Gossypium DNA Markers: Types, Numbers, and Uses

  • Mehboob-ur-Rahman
  • Yusuf Zafar
  • Andrew H. Paterson
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 3)


Numerous DNA marker systems, each with their own advantages and disadvantages, have been described for cotton. Microsatellite markers (also known as simple sequence repeats [SSRs]) are robust and, coupled with their co-dominant expression, make them the current marker of choice for phylogenetic/evolutionary studies, development of genome maps and the identification of DNA markers linked to desirable traits for use in marker-assisted selection (MAS) in cotton. Despite the advances made with such markers, there remains a need for new genomic tools, such as single nucleotide polymorphisms (SNPs), to identify further polymorphism in cotton. The allo-ploidy of the leading cultivated cotton species, together with its widespread dispersal and the selection pressure applied during domestication and scientific improvement, has resulted in a very narrow genetic base. There is thus a need to introgress novel traits from feral or wild relatives, requiring suitable markers for use in MAS. In the future more attention will be devoted to producing consensus genome maps, which will be important if the aim of ‘breeding by design’ is to be realized in cotton improvement.


Linkage Group Restriction Fragment Length Polymorphism Amplify Fragment Length Polymorphism Simple Sequence Repeat Marker Amplify Fragment Length Polymorphism Marker 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. Abdalla, A.M., Reddy, O. U. K., El-Zik, K. M. and Pepper, A. E. (2001) Genetic diversity and relationships of diploid and tetraploid cottons revealed using AFLP. Theor. Appl. Genet.102 (2/3), 222–229.Google Scholar
  2. Adams, K.L. and Wendel, J.F. (2004) Exploring the mysteries of polyploidy in cotton. Biol. J. Linn. Soc. 82,573–581.Google Scholar
  3. Aerts, J., Wetzels, Y., Cohen, N. and Aerssens, J. (2002) Data mining of public SNP database for the selection of intragenic SNPs. Hum. Mutat. 20, 162–173.PubMedGoogle Scholar
  4. Ahmad, M., Khan, M.R. and Saeed, M. (1987) Studies on factors contributing resistance in five new cultivars of cotton against insect pests. Pak. Entomol. 9 (1–2), 23–28.Google Scholar
  5. Ahmad, S., Zhang, T., Noor-ul-Islam, Shaheen, T. and Rahman, M. (2007) Identifying genetic variation in Gossypium based on single nucleotide polymorphism. Pak. J. Bot. 39(4), 1245–1250.Google Scholar
  6. Akash, M. W. (2003) Quantitative trait loci mapping for agronomic and fiber quality traits in upland cotton (Gossypium hirsutum L.) using molecular markers. PhD dissertation. Louisiana State Univ. USA.Google Scholar
  7. Ali, I. (2004) Development of genetic linkage maps for some insect non-preference traits in cotton. PhD Thesis, Univ. Agric. Faisalabad Pakistan.Google Scholar
  8. Ali, I., Ashraf, M., Rahman, M., Ullah, I., Niaz, M., Hanif, M., Hassan, M. and Zafar. Y. (2004) Screening of cotton varieties regarding hairiness trait for DNA fingerprinting. J. Nat. Sci 2(1), 91–99.Google Scholar
  9. Altaf, M.K., Stewart, J.M., Wajahatullah, M.K. and Zhang, J.F. (1997) Molecular and morphological genetics of a trispecies F2 population of cotton. In: P. Dugger, and D.A. Richter (Eds.), Proceedings of the Beltwide Cotton Production Research Conferences. National Cotton Council of America, Memphis, TN. Animal Genome VI, Jan 18–22. 1998. San Diego California, USA, pp. 448–452.Google Scholar
  10. An, C., Saha, S., Jenkins, J.N., Ma, D-P., Scheffler, B.E., Kohel, R.J., Yu, J.Z., Stelly, D.M. (2008) Cotton (Gossypium spp.) R2R3-MYB transcription factors SNP identification, phylogenomic characterization, chromosome localization, and linkage mapping. Theor. Appl. Genet. 116, 1015–1026.PubMedGoogle Scholar
  11. Asif, M., Rahman, M. and Zafar, Y. (2005) DNA fingerprinting studies of some wheat (Triticum aestivum L.) genotypes using random amplified polymorphic DNA (RAPD) analysis. Pak. J. Bot. 37(2), 271–277.Google Scholar
  12. Asif, M. (2007) Genomic Analysis for Quality Traits in Cotton (Gossypium hirsutum L.) by DNA Fingerprinting Technology. PhD Thesis, B.Z.Univ. Multan Pakistan.Google Scholar
  13. Asif, M., Rahman, M. and Zafar, Y. (2006) Genotyping Analysis of Maize (Zea mays L.). Hybrids Using DNA Fingerprinting Technology. Pak. J. Bot. 38 (5), 1425–1430.Google Scholar
  14. Aslam, M., Jiang, C., Wright, R. and Paterson, A.H. (1999) Identification of molecular markers linked to leaf curl virus disease resistance in cotton. Pak. J. Bio. Sci. 2(1), 124–126.Google Scholar
  15. Atha, D.H., Wenz, H.M., Morehead, H., Tian, J. and O’Connell, C.D. (1998) Detection of p53 point mutation by single strand conformational polymorphism (SSCP): analysis by capillary electrophoresis. Electrophoresis 19, 172–179.PubMedGoogle Scholar
  16. Baogong, J. (2004) Optimization of agrobacterium mediated cotton transformation using shoot apices explants and quantitative trait loci analysis of yield and yield component traits in upland cotton (Gossypium hirsutum). PhD thesis. Louisiana State Univ.Google Scholar
  17. Bassam, B.J., Caetano-Anollés, G. and Gresshoff, P.M. (1995) Method for profiling nucleic acids of unknown sequence using arbitrary oligonucleotide primers. US Patent 5, 413–909.Google Scholar
  18. Becelaere, G.V., Lubbers, E.L., Paterson, A.H. and Chee, P.W. (2005) Pedigree- vs. DNA Marker-Based Genetic Similarity Estimates in Cotton. Crop Sci. 45:2281–2287.Google Scholar
  19. Beckmann, J.S. and Soller, M. (1983) Restriction length polymorphisms in general improvement: methodologies, mapping and cost. Theor. Appl. Genet. 67, 35–43.Google Scholar
  20. Berger, F. (2004) Imprinting—a green variation. Science 303, 483–485.PubMedGoogle Scholar
  21. Bhatnagar, P. and Sharma P.D. (1991) Comparative incidence of sucking insect pests on different isogenic lines of cotton variety. H777. Insect Sci. 4, 170–171.Google Scholar
  22. Blair, M.W., Panaud, O. and McCouch, S.R. (1999) Inter-simple sequence repeat (ISSR) amplification for analysis of microsatellite motif frequency and fingerprinting in rice (Oryza sativa L). Theor. Appl. Genet. 98, 780–792.Google Scholar
  23. Blenda, A., Scheffler, J., Scheffler, B., Palmer, M., Lacape J.M., Yu, J.Z., Jesudurai, C., Jung, S., Muthukumar, S., Yellambalase, P., Ficklin, S., Staton, M., Eshelman, R., Ulloa, M., Saha, S., Burr, B., Liu, S., Zhang, T., Fang, D., Pepper, A., Kumpatla, S., Jacobs, J., Tomkins, J., Cantrell, R. and Main, D. (2006) The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms. B.M.C. Genomics 7, 61.Google Scholar
