MOLECULAR CHARACTERIZATION OF BIODIVERSITY IN VEGETABLES - A REVIEW

Article Id: ARCC903 | Page : 193- 201
Citation :- MOLECULAR CHARACTERIZATION OF BIODIVERSITY IN VEGETABLES - A REVIEW.Agricultural Reviews.2011.(32):193- 201
Jaskanwal Singh, R.K. Dhall* and Parjeet Singh Aulakh dhallrk2007@rediffmail.com
Address : Department of Vegetable Crops, Punjab Agricultural University, Ludhiana - 141 004, India

Abstract

Diverse genetic resources are prerequisite for any crop improvement programme, aimed at high and stable yields. In this review, the diverse molecular techniques, based on PCR, non-PCR, restriction followed by PCR and single nucleotide polymorphism (SNP) used in assessing plant genetic diversity in vegetables are discussed. Molecular tools provide valuable data on diversity through their ability to detect variation at the DNA level. Differences in gene sequence can be directly observed and described, a degree of precision previously impossible to achieve. These techniques are well established and their advantages as well as limitations have been realized and described in this work along with their applications in assessing genetic diversity in vegetable crops viz. genetic base of germplasm, predicting agronomic behavior and phylogeny. Advanced marker techniques tend to amalgamate advantageous features of several basic techniques, in order to increase the sensitivity and resolution to detect genetic discontinuity and distinctiveness.

Keywords

Vegetables Biodiversity Molecular markers Genetic diversity.

