AJPS  Vol.3 No.12 A , December 2012
Review Article: ISTR, a Retrotransposons-Based Marker to Assess Plant Genome Variability with Special Emphasis in the Genera Zea and Agave
Abstract: A review is presented for give information and highlights the advantage of ISTR as molecular marker which with the genome changes after manipulation or breeding intervention can be detected.
Cite this paper: M. Torres-Morán, N. Almaraz-Abarca and M. Escoto-Delgadillo, "Review Article: ISTR, a Retrotransposons-Based Marker to Assess Plant Genome Variability with Special Emphasis in the Genera Zea and Agave," American Journal of Plant Sciences, Vol. 3 No. 12, 2012, pp. 1820-1826. doi: 10.4236/ajps.2012.312A223.

[1]   BSPB, “Plant Breeding. The Business and Science of Crop Improvement,” British Society of Plant Breeding, 2010.

[2]   P. Escribano, M. A. Viruel and J. I. Hormaza, “Establishment of a Core Collection to Optimise the Conservation of Cherimoya (Annona cherimola Mill.) Genetic Resources Using ssr Information,” Acta Horticulturae (ISHS), Vol. 814, 2009, pp. 67-70.

[3]   K. M. Evans, F. Fernández-Fernández and C. Govan, “Harmonising Fingerprinting Protocols to Allow Comparisons Between Germplasm Collections in Pyrus,” Acta Horticulturae (ISHS), Vol. 814, 2009, pp. 103-106.

[4]   C. Miguel and L. Marum, “An Epigenetic View of Plant Cells Cultured in Vitro: Somaclonal Variation and Beyond,” Journal of Experimental Botany, Vol. 62, No. 11, 2011, pp. 1-13. doi:10.1093/jbx/err155

[5]   W. Horn, “The Pattern of Evolution and Ornamental Plant Breeding,” Acta Horticulturae (ISHS), Vol. 651, 2004, pp. 19-31.

[6]   P. Capy, G. Gasperi, C. Biemont and C. Bazin, “Stress and Transposable Elements: Co-Evolution or Useful Parasites?” Heredity, Vol. 85, 2000, pp. 101-106. doi:10.1046/j.1365-2540.2000.00751.x

[7]   J. L. Bennetzen, R. Liu, J. Ma and A. Pontaroli, “Maize Genome Structure and Rearrangement,” Maydica, Vol. 50, 2005, pp. 387-392.

[8]   V. C. Sarilar, A. Ridel, M. Rousselet, M. Falque, J-C. Tetanneur, F. Eber, A-M. Chévre, P. Brabant and K. Alix, “What Is the Impact of Allopolyploidy on Transposable Elements? A structural Approach on Newly Synthesized Brassica napus Allotetraploids,” Acta Horticulturae (ISHS), Vol. 867, 2010, pp. 113-117.

[9]   O. Omwoyo, J. V. Omondi-Muoma and J. Machuka, “Agrobacterium-Mediated Genetic Transformation of Selected Tropical Inbred and Hybrid Maize (Zea mays L.) Lines,” Plant Cell Tissue and Organ Culture, 2012 (in press). doi:10.1007/s11240-012-0247-1

[10]   W. Xiao, X. Huang, Q. Gong, X. Dai, J. Zhao. Y. Wei, and X. Huang, “Somatic Hybrids Obtained by Asymmetric Protoplast Fusion Between Musa Silk cv. Guoshanxiang (AAB) and Musa acuminate cv. Mas (AA),” Plant Cell Tissue and Organ Culture, Vol. 97, 2009, pp. 313-321. doi:10.1007/s11240-009-9530-1

[11]   S. J. Ochatt, E. M. Patat-Ochatt and A. Moessner, “Ploidy Level Determination within the Context of in Vitro Breeding,” Plant Cell Tissue and Organ Culture, Vol. 104, 2011, pp. 329-341. doi:10.1007/s11240-011-9918-6

[12]   P. SanMiguel, A. Tikhonov, Y.-K. Jin, N. Motchoulskaia, D. Zakharov, A. Melake-Berhan, P. S. Springer, K. J. Edwards, M. Lee, Z. Avramova and J. L. Bennetzen, “Nested Retrotransposons in the Intergenic Regions of the Maize Genome,” Science, Vol. 274, No. 5288, 1996, pp. 765-768. doi:10.1126/science.274.5288.765

[13]   B. Young-An and Y. Kong, “Divergent Long-Terminal-Repeat Retrotransposon Families in the Genome of Paragonimus westermani,” Korean Journal of Parasitology, Vol. 41, No. 4, 2003. pp 221-223. doi:10.3347/kjp.2003.41.4.221

