Retro transposon-markers: an overview of the recent progress in Citrus germplasm

Paper Details

Review Paper 01/10/2013
Views (239) Download (7)
current_issue_feature_image
publication_file

Retro transposon-markers: an overview of the recent progress in Citrus germplasm

Mohamed Hamdy Amar, Mohamed Abd El Salam
J. Bio. Env. Sci.3( 10), 31-41, October 2013.
Certificate: JBES 2013 [Generate Certificate]

Abstract

Citrus is a commercially important genus of the family Rutaceae and widely cultivated fruit crop in the world. Retro transposons are the most abundant class of transposable elements and they outnumber the genes in the eukaryotic genomes. Repetitive sequences make up a large part of the genome, up to 80% in certain species. Dozens or even hundreds of copies of members of some transposon families can be present in a single genome. Transposons can serve as a very rich source of identifiable polymorphisms. In this revised, several retro transposon-based marker systems such as SSAP, IRAP, REMAP and RBIP have been developed and discuss their use to visualize the genetic diversity generated by retro transposon in Citrus germplasm. Sequencing of the recent draft genome represents a valuable resource for understanding and improving of retro-transposons regions in Citrus germplasm. Therefore, sequences information of retro-transposons regions should exhibit more phylogenetic informative sites, which must be received more attention in future research in Citrus germplasm. Consequently, retro transposons integration markers are ideal tools for rapid characterization of Citrus and its related genera. This approach could be efficiently employed for conservation and management of Citrus germplasm genetic resource.

VIEWS 6

Abkenar AA, Isshiki S, Tashiro Y. 2004. Phylogenetic relationships in the “true citrus fruit trees” revealed by PCR-RFLP analysis of cpDNA. Scientia Horticulturae 102, 233- 242.

Agarwal M, Shrivastava N, Padh H. 2008. Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Reports 27,617–631.

Antonius-Klemola K, Kalendar R, Schulman AH. 2006. TRIM retro transposons occur in apple and are polymorphic between varieties but not sports. Theoretical and Applied Genetics DOI 10.1007/s00122-005-0203-0.

Arumuganathan K, Earle ED. 1991. Nuclear DNA content of some important plant species. Plant Molecular Biology Reporter 9,208–218.

Asins MJ, Monforte AJ, Mestre PF, Carbonell EA. 1999. Citrus and Prunuscopia-like retro transposons. Theoretical and Applied Genetics 99, 503-510.

Bernet GP, Asins MJ. 2003. Identification and genomic distribution of gypsy like retro transposons in Citrus and Poncirus. Theoretical and Applied Genetics 108,121–130.

Bernet GP, Mestre PF, Pina JA, Asins MJ. 2004. Molecular discrimination of lemon cultivars. Horticultural science 39, 156-159.

Biswas MK, Baig MNR, Cheng YJ, Deng XX. 2010a. Retro-transposon based genetic similarity within the genus Citrus and its relatives. Genetic Resources and Crop Evolution 57 (7), 963–972.

Biswas MK, Chai L, Amar MH, Zhang X, Deng XX. 2011. Comparative analysis of genetic diversity in Citrus germplasm collection using AFLP, SSAP, SAMPL and SSR markers. Scientia Horticulturae 129, 798–803.

Biswas MK, Xu Q, Deng XX. 2010b. Utility of RAPD, ISSR, IRAP and REMAP markers for the genetic analysis of Citrus spp. Scientia Horticulturae 124,254-261.

Branco CJS, Vieira EA, Malone G, Kopp MM, Malone E, Bernardes A, Mistura CC, Carvalho FIF, Oliveira CA. 2007. IRAP and REMAP assessments of genetic similarity in Rice (Oryza sativa .) Journal of Applied Genetics 48(2), 107–113.

Breto MP, Ruiz C, Pina JA, Asins MJ. 2001. The diversification of Citrus clementina Hort. ex Tan., a vegetatively propagated crop species. Molecular Phylogenetics and Evolution 21, 285–293.

FAOSTAT. 2010. http://faostat.fao.org/site/339/default.aspx.

Finnegan DJ. 1989. Eukaryotic transposable elements and genome evolution. Trends in Genetics 5, 103-107.

Flavell AJ, Knox MR, Pearce SR, Ellis THN. 1998. Retro transposon-based insertion polymorphisms (RBIP) for high-throughput marker analysis. The Plant Journal 16, 643-650.

Froelicher Y, Mouhaya W, Bassene JB, Costantino G, Kamiri M, Luro F, Morillon R, Ollitrault P. 2011. New universal mitochondrial PCR markers reveal new information on maternal citrus phylogeny. Tree Genetics and Genomes 7, 49-61.

Gmitter FG, Chen C, Machado MA, Alves A, Ollitrault P, Froehlicher Y, Shimizu T. 2012. Citrus genomics. Tree Genetics and Genomes 8, 611-626.

Gmitter FGJr. 1995. Origin, evolution, and breeding of the Grapefruit. Plant Breeding 13, 345– 363.

