Molecular and cytological characterization of ribosomal RNA genes in Chenopodium quinoa and Chenopodium berlandieri

Genome

Volumn 49, Issue 7, 2006, Pages 825-839

  Maughan, P J ^a   Kolano, B A ^b   Maluszynska, J ^b   Coles, N D ^a   Bonifacio, A ^c   Rojas, J ^c   Coleman, C E ^a   Stevens, M R ^a   Fairbanks, D J ^a   Parkinson, S E ^a   Jellen, E N ^a  

^a BRIGHAM YOUNG UNIVERSITY   (United States)

^b UNIVERSITY OF SILESIA   (Poland)

^c Fundacion Promocion e Investigacion de Productos Andinos Bolivia   (Bolivia)

Author keywords

5S NTS; Chenopodium; FISH; IGS; NOR; rDNA

Indexed keywords

RIBOSOMAL SPACER DNA; RIBOSOME RNA; RNA 5S; RNA, RIBOSOMAL, 45S;

ARTICLE; CHENOPODIUM QUINOA; CHROMOSOME NOR; FLUORESCENCE IN SITU HYBRIDIZATION; GENE; GENETIC POLYMORPHISM; GENETICS; GOOSEFOOT; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT;

BASE SEQUENCE; CHENOPODIUM; CHENOPODIUM QUINOA; DNA, RIBOSOMAL SPACER; EVOLUTION, MOLECULAR; GENES, PLANT; IN SITU HYBRIDIZATION, FLUORESCENCE; MOLECULAR SEQUENCE DATA; NUCLEOLUS ORGANIZER REGION; PHYLOGENY; POLYMORPHISM, GENETIC; RNA, RIBOSOMAL; RNA, RIBOSOMAL, 5S; SEQUENCE ALIGNMENT;

ACER PENSYLVANICUM; CHENOPODIUM; CHENOPODIUM BERLANDIERI; CHENOPODIUM QUINOA;

EID: 33750916144     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/G06-033     Document Type: Article

References (67)

