Abstract
The shortage of polymorphic markers for the regions of the wheat chromosomes that encode commercially valuable traits determines the need for studying the wheat microsatellite SSR loci. In this work, SSR markers for individual regions of the short arm of soft wheat chromosome 5B (5BS) were designed based on the sequence data obtained from BAC clones, and regions of the corresponding chromosome were saturated with these markers. Totally, 130 randomly selected BAC clones from 5BS library were sequenced using the IonTorrent platform and assembled in contigs using MIRA software. The assembly characteristics (N50 = 4136 bp) are comparable to the recently obtained data for wheat and related species and are acceptable for the identification of the microsatellite loci. The algorithm utilizing the properties of complex decompositions in the sliding-window mode was used to detect DNA sequences with a repeat unit of 2–4 bp. Analysis of 17770 contigs with a total length of 25879921 bp allowed for the design of 113, 79, and 67 microsatellite SSR loci with a repeat unit of 2, 3, and 4 bp, respectively. SSR markers with a motif of 3 bp were tested using nullitetrasomic lines of Chinese Spring wheat homoeologous group 5. In total, 21 markers specific for chromosome 5B were identified. Eight of these markers were mapped into the distal region of this chromosome (bin 5BS6) using a set of Chinese Spring deletion lines for 5BS. Eight and four markers were mapped to the interstitial region (bins 5BS5 and 5BS4, respectively). One marker was mapped to a pericentromeric bin. Comparative analysis of the distribution of trinucleotide microsatellites over wheat chromosome 5B, and in different cereal species, suggests that the (AAG) n repeat proliferates and is conserved during the evolution of cereals.
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References
Adonina, I.G., Goncharov, N.P., Badaeva, E.D., Sergeeva, E.M., Petrash, N.V., and Salina, E.A., (GAA)n microsatellite as an indicator of the A genome reorganization during wheat evolution and domestication, CompCytogen, 2015, vol. 9, no. 4, pp. 533–547. doi 10.3897/CompCytogen. v9i4.5120
Akhunov, E., Nicolet, C., and Dvorak, J., Single nucleotide polymorphism genotyping in polyploid wheat with the illumina goldengate assay, Theor. Appl. Genet., 2009, vol. 119, pp. 507–517. doi 10.1007/s00122-009-1059-5
Areshchenkova, T. and Ganal, M.W., Long tomato microsatellites are predominantly associated with centromeric regions, Genome, 1999, vol. 42, pp. 536–544.
Brenchley, R., Spannagl, M., Pfeifer, M., Barker, G.L.A., D’Amore, R., Allen, A.M., Mckenzie, N., Kramer, M., Kerhornou, A., Bolser, D., Kay, S., Waite, D., Trick, M., Bancroft, I., Gu, Y., et al., Analysis of the bread wheat genome using wholegenome shotgun sequencing, Nature, 2012, vol. 491, no. 7426, pp. 705–710. doi 10.1038/nature11650
Brown, S.M., Szewc-McFadden, A.K., and Kresovich, S., Development and application of simple sequence repeat (SSR) loci for plant genome analysis, in Methods in Genome Analysis in Plants, Boca Raton: CRC Press, 1996.
Chapman, J.A., Mascher, M., Buluç, A., Barry, K., Georganas, E., Session, A., Strnadova, V., Jenkins, J., Sehgal, S., Oliker, L., Schmutz, J., Yelick, K.A., Scholz, U., Waugh, R., et al., A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome, Genome Biol., 2015, vol. 16, no. 1, p. 26. doi 10.1186/s13059-015-0582-8
Chevreux, B., Wetter, T., and Suhai, S., Genome sequence assembly using trace signals and additional sequence information, Computer Science and Biology: Proc. of the German Conference on Bioinformatics, 1999, pp. 45–56.
Cuadrado, A., Schwarzacher, T., and Jouve, N., Identification of different chromatin classes in wheat using in situ hybridization with simple sequence repeat oligonucleotides, Theor. Appl. Genet., 2000, vol. 101, pp. 711–717. doi 10.1007/s001220051535
Cuadrado, A., Cardoso, M., and Jouve, N., Increasing the physical markers of wheat chromosomes using SSRs as FISH probes, Genome, 2008, vol. 51, no. 10, pp. 809–815. doi 10.1139/G08-065
Endo, T.R. and Gill, B.S., The deletion stocks of common wheat, J. Hered., 1996, vol. 87, no. 4, pp. 295–307.
Feldman, M., The origin of cultivated wheat, in The World Wheat Book, Paris: Lavoisier Publishing, 2001.
