Genotyping of Mapping Population

  • N. Manikanda Boopathi


The basic principle of plant breeding for genetic improvement of crop plants is mainly relied on selection of superior progenies from the available population based on the traits of interest (such as higher yield, improved nutritional quality, appropriate colour or fragrance preferred by the consumer). In general, such traits are not measured directly from the plants; instead, they are enumerated from some other markers or tags that are closely linked to the trait of interest. For example, rice yield is decided by higher number of productive tillers, number of grains/spikelet, etc.; other classical examples are traits such as pea seed size, colour and plant height, used by Mendel. Such tags which used to select the superior progenies from the heterogeneous mixture of population are called as markers. These markers are useful in an array of plant breeding and genetics studies including:


Polymerase Chain Reaction Polymerase Chain Reaction Product Amplify Fragment Length Polymorphism Cleave Amplify Polymorphic Sequence Cleave Amplify Polymorphic Sequence 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.


Literature Cited

  1. Bachem CWB, van der Hoeve RS, de Bruijn SM, Vreugdenhil D, Zabeau M, Visser RGF (1996) Visualisation of differential gene expression using a novel method of RNA fingerprinting based on AFLP: analysis of gene expression during potato tuber development. Plant J 9:745–753PubMedCrossRefGoogle Scholar
  2. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL et al (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3(10):e3376. doi: 10.1371/journal.pone.376 PubMedCrossRefGoogle Scholar
  3. 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 32:314–333PubMedGoogle Scholar
  4. Brody JR, Calhoun ES, Gallmeier E, Creavalle TD, Kern SE (2004) Ultra-fast high-resolution agarose electrophoresis of DNA and RNA using low-molarity conductive media. Biotechniques 37(4):598–602PubMedGoogle Scholar
  5. Caetano-Anollés G, Bassam BJDNA (1993) Amplification fingerprinting using arbitrary oligonucleotide primers. Appl Biochem Biotechnol 42:189–200PubMedCrossRefGoogle Scholar
  6. Chang RY, O’Donoughue LS, Bureau TE (2001) Inter-MITE polymorphisms (IMP): a high throughput transposon-based genome mapping and fingerprinting approach. Theor Appl Genet 102:773–781CrossRefGoogle Scholar
  7. Cronn RC, Adams KL (2003) Quantitative analysis of transcript accumulation from genes duplicated by polyploidy using cDNA-SSCP. Biotechniques 34:726–734PubMedGoogle Scholar
  8. Flavell AJ, Knox M, Pearce SR, Ellis THN (1998) Retrotransposon based insertion polymorphisms (RBIP) for high throughput marker analysis. Plant J 16:643–665PubMedCrossRefGoogle Scholar
  9. He DH, Lin ZX, Zhang XL, Nie YC, Guo XP, Zhang YX, 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  ×  Gossypium barbadense. Euphytica 153(1):181–197CrossRefGoogle Scholar
  10. Hu J, Vick BA (2003) Target region amplification polymorphism: a novel marker technique for plant genotyping. Plant Mol Biol Rep 21:289–294CrossRefGoogle Scholar
  11. Huang J, Sun M (1999) A modified AFLP with fluorescence labelled primers and automated DNA sequencer detection for efficient fingerprinting analysis in plants. Biotechnol Tech 14:277–278CrossRefGoogle Scholar
  12. Jordan SA, Humphries P (1994) Single nucleotide polymorphism in exon 2 of the BCP gene on 7q31-q35. Hum Mol Genet 3:1915PubMedCrossRefGoogle Scholar
  13. Kalendar R, Grob T, Regina M, Suoniemi A, Schulman A (1999) IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theor Appl Genet 98:704–711CrossRefGoogle Scholar
  14. Komori T, Nitta N (2005) Utilization of CAPS/dCAPS method to convert rice SNPs into PCR-based markers. Breed Sci 55:93–98CrossRefGoogle Scholar
  15. Li G, Quiros CF (2001) 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 103:455–546CrossRefGoogle Scholar
  16. Makino R, Yazyu H, Kishimoto Y, Sekiya T, Hayashi K (1992) F-SSCP: fluorescence-based polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP) analysis. PCR Methods Appl 2:10–13PubMedCrossRefGoogle Scholar
