Skip to main content
Log in

Molecular markers: It’s application in crop improvement

  • Review Article
  • Published:
Journal of Crop Science and Biotechnology Aims and scope Submit manuscript

Abstract

Over the past few decades, plant genomics research has been studied extensively bringing about a revolution in the field of plant biotechnology. Molecular markers, useful for plant genome analysis, have now become an important tool in crop improvement. The development and use of molecular markers for the detection and exploitation of DNA polymorphism is one of the most significant developments in the field of molecular genetics. The presence of various types of molecular markers, and differences in their principles, methodologies and applications require careful consideration in choosing one or more of such methods. No molecular markers are available yet that fulfill all requirements needed by researchers. In this article we attempt to review most of the available DNA markers that can be routinely employed in various aspects of plant genome analysis such as characterization of genetic variability, genome fingerprinting, genome mapping, gene localization, analysis of genome evolution, population genetics, taxonomy, plant breeding, and diagnostics. The emerging patterns make up a unique feature of the analyzed individual and are currently considered to be the ultimate tool for biological individualization.

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

  • Akagi H, Yokozeki Y, Inagaki A, Nakamura A, Fujimura T. 1996. A codominant DNA marker closely linked to the rice nuclear restorer gene, Rf-1, identified with inter-SSR finger printing. Genome 39: 1205–1209

    Article  CAS  PubMed  Google Scholar 

  • Akopyanz N, Bukanov NO, Westblom TU, Berg DE. 1992. PCR-based RFLP analysis of DNA sequence diversity in the gastric pathogen Helicobacter pylori. Nucleic Acid Res. 20: 6221–6225

    Article  CAS  PubMed  Google Scholar 

  • Avise JC. 1994. Molecular Markers, Natural History and Evolution, Chapman and Hall

  • Blair MW, Panaud O, McCouch SR. 1999. Inter-simple sequence repeats (ISSR) amplification for analysis of microsatellite motif frequency and fingerprinting in rice (Oryza sativa L.). Theor. Appl. Genet. 98: 780–792

    Article  CAS  Google Scholar 

  • Botstein D, White RL, Skolnick M, Davis RW. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32: 314 331

    PubMed  Google Scholar 

  • Brown SM, Kresovich S. 1996. In AH Paterson, ed, Genome Mapping in Plants Clandes, New York, pp. 85–93

  • Caetano-Anolles G, Bassam BJ, Gresshoff PM. 1991. DNA amplification fingerprinting using very short arbitrary oligonucleotide primers. Biotechnol. 9: 553–557

    Article  CAS  Google Scholar 

  • Chaparoo J, Werner D, O’Malley D, Sederoff R. 1992. Targeted mapping and linkage analysis in peach. Plant Genome 21: 9–11

    Google Scholar 

  • D’Ovidio R, Anderson OD. 1994. PCR analysis to distinguish between allele of a member of multi-gene family correlated with wheat bread making quality. Theor. Appl. Genet. 88: 759–763

    Article  Google Scholar 

  • Desplanque B, Boudry P, Broomberg K, Saumitou-Laprade P, Cuguen J, van Dijk H. 1999. Genetic diversity and gene flow between wild, cultivated and weedy forms of Beta vulgaris L. (Chenopodiaceae), assessed by RFLP and microsatellite markers. Theor. Appl. Genet. 98: 1194–1201

    Article  CAS  Google Scholar 

  • Di Stilio VS, Kesseli RV, Mulcahy DL. 1998. A pseudoautosomal random amplified polymorphic DNA marker for the sex chromosomes of Silene dioica. Genetics 149: 2057–2062

    PubMed  Google Scholar 

  • Ellis THN, Poyser SJ, Knox MR, Vershinin AV, Ambrose MJ. 1998. Ty1-copia class retrotransposon insertion site polymorphism for linkage and diversity analysis in pea. Mol. Gen. Genet. 260: 9–91

    CAS  PubMed  Google Scholar 

  • Flavell RB. 1995. Plant biotechnology R & D — the next ten years. Tibtech. 13: 313–319

