Assessment of genetic and epigenetic changes in virus-free garlic (Allium sativum L.) plants obtained by meristem culture followed by in vitro propagation
参考文献:Al-Zahim MA, Ford-Lloyd BV, Newbury HJ (1999) Detection of somaclonal variation in garlic (Allium sativum L.) using RAPD and cytological analysis. Plant Cell Rep 18:473–477. doi:10.1007/s002990050606 CrossRef Amir R, Hacham Y, Galili G (2002) Cystathionine γ-synthase and threonine synthase operate in concert to regulate carbon flow towards methionine in plants. Trends Plant Sci 7:153156. doi:10.1016/S1360-1385(02)02227-6 CrossRef Baránek M, Křižan B, Ondrušíková E, Pidra M (2010) DNA-methylation changes in grapevine somaclones following in vitro culture and thermotherapy. Plant Cell Tissue Organ Cult 101:11–22. doi:10.1007/s11240-009-9656-1 CrossRef Bobadilla Landey R, Cenci A, Georget F et al (2013) High genetic and epigenetic stability in Coffea arabica plants derived from embryogenic suspensions and secondary embryogenesis as revealed by AFLP, MSAP and the phenotypic variation rate. PLoS One 8:e56372. doi:10.1371/journal.pone.0056372 PubMed PubMedCentral CrossRef Brenchley R, Spannagl M, Pfeifer M et al (2012) Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 491:705–710. doi:10.1038/nature11650 PubMed PubMedCentral CrossRef Burba JL (2003) Producción de ajo, Instituto Nacional de Tecnología Agropecuaria. La Consulta, Mendoza, Argentina Carvalho MG (1981) Viroses do alho. Fitopatologia Brasileira 6:299–300 Carvalho MG, Shepherd RR, Hall DH (1981) Virus em clone de alho sem sintomas e liberto do Garlic yellow stripe virus. Fitopatologia Brasileira 6:236 Chandler VL, Walbot V (1986) DNA modification of a maize transposable element correlates with loss of activity. Proc Natl Acad Sci USA 83:1767–1771. doi:10.1073/pnas.83.6.1767 PubMed PubMedCentral CrossRef Conci VC (1997) An overview of Allium viruses in Argentina. Acta Hortic 433:593–600CrossRef Conci VC, Nome S (1991) Virus free garlic (Allium sativum L.) plants obtained by thermotherapy and meristem tip culture. J Phytopathol 132:186–192CrossRef Conci VC, Moriconi DN, Nome SF (1986) Cultivo de meristemas apicales de seis diferentes tipos clonales de ajo (Allium sativum L.). Phyton 46:187–194 Conci VC, Helguera M, Nome SF (1999) Serological and biological comparison of Onion yellow dwarf virus from onion and garlic in Argentina. Fitopatologia Brasilera 24:73–75 Conci VC, Canavelli A, Lunello P, Di Rienzo J, Nome SF, Zumelzu G, Italia R (2003) Yield losses associated with virus-infected garlic plants during five successive years. Plant Dis 87:1411–1415CrossRef Conci VC, Perotto MC, Cafrune E, Lunello P (2005) Program for intensive production of virus-free garlic plants. Acta Hortic 688:195–200CrossRef Conci VC, Canavelli A, Balzarini M (2010) The distribution of garlic viruses in leaves and bulbs during the first year of infection. J Phytopathol 158:186–193. doi:10.1111/j.1439-0434.2009.01601.x CrossRef Dann AL, Wilson CR (2011) Comparative assessment of genetic and epigenetic variation among regenerants of potato (Solanum tuberosum) derived from long-term nodal tissue-culture and cell selection. Plant Cell Rep 30:631–639. doi:10.1007/s00299-010-0983-9 PubMed CrossRef De-la-Peña C, Nic-Can G, Ojeda G et al (2012) KNOX1 is expressed and epigenetically regulated during in vitro conditions in Agave spp. BMC Plant Biol 12:203. doi:10.1186/1471-2229-12-203 PubMed PubMedCentral CrossRef Di Rienzo JA, Casanoves F, Balzarini MG, Gonzalez L, Tablada