Assessment of genetic and epigenetic stability in long-term in vitro shoot culture of pea (Pisum sativum L.)

Alwee SS, Van der Linden CG, Van der Schoot J, de Folter S, Angenent C, Cheah SC, Smulders MJM (2006) Characterization of oil palm MADS box genes in relation to the mantled flower abnormality. Plant Cell Tissue Organ Cult 85:331–344 Amberger LA, Shoemaker RC, Palmer RG (1992a) Inheritance of two independent isozyme variants in soybean plants derived from tissue culture. Theor Appl Genet 84:600–607 Amberger LA, Palmer RG, Shoemaker RC (1992b) Analysis of culture-induced variation in soybean. Crop Sci 32:1103–1108 Baranger A, Aubert G, Arnau G, Lainé AL, Deniot G, Potier J, Weinachter C, Lejeune-Hénaut I, Lallemand J, Burstin J (2004) Genetic diversity within Pisum sativum using protein- and PCR-based markers. Theor Appl Genet 108:1309–1321 Barwale UB, Widholm JM (1987) Somaclonal variation in plants regenerated from cultures of soybean. Plant Cell Rep 6:365–368 Bassam BJ, Caetano-Anolles G, Gresshoff PM (1991) Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal Biochem 196:80–83 Baurens FC, Bonnot F, Bienvenu D, Causse S, Legavre T (2003) Using SD-AFLP and MSAP to assess CCGG methylation in the banana genome. Plant Mol Biol Rep 21:339–348 Bernardi R, Natali L, Polizzi E, Cavallini A, Durante M (1995) Gene variations in pea (Pisum sativum L.) plants regenerated from long-term cultures. Agric Med 125:177–183 Bowcock A, Ruiz-Linares J, Tomfohrde E, Minch J, Kidd J, Cavallini-Sforza L (1994) High resolution human evolutionary trees with polymorphic microsatellites. Nature 368:455–457 Buntjer JB (1999) Cross Checker. Department of Plant Breeding, Wageningen University and Research Centre Cavallini A, Natali L, Polizzi E, Giordani T (1996) Variation of repetitive DNA sequences in progenies of regenerated plants of Pisum sativum. J Heredity 87:233–237 Cecchini E, Natali L, Cavallini A, Durante M (1992) DNA variations in regenerated plants of pea (Pisum sativum L). Theor Appl Genet 84:874–879 Chavanne F, Zhang DX, Liaud MF, Cerff R (1998) Structure and evolution of Cyclops: a novel giant retrotransposon of the Ty3/Gypsy family highly amplified in pea and other legume species. Plant Mol Biol 37:363–375 Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15 Ellegren H (2004) Microsatellites: simple sequences with complex evolution. Nat Rev Genet 5:435–445 Ellis THN, Poyser SJ, Knox MR, Vershinin AV, Ambrose MJ (1998) Polymorphism of insertion sites of Ty1-copia class retrotransposons and its use for linkage and diversity analysis in pea. Mol Gen Genet 260:9–19 Evans DA, Sharp WR, Medina-Filho HP (1984) Somaclonal and gametoclonal variation. Am J Bot 77:759–774 Ezhova TA, Bagrova AM, Gostimski SA (1995) Cell selection as a possible reason for the specificity of somaclonal variation in pea. Plant Breed 114:520–524 Ford R, Le Roux K, Itman C, Brouwer JB, Taylor PWJ (2002) Diversity analysis and genotyping in Pisum with sequence tagged microsatellite site (STMS) primers. Euphytica 124:397–405 Fraga M, Uriol E, Diego LB, Berdasco M, Esteller M, Cañal MJ, Rodriguez R (2002) High performance capillary electrophoretic method for the quantification of 5-methyl 2’-deoxycytidine in genomic DNA: application to plant, animal and human cancer tissues. Electrophoresis 23:1677–1681 Freytag AH, Rao-Arelli AP, Anand SC, Wrather JA, Owens LD (1989) Somaclonal variation in soybean plants regenerated from tissue culture. Plant Cell Rep 8:199–202 Gamborg OL, Miller RA, Ojima K (1968) Nutrient requirements of suspension cultures of soyabean root cells. Exp Cell Res 50:151–158 Gesteira AS, Otoni WC, Barros EG, Moreira MA (2002) RAPD-based detection of genomic instability in soybean plants derived from somatic embryogenesis. Plant Breed 121:269–271 Gostimskii SA, Bagrova AM, Ezhova TA (1995) Discovery and cytogenetic analysis of the variability in plants regenerated from tissue-culture of pea (Pisum sativum L.) Dokl Akad Nauk SSSR 283:1007–1011 Gostimsky SA, Kokaeva ZG, Konovalov FA (2005) Studying plant genome variation using molecular markers. Russ J Genet 41:378–388 Grandbastien MA (1998) Activation of plant retrotransposons under stress conditions. Trends Plant Sci 3:181–187 Griga M (2000a) Somaclonal variation in grain legumes. In: Ó Ríordain F (eds) COST Action 822: development of integrated systems for large-scale propagation of elite plants using in vitro techniques; report of activities 1998. Europ Comm, Brussels, pp 435–440 Griga M (2000b) Morphological alterations in sterile mutant of Pisum sativum obtained via somatic embryogenesis . Biol Plant 43:161–165 Griga M, Novák FJ (1990) Pea (Pisum sativum L.) In: Bajaj YPS (ed) Biotechnology in agriculture and forestry, vol 10. Legumes and oil seed crops. Springer, Berlin, pp 65–99 Griga M, Stejskal J (1994) Micropropagation of pea (Pisum sativum L.)