  24. Bligh, H. F. J., Blackhall, N. W., Edwards, K. J. and McClung, A. M. (1999) Using amplified fragment length polymorphism and simple sequence length polymorphism to identify cultivars of brown and white milled rice. Crop Sci. 39, 1715–1721.Google Scholar
  25. Bolek, Y., El-Zik, K.M., Pepper, A.E., Bell, A.A., Magill, C.W., Thaxton, P.M. and Reddy, O.U. (2005) Mapping of verticillium wilt resistance genes in cotton. Plant Sci. 168, 1581–1590.Google Scholar
  26. Botstein, D., White, R. L., Skolnik, M. and Davis, R. W. (1980) Construction of a genetic linkage map in using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32, 314–331.PubMedGoogle Scholar
  27. Bowman, D.T. (1999) Public cotton breeders – do we need them? J. Cotton Sci. 3, 139–152.Google Scholar
  28. Bowman, D.T, May, O.L. and Calhoun, D.S. (1996) Genetic base of upland cotton cultivars released between 1970 and 1990. Crop Sci. 36, 577–581.Google Scholar
  29. Bradshaw, J.E., Hackett, C.A., Meyer, R.C., Milbourne, D., McNichol, J.W., Philips, M.S. and Waugh, R. (1998) Identification of AFLP and SSR marker associated with quantitative resistance to Globodera pallida (Stone) in tetraploid potato (Solanum tuberosum subsp. tuberosum) with a view to marker-assisted selection. Theor. Appl. Genet. 97, 202–210.Google Scholar
  30. Brondani, R.P.V., Brondani, C., Tarchini, R. and Grattapaglia, D. (1998) Development, Characterisation and mapping of microsatellite markers in Eucalyptus grandis and E. urophylla. Theor. Appl. Genet. 97, 816–827.Google Scholar
  31. Brubaker, C.L. and Wendel, J.F. (1994) Re-evaluating the origin of domesticated cotton using nuclear restriction fragment length polymorphism. Am. J. Bot. 81, 1309–1326.Google Scholar
  32. Brubaker, C.L., Paterson, A.H. and Wendel, J.F. (1999) Comparative genetic mapping of allotetraploid cotton and its diploid progenitors. Genome 42, 184–203.Google Scholar
  33. Brubaker, C.L. and Wendel, J.F. (2000) RFLP diversity in cotton. In: J.N. Jenkins and S. Saha (Eds.), Genetic Improvement of Cotton: Emerging Technologies. Sci. Publishers, Inc. USA, pp. 81–102.Google Scholar
  34. Buetow, K.H., Edmonson, M. and MacDonald, R. (2001) High throughput development and characterization of a genome wide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Proc. Natl. Acad. Sci. 98, 581–584.PubMedGoogle Scholar
  35. Buteler, M.I., Jarret, R.L. and LaBonte, D. R. (1999) Sequence characterization of microsatellites in diploid and polyploid Ipomoea. Theor. Appl. Genet. 99, 123–132.Google Scholar
  36. Butter, N. S. and. Vir, B. K. (1991) Response of whitefly Bemesia tabaci (Genn.) to different cotton genotypes under glass house conditions. Ind. J. Entomol. 53 (1), 115–119.Google Scholar
  37. Caetano-Anollés, G., Bassam, B.J. and Gresshoff, P.M. (1991) DNA amplification finger- printing using very short arbitrary oligonucleotide primers. Bio/technol. 9, 553–557.Google Scholar
  38. Caetano-Anollés, G. (1996) Scanning of nucleic acids by in vitro amplification: new developments and applications. Nat. Biotech. 14, 1668–1674.Google Scholar
  39. Cai, H., Whites, P.S., Torney, D., Dishpande, A., Wang, Z., Marrone, B. and Nolan, J.P. (2000) Flow cytometry-based minisequencing: Anew plateform for high output single nucleotide polymorphism scoring. Genomics 66, 135–142.PubMedGoogle Scholar
  40. Cantrell, R.G., Pederson, J. and Liu, S. (1999) Mapping of introgressed cotton populations with DNA markers. Plant & Animal Genome VII Conference, January 17-21, San Diego, CA, USA,Google Scholar
  41. Chan, S.W.L., Zilberman, D., Xie, Z., Johansen, L.K., Carrington, J.C. and Jacobsen, S.E. (2004) RNA silencing genes control de novo DNA methylation. Science 303, 336.Google Scholar
  42. Chee, P.W., Draye, X., Jiang, C., Decanini, L., Delmonte, T., Bredhauer, B., Smith, C.W. and Paterson, A.H. (2005a) Molecular dissection of interspecific variation between Gossypium hirsutum and G. barbadense (cotton) by a backcross-self approach: I. Fiber elongation. Theor. Appl. Genet. 111, 757–763.Google Scholar
  43. Chee, P.W., Draye, X., Jiang, C., Decanini, L., Delmonte, T., Bredhauer, B., Smith, C.W. and Paterson, A.H. (2005b) Molecular dissection of phenotypic variation between Gossypium hirsutum and Gossypium barbadense (cotton) by a backcross-self approach: III. Fiber length. Theor. Appl. Genet. 111, 772–781.Google Scholar
  44. Chee, P., Jiang, C., Draye, X., Decanini, L.I., Smith, C.W., DelMonte, T.A. and Paterson, A.H. (2000) Advanced-backcross mapping of cotton QTLs. Plant & Animal Genome VIII Conference, San Diego, USA.Google Scholar
  45. Chen, J., Ennone, M.A., Li, M.S., Tylor, J.D., Rivers, P., Nelson, A.J., Slentz-Casler, K., Roses, A. and Weiner, M.P. (2000) A microsphere based essay for multiplex single nucleotide polymorphism analysis using single base chain extension. Genome Res. 10, 549–557.PubMedGoogle Scholar
  46. Chen, Z.J., Scheffler, B.E., Dennis, E., Triplett, B., Zhang, T., Chen, X., Stelly, D.M., Rabinowicz, P.D., Town, P., Arioli, T., Brubaker, C., Cantrell, R., Lacape, J., Ulloa, M., Chee, P., Gingle, A.R., Haigler, C.H., Percy, R., Saha, S., Wilkins, T., Wright, R.J., Van Deynze, A., Zhu, Y., Yu, X., Guo, W., Abdurakhmonov, I., Katageri, I., Rahman, M., Zafar, Y., Yu, J.Z., Kohel, RJ., Wendel, J. and Paterson, A.H. (2007) Towards sequencing cotton (Gossypium) genomes. Plant Physiol. 145, 1251–1263.Google Scholar
  47. Cherry, J.P., Katterman, F.R.H. and Endrizzi, J.E. (1970) Comparative studies of seed proteins of species of Gossypium by gel electrophoresis. Evolution 24, 431–447.Google Scholar
  48. Clark, R.M., Schweikert, G., Toomajian, C., Ossowski, S., Zeller, G., Shinn, P., Warthmann, N., Hu, T.T., Fu, G., Hinds, D.A., Chen, H., Frazer, K.A., Huson, D.H., Schölkopf, B., Nordborg, M., Rätsch, G., Ecker, J.R. and Weigel D. (2007) Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana. Science 317, 338–342.PubMedGoogle Scholar
  49. Comai, L., Young, K., Till, B.J., Reynolds, S.H., Greene, E.A., Codomo, C.A., Enns, L.C., Jhonson, J.E., Burtner, C., Odden, A.R. and Henikoff, S. (2004) Efficient discovery of DNA polymorphism in natural populations by Ecotilling. Plant J. 37, 778–786.PubMedGoogle Scholar