1. Appels, R., Reddy, P., McIntyre, C.L., Moran, L.B., Frankel, O.H., and Clarke, B.C. 1989. The molecular-cytogenetic analysis of grasses and its applications to studying relationships among species of the Triticease. Genome, 31: 122-133.
2. Appels, R., Baum, B.R., and Clark, B.C. 1992. The 5S DNA units of bread wheat (Triticum aestivum). Plant Syst. Evol. 183: 183-194.
3. Baker, W.J., Hedderson, T.A., and Dransfield, J. 2000. Molecular phylogenetics of Calamus (Palmae) and related rattan genera based on 5S nrRNA spacer sequence data. Mol. Phylogenet. Evol. 14: 218-231.
4. Baldwin, B.G., Sanderson, M.J., Porter, J.M., Wojciechowski, M.F., Campbell, C.S., and Donoghue, M.J. 1995. The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. Ann. Mo. Bot. Gard. 82: 247-277.
5. Baum, B.R., Bailey, L.G., and Johnson, D.A. 1996. The 5S rRNA gene units in ancestral two-rowed barley (Hordeum spontaneum C. Koch) and bulbous barley (H. bulbosum L.): sequence analysis and phylogenetic relationships with the 5S rDNA units of cultivated barley (H. vulgare L.). Genome, 39: 140-149.
6. Baum, B.R., Bailey, L.G., Belyayev, A., Raskina, O., and Nevo, E. 2004. The utility of the nontranscribed spacer of 5S rDNA units grouped into unit classes assigned to haplomes - a test on cultivated wheat and wheat progenitors. Genome, 47: 590-599.
7. Benner, M.S., Phillips, R.L., Kirihara, J.A., and Messing, J.W. 1989. Genetic analysis of methionine-rich storage protein accumulation in maize. Theor. Appl. Genet. 78: 761-767.
8. Benson, G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27: 573-580.
9. Bogenhagen, D.F., Sakonju, S., and Brown, D.D. 1980. A control region in the center of the 5S RNA gene directs specific initiation of transcription: II. The 3′ border of the region. Cell, 19: 27-35.
10. Bonifacio, A. 1990. Caracteres hereditarios y ligamiento factorial en la quinua. Agronomic Engineering thesis. University Mayor de San Simón, Cochamamba, Bolivia.
11. Capesius, I. 1991. Sequence of the 5S rRNA gene from Sinapis alba. Plant Mol. Biol. 17: 169-170.
12. Chou, C.-H., Chiang, Y.-C., and Chiang, T.-Y. 1999. Within- and between-individual length heterogeneity of the rDNA-IGS in Miscanthus sinensis var. glaber (Poaceae): phylogenetic analyses. Genome, 42: 1088-1093.
13. Cox, A.V., Bennett, M.D., and Dyer, T.A. 1992. Use of the polymerase chain reaction to detect spacer size heterogeneity in plant 5S-rRNA gene clusters and to locate such clusters in wheat (Triticum aestivum L.). Theor. Appl. Genet. 83: 684-690.
14. Cronn, R.C., Zhao, X., Paterson, A.H., and Wendel, J.F. 1996. Polymorphism and concerted evolution in a tandemly repeated gene family: 5S ribosomal DNA in diploid and allopolyploid cottons. J. Mol. Evol. 42: 685-705.
15. de Melo, N.F., and Guerra, M. 2003. Variability of the 5S and 45S rDNA sites in Passiflora L. species with distinct base chromosome numbers. Ann. Bot. 92: 309-316.
16. Ellis, T.N., Lee, D., Thomas, C.M., Simpson, P.R., Cleary, W.G., Newman, M.-A., and Burcham, K.W.G. 1988. 5S rRNA genes in pisum: sequence, long range and chromosomal organization. Mol. Gen. Genet. 214: 333-342.
17. Fernández, M., Polanco, C., Ruiz, M.L., and Pérez de la Vega, M. 2000. A comparative study of the structure of the rDNA intergenic spacer of Lens culinaris Medik., and other legume species. Genome, 43: 597-603.
18. Gandarillas, H. 1968. Razas de quinua La Paz, Bolivia, MACA, División de Investigaciones Agrícolas. Universo, Boletín Experimental No. 34
19. Gerlach, W.L., and Dyer, T.A. 1980. Sequence organization of the repeating units in the nucleus of wheat, which contain 5S rRNA genes. Nucleic Acids Res. 8: 4851-4865.
20. Hernández, P., Martín-Parras, L., Martínez-Robles, M.L., and Schvartzman, J.B. 1993. Conserved features in the mode of replication of eukaryotic ribosomal RNA genes. EMBO J. 12: 1475-1485.
21. Homsher, P.J. 1967. Cytological and taxonomic studies in Chenopodium. Ph.D. thesis, Pennsylvania State College, Pa.