Gusev, V.D., Miroshnichenko, L.A., and Chuzhanova, N.A., The detection of fractal-like structures in DNA sequences, in Information Science and Computing. Int. Book Series, No. 8: Classification, Forecasting, Data Mining, Sofia: ITHEA, 2009.
Gusev, V.D., Nemytikova, L.A., and Chuzhanova, N.A., On the complexity measures of genetic sequences, Bioinformatics, 1999, vol. 15, no. 12, pp. 994–999. doi 10.1093/bioinformatics/15.12.994
International Barley Genome Sequencing Consortium, A physical, genetic and functional sequence assembly of the barley genome, Nature, 2012, vol. 491, no. 7426, pp. 711–716. doi 10.1038/nature11543
International Wheat Genome Sequencing Consortium, A chromosomebased draft sequence of the hexaploid bread wheat (Triticum aestivum) genome, Science, 2014, vol. 345, no. 6194, p. 1251788. doi 10.1126/science.1251788
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., et al., Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation, Nature, 2013, vol. 496, no. 7443, pp. 91–95. doi 10.1038/nature12028
Langmead, B. and Salzberg, S., Fast gapped-read alignment with Bowtie 2, Nat. Methods, 2012, vol. 9, pp. 357–359.
Li, Y.-C., Korol, A.B., Beiles, A., and Nevo, E., Microsatellites: Genomic distribution, putative functions and mutational mechanisms: A review, Mol. Ecol., 2002, vol. 11, pp. 2453–2465. doi 10.1046/j.1365-294X.2002.01643.x
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., and Durbin, R., and 1000 Genome Project Data Processing Subgroup, The sequence alignment/map (SAM) format and SAMtools, Bioinformatics, 2009, vol. 25, pp. 2078–2079.
Ling, H.-Q., Zhao, S., Liu, D., Wang, J., Sun, H., Zhang, C., Fan, H., Li, D., Dong, L., Tao, Y., Gao, C., Wu, H., Li, Y., Cui, Y., et al., Draft genome of the wheat A-genome progenitor Triticum urartu, Nature, 2013, vol. 496, no. 7443, pp. 87–90. doi 10.1038/nature11997
Logacheva, M.D., Schelkunov, M.I., and Penin, A.A., Sequencing and analysis of plastid genome in mycoheterotrophic orchid Neottia nidus-avis, Genome Biol. Evol., 2011, vol. 3, pp. 1296–1303. doi 10.1093/gbe/evr102
Loman, N.J., Misra, R.V., Dallman, T.J., Constantinidou, C., Gharbia, S.E., Wain, J., and Pallen, M.J., Performance comparison of benchtop high-throughput sequencing platforms, Nat. Biotechnol., 2012, vol. 30, no. 5, pp. 434–439. doi 10.1038/nbt.2198
Mason, A.S., SSR genotyping, Methods Mol. Biol., 2015, vol. 1245, pp. 77–89. doi 10.1007/978-1-4939-1966-6_6
Pasquariello, M., Barabaschi, D., Himmelbach, A., Steuernagel, B., Ariyadasa, R., Stein, N., Gandolfi, F., Tenedini, E., Bernardis, I., Tagliafico, E., Pecchioni, N., and Francia, E., The barley Frost resistance-H2 locus, Funct. Integr. Genomic, 2014, vol. 14, no. 1, pp. 85–100. doi 10.1007/s10142-014-0360-9
Paux, E., Sourdille, P., Salse, J., Saintenac, C., Choulet, F., Leroy, P., Korol, A., Michalak, M., Kianian, S., Spielmeyer, W., Lagudah, E., Somers, D., Kilian, A., Alaux, M., Vautrin, S., et al., Physical map of the 1-Gigabase bread wheat chromosome 3B, Science, 2008, vol. 322, pp. 101–104. doi 10.1126/science.1161847
Plaschke, J., Ganal, M.W., and Röder, M.S., Detection of genetic diversity in closely related bread wheat using microsatellite markers, Theor. Appl. Genet., 1995, vol. 91, pp. 1001–1007. doi 10.1007/BF00223912
Plaschke, J., Börner, A., Wendehake, K., Ganal, M.W., and Röder, M.S., The use of wheat aneuploids for the assignment of microsatellite loci, Euphytica, 1996, vol. 89, pp. 33–40. doi 10.1007/BF00015716
Qi, L., Echalier, B., Friebe, B., and Gill, B.S., Molecular characterization of a set of wheat deletion stocks for use in chromosome bin mapping of ests, Funct. Integr. Genomics, 2003, vol. 3, pp. 39–55. doi 10.1007/s10142-002-0063-5
Qu, J. and Liu, J., A genome-wide analysis of simple sequence repeats in maize and the development of polymorphism markers from nextgeneration sequence data, BMC Res. Notes, 2013, vol. 6, p. 403. doi 10.1186/1756-0500-6-403
Sato, S., Hirakawa, H., Isobe, S., Fukai, E., Watanabe, A., Kato, M., Kawashima, K., Minami, C., Muraki, A., Nakazaki, N., Takahashi, C., Nakayama, S., Kishida, Y., Kohara, M., et al., Sequence analysis of the genome of an oil-bearing tree,Jatropha curcas L., DNA Res., 2011, vol. 18, no. 1, pp. 65–76. doi 10.1093/dnares/dsq030
Schmidt, T. and Heslop-Harrison, J.S., The physical and genomic organization of microsatellites in sugar beet, Proc. Natl. Acad. Sci. U.S.A., 1996, vol. 93, pp. 8761–8765.