    CAS  Google Scholar 

  • Freudenreich CH, Stavenhagen JB, Zakian VA. 1997. Stability of a CTG:CAG trinucleotide repeat in yeast is dependent on its orientation in the Genome. Mol. Cell Biol. 4: 2090–2098

    Google Scholar 

  • Fukuchi A, Kikuchi F, Hirochika H. 1993. DNA fingerprinting of cultivated rice with rice retrotransposon probes. Jpn. J. Genet. 68: 195–20

    Article  CAS  Google Scholar 

  • Feuillet C, Messmer M, Schachermayr G, Keller B. 1995. Genetic and physical characterization of LR 1 leaf rust resistance locus in wheat (Triticum aestivum). Mol. Gen. Genet. 248: 553–562

    Article  CAS  PubMed  Google Scholar 

  • Gale MD, Devos KM. 1998. Comparative Genetics in the Grasses. Proc. Natl. Acad. Sci. USA 95: 1971–1974

    Article  CAS  PubMed  Google Scholar 

  • Gardiner JM, Coe EH, Melia-Hancock S, Hoisington DA, Chao S. 1993. Map in maize using an immortalized F2 population. Genetics 134: 917–930

    CAS  PubMed  Google Scholar 

  • Gill KS, Lubbers EL, Gill BS, Raupp WJ, Cox TS. 1991. A genetic linkage map of Triticum tauschii (DD) and its relationship to the D genome of bread wheat (AABBDD). Genome 34: 362–374

    Google Scholar 

  • Gu WK, Weeden NF, Yu J, Wallace DH. 1995. Large-scale, cost effective screening of PCR products in marker-assisted selection applications. Theor. Appl. Genet. 91: 465–470

    Article  CAS  Google Scholar 

  • Guo PG, Bai GH, Shaner GE. 2003. AFLP and STS tagging of a major QTL for Fusarium head blight resistance in wheat. Theor. Appl. Genet. 106: 1011–1017

    CAS  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  • Jarne P, Lagoda PJL. 1996. Microsatellites, from molecules to populations and back. Trends Ecol. Evol. 11: 424–429

    Article  Google Scholar 

  • Jeffreys AJ, Wilson V, Thein SL. 1985. Hypervariable “minisatellite” regions in human DNA. Nature 314: 67–73

    Article  CAS  PubMed  Google Scholar 

  • Jongeneel CV. 2000. Searching the expressed sequence tag (EST) databases: Panning for genes. Brief. Bioinformatics 1: 76–92

    Article  CAS  PubMed  Google Scholar 

  • Joshi SP, Gupta VS, Aggarwal RK, Ranjekar PK, Brar DS. 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

    Article  CAS  Google Scholar 

  • Kantety RV, Rota ML, Matthews DE, Sorrells ME. 2002. Data mining for simple-sequence repeats in expressed sequence tags from barley, maize, rice, sorghum, and wheat. Plant Mol. Biol. 48: 501–510

    Article  CAS  PubMed  Google Scholar 

  • Konieczny A, Ausubel FM. 1993. A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J. 4: 403–410

    Article  CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Martin B, Nienhuis J, King G, Schaefer A. 1989. Restriction fragment length polymorphisms associated with water-use efficiency in tomato. Science 243: 1725–1728

    Article  CAS  PubMed  Google Scholar 

  • Mason-Gamer RJ, Weil CF, Kellogg EA. 1998. Granule-bound starch synthase: structure, function, and phylogenetic utility. Mol. Biol. Evol. 15: 1658–1673

    CAS  PubMed  Google Scholar 

  • Matsuoka Y, Mitchell SE, Kresovich S, Goodman M, Doebley J. 2002. Microsatellites in Zea-variability, patterns of mutations, and use for evolutionary studies. Theor. Appl. Genet. 104: 436–450

    Article  CAS  PubMed  Google Scholar 

  • McCouch SR, Kochert G, Yu ZH, Wang ZY, Khush GS, Coffma, WR, Tanksley SD. 1988. Molecular mapping of rice chromosomes. Theor. Appl. Genet. 76: 815–829