—in vitro system and its practical applications. In: Lumsden PJ, Nicholas JR, Davies WJ (eds) Physiology, growth and development of plants in culture. Kluwer, Dordrecht, pp 278–283 Griga M, Tejklová E, Novák FJ (1984) Hormonal regulation of growth of pea (Pisum sativum L.) shoot apices in in vitro culture. Rost Výr 30:523–530 (In Czech) Griga M, Tejklová E, Novák FJ, Kubaláková M (1986) In vitro clonal propagation of Pisum sativum L. Plant Cell Tissue Organ Cult 6:95–104 Griga M, Stejskal J, Beber K (1995) Analysis of tissue culture derived variation in pea (Pisum sativum L.)—preliminary results. Euphytica 85:335–339 Griga M, Kosturkova G, Kuchuk N, Ilieva-Stoilova M (2001) Biotechnology. In: Hedley CL (ed) Carbohydrates in grain legume seeds. Improving nutritional quality and agronomic characteristics. CABI Publishing, Wallingford Oxon, pp 145–207 Hirochika H (1993) Activation of tobacco retrotransposons during tissue culture. EMBO J 12:2521–2528 Hirochika H, Sugimoto K, Otsuki Y, Tsugawa H, Kanda M (1996) Retrotransposons of rice involved in mutations induced by tissue culture. Proc Natl Acad Sci USA 93:7783–7788 Jaligot E, Rival A, Beule T, Dussert S, Verdeil JL (2000) Somaclonal variation in oil palm (Elaeis guineensis Jacq.): the DNA methylation hypothesis. Plant Cell Rep 19:684–690 Jaligot E, Beule T, Baurens FC, Billote N, Rival A (2004) Search for methylation-sensitive amplification polymorphisms associated with the “mantled” variant phenotype in oil palm (Elaeis guineensis Jacq.). Genome 47:224–228 Jiang N, Bao ZR, Zhang XY, Hirochika H, Eddy SR, McCouch SR, Wessler SR (2003) An active DNA transposon family in rice. Nature 42:163–167 Joyce SM, Cassells AC (2002) Variation in potato microplant morphology in vitro and DNA methylation. Plant Cell Tissue Organ Cult 70:125–137 Kaeppler SM, Phillips RL (1993) DNA methylation and tissue culture-induced variation in plants. In Vitro Cell Dev Biol Plant 29:125–130 Kalendar R, Grob T, Regina M, Suoniemi A, Schulman A (1999) IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theor Appl Genet 98:704–711 Kalendar R, Tanskanen J, Immonen S, Nevo E, Schulman AH (2000) Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc Natl Acad Sci USA 97:6603–6607 Karp A (1995) Somaclonal variation as a toll for crop improvement. Euphytica 85:295–302 Kazazian HH (2004) Mobile elements: drivers of genome evolution. Science 303:1626–1632 Kidwell AG, Lisch D (1997) Transposable elements as source of variation in animals and plants. Proc Natl Acad Sci USA 94:7704–7711 Klaas M, Amasino RM (1989) DNA methylation is reduced in Dnase l-sensitive regions of plant chromatin. Plant Physiol 91:451–454 Knox MR, Ellis THN (2001) Stability and inheritance of methylation states at PstI sites in Pisum. Mol Gen Genome 265:497–507 Kohler C, Hennig L, Spillane C, Pien S, Gruissem W, Grossniklaus U (2003) The Polycomb-group protein MEDEA regulates seed development by controlling expression of the MADS-box gene PHERES1. Genes Dev 17:1540–1553 Komai F, Masuda K (2004) Plasticity in sex expression of spinach (Spinacia oleracea) regenerated from root tissues. Plant Cell Tissue Organ Cult 78:285–287 Kubis SE, Castilho AMF, Vershinin AV, Heslop-Harrison JS (2003) Retroelements, transposons and methylation status in the genome of oil palm (Elaeis guineensis) and the relationship to somaclonal variation. Plant Mol Biol 52:69–79 Kumar PS, Mathur VL (2004) Chromosomal instability in callus culture of Pisum sativum. Plant Cell Tissue Organ Cult 78:267–271 Kuznetsova OI, Ash OA, Hartina GA, Gostimskij SA (2005) RAPD and ISSR analyses of regenerated pea Pisum sativum L. plants. Russ J Genet 41:60–65 Larkin PJ, Scowcroft WR (1981) Somaclonal variation—a novel source of variability from cell cultures for plant improvement. Theor Appl Genet 60:443–455 