Skip to main content
SpringerLink
Log in

GISH-based comparative genomic analysis in Urochloa P. Beauv.

  • Original Article
  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

Abstract

The genus Urochloa P. Beauv. [syn. Brachiaria (Trin.) Griseb.] comprises species of great economic relevance as forages. The genomic constitution for the allotetraploid species Urochloa brizantha (cv. Marandu) and Urochloa decumbens (cv. Basilisk) and the diploid Urochloa ruziziensis was previously proposed as BBB1B1, B1B1B2B2 and B2B2, respectively. Evidence indicates U. ruziziensis as the ancestral donor of genome B2 in U. decumbens allotetraploidy, but the origin of the genomes B and B1 is still unknown. There are diploid genotypes of U. brizantha and U. decumbens that may be potential ancestors of the tetraploids. The aim of this study was to determine the genomic constitution and relationships between genotypes of U. brizantha (2x and 4x), U. decumbens (2x and 4x) and U. ruziziensis (2x) via genomic in situ hybridization (GISH). Additionally, chromosome number and genome size were verified for the diploid genotypes. The diploids U. brizantha and U. decumbens presented 2n = 2x = 18 chromosomes and DNA content of 1.79 and 1.44 pg, respectively. The GISH analysis revealed high homology between the diploids U. brizantha and U. decumbens, which suggests relatively short divergence time. The GISH using genomic probes from the diploid accessions on the tetraploid accessions’ chromosomes presented similar patterns, highlighting the genome B1 present in both of the tetraploids. Based on GISH results, the genomic constitution was proposed for the diploid genotypes of U. brizantha (B1B1) and U. decumbens (B1′B1′) and both were pointed as donors of genome B1 (or B1′), present in the allotetraploid genotypes.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

Abbreviations

GISH:

Genomic in situ hybridization

RAPD:

Random amplification of polymorphic DNA

CTAB:

Cetyltrimethylammonium bromide

gDNA:

Genomic DNA

SSC:

Saline sodium citrate

TNT:

Tris-NaCl-Tween-20

DAPI:

4′,6-Diamidino-2-phenylindole

H3K4me2:

Dimethylation of the lysine residue at 4th position on the N-terminal tail of histone 3

H3K9me2:

Dimethylation of the lysine residue at 9th position on the N-terminal tail of histone 3

FISH:

Fluorescent in situ hybridization

rDNA:

Ribosomal DNA

References

  1. Stevens PF (2001 onwards) Angiosperm Phylogeny Website. Version 14, July 2018 [and more or less continuously updated since]. http://www.mobot.org/MOBOT/research/APweb/. Accessed 2018

  2. Jank L, Barrios SC, Valle CB et al (2014) The value of improved pastures to Brazilian beef production. Crop Pasture Sci 65:1132–1137

    Article  Google Scholar 

  3. Valle CB, Jank L, Resende RM (2009) O melhoramento de forrageiras tropicais no Brasil. Rev Ceres 56:460–472

    Google Scholar 

  4. Valle CB, Savidan YH (1996) Genetics cytogenetics and reproductive biology of Brachiaria. In: Miles JW, Maass BL, Valle CB (eds) Brachiaria biology agronomy and improvement. Empresa Brasilera de Pesquisa Agropecuaria, Brasilia, pp 163–180

    Google Scholar 

  5. Assis GML, Euclydes RF, Cruz CD, Valle CB (2002) Genetic divergence in Brachiaria species. Crop Breed Appl Biotechnol 2:331–338. https://doi.org/10.12702/1984-7033.v02n03a02

    Article  Google Scholar 

  6. Renvoize SA, Clayton WB, Kabuye CHS (1996) Morphology, taxonomy and natural distribution of Brachiaria (Trin.) Griseb. In: Kuumble V, Miles JW, Maass BL (eds) Brachiaria: biology, agronomy and improvement. Empresa Brasilera de Pesquisa Agropecuaria, Brasilia, pp 1–15

    Google Scholar 

  7. Ambiel AC, Guaberto LM, Vanderlei TM, Neto NBM (2008) Agrupamento de acessos e cultivares de três espécies de brachiaria por RAPD. Acta Sci Agron 30:457–464. https://doi.org/10.4025/actasciagron.v30i4.5298

    Article  CAS  Google Scholar 

  8. Ambiel AC, Neto NBM, Guaberto LM, Vanderlei TM (2010) Brachiaria germplasm dissimilarity as shown by RAPD markers. Crop Breed Appl Biotechnol 10:55–64

    Article  CAS  Google Scholar 

  9. Pessoa-Filho M, Martins AM, Ferreira ME (2017) Molecular dating of phylogenetic divergence between Urochloa species based on complete chloroplast genomes. BMC Genomics 18:516. https://doi.org/10.1186/s12864-017-3904-2