22. Hori, H., and Osawa, S. 1986. Evolutionary change in 5S rRNA secondary structure and a phylogenetic tree of 352 5S rRNA species. BioSystems, 19: 163-172.
23. Hsieh, H.-M., Hou, R.-J., Chen, K.-F., Tsai, L.-C., Liu, S.-W., Liu, K.-L., Linacre, A., and Lee, J.C.-I. 2004. Establishing the rDNA IGS structure of Cannabis sativa. J. Forensic Sci. 49: 477-480.
24. Jukes, T.H., and Cantor, C.R. 1969. Evolution of protein macromolecules. In Mammalian protein metabolism. Edited by H.N. Munro. Academic Press, New York, N.Y. pp. 21-32.
25. Kellogg, E.A., and Appels, R. 1995. Intraspecific and interspecific variation in 5S RNA genes are decoupled in diploid wheat relatives. Genetics, 140: 325-343.
26. Kolano, B., Pando, L.G., and Maluszynska, J. 2001. Molecular cytogenetic studies of Chenopodium quinoa and Amaranthus caudatus. Acta Soc. Bot. Pol. 70: 85-90.
27. Kuzaff, R.K., Seveere, J.A., Soltis, D.E., Soltis, P.S., and Zimmer, E.A. 1998. The phylogenetic potential of entire 26S rDNA sequences in plants. Mol. Biol. Evol. 15: 251-263.
28. Lorz, A. 1937. Cytological investigations on five Chenopodiaceous genera with special emphasis on chromosome morphology and somatic doubling in Spinacia. Cytologia, 8: 241-276.
29. Macas, J., Navrátilová, A., and Mészáros, T. 2003. Sequence subfamilies of satellite repeats related to rDNA intergenic spacer are differentially amplified on Vicia sativa chromosomes. Chromosoma, 112: 152-158.
30. Mason, S.L., Stevens, M.R., Jellen, E.N., Bonifacio, A., Fairbanks, D.J., Coleman, C.E., McCarty, R.R., Rasmussen, A.G., Maughan, P.J. 2005. Development and use of microsatellite markers for germplasm characterization in quinoa (Chenopodium quinoa Willd.). Crop Sci. 45: 1618-1630.
31. Maughan, P.J., Bonifacio, A., Jellen, E.N., Stevens, M.R., Coleman, C.E., Ricks, M., Mason, S.L., et al. 2004. A genetic linkage map of quinoa (Chenopodium quinoa) based on AFLP, RAPD and SSR markers. Theor. Appl. Genet. 109: 1188-1195.
32. Negi, M.S., Rajagopal, J., Chauahan, N., Cronn, R., and Lakshmikumaran, M. 2002. Length and sequence heterogeneity in 5S rDNA of Populus deltoides. Genome, 45: 1181-1188.
33. Nei, M. 1987. Molecular evolutionary genetics. Columbia University Press, New York, N.Y.
34. Nickrent, D.L., and Patrick, J.A. 1998. The nuclear ribosomal DNA intergenic spacers of wild and cultivated soybean have low variation and cryptic subrepeats. Genome, 41: 183-192.
35. Partap, T., Joshi, B.D., and Galwey, N.W. 1998. Chenopods. Chenopodium spp. Promoting the conservation and use of underutilized and neglected crops. 22. Institute of Plant Genetics and Crop Plant Research, Gatersleben/ International Plant Genetic Resources Institute, Rome, Italy.
36. Penteado, M.I. de O., García, P., and Pérez de la Vega, M. 1996. Genetic variability and mating system in three species of the genus Centrosema. J. Hered. 87: 124-130.
37. Polanco, C., and Pérez de la Vega, M. 1995. Length polymorphism in the ribosomal DNA intergenic spacer of rye and slender wild oats. J. Hered. 86: 402-407.
38. Polanco, C., and Pérez de la Vega, M. 1997. Intergenic ribosomal spacer variability in hexaploid oat cultivars and landraces. Heredity, 78: 115-123.
39. Rogers, S.O., and Bendich, A.J. 1987. Ribosomal RNA genes in plants: variability in copy number and in the intergenic spacer. Plant Mol. Biol. 9: 509-520.
40. Saghai-Maroof, M.A., Soliman, K.M., Jorgensen, R.A., and Allard, R.W. 1984. Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc. Natl. Acad. Sci. U.S.A. 81: 8014-8018.
41. Saitou, N., and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
42. Sajdak, S.L., Reed, K.M., and Phillips, R.B. 1998. Intraindividual and interspecies variation in the 5S rDNA of coregonid fish. J. Mol. Evol. 46: 680-688.
43. Sastri, D.C., Hilu, K., Appels, R., Lagudah, E.S., Playford, J., and Baum, B.R. 1992. An overview of evolution in plant 5S DNA. Plant Syst. Evol. 183: 169-181.
