Skip to main content
Log in

Application of molecular markers in plant genome analysis: a review

  • Review Article
  • Published:
The Nucleus Aims and scope Submit manuscript

Abstract

Advancement in the field of molecular biology has led to the development of various molecular markers which has revolutionized our understanding of the organization and evolution of plant genomes. Detection of genetic variation in plants offers an opportunity to understand the molecular basis of several biological phenomena. The reliability and efficiency of restriction digestion and polymerase chain reaction based random DNA markers have already proved their utility in taxonomical, evolutionary and ecological studies of plants. Progresses in the field of genomics and transcriptomics have enabled plant researchers to develop molecular markers derived from exon region of the genome which are termed as genic molecular markers (GMMs). GMMs are the part of the cDNA/EST sequences that mainly characterize the functional part of the genome. Next-generation DNA sequencing has also significantly contributed towards development of microRNA specific novel functional markers at the DNA level. This review focuses on the technical aspects of different molecular markers and their applications in the genome analysis.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  1. Abdel-Rahman MM, Bayoumi SR, Barakat MN. Identification of molecular markers linked to Fusarium ear rot genes in maize plants Zea mays L. Biotechnol Biotechnol Equip. 2016;30:692–9.

    Article  CAS  Google Scholar 

  2. Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H, et al. Complementary DNA sequencing: expressed sequence tags and the human genome project. Science. 1991;252:1651–6.

    Article  CAS  PubMed  Google Scholar 

  3. Agarwal M, Shrivastava N, Padh H. Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep. 2008;27:617–31.

    Article  CAS  PubMed  Google Scholar 

  4. Andersen JR, Schrag T, Melchinger AE, Zein I, Lubberstedt T. Validation of Dwarf polymorphisms associated with flowering time in elite European inbred lines of maize (Zea mays L.). Theor Appl Genet. 2005;111:206–17.

    Article  CAS  PubMed  Google Scholar 

  5. Arnau G, Lallemand J, Bourgoin M. Fast and reliable strawberry cultivar identification using inter simple sequence repeat (ISSR) amplification. Euphytica. 2002;129:69–79.

    Article  Google Scholar 

  6. Avise JC. Molecular markers, natural history, and evolution. New York: Chapman & Hall; 1994.

    Book  Google Scholar 

  7. Becher SA, Steinmetz K, Weising K, Boury S, Peltier D, et al. Microsatellites for cultivar identification in Pelargonium. Theor Appl Genet. 2000;101:643–51.

    Article  CAS  Google Scholar 

  8. Beebee T, Rowe G. An introduction to molecular ecology. Oxford: Oxford University Press; 2004.

    Google Scholar 

  9. Biffi R, Restivo FM, Tassi F, Caporali E, Carboni A, Marziani GP, et al. A restriction fragment polymorphism probe for early diagnosis of gender in Asparagus officinalis L. Hort Sci. 1995;30:1463–4.

    CAS  Google Scholar 

  10. Botstein D, White RL, Skolnick M, Davis RW. Construction of a genetic linkage map in man using restriction fragment length polymorphism. Am J Hum Genet. 1980;32:314–31.

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Bowers JE, Dangl GS, Vignani R, Meredith CP. Isolation and characterization of new polymorphic simple sequence repeat loci in grape (Vitis vinifera L.). Genome. 1996;39:628–33.

    Article  CAS  PubMed  Google Scholar 

  12. Bredemeijer GMM, Arens P, Wouters D, Visser D, Vosman B. The use of semi-automated fluorescent microsatellite analysis for tomato cultivar identification. Theor Appl Genet. 1998;97:584–90.

    Article  CAS  Google Scholar 

  13. Brookes A. The essence of SNPs. Gene. 1999;234:177–86.

    Article  CAS  PubMed  Google Scholar 

  14. Broun P, Tanksley SD. Characterization of tomato clones with sequence similarity to human minisatellites 33.6 and 33.15. Plant Mol Biol. 1993;23:142–231.

    Article  Google Scholar 

  15. Burow MD, Blake TK. Molecular tools for the study of complex traits. In: Paterson AH, editor. Molecular dissection of complex traits. Washington, DC: CRC Press; 1998. p. 13–29.

