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Comparison of the Coffea canephora and C. arabica karyotype based on chromosomal DNA content

  • Genetics and Genomics
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Abstract

Nuclear genome size has been measured in various plants, seeing that knowledge of the DNA content is useful for taxonomic and evolutive studies, plant breeding programs and genome sequencing projects. Besides the nuclear DNA content, tools and protocols to quantify the chromosomal DNA content have been also applied, expanding the data about genomic structure. This study was conducted in order to calculate the Coffea canephora and Coffea arabica chromosomal DNA content, associating cytogenetic methodologies with flow cytometry (FCM) and image cytometry (ICM) tools. FCM analysis showed that the mean nuclear DNA content of C. canephora and C. arabica is 2C = 1.41 and 2.62 pg, respectively. The cytogenetic methodology provided prometaphase and metaphase cells exhibiting adequate chromosomes for the ICM measurements and karyogram assembly. Based on cytogenetic, FCM and ICM results; it was possible to calculate the chromosomal DNA content of the two species. The 1C chromosomal DNA content of C. canephora ranged from 0.09 (chromosome 1) to 0.05 pg (chromosome 11) and C. arabica from 0.09 (chromosome 1) to 0.03 pg (chromosome 22). The methodology presented in this study was suitable for DNA content measuring of each chromosome of C. canephora and C. arabica. The cytogenetic characterization and chromosomal DNA content analyses evidenced that C. arabica is a true allotetraploid originated from a cross between Coffea diploid species. Besides, the same analyses also reinforce that C. canephora is a possible progenitor of C. arabica.

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Abbreviations

bp:

Base pairs

pg:

Picograms

FCM:

Flow cytometry

ICM:

Image cytometry

PI:

Propidium iodide

IOD:

Integrated optical density

CV:

Coefficient of variation

References

  • Abreu IS, Carvalho CR, Clarindo WR (2008) Chromosomal DNA content of sweet pepper determined by association of cytogenetic and cytometric tools. Plant Cell Rep 27:1227–1233. doi:10.1007/s00299-008-0539-4

    Article  PubMed  CAS  Google Scholar 

  • Alan AR, Zeng H, Assani A, Shi W, McRae HE, Murch SJ, Saxena PK (2007) Assessment of genetic stability of the germplasm lines of medicinal plant Scutellaria baicalensis Georgi (huang-qin) in long-term, in vitro maintained cultures. Plant Cell Rep 26:1345–1355. doi:10.1007/s00299-007-0332-9

    Article  PubMed  CAS  Google Scholar 

  • Berthouly M, Michaux-Ferriere NM (1996) High frequency somatic embryogenesis in Coffea canephora. Plant Cell Tissue Organ Cult 44:169–176. doi:10.1007/bf00048196

    Article  Google Scholar 

  • Bogunic F, Muratovic E, Brown SC, Siljak-Yakovlev S (2003) Genome size and base composition of five Pinus species from the Balkan region. Plant Cell Rep 22:59–63. doi:10.1007/s00299-003-0653-2

    Article  PubMed  CAS  Google Scholar 

  • Caixeta ET, Carvalho CR (2000) Chromomeric pattern of maize pachytene chromosomes after trypsin treatment. Hereditas 133:183–187. doi:10.1111/j.1601-5223.2000.00183-x

    Article  PubMed  CAS  Google Scholar 

  • Carvalho CR, Saraiva LS (1993) A new heterochromatin banding pattern revealed by modified HKG banding technique for maize chromosomes. Heredity 70:515–519

    Article  Google Scholar 

  • Carvalho CR, Clarindo WR, Praça MM, Araújo FS, Carels N (2008) Genome size, base composition and karyotype of Jatropha curcas L., an important biofuel plant. Plant Sci 174:613–617. doi:10.1016/j.plantsci.2008.03.010

    Article  CAS  Google Scholar 

  • Chieco P, Derenzini M (1999) The Feulgen reaction 75 years on. Histochem Cell Biol 111:345–358. doi:10.1007/s004180050367

