Abstract
In the present study, our intention was to elucidate the genetic relation of M. acuminata subspecies and analyse the diversity of the M. balbisiana gene-pool using nuclear ribosomal gene loci based marker system. Additionally the obtained information allowed elucidating the structure and ancestry of the nuclear genomes of diploid and triploid cultivars. By establishing the nucleotide sequence of the rDNA locus for M. acuminata and partially for M. balbisiana and their comparative analysis revealed that the 5′ETS region was the most divergent between acuminata and balbisiana genomes. Based on the SNP sites identified in this region a PCR based system was built, which revealed four gene-pools among M. acuminata wild types, while M. balbisiana showed no sequence divergence. The developed markers proved to be a powerful tool in the identification of the acuminata component of diploid and triploid hybrid cultivars and discovery of unexpected genotypes.
Similar content being viewed by others
References
Auvuchanon A, Suputtitada S, Silayoi B, Apisitwanich S (2001) Musa genome discrimination using genomic in situ hybridization and SSR. In: Proceeding of the 12th annual meeting of the Thai society for genetics, Kasetsart University, Bangkok, 28–30 March 2001
Baldwin BG, Markos S (1998) Phylogenetic utility of the external transcribed spacer (ETS) of 18S–26S rDNA: congruence of ETS and ITS trees of calycadenia(Compositae). Mol Phylogenet Evol 10:449–463. doi:10.1006/mpev.1998.0545
Bartoš J, Alkhimova O, Doleželová M, De Langhe E, Doležel J (2005) Nuclear genome size and genomic distribution of ribosomal DNA in Musa and Ensete (Musaceae): taxonomic implications. Cytogenet Genome Res 109:50–57. doi:10.1159/000082381
Bena G, Jubier MF, Olivieri I, Lejeune B (1998) Ribosomal external and internal transcribed spacers: combined use in the phylogenetic analysis of Medicago (Leguminosae). J Mol Evol 46:299–306. doi:10.1007/PL00006306
Bhat KV, Jarret RL, Rana RS (1995) DNA profiling of banana and plantain cultivars using random amplified polymorphic DNA (RAPD) and restriction fragment length polymorphism (RFLP) markers. Electrophoresis 16:1736–1745
Carreel F, Faure S, Gonzalez de Leon D, Lagoda PJL, Perrier X, Bakry F, Tezenas du Montcel H, Lanaud C, Horry JP (1994) Evaluation de la diversite genetique chez les bananiers diploides (Musa spp.). Genet Sel Evol 26:125–136. doi:10.1051/gse:19940709
Carreel F, Gonzalez de Leon D, Lagoda P, Lanaud C, Jenny C, Horry JP, Tezenas du Montcel H (2002) Ascertaining maternal and paternal lineage within Musa by chloroplast and mitochondrial DNA RFLP analyses. Genome 45:679–692. doi:10.1139/g02-033
Cordesse F, Cooke R, Tremousaygue D, Greellet F, Delseny M (1993) Fine structure and evolution of the rDNA intergenic spacer in rice and other cereals. J Mol Evol 36:369–379. doi:10.1007/BF00182184
Crouch JH, Crouch HK, Constandt H, Van Gysel A, Breyne P, Montagu MV, Jarret RL, Ortiz R (1999) Comparison of PCR-based molecular marker analyses of Musa breeding populations. Mol Breed 5:233–244. doi:10.1023/A:1009649521009
Da Rocha PSCF, Bertrand H (1995) Structure and comparative analysis of the rDNA intergenic spacer of Brassica rapa: implications for the function and evolution of the Cruciferae spacer. Eur J Biochem 229:550–557. doi:10.1111/j.1432-1033.1995.tb20497.x
Daniells J, Jenny C, Karamura D, Tomekpe K (2001) Musalogue: a catalogue of Musa germplasm. Diversity in the genus Musa. Compiled by Arnaud E, Sharrock S International Network for the improvement of banana and plantain
Dolezelova M, Valarik M, Swennen R, Horry JP, Dolezel J (1998) Physical mapping of the 18S–25S and 5S ribosomal RNA genes in diploid bananas. Biol Plant 41:497–505. doi:10.1023/A:1001880030275
Fujisawa M, Yamagata H, Kamiya K, Nakamura M, Saji S, Kanamori H, Wu J, Matsumoto T, Sasaki T (2006) Sequence comparison of distal and proximal ribosomal DNA arrays in rice (Oryza sativa L.) chromosome 9S and analysis of their xanking regions. Theor Appl Genet 113:419–428. doi:10.1007/s00122-006-0307-1
Ganley ARD, Kobayashi T (2007) Highly efficient concerted evolution in the ribosomal DNA repeats: total rDNA repeat variation revealed by whole-genome shotgun sequence data. Genome Res 17:184–191. doi:10.1101/gr.5457707
Grapin A, Noyer JL, Carreel F, Dambler D, Baurens FC, Lanaud C, Lagoda PJL (1998) Diploid Musa acuminata genetic diversity assayed with sequence tagged microsatellite sites. Electrophoresis 19:1374–1380. doi:10.1002/elps.1150190829
Hammer Ø, Harper DAT, Ryan PD (2001) PAST: paleontological statistics software package for education and data analysis. Palaeontol Electronica 4:9. http://palaeo-electronica.org/ 2001-1/past/issuel.0 l.htm
