Development of Chromosome-specific Cytogenetic Markers and Merging of Linkage Fragments in Papaya

Tropical Plant Biology

Volumn 3, Issue 3, 2010, Pages 171-181

  Wai, Ching Man ^a,b   Ming, Ray ^b,c   Moore, Paul H ^b   Paull, Robert E ^a   Yu, Qingyi ^b,d  

^a UNIVERSITY OF HAWAII   (United States)

^b HAWAII AGRICULTURE RESEARCH CENTER   (United States)

^c UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^d TEXAS A AND M UNIVERSITY   (United States)

Author keywords

Carica papaya; Chromosome specific markers; Cytogenetics; Fluorescence in situ hybridization (FISH); Genetic map

Indexed keywords

CARICA PAPAYA;

EID: 77956461517     PISSN: 19359756     EISSN: 19359764     Source Type: Journal    
DOI: 10.1007/s12042-010-9054-1     Document Type: Article

References (67)

1. Blas AL, Yu Q, Chen C, Veatch O, Moore PH, Paull RE, Ming R (2009) Enrichment of a papaya high-density genetic map with AFLP markers. Genome 52: 716-725.
2. Chao S, Gardiner JM, Melia-Hancock S, Coe EH Jr (1996) Physical and genetic mapping of chromosome 9S in maize using mutations with terminal deficiencies. Genetics 143: 1785-1794.
3. Chen C, Yu Q, Hou S, Li Y, Eustice M, Skelton RL, Veatch O, Herdes RE, Diebold L, Saw J, Feng Y, Qian W, Bynum L, Wang L, Moore PH, Paull RE, Alam M, Ming R (2007) Construction of a sequence-tagged high-density genetic map of papaya for comparative structural and evolutionary genomics in brassicales. Genetics 177: 2481-2491.
4. Cheng Z, Buell CR, Wing RA, Gu M, Jiang J (2001) Toward a cytological characterization of the rice genome. Genome Res 11: 2133-2141.
5. Chung MC, Lee YI, Cheng YY, Chou YJ, Lu CF (2008) Chromosomal polymorphism of ribosomal genes in the genus Oryza. Theor Appl Genet 116: 745-753.
6. Cooper M, van Eeuwijk FA, Hammer GL, Podlich DW, Messina C (2009) Modeling QTL for complex traits: detection and context for plant breeding. Curr Opin Plant Biol 12: 231-240.
7. Creighton HB, McClintock B (1931) A correlation of cytological and genetical crossing-over in Zea Mays. Proc Natl Acad Sci USA 17: 492-497.
8. Cuadrado A, Cardoso M, Jouve N (2008) Physical organisation of simple sequence repeats (SSRs) in Triticeae: structural, functional and evolutionary implications. Cytogenet Genome Res 120: 210-219.
9. Danilova TV, Birchler JA (2008) Integrated cytogenetic map of mitotic metaphase chromosome 9 of maize: resolution, sensitivity, and banding paint development. Chromosoma 117: 345-356.
10. de Carvalho CR, Saraiva LS (1997) High-resolution HKG-banding in maize mitotic chromosomes. J Plant Res 110: 417-420.
11. de Melo NF, 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.
12. Dieguez MJ, Altieri E, Ingala LR, Perera E, Sacco F, Naranjo T (2006) Physical and genetic mapping of amplified fragment length polymorphisms and the leaf rust resistance Lr3 gene on chromosome 6BL of wheat. Theor Appl Genet 112: 251-257.
13. Dong F, Song J, Naess SK, Helgeson JP, Gebhardt C, Jiang J (2000) Development and applications of a set of chromosome-specific cytogenetic DNA markers in potato. Theor Appl Genet 101: 1001-1007.
14. Griffor MC, Vodkin LO, Singh RJ, Hymowitz T (1991) Fluorescent in situ hybridization to soybean metaphase chromosomes. Plant Mol Biol 17: 101-109.
15. Han YH, Zhang ZH, Liu JH, Lu JY, Huang SW, Jin WW (2008) Distribution of the tandem repeat sequences and karyotyping in cucumber (Cucumis sativus L.) by fluorescence in situ hybridization. Cytogenet Genome Res 122: 80-88.
16. Hizume M, Shibata F, Matsusaki Y, Garajova Z (2002) Chromosome identification and comparative karyotypic analyses of four Pinus species. Theor Appl Genet 105: 491-497.
17. Hohmann U, Endo TR, Gill KS, Gill BS (1994) Comparison of genetic and physical maps of group 7 chromosomes from Triticum aestivum L. Mol Genet Genomics 245: 644-653.
18. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436: 793-800.
19. Iovene M, Wielgus SM, Simon PW, Buell CR, Jiang J (2008) Chromatin structure and physical mapping of chromosome 6 of potato and comparative analyses with tomato. Genetics 180: 1307-1317.
20. Islam-Faridi MN, Childs KL, Klein PE, Hodnett G, Menz MA, Klein RR, Rooney WL, Mullet JE, Stelly DM, Price HJ (2002) A molecular cytogenetic map of sorghum chromosome 1. Fluorescence in situ hybridization analysis with mapped bacterial artificial chromosomes. Genetics 161: 345-353.
