A low-density genetic map of onion reveals a role for tandem duplication in the evolution of an extremely large diploid genome

Theoretical and Applied Genetics

Volumn 96, Issue 1, 1998, Pages 52-62

  King, J J ^a   Bradeen, J M ^a   Bark, O ^b   McCallum, J A ^c   Havey, M J ^a  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

^c THE NEW ZEALAND INSTITUTE FOR PLANT AND FOOD RESEARCH LIMITED   (New Zealand)

Author keywords

Allium; Duplication; Map; Onion

Indexed keywords

CHLOROPLAST DNA; GENETIC LINKAGE; GENOME ORGANIZATION; RANDOM AMPLIFIED POLYMORPHIC DNA; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SEQUENCE ANALYSIS;

ALLIUM CEPA;

EID: 0031934064     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s001220050708     Document Type: Article

References (106)

1. Ahn S, Anderson JA, Sorrells ME, Tanksley SD (1993) Homoeologous relationships of rice, wheat and maize chromosomes. Mol Gen Genet 241:483-490
2. Albini S, Jones G (1988) Synaptonemal complex spreading in Allium cepa and Allium fistulosum. II. Pachytene observations: the SC karyotype and the correspondence of late recombination nodules and chiasmata. Genome 30:399-410
3. Anderson E (1945) What is Zea mays? A report of progress. Chron Bot 9:88-92
4. Anderson P (1987) Twenty years of illegitimate recombination. Genetics 115:581-584
5. Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208-218
6. Bark OH, Havey MJ (1995) Similarities and relationships among open-pollinated populations of the bulb onion as estimated by nuclear RFLPs. Theor Appl Genet 90:607-614
7. Barnes SR, James AM, Jamieson G (1988) The organization, nucleotide sequence, and chromosomal distribution of a satellite DNA from Allium cepa. Chromosoma 92:185-192
8. Bennett MD, Smith JB (1976) Nuclear DNA amounts in angiosperms. Philos Trans R Soc London Ser B 274:227-274
9. Bennetzen JL, Freeling M (1993) Grasses as a single genetic system: genome composition, collinearity and compatibility. Trends Genet 9:259-261
10. Berninger E, Buret P (1967) Etudes des deficients chlorophyllines chez deux especes cultivées du genre Allium: l'oignon (A. cepa L.) et le poireau (A. porrum L.). Ann Amelior Plant 17:175-194
11. Bonierbale MW, Plaisted RL, Tanksley SD (1988) RFLP maps based on a common set of clones reveal modes of chromosomal evolution in potato and tomato. Genetics 120:1095-1103
12. Bradeen JM, Havey MJ (1995) Randomly amplified polymorphic DNA in bulb onion and its use to assess inbred integrity. J Am Soc Hortic Sci 120:752-758
13. Callis J, Carpenter T, Sun CW, Vierstra RD (1995) Structure and evolution of genes encoding polyubiquitin-and ubiquitin-like proteins in Arabidopsis thaliana ecotype Columbia. Genetics 139:921-939
14. Celarier RP (1956) Additional evidence for five as the basic chromosome number of the Andropogoneae. Rhodora 58:135-143
15. Chang C, Bowman JL, Dejohn AW, Lander ES, Meyerowitz EM (1988) Restriction fragment length polymorphism linkage map for Arabidopsis thaliana. Proc Natl Acad Sci USA 85:6856-6860
16. Chittenden LM, Schertz KF. Lin YR, Wing, RA, Paterson AH (1994) A detailed RFLP map of Sorghum bicolor × S. propinquum, suitable for high-density mapping, suggests ancestral duplication of Sorghum chromosomes or chromosomal segments. Theor Appl Genet 87:925 933
17. Clarke A, Jones HA, Little T (1944) Inheritance of bulb color in the onion. Genetics 29:569-575
18. Davis E (1966) An improved method of producing hybrid onion seed. J Hered 57:55-57
19. Devey ME, Fiddler TA, Liu BH, Knapp SJ, Neale DB (1994) An RFLP linkage map for loblolly pine based on a three-generation outbred pedigree. Theor Appl Genet 88:273-278
