Preparation of sub-genomic fractions enriched for particular chromosomes in polyploid wheat

Biologia Plantarum

Volumn 59, Issue 3, 2015, Pages 445-455

  Vrana J ^a   Kubalakova M ^a   Cihalikova J ^a   Valarik M ^a   Dolezel J ^a  

^a PALACKÝ UNIVERSITY   (Czech Republic)

Author keywords

chromosome sorting; complexity reduction; genome analysis

Indexed keywords

TRITICUM AESTIVUM;

EID: 84938423216     PISSN: 00063134     EISSN: 15738264     Source Type: Journal    
DOI: 10.1007/s10535-015-0522-1     Document Type: Article

References (53)

1. Bedbrook, J.R., Jones, J., O’Dell, M., Thompson, R.D., Flavell, R.B.: A molecular description of telomeric heterochromatin in Secale species. — Cell 19: 545–560, 1980.
2. Bennetzen, J.L.: Transposable element contributions to plant gene and genome evolution. — Plant mol. Biol. 42: 251–269, 2000.
3. Doležel, J., Kubaláková, M., Paux, E., Bartoš, J., Feuillet, C.: Chromosome-based genomics in the cereals. — Chromosome Res. 15: 51–66, 2007.
4. Doležel, J., Lucretti, S.: High-resolution flow karyotyping and chromosome sorting in Vicia faba lines with standard and reconstructed karyotypes. — Theor. appl. Genet. 90: 797–802, 1995.
5. Doležel, J., Macas, J., Lucretti, S.: Flow analysis and sorting of plant chromosomes. — In: Robinson, J.P., Darzynkiewicz, Z., Dean, P.N., Dressler, L.G., Orfao, A., Rabinovitch, P.S., Stewart, C.C., Tanke, H.J., Wheeless, L.L., (ed.): Current Protocols in Cytometry. Pp. 5.3.1.–5.3.33. John Wiley & Sons, New York 1999.
6. Doležel, J., Vrána, J., Šafář, J., Bartoš, J., Kubaláková, M., Šimková, H.: Chromosomes in the flow to simplify genome analysis. — Funct. Int. Genom. 12: 397–416, 2012.
7. Feuillet, C., Eversole, K.: Physical mapping of the wheat genome: A coordinated effort to lay the foundation for genome sequencing and develop tools for breeders. — Isr. J. Plant Sci. 55: 307–313, 2007.
8. Feuillet, C., Travella, S., Stein, N., Albar, L., Nublat, A., Keller, B.: Map-based isolation of the leaf rust disease resistance gene Lr10 from the hexaploid wheat (Triticum aestivum L.) genome. — Proc. nat. Acad. Sci. USA 100: 15253–15258, 2003.
9. Gill, K.S., Arumuganathan, K., Le, J.H.: Isolating individual wheat (Triticum aestivum) chromosome arm by flow cytometric analysis of ditelosomic lines. — Theor. appl. Genet. 98: 1248–1252, 1999.
10. Giorgi, D., Farina, A., Grosso, V., Gennaro, A., Ceoloni, C., Lucretti, S.: FISHIS: fluorescence in situ hybridization in suspension and chromosome flow sorting made easy. — Plos One 8: e57994, 2013.
11. Hernandez, P., Martis, M., Dorado, G., Pfeifer, M., Gálvez, S., Schaaf, S., Jouve, N., Šimková, H., Valárik, M., Doležel, J., Mayer, K.F.X.: Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content. — Plant J. 69: 377–386, 2012.
12. Huang, L., Brooks, S.A., Li, W.L., Fellers, J.P., Trick, H.N., Gill, B.S.: Map-based cloning of leaf rust resistance gene Lr21 from the large and polyploid genome of bread wheat. — Genetics 164: 655–664, 2003.
