Bazı Citrus ve akrabalarının genetik farklılık ve yakınlıklarının SSR moleküler belirteçlerle belirlenmesi

Year 2014, Volume: 27 Issue: 2, 99 - 106, 01.12.2014

İlknur Polat

Abstract

Çalışmada Aurantioideae alt familyasına ait 80 adet, Toddalioideae alt familyasına ait 1 adet Citrus ve akrabalarının genetik farklılığı ve birbiriyle olan genetik yakınlığı SSR (simple sequence repeat) moleküler belirteç tekniği kullanılarak incelenmiştir. Kullanmış olduğumuz 26 SSR primerinin 18’i polimorfizm sağlamıştır. UPGMA (unweighted-pair group method aritmetic average) dendrogram ve temel koordinat analizi (principal coordinate analysis, PCO) sonucu bireylerin birbirleriyle olan genotipik farklılıkları belirlenmiştir. Dice’ın benzerlik katsayısına göre genetik benzerlik 0.33-0.90 arasında değişim göstermiştir. En yüksek genetik benzerlik 0.90 ile Citrus montana (Wester) ve Citrus wintersii Mabb. arasında bulunmuştur. Toddalioideae alt familyasında yer alan Casimiroa tetrameria (Florida) ise 81 adet Citrus ve akrabaları içerisinde en uzak bireyi oluşturmuştur. Çalışmamızda, SSR markırlar birçok Citrus ve akrabalarının ayırt edilmesinde uygun moleküler belirteç olarak bulunmuştur.

Keywords

Citrus spp., Simple sequence repeat, Akrabalar, Moleküler belirteç

Determination of genetic diversity and relationships within some Citrus and related genera by using SSR molecular markers

Abstract

In the present study, genetic relationship and diversity of 80 Citrus and their relatives in Aurantioideae subfamily and 1 accessions in Toddalioideae subfamily were determined by simple sequence repeat (SSR) markers. From the 26 primer pairs used, 18 SSR primers generated polymorphic fragments. Genetic relationships and distance were determined by using UPGMA (unweighted-pair group method arithmetic average) dendrogram and PCO (principal coordinate analysis) analysis. The Dice similarity coefficient among the accessions ranged from 0.33 to 0.90. Citrus montana (Wester) and Citrus wintersii Mabb.in a group with 0.90 genetic similarity were determined. In contrary, Casimiroa tetrameria (Florida), in Toddalioideae subfamily, was found to be the least related sample to the remaining 81 citrus and their relatives. In our study, SSRs molecular markers were found to be suitable to distinguish many Citrus and their relatives.