44. Schaal, B.A., and Learn, G.H., Jr. 1988. Ribosomal DNA variation with and among plant populations. Ann. Mo. Bot. Gard. 75: 1207-1216.
45. Schwarzacher, T., and Heslop-Harrison, P. 2000. Practical in situ hybridization. BIOS Scientific Publisher Limited, Oxford, UK.
46. Schweizer, G., and Hemleben, V. 1989. Identification of different cultivars of Solanum tuberosum and their somatic hybrids with repetitive gene probes. Vortr. Pflanzenzuecht 15: 28-10.
47. Scoles, G.J., Gill, B.S., Xin, Z.-Y., Clarke, B.C., McIntyre, C.L., Chapman, C., and Appels, R. 1988. Frequent duplication and deletion events in the 5S RNA genes and the associated spacer regions of the Triticeae. Plant Syst. Evol. 160: 105-122.
48. Simmonds, N.W. 1971. The breeding system of Chenopodium quinoa. I. Male sterility. Heredity, 27: 73-82.
49. Soltis, D.E., Soltis, P.S., Nickrent, D.L., Johnson, L.A., Hahn, W.J., Hoot, S.B., et al. 1997. Angiosperm phylogeny inferred from 18S ribosomal DNA sequences. Ann. Mo. Bot. Gard. 84: 1-49.
50. Suzuki, A., Tanifuji, S., Komeda, Y., and Kato, A. 1996. Structural and functional characterization of the intergenic spacer region of the rDNA in Daucus carota. Plant Cell Physiol. 37: 233-238.
51. Takaiwa, F., Kikuchi, S., and Oono, K. 1990. The complete nucleotide sequence of the intergenic spacer between 25S and 17S rDNAs in rice. Plant Mol. Biol. 15: 933-935.
52. Thomas, H.M., Harper, J.A., and Morgan, W.G. 2001. Gross chromosome rearangements are occurring in an accession of the grass Lolium rigidum. Chromosome Res. 9: 585-590.
53. Todd, J.J., and Vodkin, L.O. 1996. Duplications that suppress and deletions that restore expression from a chalcone synthase multigene family. Plant Cell, 8: 687-699.
54. Tremousaygue, D., Grellet, F., Delseny, M., Delourme, R., and Renard, M. 1988. The large spacer of a nuclear ribosomal RNA gene from radish: organization and use as a probe in rapeseed breeding. Theor. Appl. Genet. 75: 298-304.
55. Udovicic, R., McFadden, G.I., and Ladiges, P.Y. 1995. Phylogeny of Eucalyptus and Angophora based on 5S rDNA spacer sequence data. Mol. Phylogenet. Evol. 4: 247-256.
56. Unfried, I., and Gruendler, P. 1990. Nucleotide sequence of the 5,8S and 25S rRNA genes and the internal transcribed spacers from Arabidopsis thaliana. Nucleic Acids Res. 18: 4011.
57. Venkateswarlu, K., Lee, S.W., and Nazar, R.N. 1991. Conserved upstream sequence elements in plant 5S ribosomal RNA-encoding genes. Gene, 105: 249-253.
58. Walters, T.W. 1987. Electrophoretic evidence for the evolutionary relationship of the tetraploid Chenopodium berlandieri to its putative diploid progenitors. Selbyana, 10: 36-55.
59. Wang, S., Tsuchiya, T., and Wilson, H.D. 1993. Chromosome studies in several species of Chenopodium from North and South America. J. Genet. Breed. 47: 163-170.
60. Ward, S.M. 2000. Allotetraploid segregation for single-gene morphological characters in quinoa (Chenopodium quinoa Willd.). Euphytica, 116: 11-16.
61. Ward, S.M. 2001. A recessive allele inhibiting saponin synthesis in two lines of Bolivian quinoa (Chenopodium quinoa Willd.) J. Hered. 92: 83-86.
62. Weiss, H., and Maluszynska J. 2000. Chromosomal rearrangement in autotetraploid plants of Arabidopsis thaliana. Hereditas, 133: 255-261.
63. Wilson, H.D. 1980. Artificial hybridization among species of Chenopodium sect. Chenopodium. Syst. Bot. 5: 253-263.
64. Wilson, H.D. 1988. Quinoa biosystematics. I: Domesticated populations. Econ. Bot. 42: 461-477.
65. Wilson, H.D. 1990. Quinua and relatives (Chenopodium sect. Chenopodium subsect.) Cellulata. Econ. Bot. 44: 92-110.
66. Wilson, H.D., and Heiser, C.B. 1979. The origin and evolutionary relationships of 'Huauzontle' (Chenopodium nuttaliae Safford), domesticated chenopod of Mexico. Am. J. Bot. 66: 198-206.
67. Yang, Y.-W., Tseng, P.-F., Tai, P.-Y., and Chang, C.-J. 1998. Phylogenetic position of Raphanus in relation to Brassica species based on 5S rRNA spacer sequence data. Bot. Bull. Acad. Sin. 39: 153-160.