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Genome-wide identification of novel genetic markers from RNA sequencing assembly of diverse Aegilops tauschii accessions.
Mol Genet Genomics. 2016 Aug; 291(4):1681-94.MG

Abstract

The wild species in the Triticeae tribe are tremendous resources for crop breeding due to their abundant natural variation. However, their huge and highly repetitive genomes have hindered the establishment of physical maps and the completeness of their genome sequences. To develop molecular markers for the efficient utilization of their valuable traits while avoiding their genome complexity, we assembled RNA sequences of ten representative accessions of Aegilops tauschii, the progenitor of the wheat D genome, and estimated single nucleotide polymorphisms (SNPs) and insertions/deletions (indels). The deduced unigenes were anchored to the chromosomes of Ae. tauschii and barley. The SNPs and indels in the anchored unigenes, covering entire chromosomes, were sufficient for linkage map construction, even in combinations between the genetically closest accessions. Interestingly, the resolution of SNP and indel distribution on barley chromosomes was slightly higher than on Ae. tauschii chromosomes. Since barley chromosomes are regarded as virtual chromosomes of Triticeae species, our strategy allows capture of genetic markers arranged on the chromosomes in order based on the conserved synteny. The resolution of these genetic markers will be comparable to that of the Ae. tauschii whose draft genome sequence is available. Our procedure should be applicable to marker development for Triticeae species, which have no draft sequences available.

Authors+Show Affiliations

Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, Japan.Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, Japan. kentaro.yoshida@port.kobe-u.ac.jp.Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan.Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan.Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, Japan.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

27142109

Citation

Nishijima, Ryo, et al. "Genome-wide Identification of Novel Genetic Markers From RNA Sequencing Assembly of Diverse Aegilops Tauschii Accessions." Molecular Genetics and Genomics : MGG, vol. 291, no. 4, 2016, pp. 1681-94.
Nishijima R, Yoshida K, Motoi Y, et al. Genome-wide identification of novel genetic markers from RNA sequencing assembly of diverse Aegilops tauschii accessions. Mol Genet Genomics. 2016;291(4):1681-94.
Nishijima, R., Yoshida, K., Motoi, Y., Sato, K., & Takumi, S. (2016). Genome-wide identification of novel genetic markers from RNA sequencing assembly of diverse Aegilops tauschii accessions. Molecular Genetics and Genomics : MGG, 291(4), 1681-94. https://doi.org/10.1007/s00438-016-1211-2
Nishijima R, et al. Genome-wide Identification of Novel Genetic Markers From RNA Sequencing Assembly of Diverse Aegilops Tauschii Accessions. Mol Genet Genomics. 2016;291(4):1681-94. PubMed PMID: 27142109.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide identification of novel genetic markers from RNA sequencing assembly of diverse Aegilops tauschii accessions. AU - Nishijima,Ryo, AU - Yoshida,Kentaro, AU - Motoi,Yuka, AU - Sato,Kazuhiro, AU - Takumi,Shigeo, Y1 - 2016/05/03/ PY - 2016/03/20/received PY - 2016/04/21/accepted PY - 2016/5/5/entrez PY - 2016/5/5/pubmed PY - 2017/1/31/medline KW - Aegilops tauschii KW - DNA markers KW - Hordeum vulgare KW - RNA sequencing KW - Synteny SP - 1681 EP - 94 JF - Molecular genetics and genomics : MGG JO - Mol Genet Genomics VL - 291 IS - 4 N2 - The wild species in the Triticeae tribe are tremendous resources for crop breeding due to their abundant natural variation. However, their huge and highly repetitive genomes have hindered the establishment of physical maps and the completeness of their genome sequences. To develop molecular markers for the efficient utilization of their valuable traits while avoiding their genome complexity, we assembled RNA sequences of ten representative accessions of Aegilops tauschii, the progenitor of the wheat D genome, and estimated single nucleotide polymorphisms (SNPs) and insertions/deletions (indels). The deduced unigenes were anchored to the chromosomes of Ae. tauschii and barley. The SNPs and indels in the anchored unigenes, covering entire chromosomes, were sufficient for linkage map construction, even in combinations between the genetically closest accessions. Interestingly, the resolution of SNP and indel distribution on barley chromosomes was slightly higher than on Ae. tauschii chromosomes. Since barley chromosomes are regarded as virtual chromosomes of Triticeae species, our strategy allows capture of genetic markers arranged on the chromosomes in order based on the conserved synteny. The resolution of these genetic markers will be comparable to that of the Ae. tauschii whose draft genome sequence is available. Our procedure should be applicable to marker development for Triticeae species, which have no draft sequences available. SN - 1617-4623 UR - https://www.unboundmedicine.com/medline/citation/27142109/Genome_wide_identification_of_novel_genetic_markers_from_RNA_sequencing_assembly_of_diverse_Aegilops_tauschii_accessions_ L2 - https://doi.org/10.1007/s00438-016-1211-2 DB - PRIME DP - Unbound Medicine ER -