Genetic Diversity in Iranian Melon Populations and Hybrids Assessed by IRAP and REMAP Markers

Authors
S. Gholamzadeh khoei
B. Abdollahi Mandoulakani
I. Bernousi
Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Urmia University, Urmia, Islamic Republic of Iran.
Abstract
Retrotransposons (RTNs) constitute informative molecular markers for plant species because of their ability to integrate into a multitude of loci throughout the genome and thereby generate insertional polymorphisms between individuals. In the present study, RTN-based molecular markers, IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism), were applied to study RTN integration events and genetic diversity in 100 melon genotypes (88 genotypes from 11 populations, three inbred lines, and 9 hybrids). A total of 94 and 262 loci were amplified using 5 IRAP and 15 REMAP primers, respectively. The percentage of polymorphic loci (PPL) in populations ranged from 39% (Zivari Shahrood) to 48% (Shadegani E). The Mantel test between IRAP and REMAP cophenetic matrices evidenced no significant correlation (r= 0.29). IRAP+REMAP-based cluster analysis using UPGMA algorithm and Dice similarity coefficient depicted 6 groups among 100 melon genotypes. AMOVA revealed the higher level of genetic variation within populations (67%) compared to among populations (33%). The mean Fst values of all groups, except for group VI, were more than 0.20, demonstrating differentiation among the populations and genetic structure of the studied melon collection.

