PENANDA DNA UNTUK ANALISIS GENETIK TANAMAN

. Zulfahmi

doi:10.24014/ja.v3i2.87

PENANDA DNA UNTUK ANALISIS GENETIK TANAMAN

. Zulfahmi

Abstract

Genetic diversity is an important aspect for plant to adapt on environment changes. Information on genetic diversity at individual, species and population levels are required for a basic consideration to formulate strategy conservation and breeding program and utilizing of genetic resources. In the last few decades, the development of DNA based molecular markers techniques has been a significant increase and its are routinely being used in ecological, evolutionary, taxonomical, phylogenetic, population genetic, identification studies of plant sciences. These DNA based markers are distinguished in two types, first non PCR based techniques such as RFLP (Restriction Fragment Length Polymorphism) and second is PCR based techniques such as RAPD (Random Amplified Polymorphic DNA), SSR (Simple Sequence Repeats) and AFLP (Amplified Fragment Length Polymorphism), Cleaved Amplified Polymorphic Sequences (CAPS), Sequence Characterized Amplified Region (SCAR), Single-Strand Conformation Polymorphism (SSCP) and DNA barcoding. These techniques are well established and their advantages as well as limitations have been realized. The review details account of techniques used in identification of markers and their applicability in plant sciences.

Keywords

DNA Markers; Plant Genetics; Assessment Diversity; Polymerace Chain Reaction (PCR)

Full Text:

PDF

References

Agarwal M, Shrivastava N, Padh H. 2008. Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep, 27: 617–631. DOI 10.1007/s00299-008-0507-z

Balding D. 1999. Forensic applications of microsatellite markers, in: Golstein, DB. and Schlötterer, C. (Eds.). Microsatellite: evolution and applications. Oxford University Press. pp. 198-210.

Botstein, D., R. White, M. Skolnick and R.W. Davis. 1980. Construction of genetic linkage map in human, using restriction fragment length polymorphism. American Journal of Human Genetics 32:314-331.

Brubaker CL, Wendel JF (1994) Reevaluating the origin of domesticated cotton (Gossypium hirsutum; Malvaceae) using nuclear restriction fragment length polymorphisms (RFLPs). Amer J Bot, 81: 1309–1326

Chase, M. W., R. S. Cowan, P. M. Hollingsworth, C. Van Den Berg, S. Madrin’an, G. Petersen, O. Seberg, T. Jorsensen, K.M. Cameron, M. Carine, N. Pedersen, T. A. J. Hedderson, F. Conrad, G. A. Salazar, J. E. Richardson, M. L. Hollingsworth, T. G. Barraclough, L. Kelly, and M. Wilkinson. 2007. A proposal for a standardised protocol to barcode all land plants. Taxon 56: 295–299.

Chen L, Ren F, Zhong H, Jiang W, and Li X. 2010. Identification and expression analysis of genes in response to high -salinity and drought stresses in Brassica napus. Acta Biochim Biophys Sin : 154–164

Cheng, K.T., H.C. Chang, C.H. Su, and F.L. Hsu. 1997. Identification of dried rhizomes of Coptis species using random amplified polymorphic DNA. Bot. Bull. Acad. Sin. 38: 241-244Dubreuil P, Dufour P, Krejci E, Causse M, De Vienne D, Gallais A, Charcosset A (1996) Organization of RFLP diversity among inbred lines of maize representing the most significant heterotic groups. Crop Science, 36:790–799

Consortium for the Barcoding of Life (CBoL) Plant Working Group. 2009. A DNA barcode for land plant. Proc. Natl.Acad. Sci. USA 106: 12794-12797.

Cuenca A, Escalante AE, Pinero D. 2003. Long distance colonization, isolation by distance and historical demography in a relictual Mexican Pinyon Pine (Pinus nelsoii Shaw) as revealed by paternally inherited genetic markers (cpSSRs). Mol. Ecol. 12: 2087-2097.

Eisen JA. 1999. Mechanistic basis for microsatellite instability, in: Golstein, D. B. and Schlötterer, C. (Eds.). Microsatellite: evolution and applications. Oxford University Press. pp. 34-48.

Ellegren, H. 2004. Microsatellites: simple sequences with complex evolution. Nature Reviews, 5: 435-445

Estoup A, Jarne P, Cornent JM. 2002. Homoplasy and mutation model at microsatellite loci and their consequnces for population genetic analysis. Mol. Ecol. 11: 1591-1604.

Gachon C, Mingam A, dan Charrier B. 2004. Real-time PCR: what relevance to plant studies? Journal of Experimental Botany, 55(402): 1445-1454. DOI: 10.1093/jxb/erh181.

Ginot Frederic, Bordelais I, Nguyen S, Gyapay G. 1996. Correction of some genotyping errors in automated fluorescent microsatellite analysis by enzymatic removal of obe base overhangs. Nucleid Acids Res, 24(3): 540-541.