21. Islam-Faridi MN, Nelson CD, Kubisiak TL (2007) Reference karyotype and cytomolecular map for loblolly pine (Pinus taeda L.). Genome 50: 241-251.
22. Jansen RC, Tesson BM, Fu J, Yang Y, McIntyre LM (2009) Defining gene and QTL networks. Curr Opin Plant Biol 12: 241-246.
23. Jiang J, Gill BS (2006) Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research. Genome 49: 1057-1068.
24. Jiang J, Gill BS, Wang GL, Ronald PC, Ward DC (1995) Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes. Proc Natl Acad Sci USA 92: 4487-4491.
25. Kato A, Vega JM, Han F, Lamb JC, Birchler JA (2005) Advances in plant chromosome identification and cytogenetic techniques. Curr Opin Plant Biol 8: 148-154.
26. Kim JS, Childs KL, Islam-Faridi MN, Menz MA, Klein RR, Klein PE, Price HJ, Mullet JE, Stelly DM (2002) Integrated karyotyping of sorghum by in situ hybridization of landed BACs. Genome 45: 402-412.
27. Kim JS, Islam-Faridi MN, Klein PE, Stelly DM, Price HJ, Klein RR, Mullet JE (2005a) Comprehensive molecular cytogenetic analysis of sorghum genome architecture: distribution of euchromatin, heterochromatin, genes and recombination in comparison to rice. Genetics 171: 1963-1976.
28. Kim JS, Klein PE, Klein RR, Price HJ, Mullet JE, Stelly DM (2005b) Molecular cytogenetic maps of sorghum linkage groups 2 and 8. Genetics 169: 955-965.
29. Kim H, Choi SR, Bae J, Hong CP, Lee SY, Hossain MJ, van Nguyen D, Jin M, Park BS, Bang JW, Bancroft I, Lim YP (2009) Sequenced BAC anchored reference genetic map that reconciles the ten individual chromosomes of Brassica rapa. BMC Genomics 10: 432.
30. Koo DH, Jo SH, Bang JW, Park HM, Lee S, Choi D (2008) Integration of cytogenetic and genetic linkage maps unveils the physical architecture of tomato chromosome 2. Genetics 179: 1211-1220.
31. Koornneef M, Fransz P, de Jong H (2003) Cytogenetic tools for Arabidopsis thaliana. Chromosome Res 11: 183-194.
32. Krishnan P, Sapra VT, Soliman KM, Zipf A (2001) FISH mapping of the 5S and 18S-28S rDNA loci in different species of Glycine. J Hered 92: 295-300.
33. Kunzel G, Korzun L, Meister A (2000) Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints. Genetics 154: 397-412.
34. Lai CW, Yu Q, Hou S, Skelton RL, Jones MR, Lewis KL, Murray J, Eustice M, Guan P, Agbayani R, Moore PH, Ming R, Presting GG (2006) Analysis of papaya BAC end sequences reveals first insights into the organization of a fruit tree genome. Mol Genet Genomics 276: 1-12.
35. Lengerova M, Kejnovsky E, Hobza R, Macas J, Grant SR, Vyskot B (2004) Multicolor FISH mapping of the dioecious model plant, Silene latifolia. Theor Appl Genet 108: 1193-1199.
36. Lim KY, Matyasek R, Lichtenstein CP, Leitch AR (2000) Molecular cytogenetic analyses and phylogenetic studies in the Nicotiana section Tomentosae. Chromosoma 109: 245-258.
37. Lysak MA, Fransz PF, Ali HB, Schubert I (2001) Chromosome painting in Arabidopsis thaliana. Plant J 28: 689-697.
38. Ma H, Moore PH, Liu Z, Kim MS, Yu Q, Fitch MM, Sekioka T, Paterson AH, Ming R (2004) High-density linkage mapping revealed suppression of recombination at the sex determination locus in papaya. Genetics 166: 419-436.
39. McClintock B (1931) The order of the genes C, Sh and Wx in Zea Mays with reference to a cytologically known point in the chromosome. Proc Natl Acad Sci USA 17: 485-491.
40. McClintock B, Hill HE (1931) The cytological identification of the chromosome associated with the R-G linkage group in ZEA MAYS. Genetics 16: 175-190.
41. Milla R, Gustafson JP (2001) Genetic and physical characterization of chromosome 4DL in wheat. Genome 44: 883-892.
42. Ming R, Moore PH, Zee FT, Abbey CA, Ma H, Paterson AH (2001) Construction and characterization of a papaya BAC library as a foundation for molecular dissection of a tree-fruit genome. Theor Appl Genet 102: 892-899.
43. Ming R et al (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452: 991-996.
44. Nagarajan N, Navajas-Perez R, Nihai P, Alam M, Ming R, Paterson AH, Salzberg SL (2008) Genome-wide analysis of repetitive elements in papaya. Tropical Plant Biol 1: 191-202.
45. Paterson AH et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551-556.
