Advertisement

Molecular Genetics and Genomics

, Volume 291, Issue 4, pp 1681–1694 | Cite as

Genome-wide identification of novel genetic markers from RNA sequencing assembly of diverse Aegilops tauschii accessions

  • Ryo Nishijima
  • Kentaro YoshidaEmail author
  • Yuka Motoi
  • Kazuhiro Sato
  • Shigeo Takumi
Original Article

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.

Keywords

Aegilops tauschii DNA markers Hordeum vulgare RNA sequencing Synteny 

Notes

Acknowledgments

Computations for the RNA sequencing assembly and alignments of short reads were performed on the NIG supercomputer at the ROIS National Institute of Genetics.

Compliance with ethical standards

Funding

This work was supported by a Grant from the Ministry of Education, Culture, Sports, Science and Technology of Japan [Grant-in-Aid for Scientific Research (B) Nos. 25292008 and 16H04862] to ST, and by MEXT as part of a Joint Research Program implemented at the Institute of Plant Science and Resources, Okayama University, Japan.

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

438_2016_1211_MOESM1_ESM.pdf (8.4 mb)
Supplementary material 1 (PDF 8597 kb)
438_2016_1211_MOESM2_ESM.pdf (20.2 mb)
Supplementary material 2 (PDF 20652 kb)