Gonzalez MA, Baraloto C, Engel J, Mori SA, Pe´ tronelli P, Rie´ ra B, Roger A, The´baud C, Chave J. 2009. Identification of Amazonian Trees with DNA Barcodes. PLoS ONE 4 (10): e7483. doi:10.1371/journal.pone.0007483

Hancock JM. 1999. Microsatellite and other simple sequences: genomic context and mutational mechanism, in: Golstein, D. B. and Schlötterer, C. (Eds.). Microsatellite: evolution and applications. Oxford University Press. pp. 1-9.

Jones CJ, Edwards KJ, Castaglione S, Winfield MO, Sala F, Wiel C van de, Bredemeijer G, Vosman B, Matthes M, Daly A, Brettschneider R, Bettini P, Buiatti M, Maestri E, Malcevschi A, Marmiroli N, Aert R, Volckaert G, Rudea J, Linacero R, Vazquez A, Karp A. 1997. Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories. Mol Breed 3: 381–390

Karsinah, Sudarsono, L. Setyobudi, dan H. Aswidinnoor. 2002. Keragaman Genetik Plasma Nutfah Jeruk Berdasarkan Analisis Penanda RAPD. Jurnal Bioteknologi Pertanian. 7(1) : 8-16.

Kress WJ, Erickson DL, Swenson NG, Thompson J, Uriarte Maria, Zimmerman JK.2010. Advances in the Use of DNA Barcodes to Build a Community Phylogeny for Tropical Trees in a Puerto Rican Forest Dynamics Plot. PLoS ONE 5(11): e15409. doi:10.1371/journal.pone.0015409

Kress, W. J., and D. L. Erickson. 2008b. DNA barcoding: Genes, genomics, and bioinformatics. Proc. Natl. Acad. Sci. USA 105: 2761–2762.

.Kress WJ and Erickson DL. 2008a. DNA Barcoding—a Windfall for Tropical Biology? Biotropica, 40(4): 405–408 DOI: 10.1111/j.1744-7429.2008.00426.x

Kress, W. J., and D. L. Erickson. 2007. A two-locus global DNA barcode for land plants: The coding rbcL gene complements the noncoding trnH-psbA spacer region. PLoS ONE 2: e508. doi:10.1371/journal.pone.0000508.

Kress, W. J., K. J.Wurdack, E. A. Zimmer, L. A. Weigt, and D. H. Janzen. 2005. Use of DNA barcodes to identify flowering plants. Proc. Natl. Acad. Sci. USA 102: 8369–8374.

Lahaye, R., M. Van Der Bank, D. Bogarin, J. Warner, F. Pupulin, G. Gigot, O. Maurin, S. Duthoit, T. G. Barraclough, and V. Savolainen. 2008. DNA barcoding the floras of biodiversity hotspots. Proc. Natl. Acad. Sci. USA 105: www.pnas.org_cgi_doi_10.1073_pnas.0709936105

Li A. dan Ge S. 2006. Genetic variation and conservation of Changnienia amoena, an endangered orchid endemic to China. Pl. Syst. Evol, 258: 251–260. DOI 10.1007/s00606-006-0410-4

Li YC, Korol AB, Fahima T, Beiles A, Nevo E. 2002. microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Mol. Ecol. 11: 2453-2465.

Lynch M, Milligan BG. 1994. Analysis of population genetic structure with RAPD markers. Mol. Ecol, 3, 91–99.

Mahdieh M, Mostajeran A, Horie T, and Katsuhara M. 2008. Drought Stress Alters Water Relations and Expression of PIP-Type Aquaporin Genes in Nicotiana tabacum Plants. Plant Cell Physiol. 49(5): 801–813. doi:10.1093/pcp/pcn054

Medri C, Ruas EA., Ruas CF, Medri PS, Medri ME, and Ruas P.M. 2011. Population genetic structure of the tropical tree species Aegiphila sellowiana (Lamiaceae). Genet. Mol. Res. 10 (4): 3186-3198.

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

Mondini L, Noorani A and. Pagnotta M. A. 2009. Assessing Plant Genetic Diversity by Molecular Tools. Diversity, 1, 19-35; doi:10.3390/d1010019

Moxon, E.R and Wills, C. 1999. DNA Microsatellites: agents of evolution? Scientific American, 280 (1): 94-99

Mullis KB, Faloona F (1987) Specific synthesis of DNA in vitro via polymerase chain reaction. Methods Enzymol, 155: 350–355

Navascues M, Emerson B.C. 2005. Chloroplast microsatellites: measures of genetic diversity and the effect of homoplasy. Mol. Ecol, 14: 1333 – 1341.

Newton CR, and Graham A. 1994. PCR: Basic Principles and Methods. EngBios Scientific Publisher, Oxford.

Nicot N, Hausman JF, Hoffmann L and Evers D. 2005. Housekeeping gene selection for real-time RT-PCR normalization in potato during biotic and abiotic stress. Journal of Experimental Botany, 56 (421): 2907–2914,doi:10.1093/jxb/eri285

Oliveira, E D, Padua J P, Zucchi M. I, Vencovsky R, Vieira M L C. 2006. Origin, evolution and genome distribution of microsatellites. Genetic and Molecular Biology, 29(2): 294-307.