    Google Scholar 

  16. Castillo A, Budak H, Varshney RK, Dorado G, Graner A, Hernandez P. Transferability and polymorphism of barley EST-SSR markers used for phylogenetic analysis in Hordeum chilense. BMC Plant Biol. 2008;8:97–105.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  17. Cheng J, Long Y, Khan MA, Wei C, Fu S, Fu J. Development and significance of RAPD-SCAR markers for the identification of Litchi chinensis Sonn. by improved RAPD amplification and molecular cloning. Electron J Biotechnol. 2015;18:35–9.

    Article  CAS  Google Scholar 

  18. Cho RJ, Mindrinos M, Richards DR, Sapolsky RJ, Anderson M, Drenkard E, Dewdney J, Reuber TL, Stammers M, Federspicl N, Theologis A, Yang WH, Hubbel E, Au M, Chung EY, Lashkari D, Lemieux B, Dean C, Lipshutz RJ, Ausubel EM, Davis RW, Oefner PJ. Genome-wide mapping with biallelic markers in Arabidopsis thaliana. Nat Genet. 1999;23:203–7.

    Article  CAS  PubMed  Google Scholar 

  19. Collard BCY, Mackill DJ. Start codon targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Mol Biol Rep. 2009;27:86–93.

    Article  CAS  Google Scholar 

  20. Cruzan M. Genetic markers in plant evolutionary ecology. Ecology. 1998;79:400–12.

    Article  Google Scholar 

  21. Danilova TV, Karlov GI. Application of inter simple sequence repeat (ISSR) polymorphism for detection of sex specific molecular markers in Hop (Humulus lupulus L.). Euphytica. 2006;151:15–21.

    Article  CAS  Google Scholar 

  22. Deshpande D, Ramakrishna W, Mulay GP, Gupta VS, Ranjekar PK. Evolutionary and polymorphic organization of knotted1 homeobox in cereals. Theor Appl Genet. 1998;97:135–40.

    Article  CAS  Google Scholar 

  23. Dikshit HK, Singh A, Singh D, Aski M, Jain N, Hegde VS. Tagging and mapping of SSR marker for rust resistance gene in lentil (Lens culinaris Medikus subsp. culinaris). Indian J Exp Biol. 2016;54:394–9.

    CAS  PubMed  Google Scholar 

  24. Dong Y, Zhu H. Single-strand conformational polymorphism analysis: basic principles and routine practice. Methods Mol Med. 2005;108:149–57.

    CAS  PubMed  Google Scholar 

  25. Falke KC, Melchinger AE, Flachenecker C, Kusterer B, Frisch M. Comparison of linkage maps from F2 and three times intermated generations in two populations of European flint maize (Zea mays L.). Theor Appl Genet. 2006;113:857–66.

    Article  CAS  PubMed  Google Scholar 

  26. Ford R, Le Roux K, Itman C, Brouwer JB, Taylor PWJ. Diversity analysis and genotyping in Pisum with sequence tagged microsatellite site (STMS) primers. Euphytica. 2002;124:397–405.

    Article  CAS  Google Scholar 

  27. Fu D, Ma BI, Mason AS, Xiao M, Wei L, An Z. MicroRNA-based molecular markers: a novel PCR-based genotyping technique in Brassica species. Plant Breed. 2013;132:375–81.

    Article  CAS  Google Scholar 

  28. Fukuchi A, Kikuchi F, Hirochika H. DNA fingerprinting of cultivated rice with rice retrotransposon probes. Jpn J Genet. 1993;68:195–204.

    Article  CAS  Google Scholar 

  29. Fukuoka S, Inoue T, Miyao A, Monna L. Mapping of sequence-tagged sites in rice by single conformation polymorphism. DNA Res. 1994;1:271–7.

    Article  CAS  PubMed  Google Scholar 

  30. Ganie SA, Mondal TK. Genome-wide development of novel miRNA-based microsatellite markers of rice (Oryza sativa) for genotyping applications. Mol Breed. 2015;35:1–12.

    Article  CAS  Google Scholar 

  31. Gaur R, Sethy NK, Choudhary S, Shokeen B, Gupta V, Bhatia S. Advancing the STMS genomic resources for defining new locations on the intra-specific genetic linkage map of chickpea (Cicer arietinum L.). BMC Genom. 2011;12:117.