Sears, E.R., Nullisomic-tetrasomic combinations in hexaploid wheat, in Chromosome Manipulations and Plant Genetics, London: Oliver and Boyd, 1966. doi 10.1007/978-1-4899-6561-5_4
Sergeeva, E.M., Afonnikov, D.A., Koltunova, M.K., Gusev, V.D., Miroshnichenko, L.A., Vrána, J., Kubaláková, M., Poncet, C., Sourdille, P., Feuillet, C., Doležel, J., and Salina, E.A., Common wheat chromosome 5B composition analysis using low-coverage 454 sequencing, Plant Genome, 2014, vol. 7, no. 2, pp. 1–16. doi 10.3835/plantgenome2013.10.0031
Sourdille, P., Singh, S., Cadalen, T., Brown-Guedira, G.L., Gay, G., Qi, L., Gill, B.S., Dufour, P., Murigneux, A., and Bernard, M., Microsatellite-based deletion bin system for the establishment of genetic-physical map relationships in wheat (Triticum aestivum L.), Funct. Integr. Genomics, 2004, vol. 4, pp. 12–25. doi 10.1007/s10142-004-0106-1
Staton, S.E., Bakken, B.H., Blackman, B.K., Chapman, M.A., Kane, N.C., Tang, S., Ungerer, M.C., Knapp, S.J., Rieseberg, L.H., and Burke, J.M., The sunflower (Helianthus annuus L.) genome reflects a recent history of biased accumulation of transposable elements, Plant J., 2012, vol. 72, no. 1, pp. 142–153. doi 10.1111/j.1365-313X.2012.05072.x
Stein, N. and Steuernagel, B., Advances in sequencing the barley genome, in Genomics of Plant Genetic Resources, Springer Netherlands, 2014. doi 10.1007/978-94-007-7572-5_16
Tautz, D. and Renz, M., Simple sequences are ubiquitious repetitive component of eukaryotic genomes, Nucleic Acids Res., 1984, vol. 12, pp. 4127–4138. doi 10.1093/nar/12.10.4127
Timonova, E.M., Dobrovol’skaya, O.B., Sergeeva, E.M., Bildanova, L.L., Sourdille, P., Feuillet, K., and Salina, E.A., A comparative genetic and cytogenetic mapping of wheat chromosome 5B using introgression lines, Russ. J. Genet., 2013, vol. 49, no. 12, pp. 1200–1206.
Zhang, Z., Deng, Y., Tan, J., Hu, S., Yu, J., and Xue, Q., A genome-wide microsatellite polymorphism database for the indica and japonica rice, DNA Res., 2007, vol. 14, pp. 37–45. doi 10.1093/dnares/dsm005
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Original Russian Text © M.A. Nesterov, D.A. Afonnikov, E.M. Sergeeva, L.A. Miroshnichenko, M.K. Bragina, A.O. Bragin, G.V. Vasiliev, E.A. Salina, 2015, published in Vavilovskii Zhurnal Genetiki i Selektsii, 2015, Vol. 19, No. 6, pp. 707–714.
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Nesterov, M.A., Afonnikov, D.A., Sergeeva, E.M. et al. Identification of microsatellite loci based on BAC sequencing data and their physical mapping into the soft wheat 5B chromosome. Russ J Genet Appl Res 6, 825–837 (2016). https://doi.org/10.1134/S2079059716070078
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DOI: https://doi.org/10.1134/S2079059716070078