GENETIC DIVERSITY OF CROCUS SATIVUS AND ITS CLOSE RELATIVE SPECIES ANALYZED BY iPBS-RETROTRANSPOSONS

Year 2017, , 243 - 252, 15.12.2017

Aysun Gedık Duygu Ates Semih Erdogmus Gonul Comertpay Muhammed Bahattin Tanyolac , Hakan Ozkan

https://doi.org/10.17557/tjfc.357426

Cited By: 7

Abstract

Saffron (Crocus L.) is a member of Crocoideae, the biggest of four subfamilies in the Iridaceae family. It has 2n = 3x = 24 chromosomes and is triploid; thus, it is sterile. In previous research, different molecular DNA markers were used but molecular characterization and genetic diversity of this complex genus have not yet been clarified. Therefore, current study aimed to determine the molecular characterization of saffron and its close relative species using inter-primer binding site (iPBS)-retrotransposon markers. Eighty-three iPBS-retrotransposon primers were used in 28 C. sativus genotypes and 17 close relative species of saffron to identify their genetic diversity. Sixteen polymorphic iPBS-retrotransposon primers generated a total of 401 polymorphic scorable bands. The mean PIC value, Nei’s genetic diversity and Shannon’s information index (I) were calculated as 0.85, 0.16 and 0.29, respectively. The results of the Unweighted Pair Group Method with Arithmetic mean UPGMA dendrogram and Principal Coordinates Analysis PCoA analysis indicated a spatial representation of the relative genetic distances among 28 saffron samples and the 17 close relative species were categorized under two distinct groups. Saffron genotypes showed very limited genetic variation and according to the iPBS-retrotransposon data, its close relatives were C. cartwrightianus and C. pallasii subsp. pallasii.

Keywords

Crocus sativus, genetic diversity, inter-primer binding site retrotransposons, saffron