  17. McCallum CM, Comai L, Greene EA, Henikoff S (2000) Targeted screening for induced mutations. Nat Biotechnol 18:455–457PubMedCrossRefGoogle Scholar
  18. Michaels SD, Amasino RMA (1998) A robust method for detecting single nucleotide changes as polymorphic markers by PCR. Plant J 14:381–385PubMedCrossRefGoogle Scholar
  19. Mullis KB, Faloona F (1987) Specific synthesis of DNA in vitro via polymerase chain reaction. Methods Enzymol 155:350–355Google Scholar
  20. Orita M, Iwahana H, Kanazawa H, Hayashi K, Sekiya T (1989) Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphism. Proc Natl Acad Sci USA 86:2766–2770PubMedCrossRefGoogle Scholar
  21. Paran I, Michelmore RW (1993) Development of reliable PCR-based markers linked to downy mildew resistance genes in lettuce. Theor Appl Genet 85:985–999CrossRefGoogle Scholar
  22. Schuelke M (2000) An economic method for the fluorescent labelling of PCR fragments. Nat Biotechnol 18:233–234PubMedCrossRefGoogle Scholar
  23. Schwartz DC, Cantor CR (1984) Separation of yeast chromosome-sized DNAs by pulsed field gradient electrophoresis. Cell 37:67–75PubMedCrossRefGoogle Scholar
  24. Tanksley SD, McCouch SR (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277:1063–1066PubMedCrossRefGoogle Scholar
  25. Tautz D, Renz M (1984) Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res 12(10):4127–4138PubMedCrossRefGoogle Scholar
  26. van den Broeck D, Maes T, Sauer M, Zethof J, De Keukeleire P, D’Hauw M, Van Montagu M, Gerats T (1998) Transposon Display identifies individual transposable elements in high copy number lines. Plant J 13:121–129PubMedGoogle Scholar
  27. 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 23:4407–4414PubMedCrossRefGoogle Scholar
  28. Wang X, Zhiyuan F, Sanwen H, Peitian S, Yumei L, Limei Y, Mu Z, Dongyu Q (2000) An extended random primer amplified region (ERPAR) marker linked to a dominant male sterility gene in cabbage (Brassica oleracea var. capitata). Euphytica 112:267–273CrossRefGoogle Scholar
  29. Waugh R, McLean K, Flavell AJ, Pearce SR, Kumar A, Thomas WTB, Powell W (1997) Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (SSAP). Mol Gen Genet 253:687–694PubMedCrossRefGoogle Scholar
  30. Weining S, Langridge P (1991) Identification and mapping of polymorphisms in cereals based on the polymerase chain reaction. Theor Appl Genet 82:209–216CrossRefGoogle Scholar
  31. Weising K, Gardner RC (1999) A set of conserved PCR primers for the analysis of simple sequence repeat polymorphisms in chloroplast genomes of dicotyledonous angiosperms. Genome 42:9–11PubMedCrossRefGoogle Scholar
  32. Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18:7213–7218PubMedCrossRefGoogle Scholar
  33. Welsh J, Chada K, Dalal SS, Ralph D, Cheng R, McClelland M (1992) Arbitrarily primed PCR fingerprinting of RNA. Nucleic Acids Res 20:4965–4970PubMedCrossRefGoogle Scholar
  34. Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1991) DNA polymorphisms amplified by arbitrary primers are usefll as genetic markers. Nucleic Acids Res 18:6531–6535CrossRefGoogle Scholar
  35. Wu KS, Jones R, Danneberger L, Scolnik P (1994) Detection of microsatellite polymorphisms without cloning. Nucleic Acids Res 22:3257–3258PubMedCrossRefGoogle Scholar

Further Readings

  1. Agarwal M, Shrivastava N, Padh H (2008) Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep 27:617–631PubMedCrossRefGoogle Scholar
  2. Eathington SR et al (2007) Molecular markers in a commercial breeding program. Crop Sci 47(S3):S154–S163Google Scholar
  3. Jena KK, Mackill DJ (2008) Molecular markers and their use in marker assisted selection in rice. Crop Sci 48:1266–1277CrossRefGoogle Scholar
  4. Lorz H, Wenzel G (2005) Molecular marker systems in plant breeding and crop improvement, Biotechnology in agriculture and forestry 55. Springer, New YorkCrossRefGoogle Scholar
  5. Van Bueren L et al (2010) The role of molecular markers and marker assisted selection in breeding for organic agriculture. Euphytica 175:51–64CrossRefGoogle Scholar

Copyright information

© Springer India 2013

Authors and Affiliations

  1. 1.Plant Molecular Biology & BioinformaticsTamil Nadu Agricultural UniversityCoimbatoreIndia

Personalised recommendations