Palai, S. K. and G. R. Rout. 2007. Identification and genetic variation among eight varieties of ginger by using random amplified polymorphism DNA markers. Plant Biotechnology, 24: 417-420.

Pagnotta, M.A.; Mondini, L.; Porceddu, E. Real-time PCR and IRAP: tools for assessing genetic variability and quantitation of WIS 2-1A and BARE-1 retrotransposons in hulled wheat. Mol. Gen. Genom. 2009, doi: 10.1007/s00438-009-0462-6

Patel RK, and Jain M. 2011. PlantRGS: AWeb Server for the Identification of Most Suitable Candidate Reference Genes for Quantitative Gene Expression Studies in Plants. DNA Research 18, 463–470. doi:10.1093/dnares/dsr032

Pereira F, Carneiro J, dan Amorin A. 2008. Identification of species with DNA based technology: current progress and challenges. Recent Patents on DNA & Gene Sequences, 2: 187-200

Provan J, Powell W, Hollingsworth PM. 2001. Choloroplast microsatellites : new tools for studies in plant ecology and evolution. TREE. 16 (3) : 142 - 147.

Powell W, Morgante M, McDevitt R, Vendramin GG, Rafalski JA. 1995. Polymorphic simple sequence repeat regions in chloroplast genomes: application to the population genetics of pines. Proc. Natl. acad. Sci.USA, 92: 7759-7763.

Powell W, Machray GC, Provan J. 1996. Polymorphism revealed by simple sequence repeats. Tren in Plant Science Reviews, 1(7):215 – 222.

Sass, C., D. P. Little, D. Wm. Stevenson, and C. D. Specht. 2007. DNA barcoding in the Cycadales: Testing the potential of proposed barcoding markers for species identification of cycads. PLoS ONE 2: e1154. doi:10.1371/journal.pone.0001154

Schlötterer, C. 2000. Evolutionary dynamics of microsatellite DNA. Chromosoma, 109: 365-371.

Schlötterer, C. 1998. Genome evolution: Are microsatellites really simple sequences?. Current Biology, 8(4):132-134.

Schlötterer, C and Tautz D. 1992. Slippage synthesis of simple sequence DNA. Nucleic Acids Res, 20(2): 211-215.

Sondur SN, Manshardt RM, dan Stiles JI. 1996. A genetic linkage map of papaya based on randomly amplified polymorphic DNA markers. Theor Appl Genet, 93: 547-553

Taberlet P, Coissac E, Pompanon F, Gielly L, Miquel C, Valentini A, Vermat T, Corthier G, Brochmann C dan Willerslev E. 2007. Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Res, 35(3): e14.doi:10.1093/nar/gkl938

Taberlet P., E. Coissac, F. Pompanon, L. Gielly, C. Miquel, A. Valentini, T. Vermat, G. Corthier, C. Brochmann, and E.Willerslev. 2006. Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Res, e1–8 doi:10.1093/nar/gkl938.

Te-chato, S., M. Lim., and M. Masahiro. 2005. Comparison of cultivar identification methods of longkong, langsat dan duku: Lansium spp. Songklanakarin J.Sci. Technol, 27(30): 465-471.

Tenover FC. 2007. Rapid Detection and Identification of Bacterial Pathogens Using Novel Molecular Technologies: Infection Control and Beyond. Medical Microbiology, 44: 418-423

Tomlinson JA, Barker I, and Boonham N. 2007. Faster, Simpler, More-Specific Methods for Improved Molecular Detection of Phytophthora ramorum in the Field. Applied and Environmental Microbiology, 73(12): 4040–4047. doi:10.1128/AEM.00161-07

Valentini A, C. Miquel and P. Taberlet. 2010. DNA Barcoding for Honey Biodiversity. Diversity, 2: 610-617; doi:10.3390/d2040610

Vos, P., Hogers, R., Bleeker, M., Reijans, M., Vandelee, T., Hornes, M., Frijters, A., Pot, J., Peleman, J., Kuiper, M., and Zabeau, M. 1995. AFLP: a new technique for DNA fingerprinting. Nucl. Acids. Res, 23: 4407-4414.

Weising K, Nybom H,Wolff K, Kahl G. 2005. DNA Fingerprinting in Plants: Principles, Methods, and Applications. Second Edition. Taylor & Francis Group. Boca Raton,

William, J.G. K., Kubelik, A. R., Livak, K. J., Rafalski, J. A., and Tingey, S. V. 1990. DNA Polymorphism Amplified by arbitrary Primers are useful as genetic marker. Nucl. Acids Res. 18:6531-6535.

Xu WF and Shi WM. 2006. Expression Profiling of the 14-3-3 Gene Family in Response to Salt Stress and Potassium and Iron Deficiencies in Young Tomato (Solanum lycopersicum) Roots: Analysis by Real-time RT–PCR. Annals of Botany, 98: 965–974, doi:10.1093/aob/mcl189

DOI: http://dx.doi.org/10.24014/ja.v3i2.87