References

• Abdullaev, F.I. 2002. Cancer chemopreventive and tumoricidal properties of saffron (Crocus sativus L.). Exp biol med. 227(1): 20-25.
• Alavi-Kia, S., S. Mohammadi, S. Aharizad and M. Moghaddam. 2008. Analysis of genetic diversity and phylogenetic relationships in Crocus genus of Iran using inter-retrotransposon amplified polymorphism. Biotechnol Biotec Eq. 22 (3): 795-800.
• Alsayied, N.F., J.A. Fernández, T. Schwarzacher and J. Heslop-Harrison. 2015. Diversity and relationships of Crocus sativus and its relatives analysed by inter-retroelement amplified polymorphism (IRAP). Ann Bot-London. 116(3): 359-368.
• Andeden, E.E., F.S. Baloch, M. Derya, B. Kilian and H. Ozkan. 2013. iPBS-Retrotransposons-based genetic diversity and relationship among wild annual Cicer species. J Plant Biochem Biot. 22(4): 453-466.
• Arslan, N., A. Ozer and R. Akdemir. 2007. Cultivation of saffron (Crocus sativus L.) and effects of organic fertilizers to the flower yield. Paper read at I International Medicinal and Aromatic Plants Conference on Culinary Herbs. 826.
• Babaei, S., M. Talebi, M. Bahar and H. Zeinali. 2014. Analysis of genetic diversity among saffron (Crocus sativus) accessions from different regions of Iran as revealed by SRAP markers. Sci Hortic-Amsterdam. 171: 27-31.
• Baloch, F.S., A. Alsaleh, L.E.S. de Miera, R. Hatipoglu, V. Ciftci, T. Karakoy, M. Yildiz and H. Ozkan. 2015a. DNA based iPBS-retrotransposon markers for investigating the population structure of pea (Pisum sativum) germplasm from Turkey. Biochem Syst Ecol. 61: 244-252.
• Baloch, F.S., M. Derya, E.E. Andeden, A. Alsaleh, G. Comertpay, B. Kilian and H. Ozkan. 2015b. Inter-primer binding site retrotransposon and inter-simple sequence repeat diversity among wild Lens species. Biochem Syst Ecol. 58: 162-168.
• Baránek, M., M. Meszáros, J. Sochorová, J. Čechová and J. Raddová. 2012. Utility of retrotransposon-derived marker systems for differentiation of presumed clones of the apricot cultivar Velkopavlovická. Sci Hortic-Amsterdam. 143: 1-6.
• Basti, A.A., E. Moshiri, A.A. Noorbala, A.H. Jamshidi, S.H. Abbasi and S. Akhondzadeh. 2007. Comparison of petal of Crocus sativus L. and fluoxetine in the treatment of depressed outpatients: a pilot double-blind randomized trial. Prog Neuro-Psychoph. 31(2): 439-442.
• Bento, M., H.S. Pereira, M. Rocheta, P. Gustafson, W. Viegas and M. Silva. 2008. Polyploidization as a retraction force in plant genome evolution: sequence rearrangements in Triticale. PLoS One. 3(1): e1402.
• Biswas, M.K., M. Baig, Y.J. Cheng and X.X. Deng. 2010. Retro-transposon based genetic similarity within the genus Citrus and its relatives. Genet Resour Crop Ev. 57(7): 963-972.
• Branco, C. J., E.A. Vieira, G. Malone, M.M. Kopp, E. Malone, A. Bernardes, C.C. Mistura, F. I. Carvalho and C.A. Oliveira. 2007. IRAP and REMAP assessments of genetic similarity in rice. J Appl Genetics. 48(2): 107-113.
• Brandizzi, F. and M. Grilli Caiola. 1998. Flow cytometric analysis of nuclear DNA in Crocus sativus and allies (Iridaceae). Plant Syst Evol. 211(3): 149-154.
• Busconi, M., L. Colli, R.A. Sánchez, M. Santaella, M. D.L.M. Pascual, O. Santana, M. Roldán and J.A. Fernández. 2015. AFLP and MS-AFLP analysis of the variation within saffron crocus (Crocus sativus L.) germplasm. PLoS One. 10(4): e0123434.
• Caiola, M.G., P. Caputo and R. Zanier. 2004. RAPD analysis in Crocus sativus L. accessions and related Crocus species. Biol Plantarum. 48(3): 375-380.