    Article  CAS  Google Scholar 

  • Meyer W, Mitchell TG, Freedman EZ, Vilgalys R. 1993. Hybridization probes for conventional DNA fingerprinting used as single primers in the polymerase chain reaction to distinguish strains of Cryptococcus neoformans. J. Clin. Microbiol. 31: 2274–2280

    CAS  PubMed  Google Scholar 

  • Miller JC, Tanksley SD. 1990. RFLP analysis of phylogenetic relationships and genetic variation in the genus Lycopersicon. Theor. Appl. Genet. 80: 437–448

    CAS  Google Scholar 

  • Morgante M, Vogel J. 1994. Compound microsatellite primers for the detection of genetic polymorphisms. US patent application no. 08/326456

  • Morgante M, Hanafey H, Powell W. 2002. Microsatellites are preferentially associated with nonrepetitive DNA in plant Genome. Nat. Genet. 30: 194–200

    Article  CAS  PubMed  Google Scholar 

  • Morjane H, Geistlinger J, Harrabi M, Weising K, Kahl G. 1994. Oligonucleotide fingerprinting detects genetic diversity among Ascochyta rabiei isolates from a single chickpea field in Tunesia. Curr. Genet. 26: 191–197

    Article  CAS  PubMed  Google Scholar 

  • Naik S, Gill KS, Prakasa Rao VS, Gupta VS, Tamhankar SA, Pujar S, Gill BS, Ranjekar PK. 1998. Identification of an STS marker linked to the Aegilops speltoides derived leaf rust resistance gene Lr28 in wheat. Theor. Appl. Genet. 97: 535–554

    Article  CAS  Google Scholar 

  • Nakamura Y, Leppert M, O’Connell P, Wolff R, Holm T, Culver M, Martin C, Fujimoto E, Hoff M, Kumlin E, White R. 1987. Variable number tandem repeat (VNTR) markers for human gene mapping. Science 235: 1616–1622

    Article  CAS  PubMed  Google Scholar 

  • Nam HG, Giraudat J, Den Boer B, Moonan F, Loos WDB, Hauge BM, Goodman HM. 1989. Restriction Fragment Length Polymorphism linkage map of Arabidopsis thaliana. Plant Cell 1: 699–705

    Article  CAS  PubMed  Google Scholar 

  • Niewohner J, Salamini F, Gebhardt C. 1995. Development of PCR assay diagnostic for RFLP markers closely linked to allele GROI and HI conferring resistance to root cyst nematode Globodera rostochinensis potato. Mol. Breed. 1: 65–78

    Article  Google Scholar 

  • Olsen M, Hood L, Cantor C, Botstein D. 1989. A common language for physical mapping of the human genome. Science 245: 1434–1435

    Article  Google Scholar 

  • Orita M, Suzuki Y, Sekiya T, Hayashi K. 1989. Rapid and sensitive detection of point mutations and DNA polymorphisms using polymerase chain reaction. Genomics 5: 874–879

    Article  CAS  PubMed  Google Scholar 

  • Pakniyat H, Powell W, Baird E, Handley LL, Robinson D, Scrimgeour EM, Nevo E, Hackett C A, Caligari PDS, Forster BP. 1997. AFLP variation in wild barley (Hordeum spontaneum C. Koch) with reference to salt tolerance and associated ecogeography. Genome 40: 332–341

    Article  CAS  PubMed  Google Scholar 

  • Paran I, Michelmore RW. 1993. Development of reliable PCR-based markers linked to downy mildew resistance genes in lettuce. Theor. Appl. Genet. 85: 985–993

    Article  CAS  Google Scholar 

  • Paran I, Kesseli R, Michelmore R. 1991. Identification of RFLP and RAPD markers linked to downy mildew resistance gene in tomato using near isogenic lines. Genome 34: 1021–1027

    CAS  PubMed  Google Scholar 

  • Pease AC, Solas D, Sullivan EJ, Cronin MT, Holmes CP, Fodor SP. 1994. Light generated oligonucleotide arrays for rapid DNA sequence analysis. Proc. Natl. Acad. Sci. USA 91: 5022–5026

