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Detection of somaclonal variation during cocoa somatic embryogenesis characterised using cleaved amplified polymorphic sequence and the new freeware Artbio

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Abstract

The scarcity and stochastic nature of genetic mutations presents a significant challenge for scientists seeking to characterise de novo mutation frequency at specific loci. Such mutations can be particularly numerous during regeneration of plants from in vitro culture and can undermine the value of germplasm conservation efforts. We used cleaved amplified polymorphic sequence (CAPS) analysis to characterise new mutations amongst a clonal population of cocoa plants regenerated via a somatic embryogenesis protocol used previously for cocoa cryopreservation. Efficacy of the CAPS system for mutation detection was greatly improved after an ‘a priori’ in silico screen of reference target sequences for actual and potential restriction enzyme recognition sites using a new freely available software called Artbio. Artbio surveys known sequences for existing restriction enzyme recognition sites but also identifies all single nucleotide polymorphism (SNP) deviations from such motifs. Using this software, we performed an in silico screen of seven loci for restriction sites and their potential mutant SNP variants that were possible from 21 restriction enzymes. The four most informative locus-enzyme combinations were then used to survey the regenerant populations for de novo mutants. We characterised the pattern of point mutations and, using the outputs of Artbio, calculated the ratio of base substitution in 114 somatic embryo-derived cocoa regenerants originating from two explant genotypes. We found 49 polymorphisms, comprising 26.3% of the samples screened, with an inferred rate of 2.8 × 10−3 substitutions/screened base. This elevated rate is of a similar order of magnitude to previous reports of de novo microsatellite length mutations arising in the crop and suggests caution should be exercised when applying somatic embryogenesis for the conservation of plant germplasm.

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References

  • Albani MC, Wilkinson MJ (1998) Inter simple sequence repeat polymerase chain reaction for the detection of somaclonal variation. Plant Breed 117:573–575

    Article  Google Scholar 

  • Bala A, Murphy P, Giller KE (2003) Distribution and diversity of rhizobia nodulating agroforestry legumes in soils from three continents in the tropics. Mol Ecol 12:917–930

    Article  CAS  PubMed  Google Scholar 

  • Blondon F, Marie D, Brown S, Kondorosi A (1994) Genome size and base composition in Medicago sativa and M. Truncatula species. Plant Genet Breed 37(2):264–270

    CAS  Google Scholar 

  • Bouman H, De Klerk GJ (2001) Measurement of the extent of somaclonal variation in begonia plants regenerated under various conditions. Comparison of three assays. Theor Appl Genet 102:111–117

    Article  CAS  Google Scholar 

  • Britt BA (1999) Molecular genetics of DNA repair in higher plants. Trends Plant Sci 4:20–22

    Article  PubMed  Google Scholar 

  • Chan TA, Hermekin H, Lengauer C, Kinzler KW, Vogelstein B (1999) 14–3-3 is required to prevent mitotic catastrophe after DNA damage. Nature 401:616–620

    Article  CAS  PubMed  Google Scholar 

  • Charters YM (2000) The potential of anchored microsatellite analysis for cocoa germplasm characterization. PhD thesis, School of Plant Sciences, Reading University

  • Cheng KC, Cahill SD, Kasai H, Nishimura S, Loeb LA (1992) 8-Hydroxyguanine, an abundant form of oxidative DNA damage, causes G-T and A-C substitutions. J Biol Chem 267(1):166–172

    CAS  PubMed  Google Scholar 

  • Clegg MT, Gaus BS, Learn GH, Morton BR (1994) Rates and patterns of chloroplast DNA evolution. Proc Natl Acad Sci USA 91:6795–6801

    Article  CAS  PubMed  Google Scholar 

  • Cotton RGH (1997) Mutation detection. Oxford University Press, Oxford

    Google Scholar 

  • Dahl F, Stenberg J, Fredriksson S, Welch K, Zhang M, Nilsson M, Bicknell D, Bodmer WF, Davis RW, Ji H (2007) Multigene amplification and massively parallel sequencing for cancer mutation discovery. Proc Natl Acad Sci USA 104(22):9387–9392