    Article  CAS  Google Scholar 

  32. Georges M, Gunawardana A, Threadgill DW, Lathrop M, Olsaker I, Mishra A, Sargeant LL, Schoeberlein A, Steele MR, Terry C, Threadgill DS, Zhao X, Holm T, Fries R, Womack JE. Characterization of a set of variable number of tandem repeat markers conserved in Bovidae. Genomics. 1991;11:24–32.

    Article  CAS  PubMed  Google Scholar 

  33. Gill KS, Lubbers EL, Gill BS, Raupp WJ, Cox TS. A genetic linkage map of ‘Triticum tauschii (DD) and its relationship to the D genome of bread wheat (AABBDD). Genome. 1991;34:362–74.

    Article  Google Scholar 

  34. Goulao L, Oliveira CM. Molecular characterisation of cultivars of apple (Malus x domestica Borkh.) using microsatellite (SSR and ISSR) markers. Euphytica. 2001;122:81–9.

    Article  CAS  Google Scholar 

  35. Gupta M, Chyi YS, Romero-Severson J, Owen JL. Amplification of DNA markers from evolutionary diverse genomes using single primers of simple-sequence repeats. Theor Appl Genet. 1994;89:998–1006.

    CAS  PubMed  Google Scholar 

  36. Gupta PK, Rustgi S, Sharma S, Singh R, Kumar N, Balyan HS. Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Mol Genet Genomics. 2003;270:315–23.

    Article  CAS  PubMed  Google Scholar 

  37. Hamada H, Kakunaga T. Potential Z-DNA forming sequences are highly dispersed in the human genome. Nature. 1982;298:396–8.

    Article  CAS  PubMed  Google Scholar 

  38. Hatada I, Hayashizaki Y, Hirotsune S, Komatsubara H, Mukai T. A genomic scanning method for higher organisms using restriction sites as landmarks. Proc Natl Acad Sci USA. 1991;88:9523–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Hayashi K, Yandell DW. How sensitive is PCR-SSCP? Hum Mutat. 1993;2:338–46.

    Article  CAS  PubMed  Google Scholar 

  40. Hayashi K. PCR-SSCP: a method for detection of mutations. Genet Anal Tech Appl. 1992;3:73–9.

    Article  Google Scholar 

  41. Heath DD, Iwama GK, Devlin RH. PCR primed with the VNTR core sequences yields species specific patterns and hypervariable probes. Nucl Acids Res. 1993;21:5782–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Helentjaris T, Slocum M, Wright S, Schaefer A, Nienhuis J. Construction of genetic linkage maps in maize and tomato using restriction fragment length polymorphisms. Theor Appl Genet. 1986;72:761–9.

    Article  CAS  PubMed  Google Scholar 

  43. Hilu KW, Borsch T, Muller K, Soltis DE, Soltis PS, Savolainen V, Chase MW, Powell MP, Alice LA, Evans R, Sauquet H, Neinhuis C, Slotta TAB, Rohwer JG, Campbell CS, Chatrou LW. Angiosperm phylogeny based on matK sequence information. Am J Bot. 2003;90:1758–76.

    Article  CAS  PubMed  Google Scholar 

  44. Hu CY, Tsai YZ, Lin SF. Development of STS and CAPS markers for variety identification and genetic diversity analysis of tea germplasm in Taiwan. Bot Stud. 2014;55:12.

    Article  PubMed  PubMed Central  Google Scholar 

  45. Hu J, Quiros CF. Identification of broccoli and cauliflower cultivars with RAPD markers. Plant Cell Rep. 1991;10:505–11.

    Article  CAS  PubMed  Google Scholar 

  46. Hu J, Vick BA. Target region amplification polymorphism: a novel marker technique for plant genotyping. Plant Mol Biol Rep. 2003;21:289–94.

    Article  CAS  Google Scholar 

  47. Hu J. Defining the sunflower (Helianthus annuus L.) linkage group ends with the Arabidopsis-type telomere sequence repeat-derived markers. Chromosome Res. 2006;14:535–48.

    Article  CAS  PubMed  Google Scholar 

  48. Jaccoud D, Peng K, Feinstein D, Kilian A. Diversity arrays: a solid state technology for sequence information independent genotyping. Nucl Acids Res. 2001;29:25.

    Article  Google Scholar 

  49. Jeffreys AJ, Neumann R, Wilson V. Repeat unit sequence variation in minisatellites: a novel source of DNA polymorphism for studying variation and mutation by single molecule analysis. Cell. 1990;60:473–85.