  50. Connell, J.P., Pammi, S., Iqbal, M.J., Huizinga, T. and Reddy, A.S. (1998) A high throughput procedure for capturing microsatellites from complex plant genomes. Plant Mol. Biol. Rep. 16, 341–349.Google Scholar
  51. Cronn, R.C., Small, R.L., Haselkorn, T. and Wendel, J.F. (2002) Rapid diversi.cation of the cotton genus (Gossypium: Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes. Am. J. Bot. 89, 707–725.PubMedGoogle Scholar
  52. Cronn, R., Small, R.L. and Wendel J.F. (1999) Duplicated genes evolve independently after polyploid formation in cotton. Proc. Natl. Acad. Sci. 96, 14406–14411.PubMedGoogle Scholar
  53. Cronn, R.C., Zhao, X.P., Paterson, A.H., 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.PubMedGoogle Scholar
  54. Draye, X., Chee, P., Jiang, C., Decanini, L., Delmonte, T., Bredhauer, R., Smith, C.W. and Paterson, A.H. (2005). Molecular dissection of phenotypic variation between Gossypium hirsutum and G. barbadense (cotton) by a backcross-self approach. II Fiber Fineness. Theor. Appl. Genet. 111, 764–771.PubMedGoogle Scholar
  55. Dudley, J.W., Saghai-Maroof, A. and Rufener, G.K. (1992) Molecular marker information and selection of parents in corn breeding programs. Crop Sci. 32, 301–304.Google Scholar
  56. Feng, C.D., Stewart, J.McD. and Zhang, J.F. (2005) STS markers linked to the Rf1 fertility restorer gene of cotton. Theor. Appl. Genet. 110, 237–243.Google Scholar
  57. Fisher, P. J., Richardson, T. E. and Gardner, R. C. (1998) Characteristics of single- and multi-copy microsatellites from Pinus radiata. Theor. Appl. Genet. 96, 969–979.Google Scholar
  58. Frelichowski, J.E.Jr., Palmer, M.B., Main, D., Tomkins, J.P., Cantrell, R.G., Stelly, D.M., Yu, J., Kohel, R.J. and Ulloa, M. (2006) Cotton genome mapping with new microsatellites from Acala 'Maxxa' BAC-ends. Mol. Genet. Gen. 275(5), 479–491.Google Scholar
  59. Fryxell, P.A. (1971) Phenetic analysis and the phylogeny of the diploid species of Gossypium L. (Malvacaea). Evolution 25, 554–562.Google Scholar
  60. Giese, H., Holm-Jensen, A.G. and Jensen, J. (1993) Localization of the laevigatum powdery mildew resistance gene to barley chromosome 2 by the use of RFLP markers. Theor. Appl. Genet. 85, 897–900.Google Scholar
  61. Gingle, A.R., Yang, H., Chee, P.W., May, O.L., Rong, J., Bowman, D.T., Lubbers, E.L., Day, J.L. and Paterson, A.H. (2006) An Integrated Web Resource for Cotton. Crop Sci. 46, 1998–2007Google Scholar
  62. Gruenbaum, Y., Naveh-Many, T., Cedar, H. and Razin, A. (1981) Sequence specificity of methylation in higher plant DNA. Nature 292, 860–862.PubMedGoogle Scholar
  63. Guo, W., Zhang, T., Shen, X., Yu, J.Z. and Kohel, R.J. (2003) Development of SCAR marker linked to a major QTL for high fiber strength and its usage in molecular-marker assisted selection in upland cotton. Crop Sci. 43(6), 2252–2257.Google Scholar
  64. Guo, W.Z., Fang, D., Yu, W.D. and Zhang, T.Z. (2005) Sequence divergence of microsatellites and phylogeny analysis in tetraploid cotton species and their putative diploid ancestors. J. Integ. Plant Biol. 47(12), 1418–1430.Google Scholar
  65. Gupta, P.K., Roy, J.K. and Parsad, A. (2001) Single nucleotide polymorphism; A paradigm for molecular marker technology and DNA polymorphism detection with emphasis with their use in plants. Curr. Sci. 80, 524–535.Google Scholar
  66. Gupta, M., Chyi, Y.S., Romero-Severson J. and Owen J.L. (1994) Amplification of DNA markers from evolutionarily diverse genomes using single primers of simple-sequence repeats. Theor. Appl. Genet. 89, 998–1006.Google Scholar
  67. Gupta, P.K. and Varshney, R.K. (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113, 163–185.Google Scholar
  68. Gut, I.J. (2001) Automation in genotyping of single nucleotide polymorphism. Hum. Mutat. 46, 416–419.Google Scholar
  69. Gutierrez, O.A., Basu, S., Saha, S., Jenkins, J.N., Shoemaker, D.B., Cheatham, C.L. and McCarty, J.C. (2002) Genetic distance among selected cotton genotypes and its relationship with F2 performance. Crop Sci. 42, 1841–1847.Google Scholar
  70. Hamada, H., Petrino, M.G. and Kakunaga, T. (1982) A novel repeat element with Z-DNA-forming potential is widely found in evolutionarily diverse eukaryotic genomes. Proc. Natl. Acad. Sci. 79, 6465–6469.PubMedGoogle Scholar
  71. Hayes, A.J. and Saghai-Maroof, M.A. (2000) Targeted resistance gene mapping in soybean using modified AFLPs. Theor. Appl. Genet. 100, 1279–1283.Google Scholar
  72. Han, Z.G., Guo, W., Song, X.L. and Zhang, T. (2004) Genetic mapping of EST-derived microsatellites from the diploid Gossypium arboreum in allotetraploid cotton. Mol. Genet. Gen. 272, 308–327.Google Scholar
  73. Han, Z.G., Wang, C., Song, X.L., Guo, W., Gou, J.Y., Li, C., Chen, X. and Zhang, T. (2006) Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton. Theor. Appl. Genet. 112, 430–439.PubMedGoogle Scholar
  74. Hawkins, J. S., Pleasants, J. and Wendel, J.F. (2005) Identification of AFLP markers that discriminate between cultivated cotton and the Hawaiian island endemic, Gossypium tomentosum Nuttall ex Seeman. Genet. Resour. Crop Evol. 52, 1069–1078.Google Scholar
  75. He, D.H., Zhong, X.L., Zhang, X. L., Nie, Y.C., Guo, X.P., Feng, C.D. and Stewart, J.McD. (2005) Mapping QTLs of traits contributing to yield and analysis of genetic effects in tetraploid cotton. Euphytica 144, 141–149.Google Scholar
  76. He, D.H., Lin, Z.X., Zhang, X.L., Nie, Y.C., Guo, X.P., Zhang, Y.X. and Li, W. (2007) QTL mapping for economic traits based on a dense genetic map of cotton with PCR-based markers using the interspecific cross of Gossypium hirsutum x Gossypium barbadense. Euphytica 153 (1–2), 181–197.Google Scholar
  77. Helentjaris, T., Slocum, M., Wright, S., Schaefer, A. and Nienhuis, J. (1986) Construction of genetic linkage maps in maize and tomato using restriction fragment length polymorphism. Theor. Appl. Genet. 72, 761–769.Google Scholar
  78. Hua, H.D., Xu, L.Z., Long, Z.X., Chun, N.Y., Ping, G.X., Xin, Z.Y. and Wu, L. (2007) QTL mapping for economic traits based on a dense genetic map of cotton with PCR-based markers using the interspecific cross of Gossypium hirsutum × Gossypium barbadense. Euphytica 153 (1–2), 181–197.Google Scholar
  79. Huang, J. and Sun, S.M. (2000) Genetic diversity and relationships of sweet potato and its wild relatives in Ipomoea series Batatas (Convolvulaceae) as revealed by inter-simple sequence repeat (ISSR) and restriction analysis of chloroplast DNA. Theor. Appl. Genet. 100, 1050–1060.Google Scholar