13. Jakobson, I., Reis, D., Tiidema, A., Peusha, H., Timofejeva, L., Valárik, M., Kladivová, M., Šimková, H., Doležel, J., Järve, K.: Fine mapping, phenotypic characterization and validation of non-race-specific resistance to powdery mildew in a wheat-Triticum militinae introgression line. — Theor. appl. Genet. 125: 609–623, 2012.
14. Kantar, M., Akpınar, B.A., Valárik, M., Lucas, S.J., Doležel, J., Hernández, P., Budak, H.: Subgenomic analysis of microRNAs in polyploid wheat. — Funct. int. Genom. 12: 465–479, 2012.
15. Kejnovský, E., Vrána, J., Matsunaga, S., Souček, P., Široký, J., Doležel, J., Vyskot, B.: Localization of male-specifically expressed MROS genes on Silene latifolia by PCR on flowsorted sex chromosomes and autosomes. — Genetics 158: 1269–1277, 2001.
16. Kubaláková, M., Kovářová, P., Suchánková, P., Číhalíková, J., Bartoš, J., Lucretti, S., Watanabe, N., Kianian, S.F., Doležel, J.: Chromosome sorting in tetraploid wheat and its potential for genome analysis. — Genetics 170: 823–829, 2005.
17. Kubaláková, M., Valárik, M., Bartoš, J., Vrána, J., Číhalíková, J., Molnár-Láng, M., Doležel, J.: Analysis and sorting of rye (Secale cereale L.) chromosomes using flow cytometry. — Genome 46: 893–905, 2003.
18. Kubaláková, M., Vrána, J., Čihalíková, J., Šimková, H., Doležel, J.: Flow karyotyping and chromosome sorting in bread wheat (Triticum aestivum L.). — Theor. appl. Genet. 104: 1362–1372, 2002.
19. Langlois, R.G., Yu, L.-C., Gray, J.W., Carrano, A.V.: Quantitative karyotyping of human chromosomes by dual beam flow cytometry. — Proc. nat. Acad. Sci. USA 79: 7876–7880, 1982.
20. Lee, J.H., Arumuganathan, K., Yen, Y., Kaeppler, S., Kaeppler, H., Baenziger, P.S.: Root tip cell cycle synchronization and metaphase-chromosome isolation suitable for flow sorting in common wheat (Triticum aestivum L.). — Genome 40: 633–638, 1997.
21. Li, I.J., Arumuganathan, K., Rines, H.W., Phillips, R.L., Riera-Lizarazu, O., Sandhu, D., Zhou, Y., Gill, K.S.: Flow cytometric sorting of maize chromosome 9 from an oat- maize chromosome addition line. — Theor. appl. Genet. 102: 658–663, 2001.
22. Lucretti, S., Doležel, J.: Bivariate flow karyotyping in broad bean (Vicia faba). — Cytometry 28: 236–242, 1997.
23. Ma, L., Xiao, Y., Huang, H., Wang, Q., Rao, W., Feng, Y., Zhang, K., Song, Q.: Direct determination of molecular haplotypes by chromosome microdissection. — Natur. Meth. 7: 299–301, 2010.
24. Ma, Y.Z., Lee, J.H., Li, L.C., Uchiyama, S., Ohmido, N., Fukui, K.: Fluorescent labeling of plant chromosomes in suspension by FISH. — Gene Genet. Syst. 80: 35–39, 2005.
25. Macas, J., Doležel, J., Gualberti, G., Pich, U., Schubert, I., Lucretti, S.: Primer-induced labelling of pea and field bean chromosomes in situ and in suspension. — Biotechniques 19: 402–408, 1995.
26. Madlung, A.: Polyploidy and its effect on evolutionary success: old questions revisited with new tools. — Heredity 110: 99–104, 2013.
27. Martis, M.M., Klemme, S., Banaei-Moghaddam, A.M., Blattner, F.R., Macas, J., Schmutzer, T., Scholz, U., Gundlach, H., Wicker, T., Šimková, H., Novák, P., Neumann, P., Kubaláková, M., Bauer, E., Haseneyer, G., Fuchs, J., Doležel, J., Stein, N., Mayer, K.F.X., Houben, A.: Selfish supernumerary chromosome reveals its origin as a mosaic of host genome and organellar sequences. — Proc. nat. Acad. Sci. USA 109: 13343–13346, 2012.
