Tarımsal Biyoteknolojide Mobil Genetik Elementlerin Moleküler Markör Olarak Kullanılması

Year 2017, , 302 - 310, 31.10.2017

Arzu Koçak Behcet İnal

https://doi.org/10.19159/tutad.310507

Abstract

Moleküler markör tekniklerinin temeli, melezleme
veya polimeraz zincir reaksiyonuna (PZR) dayanır. Farklı stratejilerin bir
kombinasyonu olarak yeni ve ileri teknikler geliştirilmiştir; örneğin cDNA’lar,
spesifik dizilerin enzim kesimi veya kullanımı, ifade edilmiş dizi etiketleri
(EST’ler), mikrosatellitler, retrotranspozonlar olarak sıralanabilir. Retrotranspozonlar
bir tür (Sınıf I) transpoze olabilen (genomda farklı yerlere entegre olabilen)
elementlerdir. Transpozon elementleri (TE) bitkilerde fiziksel olarak genomun
önemli bir kısmını oluştururlar. Retrotranspozonlar aynı zamanda, amplifikasyon
mekanizmaları ve dizilim karakteristikleri nedeniyle moleküler markör
teknikleri geliştirmek için de oldukça ideal genetik elementlerdir. Bunlardan
bazıları; Retrotranspozon-Arası Çoğaltılmış Polimorfizm, Retrotranspozon-Mikrosatellit
Çoğaltılmış Polimorfizm, Primer Bağlanma Yeri Arası Çoğaltım, Dizilim-Spesifik
Çoğaltım Polimorfizmi, Retrotranspozon Temelli İnsertion Polimorfizmi,
SINE-Arası Çoğaltılan Polimorfizm, RAPD-Retrotranspozon Çoğaltılan Polimorfizm,
Ters Dizilim Etiketli Tekrarlar, MITE-Arası Polimorfizm ve Transpoze Olabilen
Gösterim bulunmaktadır. Bu metotlar farklı tarımsal ıslah amaçları için yaygın bir
şekilde kullanılmaktadır. Bunlardan bazıları genetik çeşitliliğin, genetik
bağlantının belirlenmesi, genom haritalaması, DNA parmak izi analizi,
filogenetik, somaklonal varyasyon çalışmaları, transgenik araştırmaları,
gelişim biyolojisi ve mutagenesis çalışmalarında kullanılmaktadır. Bu çalışmada,
farklı retrotranspozon-temelli markör tiplerinin tarımsal biyoteknolojide genel
kullanım alanlarından ve potansiyel uygulamalarından bahsedilecektir.

Keywords

biyo markör, bitki, biyoteknoloji, Transpozon, ıslah

The Use of Mobile Genetic Elements as Molecular Marker in Agricultural Biotechnology

Abstract

The basis of molecular marker techniques are based on hybridization or Polymerase Chain Reaction (PCR). New
and improved techniques have been developed as a combination of different strategies such as; cDNAs, enzyme digestion or
the utilization of specific sequences; e.g. expressed sequence tags, microsatellites, and retrotransposons. Retrotransposons
are a class (Class I) of transposable elements. Transposon elements physically form an important part of the genome in
plants. Retrotransposons are also an ideal target for developing molecular marker techniques because of their amplification
mechanism and sequence characteristics. Some of these are; Inter-Retrotransposon Amplified Polymorphism,
Retrotransposon-Microsatellite Amplified Polymorphism, Inter Primer Binding Site Amplification, Sequence-Specific
Amplification Polymorphism, Retrotransposon Based Insertion Polymorphism, Inter Sine Amplified Polymorphism, RAPDRetrotransposon
Amplified Polymorphism, Inverse Sequence Tagged Repeats, Inter-MITE Polymorphism and Transposable
display. These methods are used widely for different breeding purposes. Some of those are used in determination of genetic
diversity, genetic linkage, genome mapping, DNA fingerprint analysis, phylogenetics, somaclonal variation studies,
transgenic research, developmental biology, and mutagenesis studies. In this article, the common uses and potential
applications of different retrotransposon-based marker types in agricultural biotechnology will be discussed.