M, Robledo CW (2014) InfoStat versión 2014. Grupo InfoStat, FCA, Universidad Nacional de Córdoba, Argentina. http://www.infostat.com.ar Díaz-Martínez M, Nava-Cedillo A, Guzmán-López JA et al (2012) Polymorphism and methylation patterns in Agave tequilana Weber var. “Azul” plants propagated asexually by three different methods. Plant Sci 185–186:321–330. doi:10.1016/j.plantsci.2012.01.004 PubMed CrossRef Douet, Tourmente (2007) Transcription of the 5S rRNA heterochromatic genes is epigenetically controlled in Arabidopsis thaliana and Xenopus laevis. Heredity 99:5–13. doi:10.1038/sj.hdy.6800964 PubMed CrossRef Ellis TH, Lee D, Thomas CM, Simpson PR, Cleary WG, Newman MA et al (1988) 5S rRNA genes in Pisum: sequence, long range and chromosomal organization. Mol Gen Genet 214:333–342PubMed CrossRef FAO (2014) Proposal for new work on a codex standard for garlic (Codex Alimentarius Comission, CX/FFV 14/18/10 - ADD.1; January 2014). ftp://ftp.fao.org/codex/meetings/ccffv/ccffv18/ff18_10_add1e.pdf . Accessed 10 Sept 2015 Fedoroff NV (2012) Transposable elements, epigenetics, and genome evolution. Science 80(338):758–767. doi:10.1126/science.338.6108.758 CrossRef Fraga HPF, Vieira LN, Caprestano CA et al (2012) 5-Azacytidine combined with 2,4-D improves somatic embryogenesis of Acca sellowiana (O. Berg) Burret by means of changes in global DNA methylation levels. Plant Cell Rep 31:2165–2176. doi:10.1007/s00299-012-1327-8 PubMed CrossRef Fulnecek J, Matyasek R, Kovarik A, Bezdek M (1998) Mapping of 5-methylcytosine residues in Nicotiana tabacum 5S rRNA genes by genomic sequencing. Mol Gen Genet 259:133–141PubMed CrossRef Gao X, Yang D, Cao D et al (2009) In vitro micro propagation of Freesia hybrida and the assessment of genetic and epigenetic stability in regenerated plantlets. J Plant Growth Regul 29:257–267. doi:10.1007/s00344-009-9133-4 CrossRef Garcia S, Khaitová L, Kovarík A (2012) Expression of 5S rRNA genes linked to 35S rDNA in plants, their epigenetic modification and regulatory element divergence. BMC Plant Biol 12:95. doi:10.1186/1471-2229-12-95 PubMed PubMedCentral CrossRef Goldsbrough PB, Ellis TH, Lomonossoff GP (1982) Sequence variation and methylation of the flax 5S RNA genes. Nucleic Acids Res 10:4501–4514PubMed PubMedCentral CrossRef Grellet F, Penon P (1984) Chromatin organization and methylation patterns of wheat 5S RNA genes. Plant Sci Lett 37:129–136CrossRef Helguera MP, Lunello P, Nome C, Conci VC (1997) Advances in the purification of filamentous viruses from garlic and in antisera production. Acta Hortic 433:623–630CrossRef Huang H, Han SS, Wang Y et al (2012) Variations in leaf morphology and DNA methylation following in vitro culture of Malus xiaojinensis. Plant Cell Tissue Organ Cult 111:153–161. doi:10.1007/s11240-012-0179-9 CrossRef Iciek M, Kwiecień I, Włodek L (2009) Biological properties of garlic and garlic-derived organosulfur compounds. Environ Mol Mutagen 50:247–265. doi:10.1002/em.20474 PubMed CrossRef Jakše J, Meyer JDF, Suzuki G et al (2008) Pilot sequencing of onion genomic DNA reveals fragments of transposable elements, low gene densities, and significant gene enrichment after methyl filtration. Mol Genet Genomics 280:287–292. doi:10.1007/s00438-008-0364-z PubMed CrossRef Kaeppler SM, Phillips RL (1993) Tissue culture-induced DNA methylation variation in maize. Proc Natl Acad Sci USA 90:8773–8776. doi:10.1073/pnas.90.19.8773 PubMed PubMedCentral CrossRef Kaeppler SM, Parke JL, Mueller SM et al (2000) Variation among maize