    Article  CAS  PubMed  Google Scholar 

  • Devos KM, Beales J, Ogihara Y, Doust AN (2005) Comparative sequence analysis of the Phytochrome C Gene and its upstream region in allohexaploid wheat reveals new data on the evolution of its three constituent genomes. Plant Mol Biol 58(5):625–641

    Article  CAS  PubMed  Google Scholar 

  • Fang JY, Wetten A, Hadley P (2004) Cryopreservation of cocoa (Theobroma cacao L.) somatic embryos for long-term germplasm storage. Plant Sci 166(3):669–675

    Article  CAS  Google Scholar 

  • Gautier C (2000) Compositional bias in DNA. Curr Opin Genet Dev 10:656–661

    Article  CAS  PubMed  Google Scholar 

  • González-Martínez SC, Wheeler NC, Ersoz E, Nelson CD, Neale DB (2007) Association genetics in Pinus taeda L. I. Wood Property Traits. Genetics 175:399–409

    Article  PubMed  Google Scholar 

  • Graur D, Li WH (2000) Fundamentals of molecular evolution. Sinauer, Sunderland

    Google Scholar 

  • GuhaMajumdar M, Sears BB (2005) Chloroplast DNA base substitutions: an experimental assessment. Mol Gen Genomics 273:177–183

    Article  CAS  Google Scholar 

  • Jin N, Chow CY, Liu L, Zolov SN, Bronson R, Davisson M, Petersen JL, Zhang Y, Park S, Duex JE, Goldowitz D, Meisler MH, Weisman LS (2008) VAC14 nucleates a protein complex essential for the acute interconversion of PI3P and PI(3, 5)P2 in yeast and mouse. EMBO J 27(24):3221–3234

    Article  CAS  PubMed  Google Scholar 

  • Joyce SM, Cassells AC, Jain SM (2003) Stress and aberrant phenotypes in in vitro culture. Plant Cell Tissue Organ Cult 74:103–121

    Article  CAS  Google Scholar 

  • Kaeppler SM, Phillips RL, Olhoft P (1998) Molecular basis of heritable tissue culture-induced variation in plants. Current plant science and biotechnology in agriculture. Kluwer, Dordrecht

    Google Scholar 

  • Karling S, Burge C, Campbell AM (1992) Statistical analyses of counts and distributions of restriction sites in DNA sequences. Nucl Acids Res 20:1363–1370

    Article  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16(2):111–120

    Article  CAS  PubMed  Google Scholar 

  • Kohler SW, Provost GS, Fieck A, Kretz PL, Bullock WO, Sorge JA, Putmant DL, Short JM (1991) Spectra of spontaneous and mutagen-induced mutations in the lacIgene in transgenic mice. Proc Natl Acad Sci USA 88:7958–7962

    Article  CAS  PubMed  Google Scholar 

  • Lanaud C, Risterucci AM, Pieretti I, Falque M, Bouet A, Lagoda PJL (1999) Isolation and characterization of microsatellites in Theobroma cacao L. Mol Ecol 8:2141–2143

    Article  CAS  PubMed  Google Scholar 

  • Li Z, Traore A, Maximova SN, Gupta PK (1998) Somatic embryogenesis and plant regeneration from floral explants of cocoa (Theobroma cacao L.) using thidiazuron. In Vitro Cell Dev Biol Plant 34:293–299

    Article  CAS  Google Scholar 

  • Lopez-Baez O, Bollon H, Eskes A (1993) Embryogenèse somatique de cacaoyer Theobroma cacao L. à partir de pièces florales. C R Acad Sci Paris 316:579–584

