Genome-wide polymorphisms from RNA sequencing assembly of leaf transcripts facilitate phylogenetic analysis and molecular marker development in wild einkorn wheat
A survey of genome-wide polymorphisms between closely related species is required to understand the molecular basis of the evolutionary differentiation of their genomes. Two wild diploid wheat species, namely Triticum monococcum ssp. aegilopoides and T. urartu, are closely related and harbour the Am and A genomes, respectively. The A-genome donor of tetraploid and common wheat is T. urartu, and T. monococcum ssp. monococcum is the cultivated form derived from the wild einkorn wheat subspecies aegilopoides. Although subspecies aegilopoides has been a useful genetic resource in wheat breeding, genome-wide molecular markers for this subspecies have not been sufficiently developed. Here, we describe the detection of genome-wide polymorphisms such as single-nucleotide polymorphisms (SNPs) and insertions/deletions (indels) from RNA sequencing (RNA-seq) data of leaf transcripts in 15 accessions of the two diploid wheat species. The SNPs and indels, detected using the A genome of common wheat as the reference genome, covered the entire chromosomes of these species. The polymorphism information facilitated a comparison of the genetic diversity of einkorn wheat with that of two related diploid Aegilops species, namely, Ae. tauschii and Ae. umbellulata. Cleaved amplified polymorphic sequence (CAPS) markers converted from the SNP data were efficiently developed to confirm the addition of aegilopoides subspecies chromosomes to tetraploid wheat in nascent allohexaploid lines with AABBAmAm genomes. In addition, the CAPS markers permitted linkage map construction in mapping populations of aegilopoides subspecies accessions. Therefore, these RNA-seq data provide information for further breeding of closely related species with no reference genome sequence data.
KeywordsAllopolyploidization Chromosomal synteny Molecular marker Single-nucleotide polymorphism Wheat
The authors thank Drs. N. Watanabe and K. Murai for providing seeds of two einkorn wheat accessions. Seeds of the other diploid wheat species used in this study were supplied by the National BioResource Project-Wheat, Japan (www.nbrp.jp). Computations for RNA sequence assembly of reads were performed on the NIG supercomputer at the ROIS National Institute of Genetics, Japan.
This work was supported by Grant-in-Aid for Scientific Research (B) No. 16H04862 from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan to ST, by Grant-in-Aid for Scientific Research on Innovative Areas No. 17H05842 from the MEXT to ST, and by the MEXT as part of a Joint Research Program implemented at the Institute of Plant Science and Resources, Okayama University, Japan. KY was supported by JST, PRESTO (No. JPMJPR15QB).
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Conflict of interest
The authors declare that they have no conflicts of interest.
This article does not contain any studies with human participants or animals performed by any of the authors.
- Avni R, Nave M, Barad O, Baruch K, Twardziok SO, Gundlach H, Hale I, Mascher M, Spannagl M, Wiebe K, Jordan KW, Golan G, Deek J, Ben-Zvi B, Ben-Zvi G, Himmelbach A, MacLachlan RP, Sharpe AG, Fritz A, Ben-David R, Budak H, Fashima T, Korol A, Faris JD, Hernandez A, Mikel MA, Levy AA, Steffenson B, Maccaferri M, Tuberosa R, Cattivelli L, Faccioli P, Ceriotti A, Kashkush K, Purkheirandish M, Komatsuda T, Eilam T, Sela H, Sharon A, Ohad N, Chamovitz DA, Mayer KFX, Stein N, Ronen G, Peleg Z, Pozniak CJ, Akhunov ED, Distelfeld A (2017) Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science 357:93–97CrossRefGoogle Scholar
