A historical andmodern perspective on plant cytogenetics

Briefings in Functional Genomics and Proteomics

Volumn 9, Issue 2, 2010, Pages 95-102

  Figueroa, Debbie M ^a   Bass, Hank W ^a  

^a FLORIDA STATE UNIVERSITY   (United States)

Author keywords

Bac; Chromosome; Cytology; Fish; Microscopy

Indexed keywords

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CONTIG MAPPING; CYTOGENETICS; FLUORESCENCE IN SITU HYBRIDIZATION; FUNCTIONAL GENOMICS; GENE AMPLIFICATION; GENE REARRANGEMENT; GENE STRUCTURE; GENETIC ORGANIZATION; IMMUNOCYTOCHEMISTRY; MICROSCOPY; MOLECULAR BIOLOGY; MOLECULAR PROBE; NONHUMAN; PLANT GENETICS; CYTOLOGY; GENETICS; GENOMICS; HISTORY; METHODOLOGY; PLANT; REVIEW; STATISTICAL PARAMETERS;

CYTOGENETICS; GENOMICS; HISTORY, 20TH CENTURY; HISTORY, 21ST CENTURY; IN SITU HYBRIDIZATION, FLUORESCENCE; LIMIT OF DETECTION; PLANTS;

EID: 77951996281     PISSN: 14739550     EISSN: 14774062     Source Type: Journal    
DOI: 10.1093/bfgp/elp058     Document Type: Article

References (103)