    Article  PubMed  CAS  Google Scholar 

  • Clarindo WR, Carvalho CR (2006) A high quality chromosome preparation from cell suspension aggregates culture of Coffea canephora. Cytologia 71:243–249. doi:10.1508/cytologia.71.243

    Article  Google Scholar 

  • Clarindo WR, Carvalho CR (2008) First Coffea arabica karyogram showing that this species is a true allotetraploid. Plant Syst Evol 274:237–241. doi:10.1007/s00606-008-0050-y

    Article  Google Scholar 

  • Clarindo WR, Carvalho CR, Alves BMG (2007) Mitotic evidence for the tetraploid nature of Glycine max provided by high quality karyograms. Plant Syst Evol 265:101–107. doi:10.1007/s00606-007-0522-5

    Article  Google Scholar 

  • Cros J, Gavalda MC, Chabrillange N, Recalt C, Duperray C, Hamon S (1994) Variations in the total nuclear DNA content in African Coffea species (Rubiaceae). Café Cacao Thé 38:3–10

    CAS  Google Scholar 

  • Cros J, Combes MC, Chabrillange N, Duperray C, Angles AM, Hamon S (1995) Nuclear DNA content in the subgenus Coffea (Rubiaceae): inter- and intra-specific variation in African species. Can J Bot 73:14–20

    Article  Google Scholar 

  • Doležel J, Bartoš J (2005) Plant DNA flow cytometry and estimation of nuclear genome size. Ann Bot 95:99–110. doi:10.1093/aob/mci005

    Article  PubMed  CAS  Google Scholar 

  • Doležel J, Sgorbati S, Lucretti S (1992) Comparation of three DNA fluorochromes for flow cytometric estimation of nuclear DNA content in plants. Plant Physiol 85:625–631

    Article  Google Scholar 

  • Doležel J, Greilhuber J, Lucretti S, Meister A, Lysák MA, Nardi L, Obermayer R (1998) Plant genome size estimation by flow cytometry: inter-laboratory comparison. Ann Bot 82:17–26

    Article  Google Scholar 

  • Doležel J, Lysák MA, Kubaláková M, Šimková H, Macas J, Lucretti S (2001) Sorting of plant chromosomes. In: Darzynkiewiez Z, Crissman HA, Robinson JP (eds) Cytometry, 3rd edn, part B, vol 64. Academic, San Diego, pp 3–31

    Chapter  Google Scholar 

  • Doležel J, Bartoš J, Voglmayr H, Greilhuber J (2003) Nuclear DNA and genome size of trout and human. Cytometry 51:127–128

    Article  PubMed  Google Scholar 

  • Doležel J, Kubaláková M, Bartoš J, Macas J (2004) Flow cytogenetics and plant genome mapping. Chromosome Res 12:77–91. doi:10.1023/b:chro.0000009293.15189.e5

    Article  PubMed  Google Scholar 

  • Doležel J, Kubaláková M, Paux E, Bartoš J, Feuillet C (2007) Chromosome-based genomics in the cereals. Chromosome Res 15:51–66. doi:10.1007/s10577-006-1106-x

    Google Scholar 

  • Fontes BPD (2003) Citogenética, citometria de fluxo e citometria de imagem em Coffea spp. Ph.D. thesis, Department of General Biology, The University of Viçosa, Viçosa

  • Galbraith DW, Harkins KR, Maddox JM, Ayres NM, Sharma DP, Firoozabady E (1983) Rapid flow cytometric analysis of the cell cycle in intact plant tissues. Science 220:1049–1051

    Article  PubMed  CAS  Google Scholar 

  • Greilhuber J (2005) Intraspecific variation in genome size in Angiosperms: identifying its existence. Ann Bot 95:91–98. doi:10.1093/aob/mci004