- Dubcovsky J, Luo MC, Zhong GY, Brastertter R, Desai A, Killian A, Kleinhofs A, Dvorák J (1996) Genetic map of diploid wheat, Triticum monococcum L., and its comparison with maps Hordeum vulgare L. Genetics 143:983–999Google Scholar
- Fox SE, Geniza M, Hanumappa M, Naithani S, Sullivan C, Preece J, Tiwari VK, Elser J, Leonard JM, Sage A, Gresham C, Kerhornou A, Bolser D, McCarthy F, Kersey P, Lazo GR, Jaiswal P (2014) De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum. PLoS One 9:e96855CrossRefGoogle Scholar
- Fricano A, Brandolini A, Rossini L, Sourdille P, Wunder J, Effgene S, Hidalgo A, Erba D, Piffanelli P, Salamini F (2014) Crossability of Triticum urartu and Triticum monococcum wheats, homoeologous recombination and description of a panel of interspecific introgression lines. G3 4:1931–1941CrossRefGoogle Scholar
- 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 29:644–652CrossRefGoogle Scholar
- 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 127:261–271CrossRefGoogle Scholar
- International Wheat Genome Sequencing Consortium (IWGSC) (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361.pii: eaar7191Google Scholar
- Ling HQ, Zhao S, Liu D, Wang J, Sun H, Zhang C, Fan H, Li D, Dong L, Tao Y, Gao C, Wu H, Lii Y, Cui Y, Guo X, Zheng S, Wang B, Yu K, Liang Q, Yang W, Lou X, Chen J, Feng M, Jian J, Zhang X, Luo G, Jiang Y, Liu J, Wang Z, Sha Y, Zhang B, Wu H, Tang D, Shen Q, Xue P, Zou S, Wang X, Liu X, Wang F, Yang Y, Zn X, Dong Z, Zhang K, Zhang X, Luo MC, Dvorak J, Tong Y, Wang J, Yang H, Li Z, Wang D, Zhang A, Wang J (2013) Draft genome of the wheat A-genome progenitor Triticum urartu. Nature 496:87–90CrossRefGoogle Scholar
- Ling HQ, Ma B, Shi X, Liu H, Dong L, Sun H, Cao Y, Gao Q, Zheng S, Li Y, Yu Y, Du H, Qi M, Li Y, Lu H, Yu H, Cui Y, Wang N, Chen C, Wu H, Zhao Y, Zhang J, Li Y, Zhou W, Zhang B, Hu W, van Eijk MJT, Tang J, Witsenboer HMA, Zhao S, Li Z, Zhang A, Wang D, Liang C (2018) Genome sequence of the progenitor of wheat A subgenome Triticum urartu. Nature 557:424–428CrossRefGoogle Scholar
- Luo MC, Gu YQ, Puiu D, Wang H, Twardziok SO, Deal KR, Huo N, Zhu T, Wang L, Wang Y, McGuire PE, Liu S, Long H, Ramasamy RK, Rodriguez JC, Van SL, Yuan L, Wang Z, Xia Z, Xiao L, Anderson OD, Ouyang S, Liang Y, Zimin AV, Pertea G, Qi P, Bennetzen JL, Dai X, Dawson MW, Müller HG, Kugler K, Rivarola-Duarte L, Spannagl M, Mayer KFX, Lu FH, Bevan MW, Leroy P, Li P, You FM, Sun Q, Liu Z, Lyons E, Wicker T, Salzberg SL, Devos KM, Dvorák J (2017) Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature 551:498–502CrossRefGoogle Scholar
- Mayer KFX, Martis M, Hedley PE, Simková 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, Dolezel J, Waugh R, Stein N (2011) Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell 23:1249–1263CrossRefGoogle Scholar
- Rogers WJ, Miller TE, Payne PI, Seekings JA, Sayers EJ, Holt LM, Law CN (1997) Introduction to bread wheat (Triticum aestivum L.) and assessment for bread-making quality of alleles from T. boeoticum Boiss. ssp. thaoudar at Glu-A1 encoding two high-molecular-weight subunits of glutenin. Euphytica 93:19–29CrossRefGoogle Scholar
- Sato K, Tanaka T, Shigenobu S, Motoi Y, Wu J, Itoh T (2016) Improvement of barley genome annotations by deciphering the Haruna Nijo genome. DNA Res 23:21–28Google Scholar