Hamon P, Seguin M, Perrier X, Glaszmann J-C (2003) Genetic diversity of cultivated tropical plants. Science, USA
Lebot V, Aradhya KM, Manshardt R, Meilleur B (1993) Genetic relationships among cultivated bananas and plantains from Asia and the Pacific. Euphytica 67:163–173. doi:10.1007/BF00040618
Linder CR, Goertzen LR, Heuvel BV, Francisco-Ortega J, Jansen RK (2000) The complete external transcribed spacer of 18S–26S rDNA: amplification and phylogenetic utility at low taxonomic levels in Asteraceae and closely allied families. Mol Phylogenet Evol 14:285–303. doi:10.1006/mpev.1999.0706
Newton CR, Graham A, Heptinstali LE (1989) Analysis of any point mutation in DNA. The amplification refractory mutation system. Nucleic Acids Res 17:2503–2516. doi:10.1093/nar/17.7.2503
Nicholas KB, Nicholas HB Jr (1997). GeneDoc: a tool for editing and annotating multiple sequence alignment. (www.psc.edu/biomed/genedoc)
Nwakanma DC, Pillay M, Okoli BE, Tenkouano A (2003) Sectional relationships in the genus Musa L. inferred from the PCR-RFLP of organelle DNA sequences. Theor Appl Genet 107:850–856. doi:10.1007/s00122-003-1340-y
Osuji JO, Crouch J, Harrison G, Heslop-Harrison JS (1998) Molecular cytogenetics of Musa species, cultivars and hybrids: location of 18S–5·8S–25S and 5S rDNA and telomere-like sequences. Ann Bot (Lond) 82:243–248. doi:10.1006/anbo.1998.0674
Polanco C, Vega PDL (1994) The structure of the rDNA intergenic spacer of Avena sativa L.: a comparative study. Plant Mol Biol 25:751–756. doi:10.1007/BF00029613
Raboin ML, Carreel F, Noyer JL (2005) Diploid ancestors of triploid export banana cultivars: molecular identification of 2n restitution gamete donors and n gamete donors. Mol Breed 16:333–341. doi:10.1007/s11032-005-2452-7
Sallares R, Brown TA (2004) Phylogenetic analysis of complete 5′ external transcribed spacers of the 18S ribosomal RNA genes of diploid Aegilops and related species (Triticeae, Poaceae). Genet Res Crop 51(7):701–712. doi:10.1023/B:GRES.0000034576.34036.a1
Sanderson MJ, Doyle JJ (1992) Reconstruction of organismal and gene phylogenies from data on multigene families: concerted evolution, homoplasy, and confidence. Syst Biol 41:4–17. doi:10.2307/2992502
Shepherd K (1990) Observations on Musa taxonomy. Identification of genetic diversity in the genus Musa. In: Jarret RJ (ed) Proceedings of an International Workshop held at Los Banos, Philippines, 5–10 September 1988. INIBAP, Montpellier, France, pp 158–165
Shepherd K (1999) Cytogenetics of the genus Musa. INIBAP, Montpellier, pp 39–52
Simmonds NW, Shepherd K (1955) The taxonomy and origins of the cultivated bananas. J Linn Soc Lond Bot 55:302–312. doi:10.1111/j.1095-8339.1955.tb00015.x
Soltis PS, Soltis DE, Nickrent DL, Johnson LA, Hahn WJ, Hoot SB, Sweere JA, Kuzoff RK, Kron KA, Chase MW, Swensen SM, Zimmer EA, Chaw S-M, Gillespie LJ, Kress WJ, Sytsma KJ (1997) Angiosperm phylogeny inferred from 18S ribosomal DNA sequences. Ann Missouri Bot Gard 84:1–49
Swangpol S, Volkaert H, Sotto RC, Seelanan T (2007) Utility of selected non-coding chloroplast DNA sequences for lineage assessment of Musa interspecific hybrids. J Biochem Mol Biol 40(4):577–587
Ude G, Pillay M, Nwakanma D, Tenkouano A (2002) Genetic diversity in Musa acuminata Colla and Musa balbisiana Colla and some of their natural hybrids using AFLP markers. Theor Appl Genet 104:1246–1252. doi:10.1007/s00122-002-0914-4
Valárik M, Šimková H, Hřibová E, Šafář J, Doleželová M, Doležel J (2002) Isolation, characterization and chromosome localization of repetitive DNA sequences in bananas (Musa spp.). Chrom Res 10:89–100. doi:10.1023/A:1014945730035
Volkov RA, Kostishin S, Ehrendorfer F, Schweizer D (1996) Molecular organization and evolution of the external transcribed rDNA spacer region in two diploid relatives of Nicotiana tabacum (Solanaceae). Plant Syst Evol 201:117–129. doi:10.1007/BF00989055
Acknowledgments
The present work was funded by Bioversity International (formerly International Network for Improvement of Banana and Plantain (INIBAP)). The authors are grateful to Prof. Benchamas Silayoi and Assoc. Prof. Dr. Somsak Apisitwanich for guidance and technical advice in bananas and Assoc. Prof. Dr. Jaroslav Doležel for kindly providing us with DNA from some banana wild type species.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Boonruangrod, R., Fluch, S. & Burg, K. Elucidation of origin of the present day hybrid banana cultivars using the 5′ETS rDNA sequence information. Mol Breeding 24, 77–91 (2009). https://doi.org/10.1007/s11032-009-9273-z
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11032-009-9273-z