Grzebelus D. 2006. transposon insertion polymorphism as a new source of molecular markers. Journal of Fruit and Ornamental Plant Research 14, 21-29.

Huo H, Conner JA, Ozias-Akins P. 2009. Genetic mapping of the apospory-specific genomic region in Pennisetum squamulatum using retro transposon-based molecular markers. Theoretical and Applied Genetics 119, 199-212.

Jannati M, Fotouhi R, Abad AP, Salehi Z. 2009. Genetic diversity analysis of Iranian citrus varieties using micro satellite (SSR) based markers. Journal of Horticulture and Forestry 1(7), 120-125.

Jing R, Knox MR, Lee JM, Vershinin AV, Ambrose M, Ellis THNl, Flavell AJ. 2005. Insertional polymorphism and antiquity of PDR1 retro transposon insertions in Pisum species. Genetics 171, 741–752.

Kalendar R, Antonius K, Smykal P, Schulman AH.  2010.  iPBS:  A  universal  method  for  DNA fingerprinting and retro transposon isolation. Theoretical and Applied Genetics 121, 1419-1430.

Kalendar R, Flavell AJ, Ellis T, Sjakste T, Moisy C, Schulman AH. 2011. Analysis of plant diversity with retro transposon-based molecular markers. Heredity 106, 520–530.

Kalendar R, Grob T, Regina M, Suoniemi A, Schulman A. 1999. IRAP and REMAP: Two new retro transposon-based DNA fingerprinting tech-niques. Theoretical and Applied Genetics 98,704– 711.

Kalendar R, Schulman HA. 2006. IRAP and REMAP for retro transposon-based genotyping and fingerprinting. Nature Protocols 1, 2478-2484.

Kalendar R, Vicient CM, Peleg O, Anamthawat-Jonsson K, Bolshoy A, Schulman AH. 2004. Large retro transposon derivatives: Abundance, conserved and no autonomous retro elements of barley and related genomes. Genetics 166, 1437-1450.

Kalendar R. 2011. The use of retro transposon-based molecular markers to analyze genetic diversity. Field and Vegetable Crops Research 48, 261-274.

Kazazian JrHH. 2004. Mobile elements: Drivers of genome evolution. Science 303, 1626-1632.

Khaliq I. 2009. Isolation, characterization and expression of Ty1-copia retro transposons in Agave tequilana. Ph.D thesis. University of Sussex.

Kim H, Terakami S, Nishitani C, Kurita K, Kanamori H, Katayose Y, Sawamura Y, Saito T, Yamamoto T. 2012. Development of cultivar-specific DNA markers based on retro transposon-based insertional polymorphism in Japanese pear. Breeding Science 62, 53–62.

Krueger RR, Roose ML. 2003. Use of molecular markers in the management of citrus germplasm resources. Journal of the American Society for Horticultural Science 128, 827-837.

Kumar A, Bennetzen JL. 1999. Plant retrotransposons. Annual Review of Genomics 33, 479–532.

Kumar A, Hirohiko H. 2001. Applications of retro transposons as genetic tools in plant biology. Trends in Plant Science 6, 127-134.

Leigh F, Kalendar R, Lea V, Lee D, Donini P, Schulman AH. 2003. Comparison of the utility of Barley (Hordeum vulgare) by molecular marker techniques. Molecular Genetics and Genomics 269, 464–474.

Mandoulakani BA, Piri Y, Darvishzadeh R, Bernoosi I, Jafari M. 2012. Retro element Insertional Polymorphism and Genetic Diversity in Medicago sativa Populations Revealed by IRAP and REMAP Markers. Plant Molecular Biology Reporter 30, 286–296.

Mansour A. 2007. Epigenetic activation of genomic retro transposon. Journal of Cell and Molecular Biology 6, 99-107.

Mansour A. 2008. Utilization of genomic retro transposons as cladistics markers. Journal of Cell and Molecular Biology 7, 17-28.

Nicolosi E, Deng ZN, Gentile A, , La Malfa S, Continella G, Tribulato E. 2000. Citrus phylogeny and genetic origin of important species as investigated by molecular markers. Theoretical and Applied Genetics 100, 1155 –1166.

Panaud O, Vitte C. 2005. LTR retro transposons and flowering plant genome size: emergence of the increase/decrease model. Cytogenetic and Genome Research 110 (1),91-107.

Pang XM, Hu CG, Deng XX. 2007. Phylogenetic relationships within citrus and its related genera as inferred from AFLP markers. Genetic Resources and Crop Evolution 54, 429–436.

Queen RA, Gribbon BM, James C, Jack P, Flavell AJ. 2004. Retro transposon based molecular markers for linkage and genetic diversity analysis in wheat. Molecular Genetics and Genomics 271, 91-97.

Ruiz C, Asins MJ. 2003. Comparison between Poncirus and Citrus genetic linkage maps. Theoretical and Applied Genetics 106, 826–836.

Schulman AH, Kalendar R. 2005. A movable feast: diverse retro transposons and their contribution to Barley (Hordeum vulgare) genome dynamics. Cytogenetic and Genome Research 110, 598–605.