References

  1. Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H, Kanzaki H, Matsumura H, Yoshida K, Mitsuoka C, Tamiru M, Innan H, Cano L, Kamoun S, Terauchi R (2012) Genome sequencing reveals agronomically important loci in rice using MutMap. Nat Biotechnol 30:174–178CrossRefPubMedGoogle Scholar
  2. Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J (2010) Galaxy: a web-based genome analysis tool for experimentalists. In: Current protocols in molecular biology , Chap 19.10, vol 89, pp 19.10.1–19.10.21Google Scholar
  3. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120CrossRefPubMedPubMedCentralGoogle Scholar
  4. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635CrossRefPubMedGoogle Scholar
  5. Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12:499–510CrossRefPubMedGoogle Scholar
  6. Gaut BS (2002) Evolutionary dynamics of grass genomes. New Phytol 154:15–28CrossRefGoogle Scholar
  7. Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res 15:1451–1455CrossRefPubMedPubMedCentralGoogle Scholar
  8. Goecks J, Nekrutenko A, Taylor J (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11:R86CrossRefPubMedPubMedCentralGoogle Scholar
  9. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652CrossRefPubMedPubMedCentralGoogle Scholar
  10. Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, Macmanes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, Leduc RD, Friedman N, Regev A (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8:1494–1512CrossRefPubMedGoogle Scholar
  11. Iehisa JCM, 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 Res 19:487–497CrossRefPubMedPubMedCentralGoogle Scholar
  12. Iehisa JCM, 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. Theor Appl Genet 127:261–271CrossRefPubMedGoogle Scholar
  13. International Barley Genome Sequencing Consortium (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature 491:711–716Google Scholar
  14. Jia J, Zhao S, Kong X, Li Y, Zhao G, He W, Appels R, Pfeifer M, Tao Y, Zhang X, Jing R, Zhang C, Ma Y, Gao L, Gao C, Spannagl M, Mayer KFX, Li D, Pan S, Zheng F, Hu Q, Xia X, Li J, Liang Q, Chen J, Wicker T, Gou C, Kuang H, He G, Luo Y, Keller B, Xia Q, Lu P, Wang J, Zou H, Zhang R, Xu J, Gao J, Middleton C, Quan Z, Liu G, Wang J, International Wheat Genome Sequencing Consortium, Yang H, Liu X, He Z, Mao L, Wang J (2013) Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 496:91–95CrossRefPubMedGoogle Scholar
  15. Kersey PJ, Allen JE, Armean I, Boddu S, Bolt BJ, Carvalho-Silva D, Christensen M, Davis P, Falin LJ, Grabmueller C, Humphrey J, Kerhornou A, Khobova J, Aranganathan NK, Langridge N, Lowy E, McDowall MD, Maheswari U, Nuhn M, Ong CK, Overduin B, Paulini M, Pedro H, Perry E, Spudich G, Tapanari E, Walts B, Williams G, Tello-Ruiz M, Stein J, Wei S, Ware D, Bolser DM, Howe KL, Kulesha E, Lawson D, Maslen G, Staines DM (2015) Ensembl genomes 2016: more genomes, more complexity. Nucleic Acids Res 44:574–580CrossRefGoogle Scholar
  16. Kosugi S, Natsume S, Yoshida K, MacLean D, Cano L, Kamoun S, Terauchi R (2013) Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data. PLoS One 8:e75402CrossRefPubMedPubMedCentralGoogle Scholar
  17. Kumar S, Banks TW, Cloutier S (2012) SNP discovery through next-generation sequencing and its applications. Int J Plant Genomics. doi: 10.1155/2012/831460 Google Scholar
  18. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359CrossRefPubMedPubMedCentralGoogle Scholar
  19. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Subgroup 1000 Genome Project Data Processing (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079CrossRefPubMedPubMedCentralGoogle Scholar
  20. Luo M-C, Gu YQ, You FM, Deal KR, Ma Y, Hu Y, Huo N, Wang Y, Wang J, Chen S, Jorgensen CM, Zhang Y, McGuire PE, Pasternak S, Stein JC, Ware D, Kramer M, McCombie WR, Kianian SF, Martis MM, Mayer KFX, Sehgal SK, Li W, Gill BS, Bevan MW, Šimková H, Doležel J, Weining S, Lazo GR, Anderson OD, Dvorak J (2013) A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. Proc Natl Acad Sci USA 110:7940–7945CrossRefPubMedPubMedCentralGoogle Scholar
  21. Matsumoto T, Tanaka T, Sakai H, Amano N, Kanamori H, Kurita K, Kikuta A, Kamiya K, Yamamoto M, Ikawa H, Fujii N, Hori K, Itoh T, Sato K (2011) Comprehensive sequence analysis of 24,783 barley full-length cDNAs derived from 12 clone libraries. Plant Physiol 156:20–28CrossRefPubMedPubMedCentralGoogle Scholar
  22. Matsuoka Y, Nasuda S, Ashida Y, Nitta M, Tsujimoto H, Takumi S, Kawahara T (2013) Genetic basis for spontaneous hybrid genome doubling during allopolyploid speciation of common wheat shown by natural variation analyses of the paternal species. PLoS One 8:e68310CrossRefPubMedPubMedCentralGoogle Scholar
  23. Matsuoka Y, Takumi S, Kawahara T (2015) Intraspecific lineage divergence and its association with reproductive trait change during species range expansion in central Eurasian wild wheat Aegilops tauschii Coss. (Poaceae). BMC Evol Biol 15:213CrossRefPubMedPubMedCentralGoogle Scholar
  24. Mayer KFX, Martis M, Hedley PE, Šimková H, Liu H, Morris JA, Steuernagel B, Taudien S, Roessner S, Gundlach H, Kubaláková M, Suchánková P, Murat F, Felder M, Nussbaumer T, Graner A, Salse J, Endo T, Sakai H, Tanaka T, Itoh T, Sato K, Platzer M, Matsumoto T, Scholz U, Doležel J, Waugh R, Stein N (2011) Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell 23:1249–1263CrossRefPubMedPubMedCentralGoogle Scholar
  25. Mizuno N, Yamasaki M, Matsuoka Y, Kawahara T, Takumi S (2010) Population structure of wild wheat D-genome progenitor Aegilops tauschii Coss.: implications for intraspecific lineage diversification and evolution of common wheat. Mol Ecol 19:999–1013CrossRefPubMedGoogle Scholar
  26. Nishijima R, Iehisa JCM, Matsuoka Y, Takumi S (2014) The cuticular wax inhibitor locus Iw2 in wild diploid wheat Aegilops tauschii: phenotypic survey, genetic analysis, and implications for the evolution of common wheat. BMC Plant Biol 14:246CrossRefPubMedPubMedCentralGoogle Scholar
  27. Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841–842CrossRefPubMedPubMedCentralGoogle Scholar
  28. Sehgal D, Vikram P, Sansaloni CP, Ortiz C, Saint Pierre C, Payne T, Ellis M, Amri A, Petroli CD, Wenzl P, Singh S (2015) Exploring and mobilizing the gene bank biodiversity for wheat improvement. PLoS One 10:e0132112CrossRefPubMedPubMedCentralGoogle Scholar
  29. Takagi H, Uemura A, Yaegashi H, Tamiru M, Abe A, Mitsuoka C, Utsushi H, Natsume S, Kanzaki H, Matsumura H, Saitoh H, Cano LM, Kamoun S, Terauchi R (2013) Methods MutMap-Gap: whole-genome resequencing of mutant F2 progeny bulk combined with de novo assembly of gap regions identifies the rice blast resistance gene Pii. New Phytol 200:276–283CrossRefPubMedGoogle Scholar
  30. Takumi S, Koyama K, Fujiwara K, Kobayashi F (2011) Identification of a large deletion in the first intron of the Vrn-D1 locus, associated with loss of vernalization requirement in wild wheat progenitor Aegilops tauschii Coss. Genes Genet Syst 86:183–195CrossRefPubMedGoogle Scholar
  31. Tsunewaki K (1966) Comparative gene analysis of common wheat and its ancestral species. II. Waxiness, growth habit and awnedness. Jpn J Bot 19:175–229Google Scholar
  32. Townsley BT, Covington MF, Ichihashi Y, Zumstein K, Sinha NR (2015) BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction. Front Plant Sci 6:366CrossRefPubMedPubMedCentralGoogle Scholar
  33. Wicker T, Mayer KFX, Gundlach H, Martis M, Steuernagel B, Scholz U, Šimková H, Kubaláková M, Choulet F, Taudien S, Platzer M, Feuillet C, Fahima T, Budak H, Dolezel J, Keller B, Stein N (2011) Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell 23:1706–1718CrossRefPubMedPubMedCentralGoogle Scholar
  34. Wu TD, Watanabe CK (2005) GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21:1859–1875CrossRefPubMedGoogle Scholar
  35. Yang C, Zhao L, Zhang H, Yang Z, Wang H, Wen S, Zhang C, Rustgi S, von Wettstein D, Liu B (2014) Evolution of physiological responses to salt stress in hexaploid wheat. Proc Natl Acad Sci 111:11882–11887CrossRefPubMedPubMedCentralGoogle Scholar
  36. Zhang J, Kobert K, Flouri T, Stamatakis A (2014) PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 30:614–620CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Ryo Nishijima
    • 1
  • Kentaro Yoshida
    • 1
    Email author
  • Yuka Motoi
    • 2
  • Kazuhiro Sato
    • 2
  • Shigeo Takumi
    • 1
  1. 1.Laboratory of Plant Genetics, Graduate School of Agricultural ScienceKobe UniversityKobeJapan
  2. 2.Institute of Plant Science and ResourcesOkayama UniversityKurashikiJapan

Personalised recommendations