1. Creighton HB, McClintock B. A correlation of cytological and genetical crossing-over in Zea mays. Proc Natl Acad Sci USA 1931;17:492-7.
2. McClintock B. Chromosome morphology in Zea mays. Science 1929;69:629.
3. McClintock B. The stability of broken ends of chromosomes in Zea mays. Genetics 1932;26:234-82.
4. McClintock B. The production of homozygous deficient tissues with mutant characteristics by means of the aberrant mitotic behavior of ring-shaped chromosomes. Genetics 1938;23:315-76.
5. McClintock B. The stability of broken ends of chromosomes in Zea mays. Genetics 1941;26:234-82.
6. McClintock B. The significance of responses of the genome to challenge. Science 1984;226:792-801.
7. Shastry SVS, Ranga Rao DR, Misra RN. Pachytene analysis in Oryza. I. Chromosome morphology in Oryza sativa. Indian J Genet & Plant Breed 1960;20:15-21.
8. Misra RN, Shastry SVS. Pachytene analysis in Oryza. VIII. Chromosome morphology and karyotypic variation in O. sativa. Indian J Genet & Plant Breed 1967;27:349-68.
9. Magoon ML, Shambulinguppa KG. Karyomorphology of Sorghum propinquum and its bearing on origin of 40-chromosome sorghum. Chromosoma 1961;12:460-5.
10. Barton DW. Pachytene morphology of the tomato chromosome complement. AmJ Bot 1950;37:639-43.
11. Ramanna MS, Parkken P. Structure of and homology between pachytene and somatic metaphase chromosomes of tomato. Genetica 1967;38:115-33.
12. Caspersson T, Farber S, Foley GE, et al. Chemical differentiation along metaphase chromosomes. Exp Cell Res 1968; 49:219-22.
13. Vosa CG, Marchi P. Quinacrine fluorescence and Giemsa staining in plants. Nat New Biol 1972;237:191-2.
14. Kurata N, Omura T. Karyotype analysis in rice I. A new method for identifying all chromosome pairs. Jpn J Genet 1978;54:251-5.
15. Gill BS, Kimber G. The Giemsa C-banded karyotype of rye. Proc Natl Acad Sci USA 1974;71:1247-9.
16. Linde-Laursen I. Giemsa C-banding of the chromosomes of "Emir" barley. Hereditas 1975;81:285-9.
17. Schweizer D. Differential staining of plant chromosomes. Chromosoma 1973;40:307-20.
18. Mok DWS, Mok MC. A modified Giemsa technique for identifying bean chromosomes. J Hered 1976;67:187-8.
19. Pijnacker LP, Ferwerda MA. Giemsa C-banding of potato chromosomes. Can J Genet Cytol 1984;26:415-9.
20. Yu H, Liang GH, Kofoid KD. Analysis of C-banding chromosome patterns of Sorghum. Crop Sci 1991;31:1524-7.
21. Lavania UC. Differential staining and plant chromosomes-progress in cytogenetics. Curr Sci 1978;47:255-60.
22. Gill BS, Friebe B. Plant cytogenetics at the dawn of the 21st century. Curr Opin Plant Biol 1998;1:109-15.
23. Harper LC, Cande WZ. Mapping a new frontier; development of integrated cytogenetic maps in plants. Funct Integr Genomics 2000;1:89-98.
24. Gall JG, Pardue ML. Formation and detection of RNA-DNA hybrid molecules in cytological preparations. Proc Natl Acad Sci USA 1969;63:378-83.
25. Pardue ML, Gall JG. Molecular hybridization of radioactive DNA to the DNA of cytological preparations. Proc Natl Acad Sci USA 1969;64:600-4.
26. Pardue ML, Gall JG. Nucleic acid hybridization to the DNA of cytological preparations. Methods Cell Biol 1975; 10:1-16.
27. John HA, Birnstiel Ml, Jones KW. RNA-DNA hybrids at the cytological level. Nature 1969;223:582-7.
28. Ambros PF, Matzke MA, Matzke AJ. Detection of a 17 kb unique sequence (T-DNA) in plant chromosomes by in situ hybridization. Chromosoma 1986;94:11-8.
29. Fransz PF, Stam M, Montijn BM, et al. Detection of singlecopy genes and chromosome rearrangements in Petunia hybrida by fluorescence in situ hybridization. Plant J 1996; 9:767-74.
30. Peacock WJ, Dennis ES, Rhoades MM, et al. Highly repeated DNA sequence limited to knob heterochromatin in maize. Proc Natl Acad Sci USA 1981;78:4490-4.
31. Shen DL, Wang ZF, Wu M. Gene mapping on maize pachytene chromosomes by in situ hybridization. Chromosoma 1987;95:311-4.