inbred lines and detection of quantitative trait loci for growth at low phosphorus and responsiveness to arbuscular mycorrhizal fungi. Crop Sci 40:358–364CrossRef Kashkush K, Yaakov B (2011) Methylation, transcription, and rearrangements of transposable elements in synthetic allopolyploids. Int J Plant Genomics. doi:10.1155/2011/569826 PubMed PubMedCentral Kim DW, Jung TS, Nam SH et al (2009) Garlic ESTdb: an online database and mining tool for garlic EST sequences. BMC Plant Biol 9:61. doi:10.1186/1471-2229-9-61 PubMed PubMedCentral CrossRef Kotchoni SO, Gachomo EW, Betiku E, Olusoji O (2003) A home made kit for plasmid DNA mini-preparation. Afr J Biotechnol 2:88–90CrossRef Krzymińska A, Gawłowska M, Wolko B, Bocianowski J (2008) Genetic diversity of ornamental Allium species and cultivars assessed with isozymes. J Appl Genet 49:213–220. doi:10.1007/BF03195616 PubMed CrossRef Larkin PJ, Scowcroft WR (1981) Somaclonal variation—a novel source of variability from cell cultures for plant improvement. Theor Appl Genet 60:197–214. doi:10.1007/BF02342540 PubMed CrossRef Li X, Yu X, Wang N et al (2007) Genetic and epigenetic instabilities induced by tissue culture in wild barley (Hordeum brevisubulatum (Trin.) Link). Plant Cell Tissue Organ Cult 90:153–168. doi:10.1007/s11240-007-9224-5 CrossRef Lunello P, Ducasse D, Helguera M, Nome SF, Conci VC (2002) An Argentinean isolate of Leek yellow tripe virus from leek can be transmitted to garlic. J Plant Pathol 84:11–17 Lunello P, Di Rienzo J, Conci VC (2007) Yield loss in garlic caused by leek yellow stripe virus Argentinean isolate. Plant Dis 91:153–158. doi:10.1094/PDIS-91-2-0153 CrossRef Mascia PN, Rubenstein I, Phillips RL, Wang AS, Xiang LZ (1981) Localization of the 5S rRNA genes and evidence for diversity in the 5S rDNA region of maize. Gene 15:7–20PubMed CrossRef McCallum J, Baldwin S, Shigyo M et al (2012) AlliumMap-A comparative genomics resource for cultivated Allium vegetables. BMC Genom 13:168. doi:10.1186/1471-2164-13-168 CrossRef Milne RG, Luisoni E (1977) Rapid immune electron microscopy of virus preparations. In: Maramorosch K, Koprowski H (eds) Methods in Virology, vol 6. Academic Press, New York, pp 265–281 Moriconi DN, Conci VC, Nome SF (1990) Rapid multiplication of garlic (Allium sativum L.) in vitro. Phyton 51:145–151 Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4326. doi:10.1093/nar/8.19.4321 PubMed PubMedCentral CrossRef Ngezahayo F, Xu C, Wang H et al (2009) Tissue culture-induced transpositional activity of mPing is correlated with cytosine methylation in rice. BMC Plant Biol 9:91. doi:10.1186/1471-2229-9-91 PubMed PubMedCentral CrossRef Paterson AH, Bowers JE, Bruggmann R et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–556. doi:10.1038/nature07723 PubMed CrossRef Paz RC, Rendina González AP, Ferrer MS, Masuelli RW (2015) Short-term hybridization activates Tnt1 and Tto1 Copia retrotransposons in wild tuber-bearing Solanum species. Plant Biol 17(4):860–869. doi:10.1111/plb.12301 PubMed CrossRef Peredo EL, Arroyo-García R, Revilla MÁ (2009) Epigenetic changes detected in micropropagated hop plants. J Plant Physiol 166:1101–1111. doi:10.1016/j.jplph.2008.12.015 PubMed CrossRef Perotto MC, Conci VC, Cafrune EE, Alochis P, Bracamonte R (2003) Differences in the response of garlic cultivars to the eradication of five viruses. Phyton Int J Exp Bot: 233–240 Perotto MC, Cafrune EE, Conci VC (2010) The effect of additional viral infections on garlic plants initially infected with