Smykal P. 2006. Development of an efficient retro transposon-based finger printing method for rapid pea variety identification. Journal of Applied Genetics 47, 221-230.

Sun J, Huang Y, Zhou J, Guo J, Sun Q. 2012. LTR-retro transposon diversity and transcriptional activation under phytoplasma stress in Ziziphus jujube. Tree Genetics and Genomes DOI 10.1007/s11295-012-0563-y.

Swingle WT, Reece PC. 1967. The Botany of Citrus and its Wild Relatives. In: The Citrus Industry, Reuther, W., H.J. Webber and L.D. Batchelor (Eds.). (Vol. 1), University of California Press, Berkeley, CA, USA, 190 – 430.

Syed NH, Sørensen AP, Antonise R, van de Wiel C, van der Linden CG, van ‘t, Westende W, Hooftman DA, den Nijs HC, Flavell AJ. 2006. A detailed linkage map of lettuce based on SSAP, AFLP and NBS markers. Theoretical and Applied Genetics 112, 517–527.

Tahara M, Aoki T, Suzuka S, Yamashita H, Tanaka M, Matsunaga S, Kokumai S. 2004. Isolation of an active element from a high copy-number family of retro transposons in the sweet potato genome. Molecular Genetics and Genomics 272, 116-127.

Tam SM, Mhiri C, Vogelaar A, Kerkveld M, Pearce SR, Grandbastien MA. 2005. Comparative analyses of genetic diversities within tomato and pepper collections detected by retro transposon- based SSAP, AFLP and SSR. Theoretical and Applied Genetics 110, 819-831.

Tanaka T. 1977. Fundamental discussion of Citrus classification. Studia Citrologica 14, 1–6.

Tanhuanpaa P, Kalendar R, Schulman AH, Kiviharju E. 2007. A major gene for grain cadmium accumulation in oat (Avena sativa L.). Genome 50, 588-594.

Tao NG, Xu J, Cheng YJ, Liu Hong, Guo WW, Yi HL, Deng XX. 2005. Isolation and Characterization of Copia-like Retro transposons from 12 Sweet Orange (Citrus sinensis Osbeck) Cultivars. Journal of Integrative Plant Biology 47, 1507-1515.

Ulubelde M. 1985. Turuillerin taksonomisi. Ege Bgesi Zirai Arastırma EnstitüsüYayınları 55,43 (in Turkish).

Uzun A, Yesiloglu T. 2012. Genetic Diversity in Citrus, Genetic Diversity in Plants, Prof. Mahmut Caliskan (Ed.), ISBN: 978-953-51-0185-7, InTech, DOI: 10.5772/32885. Available from: http://www.intechopen.com/books/genetic-diversity-in-plants/genetic-diversity-in-citrus.

Venturi S, Dondini L, Donini P, Sansavini S. 2006. Retro transposon characterization and fingerprinting of apple clones by S-SAP markers. Theoretical and Applied Genetics 112, 440-444.

Vitte C, Ishii T, Lamy F, Brar D, Panaud O. 2004. Genomic paleontology provides evidence for two distinct origins of Asian rice (Oryza sativa L). Molecular Genetics and Genomics 272, 504–511.

Waugh R, McLean K, Flavell AJ, Pearce SR, Kumar A, Thomas BB, Powell W. 1997. Genetic distribution of BARE-1 retro transposable elements in the Barley (Hordeum vulgare) genome revealed by sequence-specific amplification polymorphisms (S-SAP). Molecular and General Genetics 253, 687– 694.

Webber HJ. 1967. History and Development of the Citrus Industry. In: The Citrus Industry, Reuther, W, H.J. Webber and L.D. Batchelor (Eds.), (Vol.), University of California Press, Berkeley, 1-39.

Wegscheider EC. 2006. Retro transposon-based Variability in Pinot Noir Clones revealed by S-SAP. Msc thesis, University of Natural Resources and Applied Life Sciences, Vienna.

Wei J. 2007. Characterization of retro transposon elements and development of related molecular markers in citrus. PhD thesis, Huazhong Agricultural University, Wuhan, China.

Xu Q, Chen L, Ruan X, Chen D, Zhu A, Chen C, Bertrand D, Jiao W, Hao B, PLyon M, Chen J, Gao S, Xing F, Lan H, Chang J, Ge X, Le Y, Hu Q, Miao Y, Wang L, Xiao S, Biswas MK, Zeng W, Guo F, Cao H, Yang X, Xu XW, Cheng Y, Xu J, Liu J, Luo OJ, Tang Z, Guo WW, Kuang H, Zhang H, Roose ML, Nagarajan N, Deng XX, Ruan Y. 2013. The draft genome of sweet orange (Citrus sinensis). Nature Genetics 45, 59–66.

Yuan Y, dong WW, Wan-guang C, Guang-yong Q, Yu-ping H. 2010. Retro transposon Tto1 in tobacco was activated by the implantation of Low-energy N+ ion beam. Life Science Journal 7 (3), 141-147.