Liu ZL, Han FP, Tan M, Shan XH, Dong YZ, Wang XZ, Fedak G, Hao S, Bao Liu (2004) Activation of a rice endogenous retrotransposon Tos17 in tissue culture is accompanied by cytosine demethylation and causes heritable alteration in methylation pattern of flanking genomic regions. Theor Appl Genet 109:200–209 Loridon K, McPhee K, Morin J, Dubreuil P, Pilet-Nayel ML, Aubert G, Rameau C, Baranger A, Coyne C, Lejeune-Henaut I, Burstin J (2005) Microsatellite marker polymorphism and mapping in pea (Pisum sativum L.). Theor Appl Genet 111:1022–1031 Martienssen RA, Colot V (2001) DNA methylation and epigenetic inheritance in plants and filamentous fungi. Science 293:1070–1074 Matthes M, Singh R, Cheah SC, Karp A (2001) Variation in oil palm (Elaeis guineensis Jacq.) tissue culture-derived regenerants revealed by AFLPs with methylation-sensitive enzymes. Theor Appl Genet 102:971–979 McClintock B (1984) The significance of responses of the genome to challenge. Science 226:792–801 Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15:472–497 Neumann P, Požárková D, Macas J (2003) Highly abundant pea LTR retrotransposon Ogre is constitutively transcribed and partially spliced. Plant Mol Biol 53:399–410 Peraza-Echeverria S, Herrera-Valencia VA, James-Kay A (2001) Detection of DNA methylation changes in micropropagated banana plants using methylation-sensitive amplification polymorphism (MSAP). Plant Sci 161:359–367 Phillips MH, Keppler SM, Olhoft P (1994) Genetic variability of plant tissue cultures: breakdown of normal control. Proc Natl Acad Sci USA 91:5222–5226 Portis E, Acquadro A, Comino C, Lanteri S (2004) Analysis of DNA methylation during germination of pepper (Capsicum annuum L.) seeds using methylation-sensitive amplification polymorphism (MSAP). Plant Sci 166:169–178 Rahman MH, Rajora OP (2001) Microsatellite DNA somaclonal variation in micropropagated trembling aspen (Populus tremuloides). Plant Cell Rep 20:531–536 Rival A, Bertrand L, Beule T, Combes MC, Trouslot P, Lashermes P (1998) Suitability of RAPD analysis for the detection of somaclonal variants in oil palm (Elaeis guineensis Jasq.). Plant Breed 117:73–76 Rohlf M (2000) NTSYS-pc: numerical taxonomy and multivariate analysis system. Version 2.1. Department of Eclogy and Evolution. State University of New York, USA Saker MM, Adawy SS, Mohamed AA, El-Itriby HA (2006) Monitoring of cultivar identity in tissue culture-derived date palms using RAPD and AFLP analysis. Biol Plant 50:198–204 Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor Smýkal P (2006) Development of an efficient retrotransposon-based fingerprinting method for rapid pea variety identification. J Appl Genet 47:221–230 Smýkal P, Dostálová R, Hýbl M, Griga M (2004) Utility of high copy number “Ogre/Cyclop” retrotransposons for molecular genotyping of pea (Pisum sativum L.) germplasm. In: Vollmann J, Grausgruber H, Ruckenbauer P (eds) Genetic variation in plant breeding. BOKU-University of Natural Resources and Applied Life Sciences, Vienna, Austria, p 326 Stejskal J, Griga M (1992) Somatic embryogenesis and plant regeneration in Pisum sativum L. Biol Plant 34:15–22 Tenhola-Roininen T, Immonen S, Tanhuanpaa P (2006) Rye doubled haploids as a research and breeding tool—a practical point of view. Plant Breed 125:584–590 Teo CH, Tan SH, Ho CL, Faridah QF, Othman YR, Heslop-Harrison JS, Kalendar R, Schulman AH (2005) Genome constitution and classification using retrotransposon-based markers in the orphan crop banana. J Plant Biol 48:96–105 Vershinin AV, Allnutt TR, Knox MR, Ambrose MJ, Ellis NTH (2003) Transposable elements reveal the impact of introgression, rather than transposition, in Pisum diversity, evolution, and domestication. Mol Biol Evol 20:2067–2075 Vos P, Hogers R, Bleeker M, Reijans M, Vandelee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP—a new technique for DNA-fingerprinting. Nucleic Acids Res 23:4407–4414 Wessler SR (1996) Plant retrotransposons: turned on by stress. Curr Biol 6:959–961 Wilhelm E, Hristoforoglu K, Fluch S, Burg K (2005) Detection of microsatellite instability during somatic embryogenesis of oak (Quercus robur L.). Plant Cell Rep 23:790–795 Xu ML, Li XQ, Korban SS (2004) DNA-methylation alterations and exchanges during in vitro cellular differentiation in rose (Rosa hybrida L.). Theor Appl Genet 109:899–910