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Triviño NJ, Perez JG, Recio ME et al (2017) Genetic diversity and population structure of Brachiaria species and breeding populations. Crop Sci 57:2633–2644. https://doi.org/10.2135/cropsci2017.01.0045

    Article  Google Scholar 

  11. Basappa GP, Muniyamma M, Chinnappa CC (1987) An investigation of chromosome numbers in the genus Brachiaria (Poaceae: Paniceae) in relation to morphology and taxonomy. Can J Bot 65:2297–2309

    Article  Google Scholar 

  12. Valle CB, Pagliarini MS (2009), Cytogenetics, and breeding of Brachiaria. In: Singh RJ (ed) Genetic resources, chromosome engineering, and crop improvement. CRC Press, Boca Raton, pp 103–143

    Chapter  Google Scholar 

  13. Mendes-Bonato AB, Filho RGJ, Pagliarini MS et al (2002) Unusual cytological patterns of microsporogenesis in Brachiaria decumbens: abnormalities in spindle and defective cytokinesis causing precocious cellularization. Cell Biol Int 26:641–646. https://doi.org/10.1006/cbir.2002.0929

    Article  PubMed  Google Scholar 

  14. Mendes-Bonato AB, Pagliarini MS, Forli F et al (2002) Chromosome numbers and microsporogenesis in Brachiaria brizantha (Gramineae). Euphytica 125:419–425

    Article  Google Scholar 

  15. Mendes-Bonato AB, Pagliarini MS, Silva N, Valle CB (2001) Meiotic instability in invader plants of signal grass Brachiaria decumbens Stapf (Gramineae). Acta Sci 23:619–625

    Google Scholar 

  16. Mendes-Bonato AB, Risso-Pascotto C, Pagliarini MS, Valle CB (2006) Cytogenetic evidence for genome elimination during microsporogenesis in interspecific hybrid between Brachiaria ruziziensis and B. brizantha (Poaceae). Genet Mol Biol 29:711–714

    Article  Google Scholar 

  17. Mendes DV, Boldrini KR, Mendes-Bonato AB et al (2006) Cytological evidence of natural hybridization in Brachiaria brizantha Stapf (Gramineae). Bot J Linn Soc 150:441–446

    Article  Google Scholar 

  18. Paula CMP, Souza Sobrinho F, Techio VH (2017) Genomic constitution and relationship in Urochloa (Poaceae) species and hybrids. Crop Sci 57:2605–2616. https://doi.org/10.2135/cropsci2017.05.0307

    Article  CAS  Google Scholar 

  19. Lutts S, Ndikumana J, Louant BP (1991) Fertility of Brachiaria ruziziensis in interspecific crosses with Brachiaria decumbens and Brachiaria brizantha: meiotic behavior, pollen viability and seed set. Euphytica 57:267–274

    Article  Google Scholar 

  20. Ndikumana J (1985) Etude de l’hybridation entre espèces apomitcques et sexuées dans le genre Brachiaria. Universite Catholique de Louvain, Belgium

    Google Scholar 

  21. Dong F, McGrath JM, Helgeson JP, Jiang J (2001) The genetic identity of alien chromosomes in potato breeding lines revealed by sequential GISH and FISH analyses using chromosome-specific cytogenetic DNA markers. Genome. https://doi.org/10.1139/gen-44-4-729

    Article  PubMed  Google Scholar 

  22. Doyle J, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus (Madison) 12:39–40

    Google Scholar 

  23. Altinordu F, Pesuzzi L, Yu Y, He X (2016) A tool for the analysis of chromosomes: karyotype. Taxon 65(3):586–592

    Article  Google Scholar 

  24. Heslop-Harrison JSP, Schwarzacher T (2011) Organisation of the plant genome in chromosomes. Plant J 66:18–33. https://doi.org/10.1111/j.1365-313X.2011.04544.x

    Article  CAS  PubMed  Google Scholar 

  25. Dolezel J (1997) Application of flow cytometry for the study of plant genomes. J Appl Genet 3:285–302

    Google Scholar 

  26. Nielen S, Almeida LM, Carneiro VTC, Araujo ACG (2009) Physical mapping of rDNA genes corroborates allopolyploid origin in apomictic Brachiaria brizantha. Sex Plant Reprod 23:45–51. https://doi.org/10.1007/s00497-009-0124-1

    Article  CAS  PubMed  Google Scholar 

  27. De Penteado MI, Santos ACM, Rodrigues IF et al (2000) Determinação de poliploidia e avaliação da quantidade de DNA total em diferentes espécies de gênero Brachiaria. Bol Pesqui Embrapa 11:1–32