20. Devos KM, Chao S, Li QY (1994) Relationship between chromosome 9 of maize and wheat homeologous group 7 chromosomes. Genetics 138:1287-1292
21. Dubcovsky J, Luo MC, Zhong GY, Bransteitter R, Desai A, Kilian A, Kleinhofs A, Dvorak J (1996) Genetic map of diploid wheat, Triticum monococcum L., and its comparison with maps of Hordeum vulgare L. Genetics 143:983-999
22. Dunford RP, Kurata N, Laurie DA, Money TA, Minobe Y, Moore G (1995) Conservation of fine-scale DNA marker order in the genomes of rice and the Triticeae. Nucleic Acids Res 23:2724-2728
23. El-Shafie M, Davis G (1967) Inheritance of bulb color in Allium cepa. Hilgardia 9:607-622
24. Engle R, Gabelman W (1966) Inheritance and mechanism for resistance to ozone damage in onion. Proc Am Soc Hortic Sci 89:423-430
25. Feinberg A, Vogelstein B (1983) A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem 132:6-13
26. Fukuda H, Kawahara R, Sunabori S, Komamine A (1992) A gene expressed preferentially in the globular stage of somatic embryogenesis encodes elongation factor I alpha in carrot. Eur J Biochem 209:157-162
27. Funke RP, Kolchinsky A, Gresshof PM (1993) Physical mapping of a region in the soybean (Glycine max) genome containing duplicated sequences. Plant Mol Biol 22:437-446
28. Gebhardt C, Ritter E, Barone A, Debener T, Walkemeier B, Schachtschabel U. Kaufmann H, Thompson RD, Bonierbale MW, Ganal MW (1991) RFLP maps of potato and their alignment with the homoeologous tomato genome. Theor Appl Genet 83:49-57
29. Gentzbittel L, Vear F, Zhang YX, Berville A, Nicholas P (1995) Development of a consensus linkage RFLP map of cultivated sunflower (Helianthus annuus L.). Theor Appl Genet 90: 1079-1086
30. Gill KS, Lubbers EL, Gill BS, Raup WJ. Cox TS (1991) A genetic linkage map of Triticum tauschii (DD) and its relationship to the D genome of bread wheat (AABBDD). Genome 34:362-374
31. Grasser KD, Wehlfahrt T, Baumleiu H, Feix G (1993) Comparative analysis of chromosomal HMG proteins from monocotyledons and dicotyledons. Plant Mol Biol 23:619-625
32. Havey MJ (1992) Restriction enzyme analysis of the chloroplast and nuclear 45s ribosomal DNA of Allium sections Cepa and Phyllodolon. Plant Syst Evol 183:17 31
33. Havey MJ (1995) Cytoplasmic determinations using the polymerase chain reaction to aid in the extraction of maintainer lines from open-pollinated populations of onion. Theor Appl Genet 90: 263-268
34. Havey MJ, Muehlbauer FJ (1989) Linkages between restriction fragment length, isozyme, and morphological markers in lentil. Theor Appl Genet 77:395-401
35. Havey MJ, King JJ, Bradeen JM, Bark O (1997) Molecular markers and mapping in bulb onion, a forgotten monocot. HortScience 31:1116-1118
36. Helentjaris T, Slocum M, Wright S, Schaefer A, Nienhuis J (1986) Construction of genetic linkage maps in maize and tomato using restriction fragment length polymorphisms. Theor Appl Genet 72:761-769
37. Helentjaris T, Weber D. Wright S (1988) Identification of the genomic locations of duplicate nucleotide sequences in maize by analysis of restriction fragment length polymorphisms. Genetics 118:353-363
38. Horobin J (1986) Inheritance of a dwarf seed stalk character is onion. Ann Appl Biol 108:199-204
39. Hulbert S H, Bennetzen JL (1991) Recombination at the Rpl locus of maize. Mol Gen Genet 226:377-382
40. Jiang C, Lewis MA, Sink KC (1997) Combined RAPD and RFLP molecular linkage map of asparagus. Genome 40:69-70
