Retrotransposon-based molecular markers for assessment of genomic diversity

Functional Plant Biology - Tập 41 Số 8 - Trang 781 - 2014
Ahmed M. Alzohairy1, Gábor Gyulai2, Mohamed Fawzy Ramadan3, Sherif Edris4,5,6, Jamal S. M. Sabir5, Robert K. Jansen7,5, Hala F. Eissa8,9, Ahmed Bahieldin4,5
1Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
2Institute of Genetics and Biotechnology, St. István University, Gödöllő, H-2103, Hungary.
3Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
4Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt.
5King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Genomics and Biotechnology Section, Jeddah 21589, Saudi Arabia.
6Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
7Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
8Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypt
9Faculty of Biotechnology, Misr University for Science and Technology (MUST), 6th October city, Egypt

Tóm tắt

Retrotransposons (RTs) are major components of most eukaryotic genomes. They are ubiquitous, dispersed throughout the genome, and their abundance correlates with genome size. Their copy-and-paste lifestyle in the genome consists of three molecular steps involving transcription of an RNA copy from the genomic RT, followed by reverse transcription to generate cDNA, and finally, reintegration into a new location in the genome. This process leads to new genomic insertions without excision of the original element. The target sites of insertions are relatively random and independent for different taxa; however, some elements cluster together in ‘repeat seas’ or have a tendency to cluster around the centromeres and telomeres. The structure and copy number of retrotransposon families are strongly influenced by the evolutionary history of the host genome. Molecular markers play an essential role in all aspects of genetics and genomics, and RTs represent a powerful tool compared with other molecular and morphological markers. All features of integration activity, persistence, dispersion, conserved structure and sequence motifs, and high copy number suggest that RTs are appropriate genomic features for building molecular marker systems. To detect polymorphisms for RTs, marker systems generally rely on the amplification of sequences between the ends of the RT, such as (long-terminal repeat)-retrotransposons and the flanking genomic DNA. Here, we review the utility of some commonly used PCR retrotransposon-based molecular markers, including inter-primer binding sequence (IPBS), sequence-specific amplified polymorphism (SSAP), retrotransposon-based insertion polymorphism (RBIP), inter retrotransposon amplified polymorphism (IRAP), and retrotransposon-microsatellite amplified polymorphism (REMAP).

Từ khóa


Tài liệu tham khảo

Alzohairy, 2012, Life Science Journal, 9, 5019

Alzohairy, 2013, Plasmid, 69, 1, 10.1016/j.plasmid.2012.08.001

Alzohairy, 2014, Functional Plant Biology, 41, 557, 10.1071/FP13339

Baumel, 2002, Molecular Biology and Evolution, 19, 1218, 10.1093/oxfordjournals.molbev.a004182

Boyko, 2002, Plant Molecular Biology, 48, 767, 10.1023/A:1014831511810

Branco, 2007, Journal of Applied Genetics, 48, 107, 10.1007/BF03194667

Brik, 2006, TSitologiia i genetika, 3, 24

Chadha, 2005, Genome, 48, 943, 10.1139/g05-045

Chesnay, 2007, Cellular & Molecular Biology Letters, 12, 103, 10.2478/s11658-006-0054-y

Ellis, 1998, Molecular & General Genetics, 260, 9

Feschotte, 2002, Nature Reviews. Genetics, 3, 329, 10.1038/nrg793

Flavell, 1998, The Plant Journal, 16, 643, 10.1046/j.1365-313x.1998.00334.x

Gao, 2004, BMC Genomics, 5, 18, 10.1186/1471-2164-5-18

Garc�a-Mart�nez, 2003, Molecular Biology and Evolution, 20, 831, 10.1093/molbev/msg095

Hamdi, 1999, Journal of Molecular Biology, 289, 861, 10.1006/jmbi.1999.2797

Havecker, 2004, Genome Biology, 5, 225, 10.1186/gb-2004-5-6-225

Huo, 2009, Theoretical and Applied Genetics, 119, 199, 10.1007/s00122-009-1029-y

IHGSC (International Human Genome Sequencing Consortium), 2001, Nature, 409, 860, 10.1038/35057062

Jing, 2005, Genetics, 171, 741, 10.1534/genetics.105.045112

Jurka, 2007, Annual Review of Genomics and Human Genetics, 8, 241, 10.1146/annurev.genom.8.080706.092416

