Genetic variability and phylogenetic relationships studies of Aegilops L. using some molecular markers

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Genetic variability and phylogenetic relationships studies of Aegilops L. using some molecular markers

Mahjoub Asma, Mguis Khaled, Ben Brahim Nadia
Int. J. Agron. Agri. Res.8( 5), 14-25, May 2016.
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Studying of genetic relationships among Aegilops L. species is very important for broadening the cultivated wheat genepool, and monitoring genetic erosion, because the genus Aegilops includes the wild relatives of cultivated wheat which contain numerous unique alleles that are absent in modern wheat cultivars and it can contribute to broaden the genetic base of wheat and improve yield, quality and resistance to biotic and abiotic stresses of wheat. The use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in plant biotechnology and their genetics studies. There are different types of markers, morphological, biochemical and DNA based molecular markers. These DNA-based markers based on PCR (RAPD, AFLP, SSR, ISSR, IRAP), amongst others, the microsatellite DNA marker has been the most widely used, due to its easy use by simple PCR, followed by a denaturing gel electrophoresis for allele size determination, and to the high degree of information provided by its large number of alleles per locus. Day by day development of such new and specific types of markers makes their importance in understanding the genomic variability and the diversity between the same as well as different species of the plants. In this review, we will discuss about genetic variability and phylogenetic relationships studies of Aegilops L. using some molecular markers, with theirs Advantages, and disadvantages.


Aloui Mahjoub A, Mguis K, Rouaissi M, Abdellaoui R, Ben Brahim N. 2012. RAPD analysis of genetic diversity in natural populations of Aegilops geniculata Roth and Triticum durum Desf from Tunisia. Agric. Biol. J. N. Am 3(11), 466-475.

Arzani A, Khalighi MR, Shiran B, Kharazian N. 2005. Evaluation of diversity in wild relatives of wheat. Czech. J. Genet. Plant Breed 41, 112-117.

Bandopadhyay R, Sharma S, Rustgi S, Singh R, Kumar A, Balyan HS, Gupta PK. 2004. DNA polymorphism among 18 species of Triticum-Aegilops complex using wheat EST-SSRs. Plant Sci 166, 349-356.

Beckman JS, Soller M. 1990. Towards a unified approach to genetic mapping of eucaryotes based on sequence tagged microsatellite sites. Biotechnology 8, 930-932.

Belaj A, Satovic Z, Cipriani G, Baldoni L, Testolin R, Rallo L, Trujillo I. 2003. Comparative study of the discriminating capacity of RAPD, AFLP and SSR markers and of their effectiveness in establishing genetic relationships in olive. Theor Appl Genet 107, 736–744.

Bornet B, Branchard M. 2001. Non-anchored simple sequence repeat markers: reproducible and specific tools for genome fingerprinting. Plant Mol Biol Rep 19, 209–215.

Cenkci S, Yildiz M. Konuk M, Eren Y. 2008. RAPD analyses of some wild Triticum L. and Aegilops L. species and wheat cultivars in Turkey. Acta Biol. Cracovien. Botan 50(1), 35-42.

Cipriani G, Di Bella R, Testolin R. 1996. Screening RAPD primers for molecular taxonomy and cultivar fingerprinting in the genus Actinidia. Euphytica 90, 169–174.

Duran C, Appleby N, Edwards D, Batley J. 2009. Molecular genetic markers: discovery, applications, data storage and visualisation. Curr Bioinform 4, 16–27.

Fang DQ, Krueger RR, Roose ML. 1998. Phylogenetic relationships among selected Citrus germplasm accessions revealed by inter-simple sequence repeat (ISSR) markers. J Am Soc Hortic 123, 612–617.

Fathi T, Sohani MM, Samizadeh H, Mehrabi AA. 2014. Molecular genetic diversity of Aegilops triuncialis L. revealed by IRAP markers. International Journal of Biosciences 4(11), 164-170.

Fernandez ME, Figueiras AM, Benito C. 2002. The use of ISSR and RAPD markers for detecting DNA polymorphisms, genotype identification and genetic diversity among barley cultivars with known origin. Theor Appl Genet 104, 845–851.

Gao LF, Jing RL, Huo NX, Li Y, Li XP, Zhou RH, Chang XP, Tang JF, Ma ZY, Jia JZ. 2004. One hundred and one new microsatellite loci derived from ESTs (EST-SSRs) in bred wheat. Theor Appl Genet 108, 1392–1400.

Ghislain M, Spooner DM, Rodríguez F, Villamon F, Núñez C, Vásquez C, Bonierbale M. 2004. Selection of highly informative and user-friendly microsatellites (SSRs) for genotyping of cultivated potato. Theor Appl Genet 108, 881–890.

Goldstein DB, Roemer GW, Smith DA, Reich DE, Wayne RK. 1999. The use of microsatellite variation to infer population structure and demographic history in a natural model system. Genetics 151, 797–801.