[14]   H. S. Malik and T. H. Eickbush, “Phylogenetic Analysis of Ribonuclease H Domains Suggests a Late, Chimeric Origin of LTR Retrotransposable Elements and Retroviruses,” Genome Research, Vol. 11, 2001, pp. 1187-1197. doi:10.1101/gr.185101

[15]   N. Friesen, A. Brandes and J. S. Heslop-Harrison, “Diversity, Origin, and Distribution of Retrotransposons (Gypsy and Copia) in Conifers,” Molecular Biology and Evolution, Vol. 18, No. 7, 2001, pp. 1176-1188. doi:10.1093/oxfordjournals.molbev.a003905

[16]   E. R. Havecker, X. Gao and D. F. Voytas, “The Diversity of LTR Retrotransposons,” Genome Biology, 2004, Vol. 5, p. 225. doi:10.1186/gb-2004-5-6-225

[17]   A. Kumar and J. L. Bennetzen, “Plant Retrotransposons,” Annual Review of Genetics, Vol. 33, 1999, pp. 479-532. doi:10.1146/annurev.genet.33.1.479

[18]   M. A. Grandbastien, “Activation of Plant Retrotransposons under Stress Conditions,” Trends in Plant Science, Vol. 3, No. 5, 1998 pp. 181-187. doi:10.1016/S1360-1385(98)01232-1

[19]   P. SanMiguel, C. Vitte, J. L. Bennetzen and S. Hake, “The LTR-Retrotransposons in Maize,” In: Handbook of Maize, Springer, New York, 2009, pp. 307-327.

[20]   P. Bernet and M. J. Asíns, “Identification and Genomic Distribution of Gypsy-like Rretrotransposons in Citrus and Poncirus,” Theoretical and Applied Genetics, Vol. 108, No. 1, 2003, pp. 121-130. doi:10.1007/s00122-003-1382-1

[21]   W. Rohde, “Inverse Sequence-Tagged Repeat (ISTR) Analysis, a Novel and Universal PCR-based Technique for Genome Analysis in the Plant and Animal Kingdom,” Journal of Genetics and Breeding, Vol. 50, No. 3, 1996, pp. 249-261.

[22]   A. K. Rodríguez-Ponce, J. Ron-Parra, and M. I. Torres-Morán, “Determinación Molecular de la Fidelidad Genética en dos Líneas de Maíz después de Ciclos de Autofecundación,” Revista Internacional de Contaminación Ambiental, Vol. 28, No. 2, 2012, p. 146.

[23]   Y. Matzuoka, S. E. Mitchell, S. Kresovich, M. Goodman and J. Doebley, “Microsatellites in Zea—Variability, Patterns of Mutations, and Use for Evolutionary Studies,” Theoretical and Applied Genetics, Vol. 104, No. 2-3, 2002, pp.436-450. doi:10.1007/s001220100694

[24]   M. I. Torres-Morán, N. Almaraz-Abarca, A. P. Velasco-Ramírez, V. Hernández-Vargas, G. Orea-Lara, A. Cifuentes-Díaz de León, and C. Oliver-Salvador, “Taxonomic Significance of ISTR to Discriminate Species in Agavaceae,” American Journal of Agricultural and Biological Sciences, Vol. 3, 2008, pp. 661-665. doi:10.3844/ajabssp.2008.661.665

[25]   J. Sambrook and D. W. Russell, “Molecular Cloning: A Laboratory Manual,” 3rd Edition, Cold Spring Harbor Laboratory Press, New York, Vol. I, 2001.

[26]   M. I. Torres-Morán, M. M. Morales-Rivera, L. De La Cruz-Larios and A. Villalobos , “Polymorphism Identification between Off-Shoots and Micropropagated Plants of Agave tequilana and Agave cocui Using ISTRs,” Scientia-CUCBA, Vol. 8, 2006, pp. 203-206.

