Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Chromosome homologies between Citrus and Poncirus—the comparative cytogenetic map of mandarin (Citrus reticulata)

  • 448 Accesses

  • 5 Citations

Abstract

Mandarins are among the main citrus species and constitute a morphologically diverse and taxonomically controversial group. Cytogenetic studies were limited to the determination of its karyotype formula and the localization of ribosomal DNA (rDNA) sites. The cytogenetic map of Poncirus trifoliata, established by fluorescent in situ hybridization (FISH) using single-copy bacterial artificial chromosomes (BACs) together with the localization of rDNA sequences and heterochromatin (CMA/DAPI banding pattern), represented an important milestone for the cytogenetic studies of the citrus species. In this work, the cytogenetic map of Citrus reticulata cv. Cravo, one of the pure species of the genus, was built using BACs from P. trifoliata, including the citrus tristeza virus resistance locus (Ctv), to detect homeologies and structural karyotypic changes between these species. Except for chromosomes 2 and 3, heterochromatin distribution and position of BACs were maintained in comparison to P. trifoliata, indicating a high synteny between both karyotypes and supporting a close phylogenetic relationship between these species. A break of colinearity was observed between BAC clones and the CMA+ bands (including rDNA loci) from chromosomes 2 and 3, which could be mainly explained by amplification and reduction of the satellite DNA sequences that constitute the heterochromatic bands of these chromosome pairs.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2
Fig. 3

References

  1. Barkley NA, Roose ML, Krueger RR, Federici CT (2006) Assessing genetic diversity and population structure in a citrus germplasm collection utilizing simple sequence repeat markers (SSRs). Theor Appl Genet 112:1519–1531. doi:10.1007/s00122- 006-0255-9

  2. Barros e Silva AE, Marques A, Santos KGB, Guerra M (2010) The evolution of CMA bands in Citrus and related genera. Chromosome Res 18:503–514. doi:10.1007/s10577-010-9130-2

  3. Bayer RJ, Mabberley DJ, Morton C, Miller CH, Sharma IK, Pfeil BE, Rich S, Hitchcock R, Sykes S (2009) A molecular phylogeny of the orange subfamily (Rutaceae: Aurantioideae) using nine cpDNA sequences. Am J Bot 96:668–685. doi:10.3732/ajb.0800341

  4. Brasileiro-Vidal AC, dos Santos-Serejo JA, Soares Filho WS, Guerra M (2007) A simple chromosomal marker can reliably distinguishes Poncirus from Citrus species. Genetica 129:273–279. doi:10.1007/s10709-006-0007-4

  5. Bruggmann R, Bharti AK, Gundlach H, Lai J, Young S, Pontaroli AC, Wei F, Haberer G, Fuks G, Du C, Raymond C, Estep MC, Liu R, Bennetzen JL, Chan AP, Rabinowicz PD, Quackenbush J, Barbazuk WB, Wing RA, Birren B, Nusbaum C, Rounsley S, Mayer KF, Messing J (2006) Uneven chromosome contraction and expansion in the maize genome. Genome Res 16:1241–1251. doi:10.1101/gr.5338906

  6. Carvalho R, Soares Filho WS, Brasileiro-Vidal AC, Guerra M (2005) The relationship among lemons, limes and citron: a chromosomal comparison. Cytogenet Genome Res 109:276–282. doi:10.1159/000082410

  7. Coletta Filho HD, Machado MA, Targon MLPN, Moreira MCPQDG, Pompeu J Jr (1998) Analysis of the genetic diversity among mandarins (Citrus spp.) using RAPD markers. Euphytica 102:133–139. doi:10.1023/A:1018300900275

  8. Cornélio MTMN, Figueirôa ARS, Santos KGB, Carvalho R, Soares Filho WS, Guerra M (2003) Chromosomal relationships among cultivars of Citrus reticulata Blanco, its hybrids and related species. Plant Syst Evol 240:149–161. doi:10.1007/s00606- 003-0012-3

  9. Doležel J, Göhde W (1995) Sex determination in dioecious plants Melandrium album and M. rubrum using high resolution flow cytometry. Cytometry 19:103–106. doi:10.1002/cyto.990190203