Hojjatollah S, Rahiminejad MR, Heslop-harrison, JS. 2008. Retroelement Insertional Polymorphisms, Diversity and Phylogeography within Diploid, D-genome Aegilops tauschii (Triticeae, Poaceae) Sub-taxa in Iran. Annals of Botany 101, 855–861.

Holton, TA et al. 2002. Identification and mapping of polymorphic SSR markers from expressed gene sequences of barley and wheat. Mol Breed 9, 63–71.

Holubec V, Havlickova H, Hanusova R, Kostkanova E. 1993. Evaluation of Aegilops for aphid infestation, rust and powder mildew resistance and seed quality. In Damania A.B. Ed. Biodiversity and whet improvement. Chichester: John Wiley and Sons p.84-375.

Jam baranduzi A, Sofalian O, Asghari Zakaria R, Asghari A, Shokrpour M. 2013. Assessment of genetic diversity in Aegilops species in North-West of Iran using ISSR marker. YYÜ tar bil derg (yyu j agr sci) 23(2), 66–75.

Jannati M, Fotouhi R, Pourjan A, Salehi AZ. 2009. Genetic diversity analysis of Iranian Citrus varieties using microsatellite (SSR) based markers. J Hortic For 1, 120–125.

Jing R, Knox MR, Lee JM, Vershinin AV, Ambrose M, Ellis TH et al. 2005. Insertional polymorphism and antiquity of PDR1 retrotransposon insertions in Pisum species. Genetics 171, 741–752.

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.

Jones N, Ougham H, Thomas H. 1997. Markers and mapping: We are all geneticists now. New Phytologist 137, 165–177.

Kaya I, Kirisözü AÇ, Ersoy FY, Dere S, Mahinur AS. 2011. Genetic diversity and relationship analysis among accessions of Aegilops ssp. in Turkey using amplified fragment length polymorphism (AFLP) markers. African Journal of Biotechnology 10(72), 16167-16174.

Khadari B, Breton C, Moutier N, Roger JP, Besnard G, Berville A, Dosba F. 2003. The use of molecular markers for germplasm management in a French olive collection. Theor Appl Genet 106, 521– 529.

Khalighi M, Arzani A, Poursiahbidi MA. 2008. Assessment of genetic diversity in Triticum spp. And Aegilops spp. using AFLP markers. Afri. J.Biotechn 7(5), 546-552.

Konstantinos GT and Bebeli PJ. 2010. Genetic diversity of Greek Aegilops species using different types of nuclear genome markers. Molecul. Phylog. Evol 56, 951-961.

Laya A, Mohammadi R, Etminan A, Shooshtari L. 2014. Molecular discrimination of the advanced breeding lines of durum wheat (Triticum turgidum L.) based on inter simple sequence repeat markers. International Journal of Biosciences 5(12), 130-135

Lou Q, Chen J. 2007. Ty1-copia retrotransposon-based SSAP marker development and its potential in the genetic study of cucurbits. Genome 50, 802–810.

Luro F, Laigret F, Ollitrault P, Bove JM. 1995. DNA amplified fingerprinting (DAP), an useful tool for determination of genetic origin and diversity analysis in Citrus. Hort Science 30, 1063–1067.

Mahjoub A, Abdellaoui R, Ben Naceur M, Ben Brahim N. 2010. Genetic diversity of Tunisian accessions of Aegilops geniculata Roth and durum wheats (Triticum durum Desf.) using RAPD markers. Acta Bot. Gallica, 157 (1), 3-12.

Mahjoub A, El Gharbi MS, Mguis K, El Gazzeh M, Ben Brahim N. 2009. Evaluation of genetic Diversity in Aegilops geniculata Roth accessions using morphological and RAPD markers. Pakistan journal of biological Sciences 12(14), 994-1003.

Maria D, Angela P, Chialexei L. 2008. Characteristics of RAPD markers inbreeding of Cucumis sativus L. Roum Biotechnol Lett 13, 3843– 3850.

Martin-Sanchez JA, Gomez-Colmenarejo M, Del Moral J, Sin E, Montes MJ, Gonzalez-Belinchon C, Lopez-Brana I and Delibes A. 2003. A new Hessian fly resistance gene (H30) transferred from the wild grass Aegilops triuncialis to hexaploid wheat. Theor. Appl. Genet 106, 1248-1255.

Meloni M, Perini D, Filigheddu R, Binelli G. 2006. Genetic variation in five mediterranean populations of Juniperus phoenicea as revealed by inter-simple sequence repeat (ISSR) markers. Ann Bot 97, 299–304.

Mueller UG, Wolfenbarger LL. 1999. AFLP genotyping and fingerprinting. Trends Ecol. Evol 14, 389-394.

Nadot S, Bajon R, Lejeune B. 1994. The chloroplast gene rps4 as a tool for the study of Poaceae phylogeny. Plant Syst. Evol 191, 27-38.

Naghavi MR, Ghareyazi B, Hosseini G. 2005. Molecular Markers. Tehran University Press. Tehran, Iran p. 88-100.