28. Mayer, K.F.X., Martis, M., Hedley, P.E., Šimková, H., Liu, H., Morris, J.A., 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.: Unlocking the barley genome by chromosomal and comparative genomics. — Plant Cell 23: 1249–1263, 2011.
29. Neumann, P., Lysák, M., Doležel, J., Macas, J.: Isolation of chromosomes from Pisum sativum L. hairy root cultures and their analysis by flow cytometry. — Plant Sci. 137: 205–215, 1998.
30. Neumann, P., Požárková, D., Vrána, J., Doležel, J., Macas, J.: Chromosome sorting and PCR-based physical mapping in pea (Pisum sativum L.). — Chrom. Res. 10: 63–67, 2002.
31. Ng, S.B., Turner, E.H., Robertson, P.D., Flygare, S.D., Bigham, A.W., Lee, C., Shaffer, T., Wong, M., Bhattacharjee, A., Eichler, E.E., Bamshad, M., Nickerson, D.A., Shendure, J.: Targeted capture and massively parallel sequencing of 12 human exomes. — Nature 461: 272–278, 2009.
32. Paterson, A.H.: Leafing through the genomes of our major crop plants: strategies for capturing unique information. — Nat. Rev. Genet. 7: 174–184, 2006.
33. 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., Berges, H., Eversole, K., Appels, R., Šafář, J., Šimková, H., Doležel, J., Bernard, M., Feuillet, C.: A physical map of the 1-gigabase bread wheat chromosome 3B. — Science 322: 101–104, 2008.
34. Petrovská, B., Jeřábková, H., Chamrád, I., Vrána, J., Lenobel, R., Uřinovská, J., Šebela, M., Doležel, J.: Proteomic analysis of barley cell nuclei purified by flow sorting. — Cytogenet. Genome Res. 143: 78–86, 2014.
35. Pich, U., Meister, A., Macas, J., Doležel, J., Lucretti, S., Schubert, I.: Primed in situ labelling facilitates flow sorting of similar sized chromosomes. — Plant J. 7: 1039–1044, 1995.
36. Požárková, D., Koblížková, A., Román, B., Torres, A.M., Lucretti, S., Lysák, M., Doležel, J., Macas, J.: Development and characterization of microsatellite markers from chromosome 1-specific DNA libraries of Vicia faba. — Biol. Plant. 45: 337–345, 2002.
37. Šafář, J., Bartoš, J., Janda, J., Bellec, A., Kubaláková, M., Valárik, M., Pateyron, S., Weiserová, J., Tušková, R., Číhalíková, J., Vrána, J., Šimková, H., Faivre-Rampant, P., Sourdille, P., Caboche, M., Bernard, M., Doležel, J., Chalhoub, B.: Dissecting large and complex genomes: flow sorting and BAC cloning of individual chromosomes from bread wheat. — Plant J. 39: 960–968, 2004.
38. Šafář, J., Šimková, H., Kubaláková, M., Číhalíková, J., Suchánková, P., Bartoš, J., Doležel, J.: Development of chromosome-specific BAC resources for genomics of bread wheat. — Cytogenet. Genome Res. 129: 211–223, 2010.
39. Sears, E.R., Sears, L.M.S.: The telocentric chromosomes of common wheat. — In: Ramanujam, S. (ed.): Proc. 5th International Wheat Genet Symposium. Pp. 389–407. Indian Society of Genetics and Plant Breeding, IARI, New Delhi 1978.