  10. Doležel J, Sgorbati S, Lucretti S (1992) Comparison of three DNA fluorochromes for flow cytometric estimation of nuclear DNA content in plants. Physiol Plant 85:625–631. doi:10.1111/j.1399-3054.1992.tb04764.x

  11. Doležel J, Bartoš J, Voglmayr H, Greilhuber J (2003) Nuclear DNA content and genome size of trout and human. Cytometry 51A:127–128. doi:10.1002/cyto.a.10013

  12. Fang DQ, Roose ML (1997) Identification of closely related Citrus cultivars with intersimple sequence repeat markers. Theor Appl Genet 95:408–417. doi:10.1007/s001220050577

  13. Federici CT, Fang DQ, Scora RW, Roose ML (1998) Phylogenetic relationships within the genus Citrus (Rutaceae) and related genera as revealed by RFLP and RAPD analysis. Theor Appl Genet 96:812–822. doi:10.1007/s001220050807

  14. Fonsêca A, Ferreira A, Santos TRB, Mosiolek M, Bellucci E, Kami J, Gepts P, Geffroy V, Schweizer D, Santos KGB, Pedrosa-Harand A (2010) Cytogenetic map of common bean (Phaseolus vulgaris L.). Chromosome Res 18:487–502. doi:10.1007/s10577-010-9129-8

  15. Garcia-Lor A, Curk F, Snoussi-Trifa H, Morillon R, Ancillo G, Luro F, Navarro L, Ollitrault P (2013) A nuclear phylogenetic analysis: SNPs, indels and SSRs deliver new insights into the relationships in the ‘true citrus fruit trees’ group (Citrinae, Rutaceae) and the origin of cultivated species. Ann Bot 111:1–19. doi:10.1093/aob/mcs227

  16. Guerra M (1986) Reviewing the chromosome nomenclature of Levan et al. Brazil J Genet 9:741–743

  17. Guerra M (1993) Cytogenetics of Rutaceae. V. High chromosomal variability in Citrus species revealed by CMA/DAPI staining. Heredity 71:234–241. doi:10.1038/hdy.1993.131

  18. Guerra S (2007) Origem e variabilidade cariotípica da laranja-azeda (Citrus aurantium L.). Monograph, Federal University of Pernambuco

  19. Guerra M (2009) Chromosomal variability and the origin of Citrus species. In: Mahoney CL, Springer DA (eds) Genetic diversity. Nova Science Publishers, Inc., New York, pp 51–68

  20. Heslop-Harrison JS, Harrison GE, Leitch IJ (1992) Reprobing of DNA: DNA in situ hybridization preparations. Trends Genet 8:372–373. doi:10.1016/0168-9525(92)90287-E

  21. Jiang J, Gill BS, Wang G, Ronald PC, Ward DC (1995) Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosome. Proc Natl Acad Sci USA 92:4487–4491. doi:10.1073/pnas.92.10.4487

  22. Kayum M, Koç NK, Rokka VM (1998) Variation of the nuclear DNA content of species of subtribe Citrinae (Rutaceae). HortSci 33:1247–1250

  23. Luro F, Laigret F, Bové JM, Ollitrault P (1995) DNA amplified fingerprinting, a useful tool for determination of genetic origin and diversity analysis in Citrus. HortSci 30:1063–1067

  24. Marques A, Fuchs J, Ma L, Heckmann S, Guerra M, Houben A (2011) Characterization of eu- and heterochromatin of Citrus with a focus on the condensation behaviour of 45S rDNA chromatin. Cytogenet Genome Res 134:72–82. doi:10.1159/000323971

  25. Mendes S, Moraes AP, Mirkov TE, Pedrosa-Harand A (2011) Chromosome homeologies and high variation in heterochromatin distribution between Citrus L. and Poncirus Raf. as evidenced by comparative cytogenetic mapping. Chromosome Res 19:521–530. doi:10.1007/s10577-011-9203-x

  26. Moore GA (2001) Oranges and lemons: clues to the taxonomy of Citrus from molecular markers. Trends Genet 17:536–540. doi:10.1016/S0168-9525(01)02442-8

  27. Moraes AP, Lemos RR, Brasileiro-Vidal AC, Soares Filho WS, Guerra M (2007a) Chromosomal markers distinguish hybrids and non-hybrid accessions of mandarin. Cytogenet Genome Res 119:275–281. doi:10.1159/000112074