• Castillo, R., J.A. Fernández and L. Gómez-Gómez. 2005. Implications of carotenoid biosynthetic genes in apocarotenoid formation during the stigma development of Crocus sativus and its closer relatives. Plant Physiol. 139(2): 674-689.
• Comertpay, G., F. Baloch, M. Derya, E. Andeden, A. Alsaleh, H. Surek and H. Ozkan. 2015. Population structure of rice varieties used in Turkish rice breeding programs determined using simple-sequence repeat and inter-primer binding site-retrotransposon data. Genet Mol Res. 15(1).
• D’Onofrio, C., G. De Lorenzis, T. Giordani, L. Natali, A. Cavallini and G. Scalabrelli. 2010. Retrotransposon-based molecular markers for grapevine species and cultivars identification. Tree Genet Genomes. 6(3): 451-466.
• Doyle, J.J. J.L. Doyle. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin. 19:11-15.
• Erol, O., H.B. Kaya, L. Sik, M. Tuna, L. Can and M.B. Tanyolac. 2014. The genus Crocus, series Crocus (Iridaceae) in Turkey and 2 East Aegean islands: a genetic approach. Turk J Biol. 38(1): 48-62.
• Fang-Yong, C. and L. Ji-Hong. 2014. Germplasm genetic diversity of Myrica rubra in Zhejiang Province studied using inter-primer binding site and start codon-targeted polymorphism markers. Sci Hortic-Amsterdam. 170: 169-175.
• Fernández, J.A. 2004. Biology, biotechnology and biomedicine of saffron. Recent Research Developments in Plant Science. 127-159.
• Fernández, J.A. 2006. Anticancer properties of saffron, Crocus sativus Linn. Advances in phytomedicine. 2: 313-330.
• Frello, S. and J. Heslop-Harrison. 2000. Repetitive DNA sequences in Crocus vernus Hill (Iridaceae): the genomic organization and distribution of dispersed elements in the genus Crocus and its allies. Genome. 43(5): 902-909.
• Frizzi, G., M. Miranda, C. Pantani and F. Tammaro. 2007. Allozyme differentiation in four species of the Crocus cartwrightianus group and in cultivated saffron (Crocus sativus). Biochem Syst Ecol. 35(12): 859-868.
• Gailite, A. and D. Rungis. 2012. An initial investigation of the taxonomic status of Saussurea esthonica Baer ex Rupr. utilising DNA markers and sequencing. Plant Syst Evol. 298(5): 913-919.
• Goldblatt, P., T.J. Davies, J.C. Manning, M. Van Der Bank and V. Savolainen. 2006. Phylogeny of Iridaceae subfamily Crocoideae based on a combined multigene plastid DNA analysis. Aliso. 22: 399-411.
• Gribbon, B., S. Pearce, R. Kalendar, A. Schulman, L. Paulin, P. Jack, A. Kumar and A. Flavell. 1999. Phylogeny and transpositional activity of Ty1-copia group retrotransposons in cereal genomes. Mol Gen Genet. 261(6): 883-891.
• Guo, D.L., M.X. Guo, X.G. Hou and G.H. Zhang. 2014. Molecular diversity analysis of grape varieties based on iPBS markers. Biochem Syst Ecol. 52: 27-32.
• Hadizadeh, F., S. Mohajeri and M. Seifi. 2010. Extraction and purification of crocin from saffron stigmas employing a simple and efficient crystallization method. Pak J Bio Sci. 13(14): 691.
• Harpke, D., A. Carta, G. Tomović, V. Ranđelović, N. Ranđelović, F. R. Blattner and L. Peruzzi. 2015. Phylogeny, karyotype evolution and taxonomy of Crocus series Verni (Iridaceae). Plant Syst Evol. 301(1): 309-325.
• Harpke, D., S. Meng, T. Rutten, H. Kerndorff and F.R. Blattner. 2013. Phylogeny of Crocus (Iridaceae) based on one chloroplast and two nuclear loci: ancient hybridization and chromosome number evolution. Mol Phylogenet Evol. 66(3): 617-627.
• Huson, D.H. and D. Bryant. 2006. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 23(2): 254-267.
• Kafkas, S. 2006. Phylogeny, evolution and biodiversity in the genus Pistacia (Anacardiaceae). Plant genome: biodiversity and evolution 1 (part C). 525-557.