40. Shatalina, M., Wicker, T., Buchmann, J.P., Oberhaensli, S., Šimková, H., Doležel, J., Keller, B.: Genotype-specific SNP map based on whole chromosome 3B sequence information from wheat cultivars Arina and Forno. — Plant Biotechnol. J. 11: 23–32, 2013.
41. Šimková, H., Svensson, J.T., Condamine, P., Hřibová, E., Suchánková, P., Bhat, P.R., Bartoš, J., Šafář, J., Close, T.J., Doležel, J.: Coupling amplified DNA from flow-sorted chromosomes to high-density SNP mapping in barley. — BMC Genomics 9: 237, 2008.
42. Stein, N., Feuillet, C., Wicker, T., Schlagenhauf, E., Keller, B.: Subgenome chromosome walking in wheat: a 450-kb physical contig in Triticum monococcum L. spans the Lr10 resistance locus in hexaploid wheat (Triticum aestivum L.). — Proc. nat. Acad. Sci. USA 97: 13436–13441, 2000.
43. Suchánková, P., Kubaláková, M., Kovářová, P., Bartoš, J., Číhalíková, J., Molnár-Láng, M., Endo, T.R., Doležel, J.: Dissection of the nuclear genome of barley by chromosome flow sorting. — Theor. appl. Genet. 113: 651–659, 2006.
44. Uauy, C., Brevis, J.C., Dubcovsky, J.: The high grain protein content gene Gpc-B1 accelerates senescence and has pleiotropic effects on protein content in wheat. — J. exp. Bot. 57: 2785–2794, 2006.
45. Valárik, M., Bartoš, J., Kovářová, P., Kubaláková, M., De Jong, H., Doležel, J.: High-resolution FISH on super-stretched flow-sorted plant chromosomes. — Plant J. 37: 940–950, 2004.
46. Van de Peer, Y., Fawcett, J.A., Proost, S., Sterck, L., Vandepoele, K.: The flowering world: a tale of duplications. — Trends Plant Sci. 14: 680–688, 2009.
47. Vláčilová, K., Ohri, D., Vrána, J., Číhalíková, J., Kubaláková, M., Kahl, G., Doležel, J.: Development of flow cytogenetics and physical genome mapping in chickpea (Cicer arietinum L.). — Chrom. Res. 10: 695–706, 2002.
48. Vrána, J., Kubaláková, M., Šimková, H., Číhalíková, J., Lysák, M.A., Doležel J.: Flow-sorting of mitotic chromosomes in common wheat (Triticum aestivum L.). — Genetics1 56: 2033–2041, 2000.
49. Vrána, J., Šimková, H., Kubaláková, M., Číhalíková, J., Doležel, J.: Flow cytometric chromosome sorting in plants: the next generation. — Methods 57: 331–337, 2012.
50. Wenzl, P., Suchánková, P., Carling, J., Šimková, H., Huttner, E., Kubaláková, M., Sourdille, P., Paul, E., Feuillet, C., Kilian, A., Doležel, J.: Isolated chromosomes as a new and efficient source of DArT markers for the saturation of genetic maps. — Theor. appl. Genet. 121: 465–474, 2010.
51. Yang, H., Chen, X., Wong, W.H.: Completely phased genome sequencing through chromosome sorting. — Proc. nat. Acad. Sci. USA 108: 12–17, 2011.
52. Zatloukalová, P., Hřibová, E., Kubaláková, M., Suchánková, P., Šimková, H., Adoración, C., Kahl, G., Millán, T., Doležel, J.: Integration of genetic and physical maps of the chickpea (Cicer arietinum L.) genome using flow-sorted chromosomes. — Chromosome Res. 19: 729–739, 2011.
53. Zhou, S., Bechner, M.C., Place, M., Churas, C.P., Pape, L., Leong, S.A., Runnheim, R., Forrest, D.K., Goldstein, S., Livny, M., Schwartz, D.C.: Validation of rice genome sequence by optical mapping. — BMC Genom. 8: 278, 2007.