  28. Moraes AP, Soares Filho WS, Guerra M (2007b) Karyotype diversity and the origin of grapefruit. Chromosome Res 15:115–121. doi:10.1007/s10577-006-1101-2

  29. Moraes AP, Mirkov TE, Guerra M (2008) Mapping the chromosomes of Poncirus trifoliata Raf. by BAC-FISH. Cytogenet Genome Res 121:277–281. doi:10.1159/000138897

  30. Nicolosi E, Deng ZN, Gentile A, La Malfa S, Continella G, Tribulato E (2000) Citrus phylogeny and genetic origin of important species as investigated by molecular markers. Theor Appl Genet 100:1155–1166. doi:10.1007/s001220051419

  31. Ollitrault P, Dambier D, Luro F, Duperray C (1994) Nuclear genome size variations in Citrus. Fruits 49:390–393

  32. Passos OS, Cunha Sobrinho AP, Soares Filho WS (2013) Cultivares copa. In: Cunha Sobrinho AP, Magalhães AFJ, Souza AS, Passos OS, Soares Filho WS (eds) Cultura dos citros. Embrapa, Brasília. pp 293–319

  33. Pedrosa A, Guerra M, Soares Filho WS (1997) An hierarchy of activation of nucleolar organizer regions in Citrus sinensis (L.) Osbeck. Cytobios 92:43–51

  34. Pedrosa A, Schweizer D, Guerra M (2000) Cytological heterozygosity and the hybrid origin of sweet orange [Citrus sinensis (L.) Osbeck]. Theor Appl Genet 100:361–367. doi:10.1007/s001220050047

  35. Pedrosa-Harand A, Almeida CC, Mosiolek M, Blair MW, Schweizer D, Guerra M (2006) Extensive ribosomal DNA amplification during Andean common bean (Phaseolus vulgaris L.) evolution. Theor Appl Genet 112:924–933. doi:10.1007/s00122-005-0196-8

  36. Preuss S, Pikaard CS (2007) rRNA gene silencing and nucleolar dominance: insights into a chromosome-scale epigenetic on/off switch. Biochim Biophys Acta 1769:383–392. doi:10.1016/j.bbaexp.2007.02.005

  37. Silva SC, Marques A, Soares Filho WS, Mirkov TE, Pedrosa-Harand A, Guerra MS (2011) The cytogenetic map of the Poncirus trifoliata (L.) Raf.–a nomenclature system for chromosomes of all citric species. Trop Plant Biol 4:99–105. doi:10.1007/s12042-011-9072-7

  38. Singh S, Rajam MV (2009) Citrus biotechnology: achievements, limitations and future directions. Physiol Mol Biol Plant 15:3–22. doi:10.1007/s12298-009-0001-2

  39. Spiegel-Roy P, Goldschmidt EE (1996) Biology of Citrus–biology of horticultural crops. Cambridge University Press, Cambridge

  40. Sumner AT (2002) Chromosomes organization and function. Blackwell Publising, Berlim

  41. Swingle WT, Reece TC (1967) The botany of Citrus and its wild relatives. In: Reuther W, Weber HJ, Batchelor LD (eds) The Citrus industry. History, world distribution, botany and varieties. University of California Press, Berkeley, pp 190–430

  42. Tanaka T (1969) Misunderstanding with regard to Citrus classification and nomenclature. Bull Uni Osaka Pref Ser B 21:139–145

  43. Viguera E, Canceill D, Ehrlich SD (2001) Replication slippage involves DNA polymerase pausing and dissociation. EMBO J 20:2587–2595. doi:10.1093/emboj/20.10.2587

  44. Wanzenböck EM, Schöfer C, Schweizer D, Bachmair A (1997) Ribosomal transcription units integrated via T-DNA transformation associate with the nucleolus and do not require upstream repeat sequences for activity in Arabidopsis thaliana. Plant J 11:1007–1016. doi:10.1046/j.1365-313X.1997.11051007.x