  80. Iqbal, M.J., Aziz, N., Saeed, N.A., Zafar, Y. and Malik, K.A. (1997) Genetic diversity of some elite cotton varieties by RAPD analysis. Theor. Appl. Genet. 94, 139–144.PubMedGoogle Scholar
  81. Iqbal, M.J., Reddy, O.U.K., El-Zik, K.M. and Pepper, A.E. (2001) A genetic bottleneck in the evolution under domestication of upland cotton Gossypium hirsutum L. examined using DNA fingerprinting. Theor. Appl. Genet. 103, 547–554.Google Scholar
  82. Jander, G., Norris, S., Rounsley, S., Bush, D., Levin, I. and Last, R. (2002) Arabidopsis map-based cloning in the post-genome era. Plant Physiol. 129: 440–450.PubMedGoogle Scholar
  83. Jiang, C.X., Wright, R. J., El-Zik, K. M. and Paterson, A. (1998) Polyploid formation created unique avenues for response to selection in Gossypium (cotton). Proc. Natl. Acad. Sci. 95, 4419–4424.Google Scholar
  84. Jiang, C.X., Chee, P.W., Draye, X., Morrell, P.L., Smith, C.W. and Paterson, A.H. (2000) Multi-locus interactions restrict gene flow in advanced-generation interspecific populations of  polyploid Gossypium (cotton). Evolution 54, 798–814.PubMedGoogle Scholar
  85. Jixiang, W., Johnie, N.J., McCarty, J.C., Zhong, M. and Michael, S. (2007) AFLP marker associations with agronomic and fiber traits in cotton. Euphytica 153, 153–163.Google Scholar
  86. Jones, C.J., Edwards, K.J., Castaglione, S., Winfield, M.O., Sala, F., van de Wiel, C., Bredemeijer, G., Vosman, B., Matthes, M., Daly, A., Brettschneider, R., Bettini P., Buiatti, M., Maestri, E., Malcevschi, A., Marmiroli, N., Aert, R., Volckaert,G., Rueda, J., Linacero, R., Vazquez, A., and Karp, A. (1997) Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories. Mol. Breed. 3, 381–390.Google Scholar
  87. Johnson, B.L. and Thein, M.M. (1970) Assessment of evolutionary affinities in Gossypium by protein electrophoresis. Amer. J. Bot. 57, 1081–1092.Google Scholar
  88. Joshi, S.P., Gupta, V.S., Aggarwal, R.K., Ranjekar, P.K. and Brar, D.S. (2000) Genetic diversity and phylogenetic relationship as revealed by inter-simple sequence repeat (ISSR) polymorphism in the genus Oryza. Theor. Appl. Genet. 100, 1311–1320.Google Scholar
  89. Kanazin, V., Talbert, H., See, D., DeCamp, P., Nevo, E. and Blake, D. (2002) Discovery and assay of single nucleotide polymorphism in barley (Hordeum vulgare). Plant Mol. Biol. 48, 529–537.PubMedGoogle Scholar
  90. Kato, M., Miura, A., Bender, J., Jacobsen, S.E. and Kakutani, T. (2003) Role of CG and non-CG methylation in immobilization of transposons in Arabidopsis. Curr. Biol. 13, 421–426.Google Scholar
  91. Karaca, M., Saha, S., Jenkins, J.N., Zipf, A., Kohel, R. and Stelly, D.M. (2002) Simple sequence repeat (SSR) markers linked to the Ligon lintless (Li (1)) mutant in cotton. J. Heredity 93(3), 221–224.Google Scholar
  92. Karp, A., Seberg, O. and Buiatti, M. (1996) Molecular techniques in the assessment of botanical diversity. Ann. Bot. 78, 143–149.Google Scholar
  93. Kesseli, R., Paran, I. and Michelmore, R.W. (1994) Analysis of a detail linkage map of Lactuca sativa (Lettuce) constructed from RFLP and RAPD markers. Genetics 136, 1435–1446.PubMedGoogle Scholar
  94. Keyte, L.A., Percifield, R., Liu, B. and Wendel, J.F. (2006) Intraspecific DNA Methylation Polymorphism in Cotton (Gossypium hirsutum L.). J. Heredity 97(5), 444–450.Google Scholar
  95. Khan, M.A., Zhang, J. and Stewart, J.McD. (1998) Integrated molecular map based on a trispecific F2 population of cotton. Proceeding Beltwide cotton improvement conference San Diego, CA. January 5–9.Google Scholar
  96. Khan, S. A., Hussain, D., Askari, E., Stewart, J. McD., Malik, K.A. and Zafar, Y. (2000) Molecular phylogeny of Gossypium species by DNA fingerprinting. Theor. Appl. Genet. 101(5/6), 931–938.Google Scholar
  97. Kim, M.Y., Van, K., Lestari, P., Moon, J.K. and Lee, S.H. (2005) SNP identification and SNAP marker development for a GmNARK gene controlling super nodulation in soybean. Theor. Appl. Genet. 110, 1003–1010.PubMedGoogle Scholar
  98. Klein-Lankhorst, R.M., Vermunt, A., Weide, R., Liharska, T. and Zabel. P. (1991) Isolation of molecular markers for tomato (Lycopersicon esculentum) using random amplified polymorphic DNA (RAPD). Theor. Appl. Genet. 83, 108–114.Google Scholar
  99. Kohel, R.J., Yu, J. and Park, Y.H. (2001) Molecular mapping and characterization of traits controlling fiber quality in cotton. Euphytica 121, 163–172.Google Scholar
  100. Knight, R.L. and Sadd, J. (1954) The genetics of jassid resistance in cotton. III. The Kapas Purao, Kawanda and Philippines Ferguson group. J. Genet. 52, 186–198.Google Scholar
  101. Korzun, V., Rtjder, M.S., Wendehake, K., Pasqualone, A., Lotti, C., Ganal, M.W. and Blanco, A. (1999) Integration of dinucleotide microsatellites from hexaploid bread wheat into a genetic linkage map of durum wheat, Theor. Appl. Genet. 98, 1202–1207.Google Scholar
  102. Kumpatla, S.P., Manley, M.K., Horne, E.C., Gupta, M. and Thompson, S.A. (2004) An improved enrichment procedure to develop multiple repeat classes of cotton microsatellite markers. Plant Mol. Biol. Rep. 22: 85a–85iGoogle Scholar
  103. Kwok, P.Y. (2001) Methods for genotyping single nucleotide polymorphism. Annu. Rev. Gen. Hum. Genet. 2, 235–258.Google Scholar
  104. Lacape, J. M., Nguyen, T.B., Courtois, B., Belot, J.L., Giband, M., Gourlot, J.P. Gawryziak, G., Roques, S. and Hau, B. (2005) QTL Analysis of Cotton Fiber Quality Using Multiple Gossypium hirsutum x Gossypium barbadense Backcross Generations. Crop Sci. 45,123–140.Google Scholar
  105. Lacape, J.M., Nguyen, T.B., Thibivilliers, S., Bojinov, B., Courtois, B., Cantrell, R.G., Burr, B. and Hau, B. (2003) A combined RFLP-SSR-AFLP map of tetraploid cotton based on a Gossypium hirsutum x Gossypium barbadense backcross population. Genome 46, 612–626.PubMedGoogle Scholar
  106. Lacape, J.M., Dessauw, D., Rajab, M., Noyer, J.L. and Hau, B. (2007) Microsatellite diversity in tetraploid Gossypium germplasm: assembling a highly informative genotyping set of cotton SSRs. Mol. Breed. 19, 45–58.Google Scholar
  107. Lagercrantz, U., Ellegren, H. and Andersson, L. (1993) The abundance of various polymorphic microsatellite motifs differ between plants and vertebrates. Nucl. Acids Res. 21, 1111–1115.PubMedGoogle Scholar
  108. Lan, T.H., Cook, C.G. and Paterson, A.H. (1999) Identification of a RAPD marker linked to a male fertility restoration gene in cotton (Gossypium hirsutum L.). J. Agric. Gen. 4:1–5.Google Scholar
  109. Langaee, T. and Ronaghi, M. (2005) Genetic variation analyses by Pyrosequencing. Mutat. Res. 573, 96–102.PubMedGoogle Scholar