    Google Scholar 

  • Maki H (2002) Origins of spontaneous mutations: specificity and directionality of base-substitution, frameshift, and sequence-substitution mutageneses. Annu Rev Genet 36:279–303

    Article  CAS  PubMed  Google Scholar 

  • Marie D, Brown SC (1993) A cytometric exercise in plant DNA histograms, with 2C values for 70 species. Biol Cell 78:41–51

    Article  CAS  PubMed  Google Scholar 

  • Noro Y, Takano-Shimizu T, Syono K, Kishima Y, Sano Y (2007) Genetic variations in rice in vitro cultures at the EPSPs-RPS20 region. Theor Appl Genet 114(4):705–711

    Article  CAS  PubMed  Google Scholar 

  • Oh TJ, Cullis MA, Kunert K, Engelborghs I, Swennen R, Cullis CA (2007) Genomic changes associated with somaclonal variation in banana (Musa spp.). Physiol Plant 129(4):766–774

    Article  CAS  Google Scholar 

  • Paton NW, Khan SA, Hayes A, Moussouni F, Brass A, Eilbeck K, Goble CA, Hubbard SJ (2000) Conceptual modelling of genomic information. Bioinformatics 16(6):548–557

    Article  CAS  PubMed  Google Scholar 

  • Peschke VM, Phillips RL (1992) Genetic implications of somaclonal variation in plants. Adv Genet 13:41–76

    Article  Google Scholar 

  • Phillips RL, Kaeppler SM, Olhoft P (1994) Genetic instability of plant tissue cultures: breakdown of normal controls. Proc Natl Acad Sci USA 91:5222–5226

    Article  CAS  PubMed  Google Scholar 

  • Piwnica-Worms H (1999) Fools in rush in. Nature 401:535–537

    Article  CAS  PubMed  Google Scholar 

  • Radman M (1999) Enzymes of evolutionary change. Nature 401:866–869

    Article  CAS  PubMed  Google Scholar 

  • Risterucci AM, Grivet L, N’Goran J, Pieretti I, Flament MH, Lanaud C (2000) A high density linkage map of Theobroma cacao L. Theor Appl Genet 101:948–955

    Article  CAS  Google Scholar 

  • Rodríguez López CM, Wetten AC, Wilkinson MJ (2004) Detection and quantification of in vitro-culture induced chimerism using simple sequence repeats (SSR) analysis in Theobroma cacao (L.). Theor Appl Genet 110:157–166

    Article  PubMed  Google Scholar 

  • Rognes T, Seeberg E (1998) SALSA: improved protein database searching by a new algorithm for assembly of sequence fragments into gapped alignments. Bioinformatics 14:839–845

    Article  CAS  PubMed  Google Scholar 

  • Sagot M-F, Wakabayashi Y (2003) Pattern inference under many guises. In: Reed BA, Sales CL (eds) Recent advances in algorithms and combinatorics. Springer, New York, pp 245–287

    Chapter  Google Scholar 

  • Sahasrabudhe SR, Luo X, Humayun MZ (1991) Specificity of base substitutions induced by the acridine mutagen ICR-191: mispairing by guanine N7 adducts as a mutagenic mechanism. Genetics 119:981–989

    Google Scholar 

  • Sawa S, Ito T, Okada K (1997) A rapid method for detection of single base changes in Arabidopsis thaliana using the polymerase chain reaction. Plant Mol Biol Reporter 15:179–185

    Article  CAS  Google Scholar 

  • Thomas RK, Nickerson E, Simons JF, Jänne PA, Tengs T, Yuza Y, Garraway LA, LaFramboise T, Lee JC, Shah K, O’Neill K, Sasaki H, Lindeman N, Wong K-K, Borras AM, Gutmann EJ, Dragnev KH, DeBiasi R, Chen T-H, Glatt KA, Greulich H, Desany B, Lubeski CK, Brockman W, Alvarez P, Hutchison SK, Leamon JH, Ronan MT, Turenchalk GS, Egholm M, Sellers WR, Rothberg JM, Meyerson M (2006) Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing. Nature Med 12:852–855