41. Jones HA, Clarke A (1943) Inheritance of male sterility in the onion and the production of hybrid seed. Proc Am Soc Hortic Sci 43:189-194
42. Jones HA, Davis G (1944) Inbreeding and heterosis and their relation to the development of new varieties of onions. USDA Tech Bull No 874
43. Jones HA, Peterson CE (1952) Complementary factors for light-red bulb color in onions. Proc Am Soc Hortic Sci 59:457
44. Jones HA, Clarke A, Stevenson S (1944) Studies in the genetics of the onion (Allium cepa L.). Proc Am Soc Hortic Sci 44:479-484
45. Jones R, Rees H (1968) Nuclear DNA variation in Allium. Heredity 23:591-605
46. Keim P, Diers BW, Olson TC, Shoemaker RC (1990) RFLP mapping in soybean: association between marker loci and variation in quantitative traits. Genetics 126:735 742
47. Kennard WC, Poetter K, Dijkhuizen A, Meglic V, Staub JE, Havey MJ (1994) Linkages among RFLP, RAPD, isozyme, disease resistance, and morphological markers in narrow and wide crosses of cucumber. Theor Appl Genet 89:42-48
48. Kianian SF, Quiros CF (1992) Generation of a Brassica oleracea composite RFLP map: linkage arrangements among various populations and evolutionary implications. Theor Appl Genet 84:544-554
49. Kimura M (1961) Natural selection as the process of accumulating genetic information in adaptive evolution. Genet Res 2:127 140
50. Kirk JTO, Rees H, Evans G (1970) Base composition of nuclear DNA with the genus Allium. Heredity 25:507 512
51. Kleinhofs A, Kilian A, Saghai-Maroof MA, Biyashev RM, Hayes P, Chen FQ. Lapitan N, Fenwick A, Blake TK, Kanazin V (1993) A molecular, isozyme and morphological map of the barley (Hordeum vulgare) genome. Theor Appl Genet 86:705-712
52. Kosambi DD (1943) The estimation of map distances from recombination values. Ann Eugen 12:172-175
53. Krebbers E, Seurinck J, Herdies L, Cashmore AR, Timko MP (1988) Four genes in two diverged subfamilies encode the ribulose-1,5-biphosphate caroxyalse small subunit polypeptides of Arabidopsis thaliana. Plant Mol Biol 11:745-759
54. Kvarnheden A, Tandre K, Engstrom P (1995) A cdc2 homologue and closely related processed retropseudogenes from Norway spruce. Plant Mol Biol 27:391-403
55. Labani R, Elkington T (1987) Nuclear DNA variation in the genus Allium L. (Liliaceae). Heredity 59:119-128
56. Lander E, Green P, Abrahamson J, Barlow A, Daly M, Lincoln S, Newburg L (1987) MAPMAKER: an interactive computer program for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174-181
57. Landry BS, Hubert N, Etoh T, Harada JJ. Lincoln SE (1991) A genetic map for Brassica napus based on restriction fragment length polymorphisms detected with expressed DNA sequences. Genome 34:543-552
58. Leeton PRJ, Smyth DR (1993) An abundant LINE-like element amplified in the genome of Lilium speciosum. Mol Gen Genet 237:97-104
59. Leipoldt M, Schmidtke J (1982) Gene expression in phylogenetically polyploid organisms. In: Dover GA, Flavell RB (eds) Genome evolution. Academic Press, London, pp 219-236
60. Leutwiler LS, Meyerowitz EM, Tobin EM (1986) Structure and expression of three light-harvesting chlorophyll a/b binding protein genes in Arabidopsis thaliana. Nucleic Acids Res 14: 4051-4076
61. Lewis ME, Sink JC (1996) RFLP linkage map of asparagus. Genome 39:622-627
62. Matters GL, Goodenough UW (1992) A gene/pseudogene tandem duplication encodes a cysteine-rich protein expressed during zygote development in Chlamydomonas reinhardtii. Mol Gen Genet 232:81-88
63. McCouch SR, Kochert G, Yu ZH, Wang ZY, Kush GS (1988) Molecular mapping of rice chromosomes. Theor Appl Genet 76:815-829