References

  1. Anonymous (2010). In: National Horticulture Database. pp.1-5. National Horticulture Board, Ministry of Agriculture, Government of India.
  2. Archak S, Karihaloo J L and Jain A (2002) RAPD markers reveal narrowing genetic base of Indian tomato cultivars. Curr Sci 82 : 1139-1143.
  3. Atkas H, Abak K and Sensoy S (2009) Genetic diversity in some Turkish pepper (Capsicum annuum L.) genotypes revealed by AFLP analyses. African J Biotech 8 : 4378-4386.
  4. Bardakci F (2001) Random amplified polymorphic DNA (RAPD) markers. Turk J Biol 25 : 185-196.
  5. Behera T K, Gaikward A B, Singh A K and Staub J E (2008) Relative efficiency of DNA markers (RAPD, ISSR and AFLP) in detecting genetic diversity of bitter gourd (Momordica charantia L.). J Sci Food Agri 88: 733-737.
  6. Bell C J and Ecker J R (1994) Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. Genomics 19: 137-144.
  7. Beyermann B, Nürnberg P, Weihe A, Meixner M, Epplen J T and Bvrner T (1992) Fingerprinting plant genomes with oligo nucleotide probes specific for simple repetitive DNA sequences. Theor Appl Genet 83:691-694.
  8. Biswas M S, Hassan J and Hossain M M (2010) Assessment of genetic diversity in French bean (Phaseolus vulgaris L) based on RAPD marker. African J Biotech 9: 5073-5077.
  9. Blanca J, Canizares J, Roig C, Ziarsolo P, Nuez F, Pico B (2011) Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae). BMC Genom 12: 561-569.
  10. Bouck A and Vision T (2007) The molecular ecologist’s guide to expressed sequence tags. Mol Ecol 16 : 907-924.
  11. Caramante M, Rao R, Monti L M and Corrado G (2009) Discrimination of ‘San Marzano’ accessions: A comparison of minisatellite, CAPS and SSR markers in relation to morphological traits. Sci Hort 120: 560-564.
  12. Chen J, Wang H, Shen H, Chai M, Li J, Qi M and Yang W (2009) Genetic variation in tomato populations from four breeding programs revealed by single nucleotide polymorphism and simple sequence repeat markers. Scient Hort 122: 6-16.
  13. Cupic T, Tucak M, Popavic S, Bolaric S, Gryusic S and Lik V K (2009) Genetic diversity of pea genotypes assessed by pedigree, morphological and molecular data. J Food Agric Environ 7: 343-348.
  14. Demir K, Bakýr M, Sarýkamýþ G and Acunalp S (2010) Genetic diversity of eggplant (Solanum melongena) germplasm from Turkey assessed by SSR and RAPD markers. Gen Mol Res 9: 1568-1576.
  15. Helentjaris T, G King, M Slocum, C Siedestrang and S Wegman (1985) Restriction fragment polymorphisms as probes for plant diversity and their development as tools for applied plant breeding. Plant Mol Biol 5: 109-118.
  16. Hirschegger P, Jakse J, Trontelj P, Bohanec B (2010) Origins of Allium ampeloprasum horticultural groups and a molecular phylogeny of the section Allium (Allium: Alliaceae). Mol Phylogenet Evol 54: 488-497.
  17. Ipek M, Ipek A, Senalik D, Simon P W (2007) Characterization of an unusual cytoplasmic chimera detected in bolting garlic clones. J Amer Soc Hort Sci 132: 664-669.
  18. Jing Z, Tang Z, Zhang X, Luo T, Liu Q, Zhu S, Ye Z, Wang Y and Li Z (2011) Mature and origin as a marker of genetic diversity in early-mid broccoli (Brassica oleracea var.italica) based on SRAP analysis. African J Agri Res 6: 296-299.
  19. Jeong H J, Jo Y D, Park S and Kang B (2010) Identification of Capsicum species using SNP markers based on high resolution melting analysis. Genome 53: 1029-1040.
  20. Karp A, Seberg O and Buiatti M (1996) Molecular techniques in the assessment of botanical diversity. Ann Bot 78: 143-149.
  21. Karp A, Kresovich S, Bhat K V, Ayand W G and Hodgkin T (1997). Molecular tools in plant genetic resources conservation: a guide to the technologies. IPGRI Technical Bulletin No. 2, International Plant Genetic Resources Institute, Rome, Italy. Available at http:// 198.93.227.125/publicat/ techbull/TB2.pdf.
  22. Karp A, Issar P G, Ingram D S (eds.) 1998 Molecular tools for screening biodiversity. Chapman & Hall, London.
  23. Lampasona S G, Martinez L and Burba J L (2003) Genetic diversity among selected Argentinean garlic clones (Allium sativum L.) using AFLP (Amplified Fragment Length Polymorphism). Euphytica 132: 115-119.
  24. Lu X, Liu L, Gong Y, Zhao L, Song X and Zhu X (2009) Cultivar identification and genetic diversity analysis of broccoli and its related species with RAPD and ISSR markers. Sci Hort 122: 645-648.
  25. Martin-Sanz A, Caminero C, Jing R, Flavell A J and Vega M P (2011) Genetic diversity among Spanish pea (Pisum sativum L.) landraces, pea cultivars and the World Pisum sp. core collection assessed by retrotransposon-based insertion polymorphisms (RBIPs). Spanish J Agri Res 9: 166-178.
  26. Mondini L, Noorani A and Pagnotta M A (2009) Assessing plant genetic diversity by molecular tools. Diversity 1: 19-35.
  27. Mu S, Gu X, Zhang S,Wang X and Wang Y (2009) Genetic Diversity of Cucumber (Cucumis sativus L.) Germplasm by SSR. Acta Hort Sin 12: 134-141.
  28. Oumouloud A, Arnedo-Andres M S, Torres R G and Alvarez J M (2009) Morphological and molecular characterization of melon accessions resistant to Fusarium wilts. Euphytica 169: 69-79.
  29. Ovesna J, Kucera L, Kralova J, Leisova L, Stavelikova H and Velisek J (2007) Genetic diversity among garlic clonas as revealed by AFLP, phenotypic descriptors and S-amino acid levels. Veg Crop Res 66: 105-116.
  30. Renner S S, Schaefer H and Kocyan A (2007) Phylogenetics of Cucumis (Cucurbitaceae): Cucumber (C. sativus) belongs in an Asian/Australian clade far from melon (C. melo). BMC Evol Bio 7: 58-68.
  31. Richard I and Beckman J S (1995) How neutral are synonymous codon mutations? Nat Genet 10: 259-267.
  32. Tang M, He W, Hu J, Wang K, Chen P, Mou W and Yang L (2010) Genetic Diversity of Potato (Solanum tuberosum L.) in Sichuan Province. Southwest China J Agri Sci. 18: 204-211.
  33. Saiki R, Gelfand D H, Stoffel S, Scharf S J, Higuchi R, Horn G T, Mullis K B and Erlich H A (1988) Prime-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239: 487-491.
  34. Schlotterer C and Tautz D (1992) Slippage synthesis of simple sequence DNA. Nucleic Acids Res 20: 2211-2215.
  35. Singh A K, Singh M, Singh R, Kumar S and Kalloo G (2005) Genetic diversity within the genus Solanum (Solanaceae) as revealed by RAPD markers. Curr Sci 90: 711-716.
  36. Sobrino B, Briona M and Carracedoa A (2005) SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci Int 154: 181-194.
  37. Sonnante G, Stockton T, Nodari R O, Becerra Velasquez V L and Gepts P (1994) Evolution of genetic diversity during the domestication of common-bean (Phaseolus vulgaris L.) Theor Appl Genet 89: 629-635.
  38. Southern EM (1975) Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biotech 98: 503-517.
  39. Spooner D, Treuren R and de Vicente M C (2005) Molecular Markers for Genebank Management. pp. 126. Bioversity International Rome, Italy, 2005.
  40. Staub J E, Lopez-Sese A I and Fanourakis N (2004) Diversity among melon landraces (Cucumis melo L.) from Greece and their genetic relationships with other melon germplasm of diverse origins. Euphytica 136: 151-166.
  41. Staub J E, Serquen F C and Gupta M (1996) Genetic markers, map construction, and their application in plant breeding. Hort Sci 31: 729-741.
  42. Sunyaev S, Hanke J, Aydin A, Wirkner U, Zastrow I, Reich J and Bork P (1999) Prediction of nonsynonymous single nucleotide polymorphisms in human disease-associated genes. J Mol Med 77: 754-760.
  43. Vos P, Hogers R, Bleeker M, Reijans M, Van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M and Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research 23: 4407-4414.
  44. Williams J G K, Kubelik K J, Livak K J, Rafalski J A and Tingey S V (1990) DNA polymorphisms amplified by arbitrary primers are useful genetic markers. Nucleic Acids Research 18: 6531-6535.
  45. Yi S S, Akashi Y, Tanaka K, Cho T T, Khaing M T, Yoshino H, Nishida H, Yamamoto T, Win K and Kato K (2009) Molecular analysis of genetic diversity in melon landraces (Cucumis melo L.) from Myanmar and their relationship with melon germplasm from East and South Asia. Genet Resour Crop Evol 56: 1149-1161.
  46. Zabeau M and Vos P (1993) Selective restriction fragment amplification: a general method for DNA fingerprinting. EPO Patent No. 0534858A1.
  47. Zong X, Ford R, Redden R R, Guan J and Wang S (2009) Identification and analysis of genetic diversity structure with in Pisum genus based on microsatellite markers. Agric Sci China 8: 521-529.

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