• Kalendar, R., K. Antonius, P. Smýkal and A. H. Schulman. 2010. iPBS: a universal method for DNA fingerprinting and retrotransposon isolation. Theor Appl Genet. 121(8): 1419-1430.
• Kalendar, R., A. Flavell, T. Ellis, T. Sjakste, C. Moisy and A.H. Schulman. 2011. Analysis of plant diversity with retrotransposon-based molecular markers. Heredity. 106(4): 520-530.
• Kerndorff, H. and E. Pasche. 2004. Two New Taxa of the Crocus bißorus Aggregate (Liliiflorae, Iridaceae) from Turkey. Biologiezentrum Linz/Austria; download unter www.biologiezentrum.at
• Kerndorff, H. and E. Pasche. 2011. Two new taxa of Crocus (Liliiflorae, Iridaceae) from Turkey: Stapfia. 95: 4-17.
• Kerndorff, H., E. Pasche, F. Blattner and D. Harpke. 2013. A new species of Crocus (Liliiflorae, Iridaceae) from Turkey. Stapfia. 99: 141-144.
• Kerndorff, H., E. Pasche, D. Harpke and F. Blattner. 2012. Seven new species of Crocus (Liliiflorae, Iridaceae) from Turkey. Stapfia. 97: 3-16.
• Kumar, L.S. 1999. DNA markers in plant improvement: an overview. Biotechnol Adv. 17(2): 143-182.
• Kumar, P., V. Gupta, A. Misra, D. Modi and B. Pandey. 2009. Potential of molecular markers in plant biotechnology. Plant Omics. 2(4): 141.
• Larsen, B., J. Orabi, C. Pedersen and M. Ørgaard. 2015. Large intraspecific genetic variation within the Saffron-Crocus group (Crocus L., series Crocus; Iridaceae). Plant Syst Evol. 301(1): 425-437.
• Manninen, O., R. Kalendar, J. Robinson and A. Schulman. 2000. Application of BARE-1 retrotransposon markers to the mapping of a major resistance gene for net blotch in barley. Mol Gen Genet. 264(3): 325-334.
• Mathew, B. 1982. The Crocus, a revision of the genus Crocus. BT Batsford, London.
• Mehmood, A., M.J. Jaskani, S. Ahmad and R. Ahmad. 2013. Evaluation of genetic diversity in open pollinated guava by iPBS primers. Pak. J. Agri. Sci. 50(4): 591-597.
• Mir, J.I., N. Ahmed, M.H. Khan, T.A. Mokhdomi, S.H. Wani, S. Bukhari, A. Asif and R.A. Qadri. 2015. Molecular characterization of saffron-potential candidates for crop improvement. Not Sci Biol. 7(1): 81.
• Mondini, L., A. Noorani and M.A. Pagnotta. 2009. Assessing plant genetic diversity by molecular tools. Diversity .1(1): 19-35.
• Moraga, A.R., A. Trapero-Mozos, L. Gómez-Gómez and O. Ahrazem. 2010. Intersimple sequence repeat markers for molecular characterization of Crocus cartwrightianus cv. albus. Ind Crop Prod 32(2): 147-151.
• Mortazavi, S., M. Kamali Moghaddam, S. Safi and R. Salehi. 2012. Saffron petals, a by-product for dyeing of wool fibers. Prog Color Colorants Coat. 5: 75-84.
• Mousavi, S.Z. and S.Z. Bathaie. 2011. Historical uses of saffron: Identifying potential new avenues for modern research. Avicenna Journal of Phytomedicine. 1(2): 57-66.
• Negbi, M. 2003. Saffron: Crocus sativus L: CRC Press.
• Nei, M. 1987. Molecular evolutionary genetics: Columbia university press.
• Nei, M. and W.H. Li. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. P Natl Acad Sci. 76(10): 5269-5273.
• Nemli, S., T. Kianoosh and M.B. Tanyolac. 2015. Genetic diversity and population structure of common bean (Phaseolus vulgaris L.) accessions through retrotransposon-based interprimer binding sites (iPBSs) markers. Turk J Agric For. 39(6): 940-948.
• Nørbæk, R., K. Brandt, J.K. Nielsen, M. Ørgaard and N. Jacobsen. 2002. Flower pigment composition of Crocus species and cultivars used for a chemotaxonomic investigation. Biochem Syst Ecol. 30(8): 763-791.
• Ozhatay, N. 2002. Diversity of bulbous monocots in Turkey with special reference. Chromosome numbers. Pure Appl Chem. 74(4): 547-555.