64. McGrath JM, Quiros CF (1991) Inheritance of isozyme and RFLP markers in Brassica campestris and comparison with B. oleracea. Theor Appl Genet 82:668-673
65. McGrath JM, Janesco MM, Pichersky E (1993) Duplicate sequences with similarity to expressed genes in the genome of Arabidopsis thaliana. Theor Appl Genet 86:880-888
66. Moore G (1995) Cereal genome evolution: pastoral pursuits with "Lego" genomes. Curr Opin Genet Dev 5:717-724
67. Narayan RKJ (1988) Constraints upon the organization and evolution of chromosomes in Allium. Theor Appl Genet 75:319-329
68. Neale DB, Kinlaw CS, Sewell MM (1994) Genetic mapping and DNA sequencing of the loblolly pine genome. For Genet 1:197-206
69. Nichols C, Gabelman W, Larson R, Walker JC (1965) The expression and inheritance of resistance to pink root in onion seedlings. Phytopathology 55:752-756
70. Nodari RO, Tsai SM, Gilbertson RL, Gepts P (1993) Towards an integrated linkage map of common bean. 2. Development of an RFLP-based linkage map. Theor Appl Genet 85:513-520
71. O'Brien SJ (1993) Genetic maps: locus maps of complex genomes. Cold Spring Harbor Laboratory Press, New York
72. Ohno S (1970) Evolution by gene duplication. Springer, Berlin Heidelberg New York
73. Peffley E, Orozco-Castillo C (1987) Polymorphism of isozymes in plant introductions of Allium cepa L. and A. fistulosum L. Hort-Science 22:956-957
74. Pereira MG, Lee M, Bramel-Cox P, Woodman W, Doeblcy J, Whithus R (1994) Construction of an RFLP map in sorghum and comparative mapping with maize. Genome 37:236-243
75. Pichersky E (1990) Nomad DNA - A model for movement and duplication of DNA sequences in plant genomes. Plant Mol Biol 15:437-448
76. Pichersky E, Bernatzky R, Tanksley SD, Breidenbach W, Kausch A, Cashmore AR (1985) Isolation, molecular characterization, and genetic mapping of two clusters of genes encoding chlorophyll a/b binding proteins in Lycopersicon esculentum (tomato). Gene 40:247-258
77. Pichersky E, Hoffman NE, Bernatzky R, Piechulla B, Tanksley SD, Cashmore AR (1987) Molecular characterization and genetic mapping of DNA sequences encoding the Type I chlorophyll a/b binding polypeptide of photosystem I in Lycopersicon esculentum (tomato). Plant Mol Biol 9:205-216
78. Pike LM (1986) Onion breeding. In: Bassett MJ (ed) Breeding vegetable crops. AVI, Westport, Conn., pp 357-394
79. Ranjekar PK, Pallotta D, Lafontaine JG (1978) Analysis of plant genomes. V. Comparative study of molecular properties of DNAs of seven Allium species. Biochem Genet 16:957-970
80. Reinisch AJ, Dong JM, Brubaker CL, Stelly DM, Wendel, JF. Paterson A (1994) A detailed RFLP map of cotton, Gossypium hirsutum × Gossypium barbadense: chromosome organization and evolution in a disomic polyploid genome. Genetics 138:829-847
81. Restivo FM, Tassi F, Biffi R, Falavigna A, Caporali E, Carboni A. Doldi ML, Spada A, Marziani GP (1995) Linkage arrangement of RFLP loci in progenies from crosses between double haploid Asparagus officinalis L. clones. Theor Appl Genet 90:124-128
82. Robbins TP, Walker EL, Kermicle JL, Alleman M, Dellaporta SL (1991) Meiotic instability of the R-r complex arising from displaced intragenic exchange in intrachromosomal rearrangement. Genetics 129:271-283
83. SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D. Melake-Berhan A, Springer P, Edwards K, Lee M, Avramova Z. Bennetzen J (1996) Nested retrotransposons in the intergenic regions of the maize genome. Science 274:765-768
84. Schweisguth B (1973) Etude d'un nouveau type de sterilite male chez l'oignon, Allium cepa L. Ann Amelior Plant 23:221-233