32. Xu J, Earle ED. Direct and sensitive fluorescence in situ hybridization of 45S rDNA on tomato chromosomes. Genome 1994;37:1062-5.
33. Jiang J, Gill BS. Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research. Genome 2006;49:1057-68.
34. Lysak MA, Fransz PF, Ali HBM, et al. Chromosome painting in Arabidopsis thaliana. Plant J 2001;28:689-97.
35. Lysak MA, Pecinka A, Schubert I. Recent progress in chromosome painting of Arabidopsis and related species. Chromosome Res 2003;11:195-204.
36. Kato A, Lamb JC, Birchler JA. Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize. Proc Natl Acad Sci USA 2004;101:13554-9.
37. Lamb JC, Birchler JA. Retroelement genome painting: cytological visualization of retroelement expansions in the genera Zea and Tripsacum. Genetics 2006;173:1007-21.
38. Suzuki HY, Futsuhara F, Takaiwa F, et al. Localization of glutelin gene in rice chromosome by in situ hybridization. Jpn J Genet 1991;66:305-12.
39. Gustafson JP, Dille JE. Chromosome location of Oryza sativa recombination linkage groups. Proc Natl Acad Sci USA 1992;89:8646-50.
40. Woo SS, Jiang JM, Gill BS, et al. Construction and characterization of a bacterial artificial chromosome library of Sorghum bicolor. Nucleic Acids Res 1994;22:4922-31.
41. Song YC, Gustafson JP. The physical location of 14 RFLP markers in rice (Oryza sativa L.). Theor Appl Genet 1995;90: 113-9.
42. Zwick MS, Islam-Faridi MN, Czeschin DG, Jr, et al. Physical mapping of the liguleless linkage group in Sorghum bicolor using rice RFLP-selected sorghum BACs. Genetics 1998;148:1983-92.
43. Reamon-Buttner SM, Schmidt T, Jung C. AFLPs represent highly repetitive sequences in Asparagus officinalis L. Chromosome Res 1999;7:297-304.
44. Huang XQ, Zeller FJ, Hsam SLK, et al. Chromosomal location of AFLP markers in common wheat utilizing nullitetrasomic stocks. Genome 2000;43:298-305.
45. Sadder MT, Ponelies N, Born U, et al. Physical localization of single-copy sequences on pachytene chromosomes in maize (Zea mays L.) by chromosome in situ suppression hybridization. Genome 2000;43:1081-3.
46. Peters JL, Constandt H, Neyt P, et al. A physical amplified fragment-length polymorphism map of Arabidopsis. Plant Physiol 2001;127:1579-89.
47. Islam-Faridi MN, Childs KL, Klein PE, et al. A molecular cytogenetic map of sorghum chromosome 1. Fluorescence in situ hybridization analysis with mapped bacterial artificial chromosomes. Genetics 2002;161:345-53.
48. Koumbaris GL, Bass HW. A new single-locus cytogenetic mapping system for maize (Zea mays L.): overcoming FISH detection limits with marker-selected sorghum (S. propinquum L.) BAC clones. Plant J 2003;35:647-59.
49. Wang CJ, Harper L, Cande WZ. High-resolution singlecopy gene fluorescence in situ hybridization and its use in the construction of a cytogenetic map of maize chromosome Plant Cell 2006;18:529-44.
50. Amarillo FI, Bass HW. A transgenomic cytogenetic sorghum (Sorghum propinquum) bacterial artificial chromosome fluorescence in situ hybridization map of maize (Zeamays L.) pachytene chromosome 9, evidence for regions of genome hyperexpansion. Genetics 2007;177:1509-26.
51. Lamb JC, Danilova T, Bauer MJ, et al. Single-gene detection and karyotyping using small-target fluorescence in situ hybridization on maize somatic chromosomes. Genetics 2007;175:1047-58.
52. Danilova TV, Birchler JA. Integrated cytogenetic map of mitotic metaphase chromosome 9 of maize: resolution, sensitivity, and banding paint development. Chromosoma 2008; 117:345-56.
53. Albini S. A karyotype of the Arabidopsis thaliana genome derived from synaptonemal complex analysis at prophase I of meiosis. Plant J 1994;5:665-72.
54. Desel C, Jung C, Cai D, et al. High-resolution mapping of YACs and the single-copy gene Hs1(pro-1) on Beta vulgaris chromosomes by multi-colour fluorescence in situ hybridization. Plant Mol Biol 2001;45:113-22.
55. Jiang J, Hulbert SH, Gill BS, et al. Interphase fluorescence in situ hybridization mapping: a physical mapping strategy for plant species with large complex genomes. Mol Gen Genet 1996;252:497-502.