  110. Lazo, G. R., Park, Y. and Kohel. R. J. (1994) Identification of RAPD markers linked to fiber strength in Gossypium hirsutum and G. barbadense interspecific crosses. Proceeding Biochemistry of Cotton. September 28–30, 1994. Galveston, Texas.Google Scholar
  111. Lindblad-Toh, K., Wibchester, E., Daly, M.J., Wang, D.G., Hirchhof, J.N., Laviolette, J.P., Ardlie, K., Reich, D.E., Robinson, E., Sklae, P., Shah, N., Thomas, D., Fan, J.B., Grigeras, T., Warrington, J., Patil, N., Hudson, T.J. and Lander, E.S. (2000) Large–scale discovery and genotyping of single nucleotide polymorphism in mouse. Nat. Genet. 24, 381–386.PubMedGoogle Scholar
  112. Liu, S., Saha, S., Stelly, D., Burr, B. and Cantrell, R.G. (2000) Chromosomal assignment of microsatellite loci in cotton. J. Heredity 91(4), 326–32.Google Scholar
  113. Liu, B. and Wendel, J.F. (2001) Intersimple sequence repeat (ISSR) polymorphisms as a genetic marker system in cotton. Mol. Ecol. Notes 1, 205–208.Google Scholar
  114. Liu, L., Guo, W., Zhu, X. and Zhang, T. (2003) Inheritance and fine mapping of fertility restoration for cytoplasmic male sterility in Gossypium hirsutum L. Theor. Appl. Genet. 106, 461–469.PubMedGoogle Scholar
  115. Livak, K.J. (1999) Allelic discrimination using flourogenic probe and 5`nuclease assay. Genet. Anal. 14, 143–149.PubMedGoogle Scholar
  116. Lu, Y., Curtiss, J., Zhang, J., Percy, R.G. and Cantrell, R.G. (2005) Discovery of single nucleotide polymorphisms in selected fiber genes in cultivated tetraploid cotton. National Cotton Council Beltwide Cotton Conference, pp. 946.Google Scholar
  117. Maughan, P.J., Saghai Maroof, M.A., Buss, G.R. and Huestis, G.M. (1996) Amplified fragment length polymorphism (AFLP) in soybean: species diversity, inheritance and near-isogenic line analysis. Thoer. Appl. Genet. 93:392–401.Google Scholar
  118. McClelland, M. (1983) The frequency and distribution of methylatable DNA sequences in leguminous plant protein coding genes. J. Mol. Evol. 19, 346–354.PubMedGoogle Scholar
  119. McClelland, M., Mathieu-Daude, F. and Welsh, J. (1995) RNA fingerprinting and differential display using arbitrarily primed PCR. Trends in Genet. 11, 242–246.Google Scholar
  120. Mei, M., Syed, N. H., Gao, W., Thaxton, P.M., Smith, C.W., Stelly, D.M. and Chen, Z.J. (2004) Genetic mapping and QTL analysis of fiber related traits in cotton (Gossypium). Theor. Appl. Genet. 108, 280–291.PubMedGoogle Scholar
  121. Meng, L., Bregitzer, P., Zhang, S. and Lemaux, P.G. (2003) Methylation of the exon/intron region in the ubi1 promoter complex correlates with transgene silencing in barley. Plant Mol. Biol. 53,327–340.PubMedGoogle Scholar
  122. Meredith, W.R.J. (1992) Improving fiber strength through genetics and breeding. In: C.R. Benedict and G.M. Jividen (Eds.), Proceeding Cotton Fiber Cellulose: Structure, Function, and Utilization Conference, Savannah, GA. 28-31 Oct. 1992. National Cotton Council, Memphis, TN, pp. 289–302.Google Scholar
  123. Meyer, W., Mitchell, T.G., Freedman, E.Z. and Vilgalys, R. (1993) Hybridization probes for conventional DNA fingerprinting can be used as single primers in the PCR to distinguish strains of Cryptococcus neoformans. J. Clin. Microbiol. 31, 2274–2280.PubMedGoogle Scholar
  124. Mitchell, S.E., Kresovich, S., Jester, C.A., Hernandez, C.J. and Szewc-McFadden, A.K. (1997) Application of multiplex PCR and fluorescence-based, semi-automated allele sizing technology for genotyping plant genetic resources. Crop Sci. 37,617–624Google Scholar
  125. Mukhtar, M.S., Rahman, M. and Zafar, Y. (2002) Assessment of genetic diversity among wheat (Triticum aestivum L.) cultivars from a range of localities across Pakistan using random amplified polymorphic DNA (RAPD) analysis. Euphytica 128, 417–425.Google Scholar
  126. Multani, D.S. and Lyon, B.R. (1995) Genetic Fingerprinting of Australian cotton cultivars with RAPD markers. Genome 38, 1005–1008.PubMedGoogle Scholar
  127. Mumtaz, H. (2007) Identification of structural and functional genomic markers for fiber quality traits in cotton using interspecific population (G. hirsutum x G. barbadense). MPhil Thesis, QA Univ Islamabad Pakistan.Google Scholar
  128. Murtaza, N. (2006) Cotton genetic diversity study by AFLP markers. Electronic J. Biotech. 9 (4), 456–460.Google Scholar
  129. Nagaoka, T. and Ogihara, Y. (1997) Applicability of inter-simple sequence repeat polymorphisms in wheat for use as DNA markers in comparison to RFLP and RAPD markers. Theor. Appl. Genet. 94, 597–602.Google Scholar
  130. Nguyen, T.B., Giband, M., Brottier, P., Risterucci, A.M. and Lacape, J.M. (2004) Wide coverage of the tetraploid cotton genome using newly developed microsatellite markers. Theor. Appl. Genet. 109, 167–175.PubMedGoogle Scholar
  131. Niu, C., Lu, Y. and Zhang, J. (2006) Plant disease resistance gene analogues in cotton: mapping and expression. Beltwide Cotton Conference, Jan 3-6. 2006 San Antonio Texas.Google Scholar
  132. Oakeley, E.J. and Jost, J.P. (1996) Non-symmetrical cytosine methylation in tobacco pollen DNA. Plant Mol. Biol. 31, 927–930.PubMedGoogle Scholar
  133. Pan, Y.B., Burner, D.M., Ehrlich, K.C., Grisham, M.P. and Wei, Q. (1997) Analysis of primer-derived, non-specific amplification products in RAPD-PCR. Biotech. 22, 1071–1077.Google Scholar
  134. Paran, I. and Michelmore, R.W. (1993) Development of reliable PCR-based markers linked to downy mildew resistance genes in lettuce. Theor. Appl. Genet. 85, 985–993.Google Scholar
  135. Parks, C.R., Ezell, W.I., William, D.E. and Dreyer, D.L. (1975) The application of flavonoid distribution to taxonomic problems in the genus Gossypium. Bulletin of the Torrey Botanical Club 102, 350–361.Google Scholar
  136. Park, Y.H., Alabady, M.S., Ulloa, M., Sickler, B., Wilkins, T.A., Yu, J., Stelly, D.M., Kohel, R.J., El-Shihy, O.M. and Cantrell, R.G. (2005) Genetic mapping of new cotton fiber loci using EST-derived microsatellites in an interspecific recombinant inbred line cotton population. Mol. Genet. Gen. 274, 428–441Google Scholar
  137. Parnell, F.R., King, H.E. and Ruston, D.F. (1949) Jassid resistance and hairness of cotton plant. Bull. Entomol. Res. 39, 539–575.PubMedGoogle Scholar
  138. Paterson, A.H., Damon, S. Hewitt, J.D., Zamir, D., Rabinowitch, H.D., Lincoln, S.E., Lander, E.S. and Tanksley S., (1991) Mendelian factors underlying quantitative traits in tomato: comparison across species, generations, and environments. Genetics 127, 181–197.PubMedGoogle Scholar