Keywords

1. Abdollahi Mandoulakani, B., Piri, Y., Darvishzadeh, R., Bernoosi, I. and Jafari, M. 2012. Retroelement Insertional Polymorphism and Genetic Diversity in Medicago sativa Populations Revealed by IRAP and REMAP markers. Plant Mol. Biol. Rep., 8: 137-146.
2. Ausubel, F. M., Brent, R. R., Kingston, E., Moore, D. D., Seidman, J. G., Smith, J. A., Struhl, K., Albright, L. M., Coen, D. M. and Varki, A. 1995. Current Protocols in Molecular Biology. Jon Wiley, New York.
3. Biswas, M. K., Baig, M. N. R., Cheng, Y. J. and Deng, X. X. 2010. Retrotransposon Based Genetic Similarity within the Genus Citrus and Its Relatives. Genet. Resour. Crop, 7: 963-972
4. Branco, C. J. S., Vieira, E. A., Malone, G., Kopp, M. M., Malone, E., Bernardes, A., Mistura, C. C., Carvalho, F. I. F. and Oliveira, C. A. 2007. IRAP and REMAP Assessments of Genetic Similarity in Rice. J. Appl. Genet., 2: 107-113.
5. Carvalho, A., Guedes-Pinto, H. and Lima-Brito, J.E. 2012. Genetic Diversity in Old Portuguese Durum Wheat Cultivars Assessed by Retrotransposon-based Markers. Plant Mol. Biol. Rep., 30: 578-589.
6. Carvalho, A., Guedes-Pinto, H., Martins-Lopes, P. and Lima-Brito, J. E. 2010. Genetic Variability of Old Portuguese Bread Wheat Cultivars Assayed by IRAP and REMAP Markers. Ann. Appl. Biol., 156: 337-345.
7. Evanno, G., Regnaut, S. and Goudet, J. 2005. Detecting the Number of Clusters of Individuals Using the Software Structure: A Simulation Study. Mol. Ecol., 14: 2611–2620.
8. Fabriki Ourang, S., Shams-Bakhsh, M., Jalali Javaran, M. and Ahmadi, J. 2012. Analysis of Genetic Diversity of Iranian Melons (Cucumis melo L.) Using ISSR Markers. Iranian J. Biol., 22: 271-281. (in persian)
9. Falush, D., Stephens, M., Pritchard and J. K. 2007. Inference of Population Structure Using Multilocus Genotype Data: Dominant Markers and Null Alleles. Mol. Ecol. Note., 7: 574-578.
10. Garcia-Mas, J. Benjak. A., Sanseverino, W., Bourgeois, M., Mir, G., González, V. M., Hénaff, E., Câmara, F., Cozzuto, L., Lowy, E., Alioto, T., Capella-Guitérrez, S., Blanca, J., Cañizares, J., Ziarsolo, P., Gonzalez-Ibeas, D., Rodríguez-Moreno, L., Droege, M., Du, L., Alvarez-Tejado, M., Lorente-Galdós, B., Melé, M., Yang, L., Weng, Y., Navarro, A., Marques-Bonet, T., Aranda, M. A., Nuez, F., Picó, B., Gabaldón, T., Roma, G., Guigo, R., Casacuberta, J. M., Arús, P. and Puigdomènech, P. 2012. The Genome of Melon (Cucumis melo L.). Proc. Natl. Acad. Sci., 109: 11872-11877.
11. Kalendar, R., Flavell, A.J., Ellis, T. H. N., Sjakste, T., Moisy, C. and Schulman, A. H. 2011. Analysis of Plant Diversity with Retrotransposon-based Molecular Markers. Heredity, 106: 520–530.
12. Kalendar, R., Grob, T., Regina, M., Souniemi, A. and Schulman, A. H. 1999. IRAP and REMAP: Two New Retrotransposon-based DNA Fingerprinting Techniques. Theor. Appl. Genet., 98: 704-711.
13. Kirkbride, J. H. 1993. Biosystematic Monograph of the Genus Cucumis (Cucurbitaceae). Parkway Publication Boone, North Carolina, USA 159 PP.
14. Kristiina, A. K., Kalendar, R. and Schulman, A. H. 2006. TRIM Retrotransposons Occur in Apple and Are Polymorphic between Varieties but Not Sports. Theor. Appl. Genet., 112: 999-1008.
15. Lou, Q. and Chen, J. 2007. Ty1-copia Retrotransposon-based SSAP Marker Development and Its Potential in the Genetic Study of Cucurbits. Genome, 50: 802-810.
16. Mardi, M., Naghavi, M. R., Pirseyedi, S. M., Kazemi Alamooti, M., Rashidi Monfared, S., Ahkami, A. H., Omidbakhsh, M. A., Alavi, N. S., Salehi Shanjani, P. and Katsiotis, A. 2011. Comparative Assessment of SSAP, AFLP and SSR Markers for Evaluation of Genetic Diversity of Durum Wheat (Triticum turgidum L. var. durum). J. Agr. Sci. Tech., 13: 905-920
17. Nasri, S., Abdollahi Mandoulakani, B., Darvishzadeh, R. and Bernousi, I. 2013. Retrotransposon Insertional Polymorphism in Iranian Bread Wheat Cultivars and Breeding Lines Revealed by IRAP and REMAP Markers. Biochem. Genet., 51: 927-943.
18. Onofrio, C. D., Lorenzis, G. D., Giordani, T., Natali, L., Cavallini, A. and Scalabrelli, G. 2010. Retrotransposon-based Molecular Markers for Grapevine Species and Cultivars Identification. Tree Genet. Genom., 6: 451-466.
19. Peakall, R. and Smouse, P. 2006. GENEALEX 6: Genetic Analysis in Excel. Population Genetic Software for Teaching and Research. Mol. Ecol. Note., 6: 288-295.
20. Ramallo, E., Kalendar, R., Schulman, A.H. and Martinez, J. A. 2008. Reme1: A Copia Retrotransposon in Melon is Transcriptionally Induced by UV Light. Plant Mol. Biol., 66: 137-150.
21. Rohlf, F. J. 2000. NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System, Version 2.1. Exeter Software, New York.
22. Smykal, P., Bacova-Kerteszova, N., Kalendar, R., Corander, J., Schulman, A. H. and Pavelek, M. 2011. Genetic Diversity of Cultivated Flax (Linum usitatissimum L.) Germplasm Assessed by Retrotransposon-based Markers. Theor. Appl. Genet., 122: 1385-1397.
23. Tam, S. M., Mhiri, C., Vogelaar, A., Kerkveld, M., Pearce, S. R. and Le Grandbastien, M. A. 2005. Comparative Analyses of Genetic Diversities within Tomato and Pepper Collections Detected by Retrotransposon-based SSAP, AFLP and SSR. Theor. Appl. Genet., 110: 819-831.
24. Vukich, M., Schulman, A.H., Giordani, T., Natali, L., Kalendar, R. and Cavallini, A. 2009. Genetic Variability in Sunflower (Helianthus annuus L.) and in the Helianthus Genus as Assessed by Retrotransposon-based Molecular Markers. Theor. Appl. Genet., 119: 1027-1038.
25. Yap, I. V. and Nelson, R. J. 1996. Winboot: A Program for Performing Bootstrap Analysis of Binary Data to Determine the Confidence Limits of UPGMA-based Dendrograms. IRRI, Manila.
Journal of Agricultural Science and Technology
Volume 17, Issue 5
September and October 2015
Pages 1267-1277