    Article  CAS  PubMed  Google Scholar 

  • Powell W, Morgante WM, McDevitt R, Vendramin GG, Rafalski JA. 1995. Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of pines. Proc. Natl. Acad. Sci. USA 92: 7759–7763

    Article  CAS  PubMed  Google Scholar 

  • Ramakrishna W, Chowdari KV, Lagu MD, Gupta VS, Ranjekar PK. 1995. DNA fingerprinting to detect genetic variation in rice using hypervariable DNA sequences. Theor. Appl. Genet. 90: 1000–1006

    Article  CAS  Google Scholar 

  • Ratnaparkhe MB, Santra DK, Tullu A, Muehlbauer FJ. 1998. Inheritance of intersimple sequence repeat polymorphisms and linkage with a fusarium wilt resistance gene in chickpea. Theor. Appl. Genet. 96: 348–353

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  • Richardson T, Cato S, Ramser J, Kahl G, Weising K. 1995. Nucleic Acids Res. 23: 3798–3799

    Article  CAS  PubMed  Google Scholar 

  • Saal B, Wricke G. 2002. Clustering of amplified fragment length polymorphism markers in a linkage map of rye. Plant Breed. 121: 117–123

    Article  CAS  Google Scholar 

  • Sant VJ, Patankar AG, Gupta VS, Sarode ND, Mhase LB, Sainani MN, Deshmukh RB, Ranjekar PK. 1999. Potential of DNA markers in detecting divergence and analysis in heterosis in Indian elite chickpea cultivars. Theor. Appl. Genet. 98: 1217–1225

    Article  CAS  Google Scholar 

  • Sarfatti M, Katan J, Fluhr R, Zamir D. 1989. An RFLP marker in tomato linked to the Fusarium oxysporum resistance gene I2. Theor. Appl. Genet. 78: 755–759

    Article  CAS  Google Scholar 

  • Schachermayr G, Messmer MM, Feuillet C, Winzeler H, Keller B. 1995. Identification of molecular markers linked to the Agropyron elongatum-derived leaf rust resistance gene lr24 in wheat. Theor. Appl. Genet. 90: 982–990

    Article  CAS  Google Scholar 

  • Schlotterer C. 2004. The evolution of molecular markers-just a matter of fashion? Nat. Rev. Genet. 5: 63–69

    Article  CAS  PubMed  Google Scholar 

  • Sen A, Balyan HS, Sharma PC, Ramesh B, Kumar A, Roy JK, Varshney RK, Gupta PK. 1997. DNA amplification fingerprinting (DAF) as a new source of molecular markers in bread wheat. Wheat Inf. Serv. 85: 35–42

    Google Scholar 

  • Shattuck-Eidens D, Bell RN, Mitchell JT, McWorther VC. 1991. Rapid detection of maize DNA sequence variation. GATA 8: 240–245

    CAS  Google Scholar 

  • Slatkin M. 1987. Gene flow and population structure of natural populations. Science 263: 787–792

    Article  Google Scholar 

  • Sobrino B, Briona M, Carracedoa A. 2005. SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci. Int. 154: 181–194

    Article  CAS  PubMed  Google Scholar 

  • Somers DJ, Zhou Z, Bebeli P, Gustafson JP. 1996. Repetitive, genome-specific probes in wheat (Triticum aestivum L. em Thell) amplified with minisatellite core sequences. Theor. Appl. Genet. 93: 983–989

    Article  Google Scholar 

  • Tanksley SD, Ganal MW, Martin GB. 1995. Chromosome landing: A paradigm for map based gene cloning in plants with large genomes. Trends Genet. 11: 63–68

    Article  CAS  PubMed  Google Scholar 

  • Tost J, Gut IG. 2002. Genotyping single nucleotide polymorphisms by mass spectrometry. Mass Spectrom Rev. 21: 388–418

    Article  CAS  PubMed  Google Scholar 

  • Varshney RK, Graner A, Sorrells ME. 2005. Genic microsatellite markers in plants: features and applications. Trends Biotechnol. 23: 48–55