Keywords

Transposon, biomarker, plant, biotechnology, breeding

References

• Aalami, A., Safiyar, S., Mandoulakani, B.A., 2012. R-RAP: A retrotransposon-based DNA fingerprinting technique in plants. Plant Omics, 5(4): 359-364.
• Aga, E., Bryngelsson, T., 2006. Inverse sequence-tagged repeat (ISTR) analysis of genetic variability in forest coffee (Coffea arabica L.) from Ethiopia. Genetic Resources and Crop Evolution, 53(4): 721-728.
• Badge, R.M., Alisch, R.S., Moran, J.V., 2003. ATLAS: A system to selectively identify human-specific L1 insertions. The American Journal of Human Genetics, 72(4): 823-838.
• Bennetzen, J.L., 2000. Transposable element contributions to plant gene and genome evolution. Plant Molecular Biology, 42(1): 251-269.
• Branco, C.J., Vieira, E.A., Malone, G., Kopp, M.M., Malone, E., Bernardes, A., Mistura, C.C., Carvalho, F.I.F., Oliveira, C.A., 2007. IRAP and REMAP assessments of genetic similarity in rice. Journal of Applied Genetics, 48(2): 107-113.
• Buzdin, A., Ustyugova, S., Khodosevich, K., Mamedov, I., Lebedev, Y., Hunsmann, G., Sverdlov, E., 2003. Human-specific subfamilies of HERV-K (HML-2) long terminal repeats: three master genes were active simultaneously during branching of hominoid lineages. Genomics, 81(2): 149-156.
• Carvalho, A., Henrique Guedes-Pinto, H., Lima-Brito, J.E., 2012. Genetic diversity in old Portuguese durum wheat cultivars assessed by retrotransposon-based markers. Plant Molecular Biology Reporter, 30(3): 578-589.
• Chang, R.Y., O‟Donoughue, L.S., Bureau, T.E., 2001. Inter-MITE polymorphisms (IMP): a high throughput transposon-based genome mapping and fingerprinting approach. Theoretical and Applied Genetics, 102(5): 773-781.
• Chu, C.G., Tan, C.T., Yu, G.T., Zhong, S., Xu, S.S., Yan, L., 2011. A novel retrotransposon inserted in the dominant Vrn-B1 allele confers spring growth habit in tetraploid wheat (Triticum turgidum L.). G3: Genes, Genomes, Genetics, 1(7): 637-645.
• Devos, K.M., Ma, J., Pontaroli, A.C., Pratt, L.H., Bennetzen, J.L., 2005. Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat. Proceedings of the National Academy of Sciences of the United States of America, 102(52): 19243-19248.
• Esnault, C., Maestre, J., Heidmann, T., 2000. Human LINE retrotransposons generate processed pseudogenes. Nature Genetics, 24(4): 363-367
• Ewing, A.D., Ballinger, T.J., Earl, D., Broad Institute Genome Sequencing and Analysis Program and Platform, Harris, C.C., Ding, L., Wilson, R.K., Haussler, D., 2013. Retrotransposition of gene transcripts leads to structural variation in mammalian genomes. Genome Biology, 14(3): R22.
• Feng, Q., Moran, J.V., Kazazian, H.H., Boeke, J.D., 1996. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell, 87(5): 905-916.
• Feschotte, C., Jiang, N., Wessler, S.R., 2002. Plant transposable elements: Where genetics meets genomics. Nature Reviews Genetics, 3(5): 329-341.
• Flavell, A.J., Knox, M.R., Pearce, S.R., Ellis, T.H.N., 1998. Retrotransposon-based insertion polymorphisms (RBIP) for high throughput marker analysis. The Plant Journal, 16(5): 643-650.
• Hamat-Mecbur, H., Yımaz, S., Temel, A., Şahin, K., Gözükırmızı, N., 2014. Effects of epirubicin on barley seedlings. Toxicology and Industrial Health, 30(1): 52-59.