  139. Paterson, A.H., Brubaker, C.L and Wendel, J.F. (1993) A rapid method for extraction of cotton (Gossypium spp.) genome DNA suitable for RFLP or PCR analysis. Plant Mol. Biol. Rep. 11, 122–127.Google Scholar
  140. Paterson, A.H. and Zhao, X. (1995) Molecular tools for cotton improvement. In Herber D (Ed). Proceeding Beltwide Cotton Production Research Conference San Antonio, TX, 4–7 Jan., National Cotton Council of Amer., Memphis, TN.Google Scholar
  141. Paterson, A.H., Bowers, J., Burow, M., Draye, X., Elsik, C., Jiang, C., Katsar, C., Lan, T., Lin, Y. and Ming, R. (2000) Comparative genomics of plant chromosomes. Plant Cell 12, 1523–1539.PubMedGoogle Scholar
  142. Paterson, A., Estill, J., Rong, J., Williams, D. and Marler, B. (2002) Toward a genetically anchored physical map of the cotton genomes. Cotton Sci. 14 (Suppl.), 31.Google Scholar
  143. Paterson, A.H., Saranga, Y., Menz, M., Jiang, C.X. and Wright, R.J. (2003) QTL analysis of genotype x environment interactions affecting cotton fiber quality. Theor. Appl. Genet. 106, 384–396.PubMedGoogle Scholar
  144. Perring, T.M., Copper, A.D., Rodriguez, R.J., Farrarand, C.A. and Bellows, T.S. (1993) Identification of a white fly species by genomics and behavioral studies. Science 259, 74–77.PubMedGoogle Scholar
  145. Phillips, L.L. (1966) The cytology and phylogenetic of the diploid species of Gossypium. Ann. J. Bot. 53, 328–335.Google Scholar
  146. Pillay, M. and Myers, G.O. (1999) Genetic Diversity in cotton assessed by variation in ribosomal RNA genes and AFLP markers. Crop Sci. 39, 1881–1886.Google Scholar
  147. Powell, W., Machray, G.C. and Provan, J. (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci. 1, 215–222.Google Scholar
  148. Qureshi, S.N., Saha, S., Kantety, R.V. and Jenkins, J.N. (2004) EST-SSR: a new class of genetic markers in cotton. J. Cotton Sci. 8, 112–123.Google Scholar
  149. Rafalski, J.A. and Tingey, S.V. (1993) Genetic diagnostics in plant breeding: RAPDs, microsatellites and machines. Trends in Genet. 9, 275–279.Google Scholar
  150. Rahman, M. (2002) DNA markers studies in cotton. PhD Thesis, Department of Plant Breed. Genet. Univ. Agric. Faisalabad Pakistan.Google Scholar
  151. Rahman, M., Ahmed, N., Asif, M. and Zafar, Y. (2006a) Identification of DNA markers linked with cotton leaf curl disease (CLCD). International Cotton Genome Initiative (ICGI) Workshop, 18–20 Sept Brasilia Brazil. Pp. 77–78.Google Scholar
  152. Rahman, M., Asif, M., Ali, I., Hayder, Z., Malik, K.A. and Zafar, Y. (2003). DNA marker studies in cotton. Final meeting of CFC/ICAC 07 project held at ICBA, Dubai 28–30 September 2003.Google Scholar
  153. Rahman, M., Asif, M., Ullah, I., Malik, K.A. and Zafar, Y. (2005)a Overview of cotton genomic studies in Pakistan. Plant & Animal Genome Conference XIII. San Diego, CA. USA.Google Scholar
  154. Rahman, M., Aslam, N., Asif, M., Malik, T.A., Malik, K.A. and Zafar, Y. (2002a) Identification of DNA markers for cotton leaf curl disease (CLCD) in cotton (Gossypium hirsutum L.). Cotton Sci. 14, 17.Google Scholar
  155. Rahman, M., Hussain, D. and Zafar, Y. (2002b) Estimation of genetic divergence among elite cotton cultivars–genotypes by DNA fingerprinting technology. Crop Sci. 42, 2137–2144.Google Scholar
  156. Rahman, M., Malik, T.A., Hussain, D. and Zafar, Y. (2005)b Genetics of resistance to cotton leaf curl virus disease in Gossypium hirsutum. Plant Pathol. 54, 764–772.Google Scholar
  157. Rahman, M., Malik, T.A., Iqbal, M.J., Zafar, Y. and Malik, K.A. (2004) Gene tagging for salinity resistance in wheat by RAPD. Pak. J. Bot. 36 (3), 595–602.Google Scholar
  158. Rahman, M., Ullah, I., Ashraf, M. and Zafar, Y. (2008a) A study of genotypic variation for drought tolerance in cotton. Agron. Sustain. Dev. 28, 439–447.Google Scholar
  159. Rahman, M., Yasmin, T., Shaheen, H.L., Shaheen, T., Tabassam, N. and Zafar, Y. (2006b) Harvesting genetic diversity in the cotton genome. National symposium on biotechnology for economic prosperity, National Commission on Biotechnology, Green Retreat Hotel, Nathiagali, Pakistan, July 24–26, 2006. pp 38.Google Scholar
  160. Rahman, M., Yasmin, T., Tabassum, N., Ullah, I., Asif, M. and Zafar, Y. (2008b) Studying the extent of genetic diversity among Gossypium arboreum L. genotypes/cultivars using DNA fingerprinting. Genetic Res. Crop Evo. 55, 331–339.Google Scholar
  161. Rahman, M. and Zafar, Y. (2001) Genotyping of a new strain of lentil (Lens Culinaris Medik.) by DNA fingerprinting technology. Pak. J. Bot. 33 (4), 423–428.Google Scholar
  162. Rahman, M. and Zafar. Y. (2007a). Registration of NIBGE-115. Journal of Plant Registrations, 1, 51–52.Google Scholar
  163. Rahman, M. and Zafar, Y. (2007b) Registration of NIBGE-2. Int. J. Plant Registration 2,113-114.Google Scholar
  164. Rallo, P., Dorado, G. and Martin, A. (2000) Development of simple sequence repeats (SSRs) in olive tree (Olea europaea L.). Theor. Appl. Genet. 101, 984–989.Google Scholar
  165. Rana, M.K. and Bhat, K.V. (2004) A Comparison of AFLP and RAPD Markers for Genetic Diversity and Cultivar Identification in Cotton. J. Plant Biochem. Biotech. 13, 19–24.Google Scholar
  166. Reddy, A., Haisler, R.M., Yu, J. and Kohel, R.J. (1997) AFLP mapping in cotton. Plant Animal Genome Conference V, San Diego CA, USA.Google Scholar
  167. Reddy, O.U.K., Pepper, A.E., Abdurakhmonov, I., Saha, S., Jenkins, J.N., Brooks, T.B., Bolek, Y. and El-Zik, K.M. (2001) New dinucleotide and trinucleotide microsatellite marker resources for cotton genome research. J. Cotton Sci. 5, 103–113.Google Scholar
  168. Reinisch, A.J., Dong, J.M., Brubaker, C.L., Wendel, J.F. and Paterson, A.H. (1994) A detailed RFLP map of cotton, Gossypium hirsutum x Gossypium barbadense: chromosome organization and evolution in a disomic polyploid genome. Genetics 138, 829–847.PubMedGoogle Scholar
  169. Rong, J.K., Abbey, C., Bowers, J.E., Brubaker, C.L., Chang, C., Chee, P.W., Delmonte, T.A., Ding, X., Garza, J.J., Marler, B.S., Park, C., Pierce, G.J., Rainey, K.M., Rastogi, V., Schulze, K., Tronlinde, N.L., Wendel, J.F., Wilkins, T.A., Wing, R.A., Wright, R.J., Zhao, X., Zhu, L. and Paterson, A.H. (2004) A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium). Genetics 166, 389–417.PubMedGoogle Scholar