    Article  CAS  PubMed  Google Scholar 

  • Virk PS, Newbury HJ, Jackson MT, Ford-Loyd BV. 1997. In JA Callow, HJ Newbury, eds, Biotechnology and Plant Genetic Resources: Conservation and Use, pp 21–23

  • Vos P, Hogers R, Bleeker M, Reijans M, Van De Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M. 1995. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 23: 4407–4414

    Article  CAS  PubMed  Google Scholar 

  • Weising K, Nybom H, Wolff K, Meyer W 1995. DNA fingerprinting in plants and fungi. CRC Press, Boca Raton, Ann Arbor, London, Tokyo, 321 pp

    Google Scholar 

  • Welsh J, McClelland M. 1990. Fingerprinting Genomes using PCR with arbitrary primers. Nucleic Acids Res. 18: 7213–7218

    Article  CAS  PubMed  Google Scholar 

  • Williams JGK, Kublelik AR, Livak KJ, Rafalski JA, Tingey SV. 1990. DNA polymorphism’s amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18: 6531–6535

    Article  CAS  PubMed  Google Scholar 

  • Williams MNV, Pande N, Nair S, Mohan M, Bennett J. 1991. Restriction fragment polymorphism analysis of polymerase chain reaction product amplified from mapped loci of rice genomic DNA. Theor. Appl. Genet. 82: 489–498

    Article  CAS  Google Scholar 

  • Williamson VM, Ho J-Y, Wu FF, Miller N, Kaloshian I. 1994. A PCR-based marker tightly linked to the nematode resistance gene, Mi, in tomato. Theor. Appl. Genet. 87: 757–763

    Article  CAS  Google Scholar 

  • Winter P, Kahl G. 1995. Molecular marker technologies for plant improvement. World J. Microbiol. Biotechnol. 11: 438–448

    Article  CAS  Google Scholar 

  • Wu J, Krutovskii KV, Strauss SH. 1998. Abundant mitochondrial genome diversity, population differentiation, and convergent phenotypic evolution in pines. Genetics 150: 1605–1614

    CAS  PubMed  Google Scholar 

  • Xiao J, Li J, Grandillo S, Ahn SN, Yuan L, Tanksley SD, McCouch SR. 1998. Identification of trait-improving quantitative trait loci alleles from a wild rice relative, Oryzarufipogon. Genetics 150: 899–909

    CAS  PubMed  Google Scholar 

  • Yang GP, Saghai Maroof MA, Xu CG, Zhang Q, Biyashev RM. 1994. Comparative analysis of microsatellite DNA polymorphism in landraces and cultivars of rice. Mol. Gen. Genet. 245: 187–194

    Article  CAS  PubMed  Google Scholar 

  • Young ND, Menancio-Hautea D, Fatokun CA, Danesh D 1992. RFLP technology, crop improvement, and international agriculture. In G Thottappilly, LM Monti, DR Moham, AW Moore, eds, Biotechnology: Enhancing research on tropical crops in Africa. Technical Center for Agriculture and Rural Cooperation, International Institute of Tropical Agriculture, pp 221–230

  • Yu J, Hu, S, Wang J, Wong GKS, Li S, Liu B. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79–92

    Article  CAS  PubMed  Google Scholar 

  • Yu YG, Saghai Maroof MA, Buss GR, Maughan PJ, Tolin SA. 1994. RFLP and Microsatellite Mapping of a Gene for Soybean Mosaic Virus Resistance. Phytopathol. 84: 60–64

    Article  CAS  Google Scholar 

  • Zhao X, Kochert G. 1992. Characterisation and genetic mapping of short, highly repeated interspersed DNA sequence from rice (Oryzae sativa L). Mol. Gen. Genet. 2311: 353–359

    Article  Google Scholar 

  • Zietkiewicz E, Rafalski A, Labuda D. 1994. Genome fingerprinting by simple sequence repeats (SSR)-anchored PCR amplification. Genomics 20: 176–183

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Basanta Das Kumar.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kesawat, M.S., Das Kumar, B. Molecular markers: It’s application in crop improvement. J. Crop Sci. Biotechnol. 12, 169–181 (2009). https://doi.org/10.1007/s12892-009-0124-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12892-009-0124-6

Key words

Navigation