Fingerprinting and Gene Cloning

  • B. D. Singh
  • A. K. Singh


In the past two decades, molecular markers have revolutionized plant breeding activities. The DNA markers are being used for fingerprinting of crop genotypes to enable their highly precise and reliable identification. Molecular marker profiles are useful in the assessment of genetic purity seed lots of varieties and hybrids and for the determination of the crop produce purity. Molecular markers based on chloroplast/mitochondrial genome allow reliable identification of cytoplasmic male sterile lines from their maintainer lines. Furthermore, close linkage of DNA markers with genes can be exploited for positional cloning of these genes. The positional cloning procedure does not require any more information about the target gene than the distinct and readily identifiable phenotype it produces; this property is used to carry out fine mapping to identify a pair of flanking markers closely linked to this gene. The genomic region carrying the target gene is further reduced through strategies of chromosome walking, chromosome jumping, and chromosome landing. The short candidate genomic region is analyzed to identify the candidate genes and then to confirm the findings using a strategy like genetic transformation. This approach has been used for cloning of several agronomically important genes/QTLs (quantitative trait loci) in species like rice, maize, wheat, Arabidopsis, etc. The present chapter is devoted to the discussion of various aspects relevant for DNA fingerprinting of crop genotypes and those for positional cloning of genes and QTLs.


Amplify Fragment Length Polymorphism Simple Sequence Repeat Marker Amplify Fragment Length Polymorphism Marker Intellectual Property Right Maintainer Line 
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  1. Anand D, Prabhu KV, Singh AK (2012) Analysis of molecular diversity and of commercially grown Indian rice hybrids. J Plant Biochem Biotechnol 21:173–179CrossRefGoogle Scholar
  2. Arens P, Mansilla C, Deinum D et al (2010) Development and evaluation of robust molecular markers linked to disease resistance in tomato for distinctness, uniformity and stability testing. Theor Appl Genet 120:655–664PubMedCentralPubMedCrossRefGoogle Scholar
  3. Bernardo R, Kahler AL (2001) North American study on essential derivation in maize: inbreds developed without and with selection from F2 populations. Theor Appl Genet 102:986–992CrossRefGoogle Scholar
  4. Bortiri E, Jackson D, Hake S (2006) Advances in maize genomics: the emergence of positional cloning. Curr Opin Biol 9:1–8CrossRefGoogle Scholar
  5. Button P (2006) New developments in the International Union for the Protection of new varieties of plants. Acta Hortic 714:195–210Google Scholar
  6. Gresshoff PM (2005) Positional cloning of plant developmental genes. In: Meksem K, Kahl G (eds) The handbook of plant genome mapping. Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, pp 233–256CrossRefGoogle Scholar
  7. Hirosawa M, Ishikawa K, Nagase T et al (2000) Detection of spurious interruptions of protein-coding regions in cloned cDNA sequences by GeneMark analysis. Genome Res 10:1333–1341PubMedCrossRefGoogle Scholar
  8. Jeffreys AJ, Wilson V, Thein SL (1985) Hypervariable ‘minisatellite’ regions in human DNA. Nature 314:67–73PubMedCrossRefGoogle Scholar
  9. Komori T, Ohta S, Murai N et al (2004) Map-based cloning of a fertility restorer gene, Rf-1, in rice (Oryza sativa L). Plant J 37:315–325PubMedCrossRefGoogle Scholar
  10. Kuroshu RM, Watanabe J, Sugano S et al (2010) Cost-effective sequencing of full-length cDNA clones powered by a de novo-reference hybrid assembly. PLoS ONE 5:e10517. doi: 10.1371/journal.pone.0010517 PubMedCentralPubMedCrossRefGoogle Scholar
  11. Law JR, Donini P, Koebner RMD et al (1998) DNA profiling and plant variety registration. III: the statistical assessment of distinctness in wheat using amplified fragment length polymorphisms. Euphytica 102:335–342CrossRefGoogle Scholar
  12. Meyer K, Benning G, Grill E (1996) Cloning plant genes based on genetic map location. In: Paterson AH (ed) Genome mapping in plants. R.G. Landes Co., Austin, pp 137–154Google Scholar
  13. Rajendrakumar P, Biswal AK, Balachandran SM et al (2007) A mitochondrial repeat specific marker for distinguishing wild abortive type cytoplasmic male sterile rice lines from their cognate isogenic maintainer lines. Crop Sci 47:207–211CrossRefGoogle Scholar
  14. Sang X, Yang Z, Zhong B et al (2006) Assessment of purity of rice CMS lines using cpDNA marker. Euphytica 152:177–183CrossRefGoogle Scholar
  15. Singh AK, Rana MK, Singh S et al (2014a) CAAT box-derived polymorphism (CBDP): a novel promoter-targeted molecular marker for plants. J Plant Biochem Biotechnol 23:175–183CrossRefGoogle Scholar
  16. Singh VK, Singh AK, Kayastha AM et al (2014b) Bioinformatics for legume genomics research. In: Gupta S, Nadarajan N, Gupta DS (eds) Legumes in the omics era. Springer Science+Business Media, NY, pp 249–275CrossRefGoogle Scholar
  17. Smith S, Helentjaris T (1996) DNA fingerprinting and plant variety protection. In: Paterson AH (ed) Genome mapping in plants. RG Landes Co, Austin, pp 95–110Google Scholar
  18. Tanksley SD, Ganal MW, Martin GB (1995) Chromosome landing: a paradigm for map-based gene cloning in plants with large genomes. TIG 11:63–63PubMedCrossRefGoogle Scholar
  19. Yan L, Loukoianov A, Tranquilli G et al (2003) Positional cloning of the wheat vernalization gene VRN1. Proc Natl Acad Sci USA 100:6263–6268PubMedCentralPubMedCrossRefGoogle Scholar
  20. Yano M (2001) Genetic and molecular dissection of naturally occurring variation. Curr Opin Plant Biol 4:130–135PubMedCrossRefGoogle Scholar
  21. Yashitola J, Sundaram RM, Biradar SK et al (2004) A sequence specific PCR marker for distinguishing rice lines on the basis of wild abortive cytoplasm from their cognate maintainer lines. Crop Sci 44:920–924CrossRefGoogle Scholar

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© Author(s) 2015

Authors and Affiliations

  • B. D. Singh
    • 1
  • A. K. Singh
    • 2
  1. 1.School of BiotechnologyBanaras Hindu UniversityVaranasiIndia
  2. 2.Division of GeneticsIndian Agricultural Research InstituteNew DelhiIndia

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