    Article  CAS  PubMed  Google Scholar 

  50. Jeffreys AJ, Wilson V, Thein SL. Hypervariable “minisatellite” regions in human DNA. Nature. 1985;314:67–74.

    Article  CAS  PubMed  Google Scholar 

  51. Jenczewski E, Properi JM, Ronfort J. Differentiation between natural and cultivated populations of Medicago sativa (Legiminosae) from Spain: analysis with random amplified polymorphic DNA RAPD markers and comparison to allozymes. Mol Ecol. 1999;8:1317–30.

    Article  CAS  PubMed  Google Scholar 

  52. Joshi SP, Gupta VS, Aggarwal RK, Ranjekar PK, Brar DS. Genetic diversity and phylogenetic relationship as revealed by inter-simple sequence repeat (ISSR) polymorphism in the genus Oryza. Theor Appl Genet. 2000;100:1311–20.

    Article  CAS  Google Scholar 

  53. Julier C, Gouyon DD, Georges M, Guenet JL, Nakamura Y, Avner P, Lathrop GM. Minisatellite linkage maps in the mouse by cross-hybridization with human probes containing tandem repeats. Pro Natl Acad Sci USA. 1990;87:4585–9.

    Article  CAS  Google Scholar 

  54. Kendall J. Separations by the ionic migration method. Science. 1928;67:163–7.

    Article  CAS  PubMed  Google Scholar 

  55. Khaled AGA, Motawea MH, Said AA. Identification of ISSR and RAPD markers linked to yield traits in bread wheat under normal and drought conditions. Genet Eng Biotechnol. 2015;13:243–52.

    Article  Google Scholar 

  56. Kilian A, Huttner E, Wenzl P, Jaccoud D, Carling J, Caig V, Evers M, Heller-Uszynska K, Cayla C, Patarapuwadol S, Xia L, Yang S, Thomson B. The fast and the cheap: SNP and DArT-based whole genome profiling for crop improvement. In: Tuberosa R, Phillips RL, Gale M, editors. Proceedings of the international congress “In the wake of the double helix: from the green revolution to the gene revolution”, 27–31 May, 2003. Bologna: Avenue Media; 2005. p. 443–61.

    Google Scholar 

  57. Konieczny A, Ausubel FM. A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J. 1993;4:403–10.

    Article  CAS  PubMed  Google Scholar 

  58. Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970;227(5259):680–5.

    Article  CAS  PubMed  Google Scholar 

  59. Li G, Quiros CF. Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor Appl Genet. 2001;103:455–61.

    Article  CAS  Google Scholar 

  60. Litt M, Luty JA. A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet. 1989;44:397–401.

    CAS  PubMed  PubMed Central  Google Scholar 

  61. Liu Q, Wang H, Zhu L, Hu H, Sun Y. Genome-wide identification and analysis of miRNA-related single nucleotide polymorphisms (SNPs) in rice. Rice. 2013;6:10–20.

    Article  PubMed  PubMed Central  Google Scholar 

  62. Liu Y, Nie YD, Han FX, Zhao XN, Dun BQ, Lu M. et al. Allelic variation of a soluble acid invertase gene (SAI-1) and development of a functional marker in sweet sorghum [Sorghum bicolor (L.) Moench]. Mol Breed. 2014;33:721–30.

    Article  CAS  Google Scholar 

  63. Liu Z, Furnier GR. Comparison of allozyme, RFLP and RAPD markers for revealing genetic variation within and between trembling aspen and big tooth aspen. Theor Appl Genet. 1993;87:97–105.

    CAS  PubMed  Google Scholar 

  64. Lynch M, Walsh B. Genetics and analysis of quantitative traits. Sunderland, MA: Sinauer Associates; 1998.

    Google Scholar 

  65. Makino A, Sakashita H, Hidema J, Mae T, Ojima K, Osmond B. Distinctive responses of ribulose-1,5-bisphosphate carboxylase and carbonic anhydrase in wheat leaves to nitrogen nutrition and their possible relationships to CO2-transfer resistance. Plant Physiol. 1992;100:1737–43.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Mammadoy JA, Steffenson BJ, Saghai-Maroof MA. High resolution mapping of the barley leaf rust resistance gene Rph5 using barley expressed sequence tags (ESTs) and synteny with rice. Theor Appl Genet. 2005;111:1651–60.