Allexiviruses. Eur J Plant Pathol 126:489–495. doi:10.1007/s10658-009-9555-7 CrossRef Phillips RL, Kaeppler SM, Olhoft P (1994) Genetic instability of plant tissue cultures: breakdown of normal controls. Proc Natl Acad Sci USA 91:5222–5226PubMed PubMedCentral CrossRef Piccolo FM, Fisher AG (2014) Getting rid of DNA methylation. Trends Cell Biol 24:136–143. doi:10.1016/j.tcb.2013.09.001 PubMed CrossRef Pittler MH, Ernst E (2007) Clinical effectiveness of garlic (Allium sativum). Mol Nutr Food Res 51:1382–1385. doi:10.1002/mnfr.200700073 PubMed CrossRef Rafalski JA, Wiewiorowski M, Soll D (1982) Organization and nucleotide sequence of nuclear 5S rRNA genes in yellow lupin (Lupinus luteus). Nucleic Acids Res 10:7635–7642PubMed PubMedCentral CrossRef Ramírez-Malagón, Pérez-Moreno, Borodanenko et al (2006) Differential organ infection studies, potyvirus elimination, and field performance of virus-free garlic plants produced by tissue culture. Plant Cell Tissue Organ Cult 86:103–110. doi:10.1007/s11240-006-9102-6 CrossRef Rival A, Ilbert P, Labeyrie A et al (2013) Variations in genomic DNA methylation during the long-term in vitro proliferation of oil palm embryogenic suspension cultures. Plant Cell Rep 32:359–368. doi:10.1007/s00299-012-1369-y PubMed CrossRef Rivlin RS (2001) Historical perspective on the use of garlic. J Nutr 131:951–954 Rodríguez López CM, Wetten AC, Wilkinson MJ (2010) Progressive erosion of genetic and epigenetic variation in callus-derived cocoa (Theobroma cacao) plants. New Phytol 186:856–868. doi:10.1111/j.1469-8137.2010.03242.x PubMed CrossRef Rohlf FJ (1998) NTSYS-pc: numerical taxonomy system, ver. 2.1. Exeter Publications, Setauket Santos MDM, Buso GCS, Torres AC (2008) Evaluation of genetic variability in micropropagated propagules of ornamental pineapple [Ananas comosus var. bracteatus (Lindley) Coppens and Leal] using RAPD markers. Genet Mol Res 7:1097–1105. doi:10.4238/vol7-4gmr489 PubMed CrossRef Schlüter PM, Harris SA (2006) Analysis of multilocus fingerprinting data sets containing missing data. Mol Ecol Notes 6:569–572. doi:10.1111/j.1471-8286.2006.01225.x CrossRef Shahraeen N, Lesemann DE, Ghotbi T (2008) Survey for viruses infecting onion, garlic and leek crops in Iran. EPPO Bull 38:131–135. doi:10.1111/j.1365-2338.2008.01198.x CrossRef Simon PW, Jenderek MM (2003) Flowering, seed production and the genesis of garlic breeding. 23:211–244 Smulders MJM, Rus-Kortekaas W, Vosman B (1995) Tissue culture-induced DNA methylation polymorphisms in repetitive DNA of tomato calli and regenerated plants. Theor Appl Genet 91:1257–1264. doi:10.1007/BF00220938 PubMed CrossRef Sun X, Zhou S, Meng F, Liu S (2012) De novo assembly and characterization of the garlic (Allium sativum) bud transcriptome by Illumina sequencing. Plant Cell Rep 31:1823–1828. doi:10.1007/s00299-012-1295-z PubMed CrossRef Sun S, Zhong J, Li S, Wang X (2013) Tissue culture-induced somaclonal variation of decreased pollen viability in torenia (Torenia fournieri Lind.). Bot Stud 54:36. doi:10.1186/1999-3110-54-36 CrossRef Suzuki G, Ura A, Saito N et al (2001) BAC FISH analysis in Allium cepa. Genes Genet Syst 76:251–255. doi:10.1266/ggs.76.251 PubMed CrossRef Taşkin H, Baktemur G, Kurul M, Büyükalaca S (2013) Use of tissue culture techniques for producing virus-free plant in garlic and their identification through real-time PCR. Sci World J. doi:10.1155/2013/781282 Torres-Morán MI, Escoto-Delgadillo M, Molina-Moret S et al (2010) Assessment of genetic fidelity among