Keywords

Citrus spp., Simple sequence repeat, Related genera, Molecular marker

References

• Ağar A (2007) Aurantioideae Alt Familyasındaki Cinslerde Yer Alan Bazı Türlerin SSR Markırlarıyla Moleküler Karakterizasyonu. Yüksek Lisans Tezi. Çukurova Üniversitesi, Fen Bilimleri Enstitüsü, Biyoteknoloji Anabilim Dalı. Adana.
• Amar MH, Biswas MK, Zhang Z, Guo WW (2011) Exploitation of SSR, SRAP and CAPS-SNP markers for genetic diversity of Citrus germplasm collection. Scientia Horticulturae 128:220–227.
• Barkley NA, Roose ML, Krueger RR, Federici CT (2006) Assessing genetic diversity and population structure in a citrus germplasm collection utilizing simple sequence repeat markers (SSRs). Theor Appl Genet 112: 1519–1531.
• Bretó MP, Ruiz C, Pina JA, Asíns MJ (2001) The diversification of Citrus clementina Hort. ex Tan., a vegetatively propagated crop species. Molecular Phylogenetics and Evolution 21:285-93.
• Campos ET, Espinosa MAG, Warburton ML, Varela AS, Monter AV (2005) Characterization of mandarin (Citrus ssp) using morphological and AFLP markers. Interciencia 30:687-693.
• Chen C, Bowman KD, Choi YA, Dang PM, Rao MN, Huang S, Soneji JR, McCollum TG, Gmitter FG (2008) EST-SSR genetic maps for Citrus sinensis and Poncirus trifoliata. Tree Genetics & Genomes 4:1–10.
• Corazza-Nunes MJ, Machado MA, Nunes WMC, Cristofani M, Targon MLPN (2002) Assessment of genetic variability in grapefruits (C. paradisi Macf.) and pummelos (C. maxima(Burm.) Merr.) using RAPD and SSRs markers. Euphytica 126:169-76.
• Dice LR (1945) Measures of the amount of ecologic association between species. Ecology 26:297-302.
• Fang DQ, Roose ML, Krueger RR, Federici CT (1997) Fingerprinting trifoliate orange germplasm accessions with isozymes, RFLPs, and inter-simple sequence repeat markers. Theor. Appl. Genetic 95:211–219.
• Federici CT, Fang DQ, Scora RW, Roose ML (1998) Phylogenetic relationships within the genus Citrus (Rutaceae) and related genera as revealed by RFLP and RAPD analysis. Theor. Appl. Genetic 94:812–822.
• Ferrante SP, Lucretti S, Reale S, De Patrizio A, Abbate L, Tusa N, Scarano MT (2010) Assessment of the origin of new citrus tetraploid hybrids (2n 5 4x) by means of SSR markers and PCR based dosage effects. Euphytica 173:223–233.
• Gmitter FG, Grosser JW, Moore AG (1992) Citrus. In: Hammerschlag, F. and R. Litz (eds.), Biotechnology of perennial fruit crops. Pp: 335–69. CAB Int. Wallingford, UK.
• Gulsen O, Uzun A, Canan I, Seday U, Canihos E (2010) A new citrus linkage map based on SRAP, SSR, ISSR,POGP, RGA and RAPD markers. Euphytica 173:265–277.
• Gülşen O, Roose ML (2001) Limonlarda genetik çeşitlilik, bazı turunçgillerle akrabalık derecelerinin DNA markırlarının kullanılarak belirlenmesi. Bahçe 30 (1-2): 53 – 63.
• Hildebrand CE, Torney DC, Wagner RP (1992) Informativeness of polymorphic DNA markers. Los Alamos Science 20:100-102.
• Jiang D, Zhong GY, Hong QB (2006) Analysis of microsatellites in Citrus unigenes. Acta Genefica Sinica 33 (4): 345-353.
• Kacar Y, Uzun A, Polat I, Yesiloglu T, Yilmaz B, Gulsen O, Tuzcu O, Kamiloglu M, Kurt S ve Seday U (2013) Molecular characterization and genetic diversity analysis of mandarin genotypes by SSR and SRAP markers. Journal of Food, Agriculture & Environment Vol.11 (1): 516 - 521.
• Krueger RR, Navaro L (2007) Citrus Genetics, Breeding and Biothecnology. Edit: I.Khan. Chapter: “Citrus Germplasm Resources” 45-140.
• Morton CM, Grant M, Blackmore S (2003) Phylogenic relationships of the Aurantioideae inferred from chloroplast DNA sequence data. Am. J. Bot. 90: 1463–1469.
• 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. Theor. Appl. Genetic 100:1155–1166.
• Novelli VM, Cristofan M, Souza AA, Marcos A, Machado MA (2006) Development and characterization of polymorphic microsatellite markers for the sweet orange (Citrus sinensis L. Osbeck). Genetics and Molecular Biology 29: (1): 90-96.
• Polat İ (2009) Üç yapraklı (Poncirus trifoliata L. Raf.) ve üç yapraklı melezleri grubu turunçgillerin genetik akrabalık ve farklılıklarının SSR moleküler markırlarla tanımlanması. Derim 26 (2): 30-41.
• Polat İ, Turgutoglu E (2012) Bazı altıntop (Citrus paradisi) ve şadoklarda (C. maxima) genetik akrabalık ve farklılıklarının SSR markırlarıyla tanımlanması. Akdeniz Ün. Zir. Fak. Derg. 25 (1):1-7.
• Polat I, Aka-Kacar Y, Yesiloglu T, Uzun A, Tuzcu O, Gulsen O, Incesu M, Kafa G, Turgutoglu E, Anil S (2012) Molecular Characterization of Sour Orange (Citrus aurantium L.) Accessions and Their Relatives Using SSR and SRAP Markers. Genetics and Molecular Research 11 (3): 3267-3276.
• Rahman MM, Nito N (1994) Use Of Glutamate-Oxaloacetate Transaminase Isozymes For Detection Of Hybrids Among Genera Of The True Cıtrus-Fruit Trees. Scientia Horticulturae 58 (3): 197-206.
• Rohlf FJ (1993) NTSYS-PC, Numerical taxonomy and multivariate analysis system. Version 1.80. Exeter Software, Setauket, New York.
• Roose ML (2009) Use of molecular markers to understand phylogeny and genetic diversity of citrus. PCR Primers for Citrus Germplasm Characterization. http://www.plantbiology.ucr.edu/faculty/roose.html.
• Scarano MT, Abbate L, Ferrante S, Lucretti S, Reale S, Tusa N (2006) Molecular characterization of new citrus tetraploid hybrids by means of SSR markers. Proceedings of the XLIX Italian Society of Agricultural Genetics Annual Congress, Potenza, Italy – 12/15 September. C. 51.
• Smith JSC, Chin ECL, Shu H, Smith OS, Wall SJ, Senior ML, Mitchel SE, Kresorich S, Tiegle J (1997) An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.): comparisons with data from RFLPs and pedigree. Theor. Appl. Genet. 95: 163–173.
• Swingle WT, Reece PC (1967) The botany of citrus and its wild relatives. In: Reuther W. Webber, H J. Batchelor L D. (Eds.), The Citrus Industry, vol: 1. University of California Press, Berkeley, CA, USA, pp. 389–390.
• Tan ML, Song JK, Deng XX (2007) Production of two mandarin trifoliate orange hybrid populations via embryo rescue with verification by SSR analysis. Euphytica 157:155–160.
• Tanaka T (1954) Species problem in Citrus: a critical study of wild and cultivated units of Citrus, based upon field studies in their native homes. P. 9:111 in: Tanaka, T., Revisio Aurantiacearum.
• Uzun A, Yesiloglu T, Aka-Kacar Y, Tuzcu O, Gulsen O (2009a) Genetic diversity and relationships within Citrus and related genera based on sequence related amplified polymorphism markers (SRAPs). Scientia Horticulturae 121: 306–312.
• Uzun A, Gulsen O, Kafa G, Seday U (2009b) Field performance and molecular diversification of lemon selections. Scientia Horticulturae 120: 473–478.
• Uzun A (2009c) Tutunçgillerde Genetik Çeşitliliğin SRAP Markırları ile Karakterizasyonu. Doktora Tezi. Çukurova Üniversitesi, Fen Bilimleri Enstitüsü, Bahçe Bitkileri Anabilim Dalı. Adana.
• Uzun A, Yesiloglu T, Polat I, Aka-Kacar Y, Gulsen O, Yıldırım B, Tuzcu O, Tepe S, Canan I, Anıl S (2011) Evaluation of Genetic Diversity in Lemons and Some of Their Relatives Based on SRAP and SSR Markers. Plant Mol. Biol. Rep. 29: 693-701.