  45. Wu GA, Prochnik S, Jenkins J, Salse J, Hellsten U, Murat F, Perrier X, Ruiz M, Scalabrin S, Terol J, Takita MA, Labadie K, Poulain J, Couloux A, Jabbari K, Cattonaro F, Del Fabbro C, Pinosio S, Zuccolo A, Chapman J, Grimwood J, Tadeo FR, Estornell LH, Muñoz-Sanz JV, Ibanez V, Herrero-Ortega A, Aleza P, Pérez-Pérez J, Ramón D, Brunel D, Luro F, Chen C, Farmerie WG, Desany B, Kodira C, Mohiuddin M, Harkins T, Fredrikson K, Burns P, Lomsadze A, Borodovsky M, Reforgiato G, Freitas-Astúa J, Quetier F, Navarro L, Roose M, Wincker P, Schmutz J, Morgante M, Machado MA, Talon M, Jaillon O, Ollitrault P, Gmitter F, Rokhsar D (2014) Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nat Biotechnol 32:656–662. doi:10.1038/nbt.2906

  46. Xu Q, Chen LL, Ruan X, Chen D, Zhu A, Chen C, Bertrand D, Jiao WB, Hao BH, Lyon MP, Chen J, Gao S, Xing F, Lan H, Chang JW, Ge X, Lei Y, Hu Q, Miao Y, Wang L, Xiao S, Biswas MK, Zeng W, Guo F, Cao H, Yang X, Xu XW, Cheng YJ, Xu J, Liu JH, Luo OJ, Tang Z, Guo WW, Kuang H, Zhang HY, Roose ML, Nagarajan N, Deng XX, Ruan Y (2013) The draft genome of sweet orange (Citrus sinensis). Nat Genet 45:59–66. doi:10.1038/ng.2472

  47. Yamamoto M, Tominaga S (2003) High chromosomal variability of mandarins (Citrus spp.) revealed by CMA banding. Euphytica 129:267–274. doi:10.1023/A:1022284908424

  48. Yang ZN, Ye XR, Choi S, Molina J, Moonan F, Wing RA, Roose ML, Mirkov TE (2001) Construction of a 1.2-Mb contig including the citrus tristeza virus resistance gene locus using a bacterial artificial chromosome library of Poncirus trifoliata (L.) Raf. Genome 44:382–393. doi:10.1139/gen-44-3-382

Download references

Acknowledgments

We would like to thank Luiz Gustavo R. Souza and two anonymous referees for the valuable comments on the manuscript and Getúlio de Souza Vieira (Embrapa Cassava & Fruits) for his technical support in the field. This work was carried out with financial support from the Brazilian agency Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, 474330/2009-5) including a scholarship to S.C.S. (141121/2008-4) and a fellowship to A.P.-H (302953/2010-8).

Ethical standards

Experimental procedures comply with the current state and federal laws.

Conflict of interest

The authors declare that they have no conflict of interest.

Data archiving statement

The cytogenetic map has been submitted to and archived in the Citrus Genome Database (http://www.citrusgenomedb.org/tgg/data_submission).

Author information

Correspondence to Andrea Pedrosa-Harand.

Additional information

Communicated by W.-W. Guo

Electronic supplementary material

Supplemental Fig. S1

Flow cytometric DNA content (2C value) analysis of Citrus reticulata cv. Cravo using Raphanus sativus L. (2C = 1.11 pg; Doležel et al. 1992) as an internal reference standard. The coefficient of variation (CV) for mandarin ranged from 3.5 % to 4.3 %, while the standard CV ranged from 2.8 % to 3.8 %.

Supplemental Fig. S2

Mitotic metaphases from Citrus reticulata cv. Cravo stained with CMA/DAPI and hybridized in situ with 45S rDNA (ab) and different Poncirus trifoliata BACs (cf). In a and b, only CMA staining and Cy3 signals are shown, respectively, without superimposition with DAPI counterstained chromosomes. The inserts show the enlarged chromosomes pseudocoloured in gray and the BAC signals in red and green. The numbers identify the labelled chromosome pair in each case. Bar in f corresponds to 5 μm.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

da Costa Silva, S., Mendes, S., Soares Filho, W.d.S. et al. Chromosome homologies between Citrus and Poncirus—the comparative cytogenetic map of mandarin (Citrus reticulata). Tree Genetics & Genomes 11, 811 (2015). https://doi.org/10.1007/s11295-014-0811-4

Download citation

Keywords

  • BAC-FISH
  • Heteromorphism
  • Synteny
  • Heterochromatin
  • CMA/DAPI