46. Pedrosa A, Vallejos CE, Bachmair A, Schweizer D (2003) Integration of common bean (Phaseolus vulgaris L.) linkage and chromosomal maps. Theor Appl Genet 106: 205-212.
47. Peters SA, Datema E, Szinay D, van Staveren MJ, Schijlen EG, van Haarst JC, Hesselink T, Abma-Henkens MH, Bai Y, de Jong H, Stiekema WJ, Klein Lankhorst RM, van Ham RC (2009) Solanum lycopersicum cv. Heinz 1706 chromosome 6: distribution and abundance of genes and retrotransposable elements. Plant J 58: 857-869.
48. Portis E, Mauromicale G, Mauro R, Acquadro A, Scaglione D, Lanteri S (2009) Construction of a reference molecular linkage map of globe artichoke (Cynara cardunculus var. scolymus). Theor Appl Genet 120: 59-70.
49. Ren Y, Zhang Z, Liu J, Staub JE, Han Y, Cheng Z, Li X, Lu J, Miao H, Kang H, Xie B, Gu X, Wang X, Du Y, Jin W, Huang S (2009) An integrated genetic and cytogenetic map of the cucumber genome. PLoS ONE 4: e5795.
50. Robledo G, Lavia GI, Seijo G (2009) Species relations among wild Arachis species with the A genome as revealed by FISH mapping of rDNA loci and heterochromatin detection. Theor Appl Genet 118: 1295-1307.
51. Rosato M, Castro M, Rossello JA (2008) Relationships of the woody Medicago species (section Dendrotelis) assessed by molecular cytogenetic analyses. Ann Bot 102: 15-22.
52. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365-386.
53. Saintenac C, Falque M, Martin OC, Paux E, Feuillet C, Sourdille P (2009) Detailed recombination studies along chromosome 3B provide new insights on crossover distribution in wheat (Triticum aestivum L.). Genetics 181: 393-403.
54. Schubert I, Fransz PF, Fuchs J, de Jong JH (2001) Chromosome painting in plants. Methods Cell Sci 23: 57-69.
55. Shishido R, Sano Y, Fukui K (2000) Ribosomal DNAs: an exception to the conservation of gene order in rice genomes. Mol Genet Genomics 263: 586-591.
56. Storey WB (1953) Genetics of papaya. J Heredity 44: 70-78.
57. Taketa S, Harrison GE, Heslop-Harrison JS (1999) Comparative physical mapping of the 5S and 18S-25S rDNA in nine wild Hordeum species and cytotypes. Theor Appl Genet 98: 1-9.
58. Tang X, Szinay D, Lang C, Ramanna MS, van der Vossen EA, Datema E, Lankhorst RK, de Boer J, Peters SA, Bachem C, Stiekema W, Visser RG, de Jong H, Bai Y (2008) Cross-species bacterial artificial chromosome-fluorescence in situ hybridization painting of the tomato and potato chromosome 6 reveals undescribed chromosomal rearrangements. Genetics 180: 1319-1328.
59. Tang X, de Boer JM, van Eck HJ, Bachem C, Visser RG, de Jong H (2009) Assignment of genetic linkage maps to diploid Solanum tuberosum pachytene chromosomes by BAC-FISH technology. Chromosome Res 17: 899-915.
60. Walling JG, Shoemaker R, Young N, Mudge J, Jackson S (2006) Chromosome-level homeology in paleopolyploid soybean (Glycine max) revealed through integration of genetic and chromosome maps. Genetics 172: 1893-1900.
61. Wang Y, Tang X, Cheng Z, Mueller L, Giovannoni J, Tanksley SD (2006) Euchromatin and pericentromeric heterochromatin: comparative composition in the tomato genome. Genetics 172: 2529-2540.
62. Wang K, Guo W, Zhang T (2007) Development of one set of chromosome-specific microsatellite-containing BACs and their physical mapping in Gossypium hirsutum L. Theor Appl Genet 115: 675-682.
63. Wang K, Guan B, Guo W, Zhou B, Hu Y, Zhu Y, Zhang T (2008) Completely distinguishing individual A-genome chromosomes and their karyotyping analysis by multiple bacterial artificial chromosome-fluorescence in situ hybridization. Genetics 178: 1117-1122.
64. Watson JD, Crick FH (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171: 737-738.
65. Yu Q, Tong E, Skelton RL, Bowers JE, Jones MR, Murray JE, Hou S, Guan P, Acob RA, Luo MC, Moore PH, Alam M, Paterson AH, Ming R (2009) A physical map of the papaya genome with integrated genetic map and genome sequence. BMC Genomics 10: 371.
66. Zhang D, Yang Q, Bao W, Zhang Y, Han B, Xue Y, Cheng Z (2005) Molecular cytogenetic characterization of the Antirrhinum majus genome. Genetics 169: 325-335.
67. Zhang W, Wang X, Yu Q, Ming R, Jiang J (2008) DNA methylation and heterochromatinization in the male-specific region of the primitive Y chromosome of papaya. Genome Res 18: 1938-1943.