Nevo E, Korol AB, Beiles A, Fahima T. 2002. Evolution of Wild Emmer and Wheat Improvement. Population Genetics, Genetic Resources and Genome Organization of Wheat’s Progenitor, Triticum dicoccoides. Springer, Heidelberg. plant Eriogonum ovalifolium var. vineum. Conservation Genetics 4, 337-352.

Nicot N. et al. 2004. Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs). Theor Appl Genet 109, 800–805.

Pillay M, Myers GO. 1999. Genetic diversity assessed by variation in ribosomal RNA genes and AFLP markers. Crop Science 39, 1881-1886.

Pradeep Redy M, Sarla N, Siddiq A. 2002. Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding. Euphytica 128, 9–17.

Queen RA, Gribbon BM, James C, Jack P, Flavell AJ. 2004. Retrotransposon-based molecular markers for linkage and genetic diversity analysis in wheat. Mol Genet Genomics 271, 91–97.

Qui J, van Santen E, Tuzun S, Campos-Andrada M. 1999. Genetic analysis of Lupinus luteus and L. cosentinii using fluorescence labelled AFLP primers. 9th Int. Lupin Conf.

Ratnaparkhe MB, Santra DK, Tullu A, Muehlbauer FJ. 1998. Inheritance of inter simple sequence repeat polymorphism and linkage with Fusarium wilt resistance gene in chickpea. Theor Appl Genet 96, 348–353.

Rouf Mian MA, Hopkins AA, Zwonitzer JC. 2002. Determination of genetic diversity in tall fescue with AFLP markers. Crop Sci 42, 944- 950.

Russell JR, Fuller JD, Macaulay M, Hatz BG, Jahoor A, Powell W, Waugh R. 1997. Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theor. Appl. Genet 95, 714-72

San Miguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL. 1998. The paleontology of intergene retrotransposons of maize. Nat Genet 20, 43–45.

Sanz AM, Gonzalez SG, Syed NH, Suso MJ, Saldana CC, Flavell AJ. 2007. Genetic diversity analysis in Vicia species using retrotransposon-based SSAP markers. Mol Genet Genomics 278, 433–441.

Schaal BA, Hayworth DA, Olsen KM, Rauscher JT, Smith WA. 1998. Phylogeographic studies in plants: problems and prospects. Mol Ecol 7, 465–474.

Schaal BA, Leverich WJ, Rogstad SH. 1991. A comparison of methods for assessing genetic variation in plant conservation biology. In: Falk DA, Holsinger KE. Eds. Genetics and conservation of rare plants. Oxford University Press, New York p.123–134.

Schoenenberger N, Felber F, Savova-Bianchi D, Guadagnuolo R. 2005. Introgression of wheat DNA markers from A, B and D genomes in early generation progeny of Aegilops cylindrica Host · Triticum aestivum L. hybrids. Theor Appl Genet 111, 1338–1346.

Sharma A, Ajay NG, Mahadik KR. 2008. Molecular markers: New prospects in plant genome analysis. Phco. Rev 2(3), 23-34.

Smykal P. 2006. Development of an efficient retrotransposon-based fingerprinting method for rapid pea variety identification. Journal of Applied Genetics 47, 221–230.

Soleimani VD, Baum BR, Johnson DA. 2002. AFLP and pedigree-based genetic diversity estimates in modern cultivars of durum wheat (Triticum turgidum L. subsp. durum (Desf.) Husn.). Theor Appl Genet 104, 350–357.

Sorrells ME, Wilson WA. 1997. Direct classification and selection of superior alleles for crop improvement. Crop Sci 37, 691–697.

Tautz D. 1989. Hypervariability of simple sequence repeats as a general source for polymorphic DNA markers. Nucleic Acids Res 17, 6463–6471.

Van Slageren MW. 1994. Wild Wheats: a monograph of Aegilops L. and Amblyopyrum (Jaub. and Spach) Eig (Poaceae). Wageningen Agricultural University Papers 94–7, Wageningen, the Netherlands.

Virk PS, Zhu J, Newburg HJ, Bryan GJ, Jackson MT, Ford- Lloyd BV. 2001. Effectiveness of different classes of molecular markers for classifying and revealing variation in rice germplasm. Euphytica 112, 275–284.

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). Mol Genet Genomics 272, 504–511.

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

Williams JGK, Kublik AR, Livak KJ, Rafalsky JA, Tingey SV. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acid Res 18, 6531–6535.

Yildirim F, Akkaya MS. 2006. DNA fingerprinting and genetic characterization of Anatolian Triticum sp. using AFLP markers. Genet. Resour. Crop Eviron 53, 1033-1042.

Yu JK, Dake TM, Singh S, Benscher D, Li W, Gill B, Sorrells ME. 2004. Development and mapping of EST-derived simple sequence repeat markers for hexaploid wheat. Genome / National Research Council Canada 47(5), 805-818.

Zietkiewicz E,  Rafalski  A,  Labuda  D.  1994. Genome  fingerprinting  by  simple  sequence  repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20, 176–183.