    Google Scholar 

  28. Pinheiro AA (2000) Duplication of the chromosome number of diploid Brachiaria brizantha plants using colchicine. Plant Cell Rep 18:274–278

    Article  Google Scholar 

  29. Ricci GCL, Souza-Kaneshima AM, Felismino MF et al (2011) Chromosome numbers and meiotic analysis in the pre-breeding of Brachiaria decumbens (Poaceae). Indian Acad Sci 90:289–294

    Google Scholar 

  30. Ishigaki G, Gondo T, Ebina M et al (2010) Estimation of genome size in Brachiaria species. Grassl Sci 56:240–242. https://doi.org/10.1111/j.1744-697X.2010.00200.x

    Article  Google Scholar 

  31. Timbó AL, Pereira RC, Souza Sobrinho F, Davide LC (2014) Nuclear DNA content and chromosome numbereira in Brachiaria spp. genotypes. Rev Cienc Agron 45:62–67

    Article  Google Scholar 

  32. Leitch IJ, Soltis DE, Soltis PS, Bennett MD (2005) Evolution of DNA amounts across land plants (Embryophyta). Ann Bot 95:207–217. https://doi.org/10.1093/aob/mci014

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Bennetzen JL, Ma J, Devos KM (2005) Mechanisms of recent genome size variation in flowering plants. Ann Bot 95:127–132. https://doi.org/10.1093/aob/mci008

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Belyayev A, Raskina O, Nevo E (2001) Evolutionary dynamics and chromosomal distribution of repetitive sequences on chromosomes of Aegilops speltoides revealed by genomic in situ hybridization. Heredity (Edinburgh) 86:738–742. https://doi.org/10.1046/j.1365-2540.2001.00891.x

    Article  CAS  Google Scholar 

  35. Maluszynska J, Hasterok R (2005) Identification of individual chromosomes and parental genomes in Brassica juncea using GISH and FISH. Cytogenet Genome Res 109:310–314. https://doi.org/10.1159/000082414

    Article  CAS  PubMed  Google Scholar 

  36. Paula CM, Sobrinho FS, Techio VH (2016) Chromosomal distribution of H3K4me2, H3K9me2 and 5-methylcytosine: variations associated with polyploidy and hybridization in Brachiaria (Poaceae). Plant Cell Rep 35:1359–1369

    Article  Google Scholar 

  37. Li C, Zhang D, Ge S et al (2001) Identification of genome constitution of Oryza malampuzhaensis, O. minuta, and O. punctata by multicolour genomic in situ hybridization. Theor Appl Genet 103:204–211

    Article  CAS  Google Scholar 

  38. Jenkins G, Mur L, Bablak P et al (2004) Prospects for functional genomics in a new model grass. In: Leister D (ed) Plant functional genomics. CRC Press, Boca Raton

    Google Scholar 

  39. Roa F, Guerra M (2015) Non-random distribution of 5S rDNA sites and its association with 45S rDNA in plant chromosomes. Cytogenet Genome Res 146:243–249. https://doi.org/10.1159/000440930

    Article  CAS  PubMed  Google Scholar 

  40. Watson JM, Riha K (2010) Comparative biology of telomeres: where plants stand. FEBS Lett 584:3752–3759. https://doi.org/10.1016/j.febslet.2010.06.017

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Majka J, Majka M, Kwiatek M, Wiśniewska H (2017) Similarities and differences in the nuclear genome organization within Pooideae species revealed by comparative genomic in situ hybridization (GISH). J Appl Genet 58:151–161. https://doi.org/10.1007/s13353-016-0369-y

    Article  CAS  PubMed  Google Scholar 

  42. Salina EA, Sergeeva EM, Adonina IG et al (2009) Isolation and sequence analysis of the wheat B genome subtelomeric DNA. BMC Genomics 10:414. https://doi.org/10.1186/1471-2164-10-414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Nani TF, Pereira DL, Souza Sobrinho F, Techio VH (2016) Physical map of repetitive DNA sites in Brachiaria spp.: intravarietal and interspecific polymorphisms. Crop Sci 56:1769–1783. https://doi.org/10.2135/cropsci2015.12.0760

    Article  CAS  Google Scholar 

  44. Flavell RB, Gale MD, O’dell M et al (1993) Molecular organization of genes and repeats in the large cereal genomes and implications for the isolation of genes by chromosome walking. Chromosomes today. Springer, Dordrecht, pp 199–213

    Chapter  Google Scholar 

  45. Schnable PS, Ware D, Fulton RS et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115. https://doi.org/10.1126/science.1178534