    Article  CAS  Google Scholar 

  67. Manoj P, Banerjee NS, Ravichandran P. Development of sex-associated SCAR markers in Piper longum L. PGR Newsl. 2005;141:44–50.

    Google Scholar 

  68. Markert CL, Moller F. Multiple forms of enzymes, tissue, ontogenetic and species specific pattern. Pro Natl Acad Sci USA. 1959;45:753–63.

    Article  CAS  Google Scholar 

  69. McCouch SR, Kochert G, Yu ZH, Wang ZY, Khush GS, Coffman WR, et al. Molecular mapping of rice genomes. Theor Appl Genet. 1988;76:815–29.

    Article  CAS  PubMed  Google Scholar 

  70. McDermott JM, Brandle U, Dutly F, Haemmerli UA, Keller S, Muller KE, Wolf MS. Genetic variation in powdery mildew of barley: development of RAPD, SCAR and VNTR markers. Phytopathology. 1994;84:1316–21.

    Article  CAS  Google Scholar 

  71. Meyer W, Michell TG, Freedman EZ, Vilgalys R. Hybridization probes for conventional DNA fingerprinting used as single primers in polymerase chain reaction to distinguish strain of Cryptococcus neoformans. J Clin Microbiol. 1993;31:2274–80.

    CAS  PubMed  PubMed Central  Google Scholar 

  72. Michaels SD, Amasino RM. A robust method for detecting single nucleotide changes as polymorphic markers by PCR. Plant J. 1998;14:381–5.

    Article  CAS  PubMed  Google Scholar 

  73. Milewicz M, Sawicki J. Sex-linked markers in dioecious plants. Plant Omics J. 2013;6:144–9.

    Google Scholar 

  74. Ming R, Wang J, Moore PH, Paterson AH. Sex chromosomes in flowering plants. Am J Bot. 2007;94:141–56.

    Article  PubMed  Google Scholar 

  75. Mishra RK, Gangadhar BH, Nookaraju A, Kumar S, Park SW. Development of EST-derived SSR markers in pea (Pisum sativum) and their potential utility for genetic mapping and transferability. Plant Breed. 2012;131:118–24.

    Article  CAS  Google Scholar 

  76. Moore G, Lucas H, Batty N, Flavell R. A family of retrotransposons and associated genomic variation in wheat. Genomics. 1991;10:461–8.

    Article  CAS  PubMed  Google Scholar 

  77. Mullis KB, Ferre F, Gibbs RA. The polymerase chain reaction. Basel: Birkhauser; 1994.

    Book  Google Scholar 

  78. Murphy RW, Sites JW Jr, Buth DG, Haufler CH. Proteins: isozyme electrophoresis, in: Molecular systematics, 2nd ed. Hillis DM, Moritz C and Mable BK (eds.), Sinauer Associates, Sunderland, MA. 1996; pp. 51–120.

  79. Nakamura Y, Carison M, Krapcho K, Kanamori M, White R. New approach for isolation of VNTR markers. Am J Hum Genet. 1988;43(6):854–9.

    CAS  PubMed  PubMed Central  Google Scholar 

  80. Nanda S, Kar B, Nayak S, Jha S, Joshi RK. Development of an ISSR based STS marker for sex identification in pointed gourd (Trichosanthes dioica Roxb.). Sci Hort. 2013;150:11–5.

    Article  CAS  Google Scholar 

  81. Nickrent DL, Soltis DE. A comparison of angiosperm phylogenies from nuclear 18 s rDNA and rbcL sequences. Ann Miss Bot Gard. 1995;82:208–34.

    Article  Google Scholar 

  82. Nithin C, Patwa N, Thomas A, Bahadur RP, Basak J. Computational prediction of miRNAs and their targets in Phaseolus vulgaris using simple sequence repeat signatures. BMC Plant Biol. 2015;15:140.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  83. Olsen M, Hood L, Cantor C, Botstein D. A common language for physical mapping of the human genome. Science. 1989;245:1434–5.

    Article  Google Scholar 

  84. Orita M, Iwahana H, Kanazawa H, Hayashi K, Sekiya T. Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc Natl Acad Sci USA. 1989;86:2766–70.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Paran I, Michelmore RW. Development of reliable PCR-based markers linked to downy mildew resistance genes in lettuce. Theor Appl Genet. 1993;85:985–93.