56. Khrustaleva LI, Kik C. Localization of single-copy T-DNA insertion in transgenic shallots (Allium cepa) by using ultrasensitive FISH with tyramide signal amplification. Plant J 2001;25:699-707.
57. Stephens JL, Brown SE, Lapitan NL, et al. Physical mapping of barley genes using an ultrasensitive fluorescence in situ hybridization technique. Genome 2004;47:179-89.
58. Zhong XB, de Jong JH, Zabel P. Preparation of tomato meiotic pachytene and mitotic metaphase chromosomes suitable for fluorescence in situ hybridization (FISH). Chromosome Res 1996;4:24-8.
59. Lawrence CJ, Seigfried TE, Bass HW, et al. Predicting chromosomal locations of genetically mapped loci in maize using the Morgan2McClintock Translator. Genetics 2006;172: 2007-9.
60. Cheng Z, Buell CR, Wing RA, et al. Resolution of fluorescence in-situ hybridization mapping on rice mitotic prometaphase chromosomes, meiotic pachytene chromosomes and extended DNA fibers. Chromosome Res 2002;10:379-87.
61. de Jong JH, Fransz P, Zabel P. High resolution FISH in plants-techniques and applications. Trends Plant Sci 1999;4: 258-63.
62. Jiang J, Gill BS, Wang GL, et al. Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes. Proc Natl Acad Sci USA 1995;92:4487-91.
63. Fransz PF, Armstrong S, de Jong JH, et al. Integrated cytogenetic map of chromosome arm 4S of A. thaliana: structural organization of heterochromatic knob and centromere region. Cell 2000;100:367-76.
64. Zoller JF, Herrmann RG, Wanner G. Chromosome condensation in mitosis and meiosis of rye (Secale cereale L.). Cytogenet Genome Res 2004;105:134-44.
65. Valarik M, Bartos J, Kovarova P, et al. High-resolution FISH on super-stretched flow-sorted plant chromosomes. Plant J 2004;37:940-50.
66. Koo DH, Jiang J. Super-stretched pachytene chromosomes for fluorescence in situ hybridization mapping and immunodetection of DNA methylation. PlantJ 2009;59:509-16.
67. Jackson SA, Wang ML, Goodman HM, et al. Application of fiber-FISH in physical mapping of Arabidopsis thaliana. Genome 1998;41:566-72.
68. Jin WW, Melo JR, Nagaki K, et al. Maize centromeres: organization and functional adaptation in the genetic background of oat. Plant Cell 2004;16:571-81.
69. Lilly JW, Havey MJ, Jackson SA, et al. Cytogenomic analyses reveal the structural plasticity of the chloroplast genome in higher plants. Plant Cell 2001;13:245-54.
70. Nagaki K, Cheng Z, Ouyang S, et al. Sequencing of a rice centromere uncovers active genes. Nat Genet 2004;36: 138-45.
71. Fransz PF, Alonso-Blanco C, Liharska TB, et al. Highresolution physical mapping in Arabidopsis thaliana and tomato by fluorescence in situ hybridization to extended DNA fibres. Plant J 1996;9:421-30.
72. The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000;408:796-815.
73. Dong F, Song J, Naess SK, et al. Development and application of a set of chromosome-specific cytogenetic DNA markers in potato. Theor Appl Genet 2000;101:1001-7.
74. Fransz P, Armstrong S, Alonso-Blanco C, et al. Cytogenetics for the model system Arabidopsis thaliana. Plant J 1998;13: 867-76.
75. Islam-Faridi MN, Nelson CD, Kubisiak TL. Reference karyotype and cytomolecular map for loblolly pine (Pinus taeda L.). Genome 2007;50:241-51.
76. Moraes AP, Mirkov TE, Guerra M. Mapping the chromosomes of Poncirus trifoliata Raf. by BAC-FISH. Cytogenet Genome Res 2008;121:277-81.
77. Koo DH, Jo SH, Bang JW, et al. Integration of cytogenetic and genetic linkage maps unveils the physical architecture of tomato chromosome 2. Genetics 2008;179:1211-20.
78. Szinay D, Chang SB, Khrustaleva L, et al. High-resolution chromosome mapping of BACs using multi-colour FISH and pooled-BAC FISH as a backbone for sequencing tomato chromosome 6. PlantJ 2008;56:627-37.
79. Tang XM, Szinay D, Lang C, et al. Cross-species bacterial artificial chromosome-fluorescence in situ hybridization painting of the tomato and potato chromosome 6 reveals undescribed chromosomal rearrangements. Genetics 2008; 180:1319-28.