85. Schwimmer S, Weston W (1961) Enzymatic development of pyruvic acid in onion as a measure of pungency. J Agric Food Chem 9:301-304
86. Shiozaki K, Akhavan-Niaki H, McGowan CH, Russell P (1994) Protein phosphatase 2C, encoded by ptcl + , is important in the heat shock response of Schizosaccharomyces pombe. Mol Cell Biol 14:3742-3751
87. Shoemaker RC, Polzin K, Labate J, Specht J, Brummer EC, Olson T, Young N, Concibido V, Wilcox J, Tamulonis J, Kochert G, Boersma H (1996) Genome duplication in soybean (Glycine subgenus soja). Genetics 144:329 338
88. Slocum MK, Figdore SS, Kennard WC, Suzuki JY, Osborn TC (1990) Linkage arrangement of restriction fragment length polymorphism loci in Brassica oleracea. Theor Appl Genet 80:57 64
89. Smith GP (1976) Evolution of repeated DNA sequences by unequal crossover. Science 191:528-535
90. Song KM, Suzuki JY, Slocum MK, Williams PH, Osborn TC (1991) A linkage map of Brassica rapa (syn. campestris) based on restriction fragment length polymorphism loci. Theor Appl Genet 82:296-304
91. Sparrow AH, Nauman AF (1976) Evolution of genome size by DNA doublings. Science 192:524-529
92. Stack SM, Comings DE (1979) The chromosomes and DNA of Allium cepa. Chromosoma 70:161-181
93. Sugita M, Manzara T, Pichersky E, Cashmore AR, Gruissem W (1987) Genome organization, sequence analysis, and expression of all five genes encoding the small subunit of ribulose-1.5-biphosphate carboxylase/oxygenase from tomato. Mol Gen Genet 209:247-256
94. Tanksley SD, Bernatzky R, Lapitan NL, Prince JP (1988) Conservation of gene repertoire but not gene order in pepper and tomato. Proc Natl Acad Sci USA 85:6419 6423
95. Tanksley SD, Ganal MW, Prince JP, de Vicente MC, Bonierbale MW, Brown P, Fulton T, Giovannoni J, Grandillo S, Martin G, Messeguer R, Miller J, Miller L, Paterson A, Pineda O, Roder M, Wing R, Wu W, Young N (1992) High-density molecular linkage maps of the tomato and potato genomes. Genetics 132: 1141-1160
96. Tartof KD (1988) Unequal crossing over then and now. Genetics 120:1-6
97. Ueki J, Morioka S, Komari T, Kumashiro T (1995) Purification and characterization of phospholipase D (PLD) from rice (Oryza sativa L.) and cloning of cDNA for PLD from rice and maize (Zea mays L.) Plant Cell Physiol 36:903-914
98. Van Damme EJM, Smeets K, Torrekens S, Van Leuven F, Peumans WJ (1992) Isolation and characterization of alliinase cDNA clones from garlic (Allium sativum L.) and related species. Eur J Biochem 209:751-757
99. Van Damme EJM, Smeets K, Engelborghs I, Aelbers H, Balzarini J, Pusztai A, van Leuven F, Goldstein IJ, Peumans WJ (1993) Cloning and characterization of the lectin cDNA clones from onion, shallot and leek. Plant Mol Biol 23:365-376
100. Van Raamsdonk L, Wietsma W, de Vries J (1992) Crossing experiments in Allium L. section Cepa. Bot J Linn Soc 109:293-303
101. Vanin EF (1985) Processed pseudogenes: characteristics and evolution. Annu Rev Genet 19:253-272
102. Veit B, Vollbrecht E, Mathern J, Hake S (1990) A tandem duplication causes the Kn1-0 allele of Knotted, a dominant morphological mutant of maize. Genetics 125:623-631
103. Vosa C (1976) Heterochromatic patterns in Allium. I. The relationship between the species of the cepa group and its allies. Heredity 36:383-392
104. Whitkus R, Doebley J, Lee M (1992) Comparative mapping of sorghum and maize. Genetics 132:1119-1130
105. Xu GW, Magill CW, Schertz KF, Hart GE (1994) A RFLP linkage map of Sorghum bicolor (L.) Moench. Theor Appl Genet 89:139-145
106. Yang XF, Quiros CF (1995) Construction of a genetic linkage map in celery using DNA-based markers. Genome 38:36-44