    Article  CAS  PubMed  Google Scholar 

  86. Powell W, Morgante M, Andre C, Hanafey M, Vogel J, et al. The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed. 1996;2:225–38.

    Article  CAS  Google Scholar 

  87. Ramkumar G, Sivaranjani AKP, Pandey MK, Sakthivel K, Rani NS, Sudarshan I, et al. Development of a PCR-based SNP marker system for effective selection of kernel length and kernel elongation in rice. Mol Breed. 2010;26:735–40.

    Article  Google Scholar 

  88. Reddy PM, Sarla N, Siddiq EA. Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding. Euphytica. 2002;128:9–17.

    Article  Google Scholar 

  89. Réjon CR, Jamilena M, Ramos MG, Parker JS, Rejon MR. Cytogenetic and molecular analysis of the multiple sex-chromosome system of Rumex acetosa. Heredity. 1994;72:209–15.

    Article  Google Scholar 

  90. Roy SK, Gangopadhyay G, Ghose K, Dey S, Basu D, Mukherjee KK. A cDNA-AFLP approach to look for differentially expressed gene fragments in dioecious pointed gourd (Trichosanthes dioica Roxb.) for understanding sex expression. Curr Sci. 2008;94:381–5.

    CAS  Google Scholar 

  91. Russell J, Booth A, Fuller J, Harrower B, Hedley P. A comparison of sequence-based polymorphism and haplotype content in transcribed and anonymous regions of the barley genome. Genome. 2004;47:389–98.

    Article  CAS  PubMed  Google Scholar 

  92. Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, et al. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science. 1988;239:487–91.

    Article  CAS  PubMed  Google Scholar 

  93. Savolainen V, Chase MW, Hoot SB, Morton CM, Soltis DE, Bayer C, Fay MF, De Bruijn AY, Sullivan S, Qiu YL. Phylogenetics of flowering plants based on combined analysis of plastid atpB and rbcL gene sequences. Syst Biol. 2000;49:306–62.

    Article  CAS  PubMed  Google Scholar 

  94. Sax K. The association of size differences with seed-coat pattern and pigmentation in Phaseolus vulgaris. Genetics. 1923;8:552–60.

    CAS  PubMed  PubMed Central  Google Scholar 

  95. See D, Kanazin V, Talbert H, Blake TK. Electrophoretic detection of single nucleotide polymorphisms. Biotechniques. 2000;28:710–6.

    CAS  PubMed  Google Scholar 

  96. Soller M. Beckmann JS Genetic polymorphism in varietal identification and genetic improvement. Theor Appl Genet. 1983;67:25–33.

    Article  CAS  PubMed  Google Scholar 

  97. Soltis DE. Soltis PS Phylogenetic relationships in Saxifragaceae sensu lato: a comparison of topologies based on 18S rDNA and rbcL sequences. Am J Bot. 1997;84:504–22.

    Article  CAS  PubMed  Google Scholar 

  98. Soltis DE, Soltis PS, Cleggy MT, Durbin M. Sequence divergence and phylogenetic-relationships in Saxifragaceae sensu lato. Proc Natl Acad Sci USA. 1990;87:4640–4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Song QJ, Marek LF, Shoemaker RC. A new integrated genetic linkage map of the soybean. Theor Appl Genet. 2004;109:122–8.

    Article  CAS  PubMed  Google Scholar 

  100. Sturtevant AH. The linear arrangement of six sex-linked factors in Drosophila, as shown by their mode of association. J Exp Zool. 1913;14:43–59.

    Article  Google Scholar 

  101. Tanksley SD, McCouch SR. Seed banks and molecular maps: unlocking genetic potential from the wild. Science. 1997;277:1063–6.

    Article  CAS  PubMed  Google Scholar 

  102. Tanksley SD. Molecular markers in plant breeding. Plant Mol Biol Rep. 1983;1:3–8.

    Article  CAS  Google Scholar 

  103. Tautz D, Trice M, Dover GA. Cryptic simplicity in DNA is a major source of genetic variation. Nature. 1986;322:652–6.

    Article  CAS  PubMed  Google Scholar 

  104. Thomas MR, Scott NS. Microsatellite repeats in grapevine reveal DNA polymorphisms when analysed as sequence-tagged sites (STSs). Theor Appl Genet. 1993;86:985–90.

