ae. tauschii accessions. Because almost all of the SNP markers were polymorphic between L1 and L2, and the D-genome donor of common wheat is presumed to belong to L2, these markers are available for D-genome typing in crosses between common wheat varieties and L1-derived synthetic wheat. Due to the conserved synteny between wheat and barley chromosomes, the high-density expressed sequence tag barley map and the hypothetical gene order in barley can be applied to develop markers on target chromosomal regions in wheat. SN - 1756-1663 UR - https://www.unboundmedicine.com/medline/citation/23125207/Discovery_of_high_confidence_single_nucleotide_polymorphisms_from_large_scale_de_novo_analysis_of_leaf_transcripts_of_Aegilops_tauschii_a_wild_wheat_progenitor_ L2 - https://academic.oup.com/dnaresearch/article-lookup/doi/10.1093/dnares/dss028 DB - PRIME DP - Unbound Medicine ER -