Kalendar, 2011, Field and Vegetable Crops Research, 48, 261

Kalendar, 2006, Nature Protocols, 1, 2478, 10.1038/nprot.2006.377

Kalendar, 1999, Theoretical and Applied Genetics, 98, 704, 10.1007/s001220051124

Kalendar, 2010, Theoretical and Applied Genetics, 121, 1419, 10.1007/s00122-010-1398-2

Lanteri, 2006, Theoretical and Applied Genetics, 112, 1532, 10.1007/s00122-006-0256-8

Leigh, 2003, Molecular Genetics and Genomics, 269, 464, 10.1007/s00438-003-0850-2

Manninen, 2000, Molecular & General Genetics, 264, 325, 10.1007/s004380000326

Manninen, 2006, Genome, 49, 1564, 10.1139/g06-119

Mansour, 2007, Journal of Cell and Molecular Biology, 6, 99

Mansour, 2008, Journal of Cell and Molecular Biology, 7, 17

Mansour, 2009, Plant Stress, 3, 33

Mansour, 2010, Genes, Genomes and Genomics, 4, 41

Nagy, 2006, Genome, 49, 289, 10.1139/G05-109

Nair, 2005, Euphytica, 144, 285, 10.1007/s10681-005-7321-2

Petit, 2007, Molecular Genetics and Genomics, 278, 1, 10.1007/s00438-007-0226-0

Poczai, 2013, Plant Methods, 9, 6, 10.1186/1746-4811-9-6

Queen, 2004, Molecular Genetics and Genomics, 271, 91, 10.1007/s00438-003-0960-x

Ramallo, 2008, Plant Molecular Biology, 66, 137, 10.1007/s11103-007-9258-4

Ribaut, 1998, Trends in Plant Science, 3, 236, 10.1016/S1360-1385(98)01240-0

Rice Chromosome 10 Sequencing Consortium, 2003, Science, 300, 1566, 10.1126/science.1083523

Roos, 2004, Proceedings of the National Academy of Sciences of the United States of America, 101, 10�650, 10.1073/pnas.0403852101

Sabot, 2006, Heredity, 97, 381, 10.1038/sj.hdy.6800903

Sanz, 2007, Molecular Genetics and Genomics, 278, 433, 10.1007/s00438-007-0261-x

Shedlock, 2000, BioEssays, 22, 148, 10.1002/(SICI)1521-1878(200002)22:2<148::AID-BIES6>3.0.CO;2-Z

Syed, 2006, Theoretical and Applied Genetics, 112, 517, 10.1007/s00122-005-0155-4

Tahara, 2004, Molecular Genetics and Genomics, 272, 116, 10.1007/s00438-004-1044-2

Tam, 2005, Theoretical and Applied Genetics, 110, 819, 10.1007/s00122-004-1837-z

Tanhuanp��, 2007, Genome, 50, 588, 10.1139/G07-036

Tatout, 1999, Molecular Biology and Evolution, 16, 1614, 10.1093/oxfordjournals.molbev.a026074

Teo, 2002, Journal of Biochemistry, Molecular Biology, and Biophysics, 6, 193, 10.1080/10258140290022329

Teo, 2005, Journal of Plant Biology, 48, 96, 10.1007/BF03030568

Tsumura, 1996, Theoretical and Applied Genetics, 92, 40, 10.1007/BF00222949

Venturi, 2006, Theoretical and Applied Genetics, 112, 440, 10.1007/s00122-005-0143-8

Vershinin, 2003, Molecular Biology and Evolution, 20, 2067, 10.1093/molbev/msg220

Vitte, 2005, Cytogenetic and Genome Research, 110, 91, 10.1159/000084941

Vos, 1995, Nucleic Acids Research, 23, 4407, 10.1093/nar/23.21.4407

Waugh, 1997, Molecular & General Genetics, 253, 687, 10.1007/s004380050372

Xiong, 1990, The EMBO Journal, 9, 3353, 10.1002/j.1460-2075.1990.tb07536.x

Yu, 2000, Genome, 43, 736, 10.1139/gen-43-5-736

Thông tin
Thông tin xuất bản

Functional Plant Biology

Tập 41 Số 8

781

Thông tin tác giả