    Article  CAS  PubMed  Google Scholar 

  105. Torado A, Koike M, Mochida K, Ogihara Y. SSR-based linkage map with new markers using an intraspecific population of common wheat. Theor Appl Genet. 2006;112:1042–51.

    Article  CAS  Google Scholar 

  106. Varshney RK, Marcel TC, Ramsay L, Russell J, Roder MS, et al. A high density barley microsatellite consensus map with 775 SSR loci. Theor Appl Genet. 2007;114:1091–113.

    Article  CAS  PubMed  Google Scholar 

  107. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kulper M, Zabeau M. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 1995;23(21):4407–14.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Wang D, Li Y, Li Z. Identification of a male-specific amplified fragment length polymorphism (AFLP) and a sequence characterized amplified region (SCAR) marker in Eucommia ulmoides Oliv. Int J Mol Sci. 2011;12:857–64.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  109. Weiland JJ, Yu MH. A cleaved amplified polymorphic sequence (CAPS) marker associated with root-knot nematode resistance in sugarbeet. Crop Sci. 2003;43:1814–8.

    Article  CAS  Google Scholar 

  110. Weising K, Nybom H, Wolff K, Kahl G. DNA fingerprinting in plants: principles, methods, and applications. 2nd ed. Boca Raton: CRC Press, Taylor & Francis Group; 2005.

    Book  Google Scholar 

  111. Weising K, Nybom H, Wolff K, Meyer W. DNA fingerprinting in plants and fungi. Boca Rato: CRC Press; 1995.

    Google Scholar 

  112. Welsh J, McClelland M. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 1990;18:7213–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Wenzl P, Carling J, Kurna D, Jaccound D, Huttner E, Kleinhofs A, Kilian A. Diversity arrays technology (Dart) for whole genome profiling of barley. Proc Natl Acad Sci USA. 2004;101(26):9915–20.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Williams NMV, Pande N, Nair S, Mohan M, Bennett J. Restriction fragment length polymorphism analysis of polymerase chain reaction products amplified from mapped loci of rice (Oryza sativa L.) genomic DNA. Theor Appl Genet. 1990;82:489–98.

    Article  Google Scholar 

  115. Winberg BC, Zhou Z, Dallas JF, McIntyre CL, Gustafson JP. Characterization of minisatellite sequences from Oryza sativa. Genome. 1993;36:978–83.

    Article  CAS  PubMed  Google Scholar 

  116. Winter P, Kahl G. Molecular marker technologies for plant improvement. World J Microbiol Biotechnol. 1995;11:438–48.

    Article  CAS  PubMed  Google Scholar 

  117. Wolff K, Zietkiewicz E, Hofstra H. Identification of chrysanthemum cultivars and stability of fingerprint patterns. Theor Appl Genet. 1995;91:439–47.

    Article  CAS  PubMed  Google Scholar 

  118. Wong Z, Wilson V, Jeffreys AJ, Thein SL. Cloning a selected fragment from a human DNA “fingerprint”: isolation of an extremely polymorphic minisatellite. Nucleic Acids Res. 1986;14:4605–16.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Wu KS, Jones R, Danneberger L, Scolnik A. Detection of microsatellite polymorphisms without cloning. Nucleic Acids Res. 1994;22:3257–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Zabeau M, Vos P. Selective restriction fragment amplification: a general method for DNA fingerprinting. European Patent Office. Publication 0534858 A1 Bulletin. 1993; 93(13).

  121. Zhou L, Chen Z, Lang X, Du B, Liu K, Yang G, et al. Development and validation of a PCR-based functional marker system for the brown planthopper resistance gene Bph14 in rice. Breed Sci. 2013;63:347–52.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Zietkiewicz E, Rafalski A, Labuda D. Genome fingerprinting by simple sequence repeat (SSR) anchored polymerase chain reaction amplification. Genomics. 1994;20:176–83.

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

S. Saha and P. Ghosh thankfully acknowledge University Grants Commission, New Delhi for the award of Postdoctoral Fellowship and Emeritus Fellowship, respectively.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Parthadeb Ghosh.

Additional information

figure a

In Honour of Prof AK Sharma, the Founder and Editor-in-Chief of the Nucleus

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Adhikari, S., Saha, S., Biswas, A. et al. Application of molecular markers in plant genome analysis: a review. Nucleus 60, 283–297 (2017). https://doi.org/10.1007/s13237-017-0214-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13237-017-0214-7

Keywords

Navigation