• Hubby, J.L., Lewontin, R.C., 1966. A molecular approach to the study of genic heterozygosity in natural populations. I. the number of alleles at different loci in Drosophila pseudoobscura. Genetics, 54(2): 577-594.
• Iskow, R.C., McCabe, M.T., Mills, R.E., Torene, S., Pittard, W.S., Neuwald, A.F., Van Meir, E.G., Vertino, P.M., Devine, S.E., 2010. Natural mutagenesis of human genomes by endogenous retrotransposons. Cell, 141(7): 1253-1261.
• Kalendar, R., Antonius, K., Smykal, P., Schulman, A.H., 2010. iPBS: A universal method for DNA fingerprinting and retrotransposon isolation. Theoretical and Applied Genetics, 121(8): 1419-1430.
• Kalendar, R., Flavell, A.J., Ellis, T.H.N., Sjakste, T., Moisy, C., Schulman, A.H., 2011. Analysis of plant diversity with retrotransposon-based molecular markers. Heredity, 106(4): 520-530.
• Kalendar, R., Grob, T., Regina, M., Suoniemi, A., Schulman, A.H., 1999. IRAP and REMAP: Two new retrotransposon-based DNA fingerprinting techniques. Theoretical and Applied Genetics, 98(5): 704-711.
• Kalendar, R., Schulman, A.H., 2006. IRAP and REMAP for retrotransposon-based genotyping and fingerprinting. Nature Protocols, 1(5): 2478-2484.
• Kang, H.W., Kang, K.K., 2008. Genomic characterization of Oryza species-specific CACTA-like transposon element and its application for genomic fingerprinting of rice varieties. Molecular Breeding, 21(3): 283-292.
• Kejnovsky, E., Hobza, R., Cermak, T., Kubat, Z., Vyskot, B., 2009. The role of repetitive DNA in structure and evolution of sex chromosomes in plants. Heredity, 102(6): 533-541.
• Kumar, A., Bennetzen, J.L., 1999. Plant retrotransposons. Annual Reviews in Genetics, 33(1): 479-532.
• Kwon, S.J., Kim, D.H., Lim, M.H., Long, Y., Meng, J.L., Lim, K.B., Kim, J.A., Kim, J.S., Jin, M., Kim, H.I., Ahn, S.N., Wessler, S.R., Yang, T.J., Park, B.S., 2007. Terminal repeat retrotransposon in miniature (TRIM) as DNA markers in Brassica relatives. Molecular Genetics and Genomics, 278(4): 361-370.
• Kwon, S.J., Park, K.C., Kim, J.H., Lee, J.K., Kim, N.S., 2005. Rim 2/Hipa CACTA transposon display; A new genetic marker technique in Oryza species. BMC Genetics, 15(6): 1-13.
• Leigh, F., Kalendar, R., Lea, V., Lee, D., Donini, P., Schulman, A.H., 2003. Comparison of the utility of barley retrotransposon families for genetic analysis by molecular marker techniques. Molecular Genetics Genomics, 269(4): 464-474.
• Li, Y.C., Korol, A.B., Fahima, T., 2002. Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Molecular Ecology, 11(12): 2453-2465.
• Lopes, F.R., Jjingo, D., Da Silva, C.R., Andrade, A.C., Marraccini, P., Teixeira, J.B., Carazzolle, M.F., Pereira, G.A., Pereira, L.F., Vanzela, A.L., Wang, L., Jordan, I.K., Carareto, C.M., 2013. Transcriptional activity, chromosomal distribution and expression effects of transposable elements in Coffea genomes. Plos One, 8(11): e78931.
• Mamedov, I.Z., Arzumanyan, E.S., Amosova, A.L., Lebedev, Y.B., Sverdlov, E.D., 2005. Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach. Nucleic Acids Research, 33(2): e16.
• Manninen, O., Kalendar, R., Robinson, J., Schulman, A.H., 2000. Application of BARE-1 retrotransposon markers to the mapping of a major resistance gene for net blotch in barley. Molecular and General Genetics, 264(3): 325-334.
