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RNA-seq analysis reveals considerable genetic diversity and provides genetic markers saturating all chromosomes in the diploid wild wheat relative Aegilops umbellulata.
BMC Plant Biol. 2018 Nov 08; 18(1):271.BP

Abstract

BACKGROUND

Aegilops umbellulata Zhuk. (2n = 14), a wild diploid wheat relative, has been the source of trait improvement in wheat breeding. Intraspecific genetic variation of Ae. umbellulata, however, has not been well studied and the genomic information in this species is limited.

RESULTS

To develop novel genetic markers distributed over all chromosomes of Ae. umbellulata and to evaluate its genetic diversity, we performed RNA sequencing of 12 representative accessions and reconstructed transcripts by de novo assembly of reads for each accession. A large number of single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) were obtained and anchored to the pseudomolecules of Ae. tauschii and barley (Hordeum vulgare L.), which were regarded as virtual chromosomes of Ae. umbellulata. Interestingly, genetic diversity in Ae. umbellulata was higher than in Ae. tauschii, despite the narrow habitat of Ae. umbellulata. Comparative analyses of nucleotide polymorphisms between Ae. umbellulata and Ae. tauschii revealed no clear lineage differentiation and existence of alleles with rarer frequencies predominantly in Ae. umbellulata, with patterns clearly distinct from those in Ae. tauschii.

CONCLUSIONS

The anchored SNPs, covering all chromosomes, provide sufficient genetic markers between Ae. umbellulata accessions. The alleles with rarer frequencies might be the main source of the high genetic diversity in Ae. umbellulata.

Authors+Show Affiliations

Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada-ku, Kobe, 657-8501, Japan.Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada-ku, Kobe, 657-8501, Japan. kentaro.yoshida@port.kobe-u.ac.jp.Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada-ku, Kobe, 657-8501, Japan.Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada-ku, Kobe, 657-8501, Japan.Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan.Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan.Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada-ku, Kobe, 657-8501, Japan.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

30409135

Citation

Okada, Moeko, et al. "RNA-seq Analysis Reveals Considerable Genetic Diversity and Provides Genetic Markers Saturating All Chromosomes in the Diploid Wild Wheat Relative Aegilops Umbellulata." BMC Plant Biology, vol. 18, no. 1, 2018, p. 271.
Okada M, Yoshida K, Nishijima R, et al. RNA-seq analysis reveals considerable genetic diversity and provides genetic markers saturating all chromosomes in the diploid wild wheat relative Aegilops umbellulata. BMC Plant Biol. 2018;18(1):271.
Okada, M., Yoshida, K., Nishijima, R., Michikawa, A., Motoi, Y., Sato, K., & Takumi, S. (2018). RNA-seq analysis reveals considerable genetic diversity and provides genetic markers saturating all chromosomes in the diploid wild wheat relative Aegilops umbellulata. BMC Plant Biology, 18(1), 271. https://doi.org/10.1186/s12870-018-1498-8
Okada M, et al. RNA-seq Analysis Reveals Considerable Genetic Diversity and Provides Genetic Markers Saturating All Chromosomes in the Diploid Wild Wheat Relative Aegilops Umbellulata. BMC Plant Biol. 2018 Nov 8;18(1):271. PubMed PMID: 30409135.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - RNA-seq analysis reveals considerable genetic diversity and provides genetic markers saturating all chromosomes in the diploid wild wheat relative Aegilops umbellulata. AU - Okada,Moeko, AU - Yoshida,Kentaro, AU - Nishijima,Ryo, AU - Michikawa,Asami, AU - Motoi,Yuka, AU - Sato,Kazuhiro, AU - Takumi,Shigeo, Y1 - 2018/11/08/ PY - 2018/01/29/received PY - 2018/10/25/accepted PY - 2018/11/10/entrez PY - 2018/11/10/pubmed PY - 2018/11/20/medline KW - Aegilops tauschii KW - Aegilops umbellulata KW - Barley KW - DNA markers KW - RNA sequencing KW - Synteny SP - 271 EP - 271 JF - BMC plant biology JO - BMC Plant Biol VL - 18 IS - 1 N2 - BACKGROUND: Aegilops umbellulata Zhuk. (2n = 14), a wild diploid wheat relative, has been the source of trait improvement in wheat breeding. Intraspecific genetic variation of Ae. umbellulata, however, has not been well studied and the genomic information in this species is limited. RESULTS: To develop novel genetic markers distributed over all chromosomes of Ae. umbellulata and to evaluate its genetic diversity, we performed RNA sequencing of 12 representative accessions and reconstructed transcripts by de novo assembly of reads for each accession. A large number of single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) were obtained and anchored to the pseudomolecules of Ae. tauschii and barley (Hordeum vulgare L.), which were regarded as virtual chromosomes of Ae. umbellulata. Interestingly, genetic diversity in Ae. umbellulata was higher than in Ae. tauschii, despite the narrow habitat of Ae. umbellulata. Comparative analyses of nucleotide polymorphisms between Ae. umbellulata and Ae. tauschii revealed no clear lineage differentiation and existence of alleles with rarer frequencies predominantly in Ae. umbellulata, with patterns clearly distinct from those in Ae. tauschii. CONCLUSIONS: The anchored SNPs, covering all chromosomes, provide sufficient genetic markers between Ae. umbellulata accessions. The alleles with rarer frequencies might be the main source of the high genetic diversity in Ae. umbellulata. SN - 1471-2229 UR - https://www.unboundmedicine.com/medline/citation/30409135/RNA_seq_analysis_reveals_considerable_genetic_diversity_and_provides_genetic_markers_saturating_all_chromosomes_in_the_diploid_wild_wheat_relative_Aegilops_umbellulata_ L2 - https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-018-1498-8 DB - PRIME DP - Unbound Medicine ER -