    Article  CAS  PubMed  Google Scholar 

  46. Biscotti MA, Olmo E, Heslop-Harrison JS (2015) Repetitive DNA in eukaryotic genomes. Chromosom Res 23:415–420. https://doi.org/10.1007/s10577-015-9499-z

    Article  CAS  Google Scholar 

  47. López-Flores I, Garrido-Ramos MA (2012) The repetitive DNA content of eukaryotic genomes. Repetitive DNA 7:1–28. https://doi.org/10.1159/000337118

    Article  Google Scholar 

  48. Morrone O, Zuloaga FO (1992) Revision de las especies sudamericanas nativas e introducidas de los generos Brachiaria y Urochloa (Poaceae: Panicoideae: Paniceae). Darwiniana 31:43–109

    Google Scholar 

  49. Maass BL (2004) Identifying and naming Brachiaria species. In: Miles JW, Valle CB (eds) Brachiaria: biology, agronomy and improvement. Empresa Brasilera de Pesquisa Agropecuaria, Brasilia, pp 9–12

    Google Scholar 

  50. Akiyama Y, Yamada-Akiyama H, Ebina M (2010) Morphological diversity of chromosomes bearing ribosomal DNA loci in Brachiaria species. Grassl Sci 56:217–223. https://doi.org/10.1111/j.1744-697X.2010.00197.x

    Article  Google Scholar 

  51. Nielen S, Almeida LM, Carneiro VTC, Araujo ACG (2010) Physical mapping of rDNA genes corroborates allopolyploid origin in apomictic Brachiaria brizantha. Sex Plant Reprod 23:45–51. https://doi.org/10.1007/s00497-009-0124-1

    Article  CAS  PubMed  Google Scholar 

  52. Renny-Byfield S, Wendel JF (2014) Doubling down on genomes: polyploidy and crop plants. Am J Bot 101:1711–1725. https://doi.org/10.3732/ajb.1400119

    Article  PubMed  Google Scholar 

  53. Gaut B, Thierry d’Ennenquin M, Peek A, Sawkins N (2000) Maize as a model for the evolution of plant nuclear genomes. Proc Natl Acad Sci U S A 97:7008–7015

    Article  CAS  Google Scholar 

  54. Ermolaeva M, Wu M, Eisen J, Salzberg S (2003) The age of the Arabidopsis thaliana genome duplication. Plant Mol Biol 51:859–866

    Article  CAS  Google Scholar 

  55. Doyle JA, Endress PK (2000) Morphological phylogenetic analysis of basal angiosperms: comparison and combination with molecular data. Int J Plant Sci 161:121–153

    Article  Google Scholar 

Download references

Acknowledgements

The authors thank the support of the Foundation for Research Support of the State of Minas Gerais (FAPEMIG), the Coordination for the Improvement of Higher Education Personnel (CAPES), the National Council for Scientific and Technological Development (CNPq) for financial support for the development of this study. All authors read and approved the final manuscript.

Author information

Authors and Affiliations

  1. Department of Biology/DBI – Plant Cytogenetics Laboratory, Federal University of Lavras (UFLA), P.O. Box 3037, Lavras, Minas Gerais, Brazil

    Caio T. R. Corrêa, Nathalia G. Z. Bonetti, Giovana A. Torres & Vânia H. Techio

  2. Embrapa Gado de Corte – Campo Grande, Campo Grande, Mato Grosso do Sul, Brazil

    Sanzio C. L. Barrios & Cacilda B. do Valle

Authors
  1. Caio T. R. Corrêa
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Nathalia G. Z. Bonetti
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sanzio C. L. Barrios
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Cacilda B. do Valle
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Giovana A. Torres
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Vânia H. Techio
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

CTRC—carried oed out flow cytometry analysis, helped prepared slides and image processing. SCLB and CBV—responsible for the breeding program of Urochloa; provided hybrid seeds of Urochloa and reviewed the manuscript. GAT—helped the GISH analysis and has been involved in drafting the manuscript. VHT—conceived the study, participated in its design and coordination and helped to draft the manuscript.

Corresponding author

Correspondence to Vânia H. Techio.

Ethics declarations

Conflict of interest

The authors declare that there is no conflict of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

This study is part of C.T.R. Correa’s thesis and the abstract can be found in the repository: http://repositorio.ufla.br/jspui/handle/1/33642.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Corrêa, C.T.R., Bonetti, N.G.Z., Barrios, S.C.L. et al. GISH-based comparative genomic analysis in Urochloa P. Beauv.. Mol Biol Rep 47, 887–896 (2020). https://doi.org/10.1007/s11033-019-05179-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-019-05179-7

Keywords

Search

Navigation