• Mathias, S.L., Scott, A.F., Kazazian, H.H., Boeke, J.D., Gabriel, A., 1991. Reverse transcriptase encoded by a human transposable element. Science, 254(5039): 1808-1810.
• Mazaheri, M., Kianian, P.M.A., Mergoum, M., Valentini, G.L., Seetan, R., Pirseyedi, S.M., Kumar, A., Gu, Y.Q., Stein, N., Kubaláková, M., Doležel, J., Denton, A.M., Kianian, S.F., 2014. Transposable element junctions in marker development and genomic characterization of barley. The Plant Genome, 7: 1-8.
• McKie, A.B., Iwamura, T., Leung, H.Y., Hollingsworth, M.A., Lemoine, N.R., 1997. Alu-polymerase chain reaction genomic fingerprinting technique identifies multiple genetic loci associated with pancreatic tumourigenesis. Genes, Chromosomes and Cancer, 18(1): 30-41.
• Menconi, G., Battaglia, G., Grossi, R., Pisanti, N., Marangoni, R., 2013. Mobilomics in Saccharomyces cerevisiae strains. BMC Bioinformatics, 14: 102.
• Nair, A.S., Teo, C.H., Trude, S., Pat, H.H., 2005. Genome classification of banana cultivars from South India using IRAP markers. Euphytica, 144(3): 285-290.
• Nasri, S., Mandoulakani, B.A., Darvishzadeh, R., Bernousi, I., 2013. Retrotransposon insertional polymorphism in Iranian bread wheat cultivars and breeding lines revealed by IRAP and REMAP markers. Biochemical Genetics, 51(11-12): 927-943.
• Ovchinnikov, I., Troxel, A.B., Swergold, G.D., 2001. Genomic characterization of recent human LINE-1 insertions: evidence supporting random insertion. Genome Research, 11(12): 2050-2058.
• Pandotra, P., Gupta, A.P., Gandhiram, Husian, M.K., Gupta, S., 2013. Genetic and chemo-divergence in eighteen core collection of Zingiber officinale from North-West Himalayas. Scientia Horticulturae, 160(2013): 283-291.
• Poczai, P., Varga, I., Laos, M., Cseh, A., Bell, N., Valkonen, J.P.T., Hyvonen, J., 2013. Advances in plant gene-targeted and functional markers: A review. Plant Methods, 19(1): 6.
• Ramsay, L., Macaulay, M., Cardle, L., Morgante, M., Degli-Ivanissevich, S., Maestri, E., Powell, W., Waugh, R., 1999. Intimate association of microsatellite repeats with retrotransposons and other dispersed repetitive elements in barley. Plant Journal, 17(4): 415-425.
• Roy, A.M., Carroll, M.L., Kass, D.H., Nguyen, S.V., Salem, A.H., Batzer, M.A., Deininger, P.L., 1999. Recently integrated human Alu repeats: finding needles in the haystack. Genetica, 107(1-3): 149-161.
• Saha, S., Karaca, M., Jenkins, J.N., Zipf, A.E., Reddy, O.U.K., Kantety, R.V., 2003. Simple sequence repeats as useful resources to study transcribed genes of cotton. Euphytica, 130(3): 355-364.
• Schrider, D.R., Navarro, F.C.P., Galante, P.A., Parmigiani, R.B., Camargo, A.A., Hahn, M.W., De Souza, S.J., 2013. Gene copy-number polymorphism caused by retrotransposition in humans. Plos Genetics, 9(1): e1003242.
• Schulman, A.H., Kalendar, R., 2005. A movable feast: Diverse retrotransposons and their contribution to barley genome dynamics. Cytogenetics and Genome Research, 110(1-4): 598-605.
• Seibt, K.M., Wenke, T., Wollrab, C., Junghans, H., Muders, K., Dehmer, K.J., Diekmann, K., Schmidt, T., 2012. Development and application of SINE-based markers for genotyping of potato varieties. Theoretical and Applied Genetics, 125(1): 185-196.