  170. Rungis, D., Llewellyn, D., Dennis, E.S. and Lyon, B.R. (2005) Simple sequence repeat (SSR) markers reveal low levels of polymorphism between cotton (Gossypium hirsutum L.) cultivars. Austr. J. Agri. Res. 56, 301–307.Google Scholar
  171. Shah, M.R., Kumpatla, S.P., Gupta, M. and Thompson, S.A. (2004) SSR-Based SNP discovery: an economical approach for the development of SNP markers in cotton. Plant & Animal Genomes XII Conference, San Diego, USA.Google Scholar
  172. Saha, S., Karaca, M., Jenkins, J.N., Zipf, A.E., Reddy, O.U.K. and Kantety, R.V. (2003) Simple sequence repeats as useful resources to study transcribed genes of cotton. Euphytica 130(3), 355–364.Google Scholar
  173. Saal, B., Plieske, J., Hu, J., Quiros, C.F. and Struss, D. (2001) Microsatellite markers for genome analysis in Brassica. II. Assignment of rapeseed microsatellites to the A and C genomes and genetic mapping in Brassica oleracea L. Theor. Appl. Genet. 102 (5), 695–699.Google Scholar
  174. Saranga, Y., Menz, M., Jiang, C.X., Wright, R.J., Yakir, D. and Paterson. A.H. (2001) Genomic dissection of genotype x environment interactions conferring adaptation of cotton to arid conditions. Genome Res. 11, 1988–1995.PubMedGoogle Scholar
  175. Schmid, K.J., So¨rensen T.R., Stracke, R., ¨rje´k, O.T., Altmann, T., Mitchell-Olds, T. and Weisshaar B. (2003) Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana. Genome Res 13:1250–1257.PubMedGoogle Scholar
  176. Schneider, K., Weisshaar, B., Borchardt, D.C. and Salamini, F. (2001) SNP frequency and allelic haplotype structure of Beta vulgaris expressed genes. Mol. Breed. 8, 63–74.Google Scholar
  177. Schon, C.C., Lee, M., Melchinger, A.E., Guthrie, W.D. and Woodman, W.L. (1993) Mapping and characterization of quantitative trait loci affecting resistance against second generation European corn borer in maize with the aid of RFLPs. Heredity 70, 648–659.Google Scholar
  178. Shaheen, H.L. (2005) Global view of genetic diversity among cotton cultivars/genotypes by microsatellite analysis. MPhil Thesis. Department of Botany Univ. Agric. Faisalabad Pakistan.Google Scholar
  179. Shaheen, T., Rahman, M. and Zafar, Y. (2006) Chloroplast RPS8 gene of cotton reveals the conserved nature through out taxa. Pak J Bot. 38 (5): 1467–1476.Google Scholar
  180. Shappley, Z.W., Jenkins, J.N., Watson, C.E., Kahler, A.L. and Meredith, W.R. (1996) Establishment of molecular markers and linkage groups in two F2 populations of upland cotton. Theor. Appl. Genet. 92, 915–919.Google Scholar
  181. Shappley, Z.W., Jenkins, J.N., Zhu, J. and McCarty, J.C. (1998) Quantitative trait loci associated with agronomic and fiber traits of Upland Cotton. J. Cotton Sci. 4, 153–163.Google Scholar
  182. Shen, X., Guo, W., Zhu, X., Yuan, Y., Yu, J.Z., Kohel, R.J. and Zhang, T. (2005) Molecular mapping of QTLs for fiber qualities in three diverse lines in Upland cotton using SSR markers. Mol. Breed. 15 (2), 169–181.Google Scholar
  183. Shen, X., Guo, W., Lu, Q., Zhu, X., Yuan, Y. and Zhang, T. (2007) Genetic mapping of quantitative trait loci for fiber quality and yield trait by RIL approach in Upland cotton. Euphytica 155, 371–380.Google Scholar
  184. Shi, M.M. (2001) Enabling large scale pharmacogenetic studies by high-throughput mutation detection and genotyping technologies. Clin. Chem. 47, 164–172.PubMedGoogle Scholar
  185. Small, R.L., Ryburn, J.A. and Wendel, J.F. (1999) Low levels of nucleotide diversity at homoeologous Adh loci in allotetraploid cotton (Gossypium L.). Mol. Biol. Evol. 16, 491–501.PubMedGoogle Scholar
  186. Song, X. L., Wang, K., Guo, W.Z., Zhang, J. and Zhang, T.Z. (2005) A comparison of genetic maps constructed from haploid and BC1 mapping populations from the same crossing between Gossypium hirsutum L. 3 G. barbadense L. Genome 48, 378–390.PubMedGoogle Scholar
  187. Struss, D. and Plieske, J. (1998) The use of microsatellite markers for detection of genetic diversity in barley populations. Theor. Appl. Genet. 97, 308–315.Google Scholar
  188. Syvanen, A.C. (2001) Assessing genetic variation genotyping single nucleotide polymorphism. Nat. Rev. Genet. 2, 930–942.PubMedGoogle Scholar
  189. Tabassam, N., Rahman, M. and Zafar Y. (2006) DNA-based genotyping of sorghum hybrids. Pak. J. Bot. 38, 1599–1604.Google Scholar
  190. Tatineni, V., Cantrell, R.G. and Davis, D.D. (1996) Genetic diversity in elite cotton germplasm determined by morphological characteristics and RAPD. Crop Sci. 36, 186–192.Google Scholar
  191. Taylor, G.D., Briley, D., Nguyen, Q., Long, K., Iannone, M.A., Li, M.S., Ye, F., Ashari, A., Lai, A., Wagner, M., Chen, J. and Weiner, M.P. (2001) Flow cytometric platforms for high-throughput single nucleotide polymorphism analysis. Biotech. 30, 661–669.Google Scholar
  192. Temnykh, S., Park, W.D., Ayres, N., Cartinhour, S., Hauck, N., Lipovick, L., Cho, Y.G., Ishii, T. and McCouch, S.R. (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor. Appl. Genet. 100, 697–712.Google Scholar
  193. Tenaillon, M., Sawkins, M., Long, A., Gaut, R., Doebley, J. and Gaut, B. (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays). Proc. Natl. Acad. Sci. 98, 9161–9166.PubMedGoogle Scholar
  194. Tsuchihashi, Z. and Dracopoli, N.C. (2002) Progress in high throughput SNP genotyping methods. Pharmacogenomics J. 2, 103–110.PubMedGoogle Scholar
  195. The International HapMap Consortium. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 851, 451–461.Google Scholar
  196. Thuillet, A.C., Bataillon, T., Sourdille, P. and David, J.L. (2004) Factors affecting polymorphism at microsatellite loci in bread wheat [Triticum aestivum (L.) Thell]: effects of mutation processes and physical distance from the centromere. Theor. Appl. Genet. 108(2), 368–377.PubMedGoogle Scholar
  197. Udall, J.A., Quijada, P.A., Lambert, B. and Osborn, T.C. (2006) Quantitative trait analysis of seed yield and other complex traits in hybrid spring rapeseed (Brassica napus L.): 2. Identification of alleles from unadapted germplasm. Theor. Appl. Genet. 113, 597–609.PubMedGoogle Scholar
  198. Ulloa, M. and Meredith, W.R. (2000) Genetic linkage map and QTL analysis of agronomic and fiber quality traits in an intraspecific population. J. Cotton Sci. 4, 161–170.Google Scholar
  199. Ulloa, M., Meredith, W.R., Shappley, Z.W. and Kahler, A.L. (2002) RFLP genetic linkage maps from four F2:3 populations and a joinmap of Gossypium hirsutum L. Theor. Appl. Genet. 104, 200–208.PubMedGoogle Scholar