80. Iovene M, Wielgus SM, Simon PW, et al. Chromatin structure and physical mapping of chromosome 6 of potato and comparative analyses with tomato. Genetics 2008;180: 1307-17.
81. Stack SM, Royer SM, Shearer LA, et al. Role of fluorescence in situ hybridization in sequencing the tomato genome. Cytogenet Genome Res 2009;124:339-50.
82. Okagaki RJ, Jacobs MS, Stec AO, et al. Maize centromere mapping: a comparison of physical and genetic strategies. J Hered 2008;99:85-93.
83. Feng Q, Zhang Y, Hao P, et al. Sequence and analysis of rice chromosome 4. Nature 2002;420:316-20.
84. Sasaki T, Matsumoto T, Yamamoto K, et al. The genome sequence and structure of rice chromosome 1. Nature 2002; 420:312-6.
85. Peterson DG, Lapitan NL, Stack SM. Localization of singleand low-copy sequences on tomato synaptonemal complex spreads using fluorescence in situ hybridization (FISH). Genetics 1999;152:427-39.
86. Visser RGF, Bachem CWB, de Boer JM, et al. Sequencing the potato genome: outline and first results to come from the elucidation of the sequence of the world's third most important food crop. AmJ Potato Res 2009;86:417-29.
87. Jackson SA, Cheng ZK, Wang ML, et al. Comparative fluorescence in situ hybridization mapping of a 431-kb Arabidopsis thaliana bacterial artificial chromosome contig reveals the role of chromosomal duplications in the expansion of the Brassica rapa genome. Genetics 2000;156:833-8.
88. Mandakova T, Lysak MA. Chromosomal phylogeny and karyotype evolution in x = 7 crucifer species (Brassicaceae). Plant Cell 2008;20:2559-70.
89. Draye X, Lin YR, Qian XY, et al. Toward integration of comparative genetic, physical, diversity, and cytomolecular maps for grasses and grains, using the sorghum genome as a foundation. Plant Physiol 2001;125:1325-41.
90. Lysak MA, Koch MA, Pecinka A, et al. Chromosome triplication found across the tribe Brassiceae. Genome Res 2005; 15:516-25.
91. Yan H, Ito H, Nobuta K, et al. Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromere. Plant Cell 2006;18:2123-33.
92. Zhong CX, Marshall JB, Topp C, et al. Centromeric retroelements and satellites interact with maize kinetochore protein CENH3. Plant Cell 2002;14:2825-36.
93. Zhang WL, Lee HR, Koo DH, et al. Epigenetic modification of centromeric chromatin: hypomethylation of DNA sequences in the CENH3-associated chromatin in Arabidopsis thaliana and maize. Plant Cell 2008;20:25-34.
94. Carlson SR, Rudgers GW, Zieler H, et al. Meiotic transmission of an in vitro-assembled autonomous maize minichromosome. PLoS Genet 2007;3:1965-74.
95. Yu W, Han F, Gao Z, et al. Construction and behavior of engineered minichromosomes in maize. Proc Natl Acad Sci USA 2007;104:8924-9.
96. Ananiev EV, Wu C, Chamberlin MA, et al. Artificial chromosome formation in maize (Zea mays L.). Chromosoma 2009;118:157-177.
97. Huang B, Jones SA, Brandenburg B, et al. Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution. Nat Methods 2008;5: 1047-52.
98. Huang B, Wang W, Bates M, et al. Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science 2008;319:810-3.
99. Rust MJ, Bates M, Zhuang X. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat Methods 2006;3:793-5.
100. Carlton PM. Three-dimensional structured illumination microscopy and its application to chromosome structure. Chromosome Res 2008;16:351-65. 101
101. Wang CJ, Carlton PM, Golubovskaya IN, et al. Interlock formation and coiling of meiotic chromosome axes during synapsis. Genetics 2009;183:905-15.
102. Gustafsson MG, Shao L, Carlton PM, et al. Threedimensional resolution doubling in wide-field fluorescence microscopy by structured illumination. Biophys J 2008;94: 4957-70.
103. Ananiev EV, Phillips RL, Rines HW. Chromosome-specific molecular organization of maize (Zea mays L.) centromeric regions. Proc Natl Acad Sci USA 1998;95:13073-8.