• Pearce, S.R., D. Li, A. Flavell, G. Harrison, J. Heslop-Harrison and A. Kumar. 1996. TheTy1-copia group retrotransposons inVicia species: copy number, sequence heterogeneity and chromosomal localisation. Mol Gen Genet. 250(3): 305-315.
• Peruzzi, L. and A. Carta. 2011. Crocus ilvensis sp. nov.(sect. Crocus, Iridaceae), endemic to Elba Island (Tuscan archipelago, Italy). Nord J Bot. 29(1):ö6-13.
• Petersen, G., O. Seberg, S. Thorsøe, T. Jørgensen and B. Mathew. 2008. A phylogeny of the genus Crocus (Iridaceae) based on sequence data from five plastid regions. Taxon. 57(2): 487-499.
• Pitsikas, N. and N. Sakellaridis. 2006. Crocus sativus L. extracts antagonize memory impairments in different behavioural tasks in the rat. Behav Brain Res. 173(1): 112-115.
• Rohlf, F. 2000. NTSYS-pc Numerical taxonomy and multivariate analysis system, version 2.01. Setauket New York: Applied Biostatistics: Inc.
• Rubio-Moraga, A., R. Castillo-López, L. Gómez-Gómez and O. Ahrazem. 2009. Saffron is a monomorphic species as revealed by RAPD, ISSR and microsatellite analyses. BMC research notes. 2(1): 1.
• Saeidi, H., M.R. Rahiminejad and J. Heslop-Harrison. 2008. Retroelement insertional polymorphisms, diversity and phylogeography within diploid, D-genome Aegilops tauschii (Triticeae, Poaceae) sub-taxa in Iran. Ann Bot-London. 101(6): 855-861.
• SanMiguel, P., A. Tikhonov, Y.K. Jin and N. Motchoulskaia. 1996. Nested retrotransposons in the intergenic regions of the maize genome. Science. 274(5288): 765.
• Schneider, I., H. Kerndorff and E. Pasche. 2012. Chromosome numbers of Turkish Crocus (Liliiflorae, Iridaceae) and their geographical distribution. Feddes repertorium. 123(1): 73-79.
• Schulman, A.H., A.J. Flavell and T.N. Ellis. 2004. The application of LTR retrotransposons as molecular markers in plants. Mobile Genetic Elements: Protocols and Genomic Applications. 145-173.
• Schulman, A.H., A.J. Flavell, E. Paux and T.N. Ellis. 2012. The application of LTR retrotransposons as molecular markers in plants. Mobile Genetic Elements: Protocols and Genomic Applications. 115-153.
• Seberg, O. and G. Petersen. 2009. How many loci does it take to DNA barcode a crocus? PLoS One. 4(2): e4598.
• Smýkal, P., N. Bačová-Kerteszová, R. Kalendar, J. Corander, A.H. Schulman and M. Pavelek. 2011. Genetic diversity of cultivated flax (Linum usitatissimum L.) germplasm assessed by retrotransposon-based markers. Theor Appl Genet. 122(7): 1385-1397.
• Tam, S.M., C. Mhiri, A. Vogelaar, M. Kerkveld, S.R. Pearce and M.A. Grandbastien. 2005. Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and SSR. Theor Appl Genet. 110(5): 819-831.
• Verma, S. and A. Bordia. 1998. Antioxidant property of Saffron in man. Indian J Med Sci. 52(5): 205-207.
• Weising, K., H. Nybom, M. Pfenninger, K. Wolff and G. Kahl. 2005. DNA fingerprinting in plants: principles, methods, and applications: CRC press.
• Yildiz, M., M. Kocak and F. Baloch. 2015. Genetic bottlenecks in Turkish okra germplasm and utility of iPBS retrotransposon markers for genetic diversity assessment. Genet Mol Res. 14(3): 10588-10602.
• Yuzbasioglu, S., S. Aslan and N. Ozhatay. 2015. Crocus thracicus (Iridaceae), a new species from north-western Turkey. DOI: http://dx.doi.org/10.11646/phytotaxa.197.3.4.
• Zubor, A., G. Surányi, Z. Győri, G. Borbély and J. Prokisch. 2003. Molecular biological approach of the systematics of Crocus sativus L. and its allies. Paper read at I International Symposium on Saffron Biology and Biotechnology. 650