  200. Ulloa, M., Saha, S., Jenkins, J.N., Meredith, W.R., Mccarty, J.J.C., and Stelly, D.M. (2005) Chromosomal assignment of RFLP linkage groups harboring important QTLs on an intraspecific cotton (Gossypium hirsutum L.) Joinmap. J. Heredity 96(2), 132–144.Google Scholar
  201. Valicek, P. (1978) Wild and cultivated cottons. Cottoned fibres tropicles (English Eds.) 33, 363–387.Google Scholar
  202. Van Esbroeck, G.A., Bowman, D.T., May, O.L and Calhoun, D.S. (1999) Genetic similarity indices for ancestral cotton cultivars and their impact on genetic diversity estimates of modern cultivars. Crop Sci. 39, 323–328.Google Scholar
  203. Vos, P., Hogers, R., Blecker, M., Reijans, M., Lee, T., Hornes, M., Frijters, A., Pot, J., Peleman, J., Kuiper, M. and Zabeau, M. (1995) AFLP: a new technique for DNA fingerprinting. Nucl. Acids Res. 23, 4407–4414.PubMedGoogle Scholar
  204. Wang, G.L., Dong, J.M. and Paterson, A.H. (1995) The distribution of Gossypium hirsutum chromatin in Gossypium barbadense germplasm: molecular analysis of introgressive plant breeding. Theor. Appl. Genet. 91, 1153–1161.Google Scholar
  205. Wang, H-M., Lin, Z-X., Zhang, X-L., Chen, W., Guo, X-P., Nie, Y-C. and Li Y-H. (2008) Mapping and quantitative trait loci analysis of verticillium wilt resistance genes in cotton. Journal of Integrative Plant Biol. 50(2), 174–182.Google Scholar
  206. Welsh, J. and McClelland, M. (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucl. Acids Res. 18, 7213–7218.PubMedGoogle Scholar
  207. Wendel, J.F. and Albert, V.A. (1992) Phylogenetics of the cotton genus (Gossypium)-character-state weighted parsimony analysis of chloroplast-DNA restriction site data and its systematic and biogeographic implications. Syst. Bot. 17, 115–143.Google Scholar
  208. Wendel, J.F., Brubaker, C.L. (1993) RFLP diversity in Gossypium hirsutum L. and new insights into the domestication of cotton. Amer J Bot 80: 71.Google Scholar
  209. Wendel, J.F., Brubaker, C.L. and Percival, A.E. (1992) Genetic diversity in Gossypium hirsutum and the origin of upland cotton. Am. J. Bot. 79, 1291–1310.Google Scholar
  210. Williams, J.G.K., Kubelik, A.R., Livak, K.J., Rafalski, J.A. and Tingey, S.V. (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucl. Acids Res. 18, 6531–6535.PubMedGoogle Scholar
  211. Wolfe, A.D., Xiang, Q.Y. and Kephart, S.R. (1998) Assessing hybridization in natural populations of Penstemon (Scrophulariaceae) using hypervariable intersimple sequence repeat (ISSR) bands. Mol. Ecol. 7, 1107–1125.PubMedGoogle Scholar
  212. Wright, R.J., Thaxton, P.M., El-Zik, K.M. and Paterson, A.H. (1999) Molecular mapping of genes affecting pubescence of cotton. J. Heredity 90 (1), 215–219.Google Scholar
  213. Wright, R., Thaxton, P., Paterson, A.H. and El-Zik, K. (1998) Polyploid formation in Gossypium has created novel avenues for response to selection for disease resistance. Genetics 149, 1987–1996.PubMedGoogle Scholar
  214. Xu, M.L., Melchinger, A.E., Xia, X.C. and Lübberstedt, T. (1999) High-resolution mapping of loci conferring resistance to sugarcane mosaic virus in maize using RFLP, SSR and AFLP markers. Mol. Gen. Genet. 261, 574–581.PubMedGoogle Scholar
  215. Yasmin, T. (2005). DNA based characterisation of different cultivated cotton strains. MPhil Thesis, Department of Botany Univ. Agric. Faisalabad Pakistan.Google Scholar
  216. Ye, F., Li, M.S., Taylor, J.D., Nguyen, Q., Colton, H.M., Casey, W.M., Wagner, M., Weiner, M.P. and Chen, J. (2001) Fluorescent microsphere-based readout technology for multiple human single nucleotide polymorphism analysis and bacterial identification. Hum. Mutat. 17, 305–316.PubMedGoogle Scholar
  217. Yu, J., Park, Y., Lazo, G.R., Wolff, N.C. and Kohel, R.J. (1996) Molecular mapping of the cotton genome and its applications to cotton improvement. Proceeding Beltwide Cotton Conference. pp. 636.Google Scholar
  218. Yu, J., Kohel, R.J., Xu, Z., Dong, J., Zhang, H., Stelly, D.M., Zhu, Y. and Covaleda, L. (2005) Physical mapping of fiber development genes in cotton. Plant & Animal Genome XIII Conference, Town & Country Hotel, San Diego, CA, pp. 225.Google Scholar
  219. Zhang, J. and Stewart, J.McD. (2004) Identification of molecular markers linked to the fertility restorer genes for CMS-D8 in cotton. Crop Sci. 44, 1209–1217.Google Scholar
  220. Zhang, J., Guo, W. and Zhang, T. (2002) Molecular linkage map of allotetraploid cotton (Gossypium hirsutum L. x Gossypium barbadense L.) with a haploid population. Theor. Appl. Genet. 105 (8), 1166–1174.PubMedGoogle Scholar
  221. Zhang, J., Pang, M.X., Niu, C., Wang, W., Percy, R.G., Cantrell, R.G. and Stewart, J. McD. (2007) AFLP-based SNP discovery in cotton, Plant & Animal Genome XV Conference, Town & Country Hotel, San Diego, CA, pp 169.Google Scholar
  222. Zhang, J., Stewart, J.McD. and Wang, T. (2005) Linkage analysis between gametophytic restorer Rf 2 gene and genetic markers in cotton. Crop Sci. 45, 147–156.Google Scholar
  223. Zhang, T.Z., Yuan, Y., Yu, J., Guo, W. and Kohel, R.J. (2003) Molecular tagging of a major QTL for fiber strength in Upland cotton and its marker-assisted selection. Theor. Appl. Genet. 106, 262–268.PubMedGoogle Scholar
  224. Zhang, Q. and Yu, S. (1999) Molecular markers-based gene tagging and its impact on rice improvement. In: J.S. Nanda (Ed.), Rice Breeding and Genetics-Research Priorities and Challenges, Science Publishers Inc., Enfield, New Hampshire, pp. 241–270.Google Scholar
  225. Zhang, J.F. and Stewart. J.McD. (2001). Inheritance and genetic relationships of the D8 and D2-2 restorer genes for cotton cytoplasmic male sterility. Crop Sci. 41, 289–294.Google Scholar
  226. Zhao, X.P., Lin, Y.R. and Paterson, A.H. (1994) Characterization and genetic mapping of DNA microsatellites from cotton. Plant & Animal genome II conference, Town & Country Conference Center, San Diego, CA.Google Scholar
  227. Zhu, J., Gale, M.D., Quarrie, S., Jackson, M.T. and Bryan, G.J. (1998) AFLP markers for the study of rice biodiversity. Theor. Appl. Genet. 96, 602–611.Google Scholar
  228. Zhu, Y.L., Song, Q.J., Hyten, D.L., Van, T.C.P., Matukumalli, L.K., Grimm, D.R., Hyatt. S.M., Fickus, E.W., Young, N.D. and Cregan, P.B. (2003) Single n`ucleotide polymorphism in soybean. Genetics 168, 1123–1134.Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Mehboob-ur-Rahman
    • 1
  • Yusuf Zafar
  • Andrew H. Paterson
  1. 1.Plant Genomics & Mol Breeding Labs. National Institute for Biotechnology & Genetic Engineering (NIBGE)Pakistan

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