[27]   M. I. Torres-Morán, M. Escoto-Delgadillo, S. Molina-Moret, D. M. Rivera-Rodríguez, A. P. Velasco-Ramírez, D. Infante and L.Portillo, “Assessment of Genetic Fidelity Among Agave tequilana Plants Propagated Asexually via Rhizomes versus in Vitro Culture,” Plant Cell Tissue and Organ Culture, Vol. 103, No. 3, 2010, pp. 403-409. doi:10.1007/s11240-010-9777-6

[28]   M. Díaz-Martínez, A. Nava-Cedillob, J. A. Guzmán-López, R. Escobar-Guzmán and J. Simpson, “Polymorphism and Methylation Patterns in Agave tequilana Weber var. ‘Azul’ Plants Propagated Asexually by Three Different Methods,” Plant Science, Vol. 185-186, 2012, pp. 321-330. doi:10.1016/j.plantsci.2012.01.004

[29]   A. Bousios, I. Saldana-Oyarzabal, A. Valenzuela-Zapata, C. Wood and S. R. Pearce, “Isolation and Characterization of Ty1-Copia Retrotransposon Sequences in the Blue Agave (Agave tequilana Weber var. azul) and Therir Development as SSAP Markers for Phylogenetics Analysis,” Plant Science, Vol. 172, No. 2, 2007, pp. 291-298. doi:10.1016/j.plantsci.2006.09.002

[30]   I. Khaliq, M. A. Khan and S. Pearce, “Ty1-Copia Retrotransposons are Heterogeneous, Extremely High Copy Number and are Major Players in the Genome Organization and Evolution of Agave tequilana,” Genetic Resources and Crop Evolution, Vol. 59, No. 4, 2012, pp. 575-587. doi:10.1007/s10722-011-9705-6

[31]   H. S. Gentry, “Agaves of Continental North America,” The University of Arizona Press, Tucson, 1982.

[32]   N. Almaraz-Abarca, A. Delgado-Alvarado, V. Hernández-Vargas, M. Ortega-Chávez, G. Orea-Lara, A. Cifuentes-Díaz de León, J. A. ávila-Reyes and R. Mu?iz-Martínez, “Profiling of Phenolic Compounds of Somatic and Reproductive Tissue of Agave durangensis Gentry (Agavaceae),” American Journal of Applied Science, Vol. 6, 2009, pp. 1076-1085. doi:10.3844/ajassp.2009.1076.1085

[33]   M. Nei, “Estimation of Average Heterozygosity and Genetic Distance from a Small Numer of Individuals,” Genetics, Vol. 89, No. 3, 1978, pp. 583-590.

[34]   J. W. Sites and J. C. Marshall, “Operational Criteria for Delimiting Species,” Annual Review of Ecology, Evolution, and Systematics, Vol. 35, 2004, pp. 199-227. doi:10.1146/annurev.ecolsys.35.112202.130128

[35]   E. R. Sensi, W. Vignani, W. Rohde and S. Bricolti, “Characterization of Genetic Biodiversity with Vitis vinífera L. Sangiovese and Colorino Genotypes by AFLP and ISTR, DNA Marker Technology,” Vitis, Vol. 35, 1996, pp. 183-188.

[36]   J. R. Demey, E. Gamez, S. Molina and D. Infante, “Comparative Study of the Discriminating Capacity of AFLP and ISTR Markers for Genetic Analysis of Agave fourcroydes,” Plant Molecular Biology Reporter, Vol. 22, No. 1, 2004, pp. 29-35. doi:10.1007/BF02773346

[37]   M. J. Alonso, R. Cueto, Y. Santos, W. Romero, R. Llauger and W. Rohde, “Morphological and Molecular Variability of one Population of Green Coconut Plant in the Baracoa Region,” Cultivos Tropicales, Vol. 28, 2007, pp. 69-75.

[38]   J. L. Hamrick, and M. J. W. Godt, “Allozyme Diversity in Plant Species,” In: H. D. Brown, M. T. Clegg, A. L. Kahler and B. S. Weir, Eds., Plant Population Genetics, Breeding, and Genetic Resource, Sinauer, Massachusetts, 1989, pp. 43-63.

[39]   P. Keim, W. Beavis, J. Schupp and R. Freestone, “Evaluation of Soybean RFLP Marker Diversity in Adapted Germplasm,” Theorical and Applied Genetics, Vol. 85, No. 2-3, pp. 205-212.

[40]   X. Guo and R. C. Elston, “Linkage Information Content of Polymorphic Genetic Markers,” Human Heredity, Vol. 49, No. 2, 1999, pp.112-118. doi:10.1159/000022855

[41]   D. V. Sehgal, V. R. Rajpal, S. N. Raina, T. Sasanuma and T. Sasakuma, “Assaying Polymorphism at DNA Level for Genetic Diversity Diagnostics of the Safflower (Carthamus tinctorius L.) World Germoplasm Resources,” Genetica, Vol. 135, No. 3, 2009, pp.457-470. doi:10.1007/s10709-008-9292-4

[42]   R. Highton, “Taxonomic Treatment of Genetically Differentiated Populations,” Herpetologica, Vol. 46, 1990, pp. 114-121.