• Sheen, F.M., Sherry, S.T., Risch, G.M., Robichaux, M., Nasidze, I., Stoneking, M., Batzer, M.A., Swergold, G.D., 2000. Reading between the LINEs: human genomic variation induced by LINE-1 retrotransposition. Genome Research, 10(10): 1496-1508.
• Soorni, A., Nazeri, V., Fattahi, R., Khadivi-Khub, A., 2013. DNA fingerprinting of Leonurus cardiaca L. germplasm in Iran using amplified fragment length polymorphism and interretrotransposon amplified polymorphism. Biochemical Systematics and Ecology, 50: 438-447.
• Sveinbjörnsson, J.I., Halldórsson, B.V., 2012. PAIR: polymorphic Alu insertion recognition. BMC Bioinformatics, 13(6): S7.
• Teo, C.H., Tan, S.H., Ho, C.L., Faridah, Q.Z., Othman, Y.R., Heslop-Harrison, J.S., Kalendar, R., Schulman, A.H., 2005. Genome constitution and classification using retrotransposon-based markers in the orphan crop banana. Journal of Plant Biology, 48(1): 96-105.
• 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. The Plant Journal, 13(1): 121-129.
• Vicient, C.M., Jaaskelainen, M., Kalendar, R., Schulman, A.H., 2001. Active retrotransposons are a common feature of grass genomes. Plant Physiology, 125(3): 1283-1292.
• Vicient, C.M., Suoniemi, A., Anamthawat-Johnsson, K., Tanskanen, J., Beharav, A., Nevo, E., Schulman, A.H., 1999. Retrotransposon BARE-1 and its role in genome evolution in the genus Hordeum. Plant Cell, 11(9): 1769-1784.
• Vos, P., Hogers, R., Bleeker, M., Reijans, M., Van De Lee, T., Hornes, M., Frijters, A., Pot, J., Peleman, J., Kuiper, M., Zabeau, M., 1993. AFLP: A new technique for DNA fingerprinting. Nucleic Acids Research, 23(21): 4407-4414.
• Waugh, R., McLean, K., Flavell, A.J., Pearce, S.R., Kumar, A., Thomas, B.B., Powell, W., 1997. Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP). Molecular and General Genetics, 253(6): 687-694.
• Wicker, T., Sabot, F.,Hua-Van, A., Bennetzen, J.L., Capy, P., Chalhoub, B., Flavell, A., Leroy, P., Morqante, M., Panaud, O., Paux, E., SanMiguel, P., Schulman, A.H., 2007. A unifed classifcation system for eukaryotic transposable elements. Nature Reviews Genetics, 8(12): 973-982.
• Witherspoon, D., Xing, J., Zhang, Y., Watkins, W.S., Batzer, M.A., Jorde, L.B., 2010. Mobile element scanning (ME-Scan) by targeted high-throughput sequencing. BMC Genomics, 11: 410.
• Witte, C.P., Le, Q.H., Bureau, T., Kumar, A., 2001. Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes. Proceedings of the National Academy of Sciences USA, 98(24): 13778-13783.
• Wong, K., Adams, D.J., Keane, T.M., 2013. Go retro and get a GRIP. Genome Biology, 14(3): 1-3.
• Wong, K., Keane, T.M., Stalker, J., Adams, D.J., 2010. Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly. Genome Biology, 11(12): R128.
• Xing, J., Witherspoon, D.J., Jorde, L.B., 2013. Mobile element biology: new possibilities with high-throughput sequencing. Trends in Genetics, 29(5): 280-289.
• You, F.M, Wanjugi, H., Huo, N., Lazo, G.R., Luo, M.C., Anderson, O.D., Dvorak, J., Gu, Y.Q., 2010. RJPrimers: unique transposable element insertion junction discovery and PCR primer design for marker development. Nucleic Acids Research, 38(2): 313-320.
• Zietkiewicz, E., Rafalski, A., Labuda, D., 1989. Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics, 20(2): 176-183.