    Article  PubMed  CAS  Google Scholar 

  • Greilhuber J, Ebert I (1994) Genome size variation in Pisum sativum. Genome 37:646–655

    Article  PubMed  CAS  Google Scholar 

  • Hardie DC, Gregory TR, Hebert PDN (2002) From pixels to picograms: a beginners’ guide to genome quantification by Feulgen image analysis densitometry. J Histochem Cytochem 50:735–749

    PubMed  CAS  Google Scholar 

  • Kovářová P, Navrátilová A, Macas J, Doležel J (2007) Chromosome analysis and sorting in Vicia sativa using flow cytometry. Biol Plant 51:43–48

    Article  Google Scholar 

  • Lashermes P, Cros J, Combes MC, Trouslot P, Anthony F, Hamon S, Charrier A (1996) Inheritance and restriction fragment length polymorphism of chloroplast DNA in the genus Coffea L. Theor Appl Genet 93:626–632. doi:10.1007/BF00417958

    Article  CAS  Google Scholar 

  • Lashermes P, Combes MC, Trouslot P, Charrier A (1997) Phylogenetic relationships of coffee-tree species (Coffea L.) as inferred from ITS sequences of nuclear ribosomal DNA. Theor Appl Genet 94:947–955. doi:10.1007/s001220050500

    Article  CAS  Google Scholar 

  • Lashermes P, Combes MC, Robert J, Trouslot P, D’Hont A, Anthony F, Charrier A (1999) Molecular characterization and origin of the Coffea arabica L. genome. Mol Gen Genet 261:259–266

    Article  PubMed  CAS  Google Scholar 

  • Lee JH, Arumuganathan K, Kaeppler SM, Park SW, Kim KY, Chung YS, Kim DH, Fukui K (2002) Variability of chromosomal DNA contents in maize (Zea mays L.) inbred and hybrid lines. Planta 215:666–671. doi:10.1007/s00425-002-0793-6

    Article  PubMed  CAS  Google Scholar 

  • Lee JH, Ma Y, Wako T, Li LC, Kim KY, Park SW, Uchiyama S, Fukui K (2004) Flow karyotypes and chromosomal DNA contents of genus Triticum species and rye (Secale cereale). Chromosome Res 12:93–102. doi:10.1023/B:CHRO.0000009327.45035.84

    Article  PubMed  CAS  Google Scholar 

  • Loureiro J, Rodriguez E, Doležel J, Santos C (2006a) Comparison of four nuclear isolation buffers for plant DNA flow cytometry. Ann Bot 98:679–689. doi:10.1093/aob/mcl141

    Article  PubMed  CAS  Google Scholar 

  • Loureiro J, Rodriguez E, Doležel J, Santos C (2006b) Flow cytometric and microscopic analysis of the effect of tannic acid on plant nuclei and estimation of DNA content. Ann Bot 98:515–527. doi:10.1093/aob/mcl140

    Article  PubMed  CAS  Google Scholar 

  • Lucretti S, Doležel J, Schubert I, Fuchs J (1993) Flow karyotyping and sorting of Vicia faba chromosomes. Theor Appl Genet 85:665–672. doi:10.1007/bf00225003

    Article  Google Scholar 

  • Mahé L, Combes M, Lashermes P (2007) Comparison between a coffee single copy chromosomal region and Arabidopsis duplicated counterparts evidenced high level synteny between the coffee genome and the ancestral Arabidopsis genome. Plant Mol Biol 64:699–711. doi:10.1007/s11103-007-9191-6

    Article  PubMed  CAS  Google Scholar 

  • Neumann P, Lysák M, Doležel J, Macas J (1998) Isolation of chromosomes from Pisum sativum L. hairy root cultures and their analysis by flow cytometry. Plant Sci 137:205–215. doi:10.1016/S0168-9452(98)00141-1

    Article  CAS  Google Scholar 

  • Noirot M, Barre P, Duperray C, Louarn J, Hamon S (2003a) Effects of caffeine and chlorogenic acid on propidium iodide accessibility to DNA: consequences on genome size evaluation in coffee tree. Ann Bot 92:259–264. doi:10.1093/aob/mcg139