Agave tequilana plants propagated asexually via rhizomes versus in vitro culture. Plant Cell Tissue Organ Cult 103:403–409. doi:10.1007/s11240-010-9777-6 CrossRef Us-Camas R, Rivera-Solís G, Duarte-Aké F, De-la-Peña C (2014) In vitro culture: an epigenetic challenge for plants. Plant Cell Tissue Organ Cult 118:187–201. doi:10.1007/s11240-014-0482-8 CrossRef Vitte C, Estep MC, Leebens-Mack J, Bennetzen JL (2013) Young, intact and nested retrotransposons are abundant in the onion and asparagus genomes. Ann Bot 112:881–889. doi:10.1093/aob/mct155 PubMed PubMedCentral CrossRef Volk GM, Henk AD, Richards CM (2004) Genetic diversity among US garlic clones as detected using AFLP methods. J Am Soc Hortic Sci 129:559–569 Vos P, Hogers R, Bleeker M et al (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414. doi:10.1093/nar/23.21.4407 PubMed PubMedCentral CrossRef Wang QM, Wang YZ, Sun LL et al (2012) Direct and indirect organogenesis of Clivia miniata and assessment of DNA methylation changes in various regenerated plantlets. Plant Cell Rep 31:1283–1296. doi:10.1007/s00299-012-1248-6 PubMed CrossRef Wang X, Wu R, Lin X et al (2013) Tissue culture-induced genetic and epigenetic alterations in rice pure-lines, F1 hybrids and polyploids. BMC Plant Biol 13:77. doi:10.1186/1471-2229-13-77 PubMed PubMedCentral CrossRef Wu Y, Wu R, Zhang B et al (2011) Epigenetic instability in genetically stable micro propagated plants of Gardenia jasminoides Ellis. Plant Growth Regul 66:137–143. doi:10.1007/s10725-011-9637-3 CrossRef Xiong LZ, Xu CG, Saghai Maroof MA, Zhang Q (1999) Patterns of cytosine methylation in an elite rice hybrid and its parental lines, detected by a methylation-sensitive amplification polymorphism technique. Mol Gen Genet 261:439–446. doi:10.1007/s004380050986 PubMed CrossRef Xu M, Li X, Korban SS (2004) DNA-methylation alterations and exchanges during in vitro cellular differentiation in rose (Rosa hybrida L.). Theor Appl Genet 109:899–910. doi:10.1007/s00122-004-1717-6 PubMed CrossRef Yap I, Nelson RJ (1996) WinBoot: a program for performing bootstrap analysis of binary data to determine the confidence limits of UPGMA-based dendrograms. International Rice Research Institute, Manila Yu J, Hu S, Wang J et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79–92. doi:10.1126/science.1068037 PubMed CrossRef
1. Laboratorio de Biología Molecular, Instituto de Biología Agrícola de Mendoza, Consejo Nacional de Investigaciones Científicas y Técnicas (IBAM-CONICET), Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Almirante Brown 500, Chacras de Coria, Mendoza, Argentina 2. CIGEOBIO (FCEFyN, UNSJ/CONICET), Av. Ignacio de la Roza 590 (Oeste), J5402DCS, Rivadavia, San Juan, Argentina 3. Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV), Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), Camino 60 cuadras km 5.5 (Av. 11 de setiembre 4755), Córdoba, Córdoba, Argentina 4. Instituto de Patología Vegetal (IPAVE), Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), Camino 60 cuadras km 5.5 (Av. 11 de setiembre 4755), Córdoba, Córdoba, Argentina 5. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Córdoba, Argentina 6. EEA Mendoza, Instituto Nacional de Tecnología Agropecuaria (INTA), San Martín 3853, (5507), Luján de Cuyo, Mendoza, Argentina
Key message This is the first report assessing epigenetic variation in garlic. High genetic and epigenetic polymorphism during in vitro culture was detected. Sequencing of MSAP fragments revealed homology with ESTs.