    Article  CAS  PubMed  Google Scholar 

  • Thomas RK, Baker AC, Debiasi RM, Winckler W, Laframboise T, Lin WM, Wang M, Feng W, Zander T, Macconnaill LE, Lee JC, Nicoletti R, Hatton C, Goyette M, Girard L, Majmudar K, Ziaugra L, Wong KK, Gabriel S, Beroukhim R, Peyton M, Barretina J, Dutt A, Emery C (2007) High-throughput oncogene mutation profiling in human cancer. Nature Genet 39:347–351

    Article  CAS  PubMed  Google Scholar 

  • Traore A, Maximova SN, Guiltinan MJ (2003) Micropropagation of Theobroma cacao L. using somatic embryo-derived plants. In vitro Cell Dev Biol Plant 39:332–337

    Article  CAS  Google Scholar 

  • Vettori C, Vendramin GG, Anzidei M, Pastorelli R, Paffetti D, Glannini R (2004) Geographic distribution of chloroplast variation in Italian populations of beech (Fagus sylvatica L.). Theor Appl Genet 109:1–9

    Article  CAS  PubMed  Google Scholar 

  • Wang D, Kreutzer DA, Essigmann JM (1998) Mutagenicity and repair of oxidative DNA damage: insights from studies using defined lesions. Mutat Res 400(1–2):99–115

    CAS  PubMed  Google Scholar 

  • Whittaker JC, Harbord RM, Boxall N, Mackay I, Dawson G, Sibly RM (2003) Likelihood-based estimation of microsatellite mutation rates. Genetics 164:781–787

    PubMed  Google Scholar 

  • Wolfe KH, Sharp PM, Wen-Hsiung L (1987) Rates of nucleotide substitutions vary greatly among plant mitochondrial, chloroplast and nuclear DNAs. Proc Natl Acad Sci USA 84:9054–9058

    Article  CAS  PubMed  Google Scholar 

  • Wolfe KH, Sharp PM, Wen-Hsiung L (1989) Rates of synonymous substitutions in plant nuclear genes. Mol Evol 29:208–211

    Article  CAS  Google Scholar 

  • Yu J, Buckler ES (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotech 17(2):155–160

    CAS  PubMed  Google Scholar 

  • Zakeri S, Mehrizi AA, Djadid ND, Snounou G (2006) Circumsporozoite protein gene diversity among temperate and tropical Plasmodium vivax isolates from Iran. Trop Med Int Health 11(5):729–737

    Article  CAS  PubMed  Google Scholar 

  • Zoldos V, Papes D, Brown SC, Panaud O, Siljak-Yakovlev S (1998) Genome size and base composition of seven Quercus species: inter- and intra-population. Genome 41:162–168

    Article  CAS  Google Scholar 

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Acknowledgments

We thank Cocoa Research UK for funding this study.

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Authors and Affiliations

  1. School of Biological Sciences, Reading University, Whiteknights, Reading, RG6 6AS, UK

    Andrew C. Wetten

  2. Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Penglais, Ceredigion, SY23 3DA, UK

    Carlos M. Rodríguez López & Michael J. Wilkinson

  3. Fundación de Estudios Portuarios, 38006, S/C de Tenerife, Spain

    Hector Sicilia Bravo

Authors
  1. Carlos M. Rodríguez López
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  2. Hector Sicilia Bravo
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Correspondence to Carlos M. Rodríguez López.

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Rodríguez López, C.M., Bravo, H.S., Wetten, A.C. et al. Detection of somaclonal variation during cocoa somatic embryogenesis characterised using cleaved amplified polymorphic sequence and the new freeware Artbio. Mol Breeding 25, 501–516 (2010). https://doi.org/10.1007/s11032-009-9348-x

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