    Article  PubMed  CAS  Google Scholar 

  • Noirot M, Poncet V, Barre P, Hamon P, Hamon S, Kochko A (2003b) Genome size variations in diploid African Coffea species. Ann Bot 92:709–714. doi:10.1093/aob/mcg183

    Article  PubMed  CAS  Google Scholar 

  • Otto FJ (1990) DAPI staining of fixed cells for high-resolution flow cytometry of nuclear DNA. In: Darzynkiewiez Z, Crissman HA, Robinson JP (eds) Methods in cell biology, vol 33. Academic, San Diego, pp 105–110

    Google Scholar 

  • Pinto G, Loureiro J, Lopes T, Santos C (2004) Analysis of the genetic stability of Eucalyptus globulus Labill. somatic embryos by flow cytometry. Theor Appl Genet 109:580–587. doi:10.1007/s00122-004-1655-3

    CAS  Google Scholar 

  • Puech M, Giroud F (1999) Standardization of DNA quantitation by image analysis: quality control of instrumentation. Cytometry 36:11–17

    Article  PubMed  CAS  Google Scholar 

  • Raina SN, Mukai Y, Yamamoto M (1998) In situ hybridization identifies the diploid progenitor species of Coffea arabica (Rubiaceae). Theor Appl Genet 97:1204–1209. doi:10.1007/s001220051011

    Article  Google Scholar 

  • Rijo L (1974) Observações cariológicas no cafeeiro ‘Híbrido de Timor’. Port Acta Biol 8:157–168

    Google Scholar 

  • Rossi AAB, Clarindo WR, Carvalho CR, Oliveira LO (2008) Karyotype and nuclear DNA content of Psychotria ipecacuanha: a medicinal species. Cytologia 73:53–60

    Article  Google Scholar 

  • Van Boxtel J, Berthouly M (1996) High frequency somatic embryogenesis from coffee leaves. Factors influencing embryogenesis and subsequent proliferation and regeneration in liquid medium. Plant Cell Tissue Organ Cult 44:4–17. doi:10.1007/bf00045907

    Article  Google Scholar 

  • Veuskens J, Marie D, Hinnisdaels S, Brown SC (1999) Analysis and sorting of plant chromosomes by flow cytometry. In: Radbruch A (ed) Flow cytometry and cell sorting, Springer Lab Manual, 2nd edn. Springer, Berlin, pp 277–292

    Google Scholar 

  • Vilhar B, Dermastia M (2002) Standardization of instrumentation in plant DNA image cytometry. Acta Bot Croat 61:11–26

    CAS  Google Scholar 

  • Vilhar B, Greilhuber J, Koce JD, Temsch EM, Dermastia M (2001) Plant genome size measurement with DNA image cytometry. Ann Bot 87:719–728. doi:10.1006/anbo.2001.1394

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

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Acknowledgments

We thank CNPq—Conselho Nacional de Desenvolvimento Científico e Tecnológico, CBP&D/Café—Consórcio Brasileiro de Pesquisa e Desenvolvimento do Café and FAPEMIG—Fundação de Amparo à Pesquisa do Estado de Minas Gerais, Brazil, for their financial support.

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Authors and Affiliations

  1. Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil

    Wellington Ronildo Clarindo & Carlos Roberto Carvalho

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  1. Wellington Ronildo Clarindo
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  2. Carlos Roberto Carvalho
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Correspondence to Carlos Roberto Carvalho.

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Communicated by J. C. Register.

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Clarindo, W.R., Carvalho, C.R. Comparison of the Coffea canephora and C. arabica karyotype based on chromosomal DNA content. Plant Cell Rep 28, 73–81 (2009). https://doi.org/10.1007/s00299-008-0621-y

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  • DOI: https://doi.org/10.1007/s00299-008-0621-y

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