SSR Markers in Genetic Diversity Assessment of Fig Ficus carica L. Populations in Kurdistan Region – Iraq
DOI:
https://doi.org/10.25271/sjuoz.2020.8.4.758Keywords:
Fig, Nucleic acids, SSR, Genetic diversityAbstract
In the current study, simple sequence repeats (SSR) markers were used to assess the phylogenetic relationships and to investigate genetic polymorphism among 28 fig landraces in Kurdistan Region-Iraq. Fifteen SSR loci produced 73 alleles were produced across all studied genotypes. The observed heterozygosity (Ho) was (0.000) detected with all primers. The expected heterozygosity (He) was ranged from 0.000 to 0.875. The Polymorphic information content PIC was ranged from 0.000 to 0.843, and Fixation index values were ranged from +0.999 to +1.000. The SSR profiles produced were further used for assessing similarities (genetic distance) between the cultivars studied. Genetic distance calculation was achieved using computer software (NTSYS-PC). The genetic distances among the studied genotypes were ranged between (0.1029-0.9485). Genetic distances were supported by the developed dendrogram using UPGMA method. This dendrogram was split into two major groups, and each group was further divided into subgroups. The product of the general data and study of the clusters suggested that almost all the fig cultivars revealed significant genetic diversities. The microsatellite markers allowed clearly the differentiation between studied fig landraces and gave the reliability of these markers in fingerprinting of fig genotypes. It is worth to mention that the study findings will help the management of fig genotypes and might help the selection of landraces for future breeding program in this region.
References
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Baraket, G., Abdelkrim, A., Mars, M., & Hannachi, A. S. (2011). Comparative Assessment of SSR and AFLP Markers for Evaluation of Genetic Diversity and Conservation of Fig, Ficus carica L. Plant Mol Biol Rep, 29: 171–184.
Botstein, D., White, R. L., Skolnick, M. H., & Davis, R.W. (1980). Construction of a genetic map in man using restriction fragment length polymorphisms. American Journal of Human Genetic, 32: 314-331.
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Cervera, M. T., Remington, D., Frigerio, J. M., Storme , V., Ivens, B., Boerjan, W., & Plomion, C. (2000). Improved AFLP analysis of tree species. Canadian Journal of Forest Research, 30 (10): 1608-1616.
Chatti, K. G. B. A. A., Saddoud, O., Mars, M., Trifi, M., & Salhihannachi, A. (2010). Development of molecular toolls for characterization and genetic diversity analysis in Tunisian fig (Ficus carica L.) cultivars. Biochemical Genetics, 48 (9-10): 789-806.
Cooper, G. (1995). Analysis of genetic variation and sperm competition in Dragon flies. D. Phil. Thesis, Oxford University.
Dehgan, B. (1998). Landscape Plants for Subtropical Climates. University Press of Florida, Gainesville, FL.
Esselman E. J., Crawford, D. J., Brauner, S., Stuessy, Anderson, T. F., G. J., & Silva, O. M. (2000). RAPD marker diversity within and divergence among species of Dendroseris (Asteraceae: Lactuceae). American Journal of Botany, 87: 591–596.
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Flaishman, M., Rodov, V., & Stover, E. (2008). The Fig: Botany, Horticulture, and Breeding, Horticultural Reviews, 34: 113-197.
Fornari, B., Malvolti, M. E., Taurchini, D., Fineschi, S., Beritognolo, I., McCaglia, E., & Cannata, F. (2001). Isozyme and organellar DNA analysis of genetic diversity in natural/ naturalized European and Asiatic walnut (Juglans regia) populations. Acta Hort, 544: 167-178.
Ganopoulos, I. A., Xanthopulou, A., Molassiotis, E., Karagiannis, T., Moysiadis, P., Katsaris, F., Aravanopoulos, A., Tsaftaris, A., Kalivas, A., & Madesis, P. (2015). Mediterranean basin (Ficus carica L.) from genetic diversity and structure to authentication of protected designation of origin cultivar using microsatellite markers. Trees, 29 (6): 1959-1971.
Giraldo, E., Lopez-corrales, M., & Jose Ignacio Hormaza, J. I. (2010). Optimization of the management of an ex-situ germplasm bank in common fig with SSR. American Journal of Horticulture Science, 133: 69-77.
Goldstein, D.B., & Schlotterer, C. (1999). Microsatellites, evolution and applications. Oxford University Press, New York.
Govindaraij, M., Vetriventhan, M., & Srinivasan, M. (2015). Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives. Genetics Research International, 2015, 1-14. Article ID 431487.
Guasmi, F., Ferchichi, A., Farés, K., & Touil, L. (2006). Identification and differentiation of Ficus carica L. cultivars using inter simple sequence repeat markers. Afr. J. Biotechnol, 5: 1370-1374.
Gupta, P.K., Varshney, R.K., Sharma, P.C., & Ramesh, B. (1999). Molecular markers and their applications in wheat breeding. Plant Breed, 118: 369-390.
Gregory T. R. (2008). Understanding Evolutionary Trees. Evo Edu Outreach, 1(2): 121-137.
Ikegami, H., Nogata, H., Hirashima, K., Mitsuo Awamura, M., & Nakahara, T. (2009). Analysis of genetic diversity among European and Asian fig varieties (Ficus carica L.) using ISSR, RAPD, and SSR markers. Genetic Resources and Crop Evolution, 56: 201-209.
Jarne, P., & Lagoda, P. (1996). Microsatellites, from molecules to populations and back. Trends Ecol. Evol, 11: 424-429.
Khadari, B., Ater, M., Mamouni, A., Roger, J. P., & Kjellberg, F. (2004). Molecular characterization of Moroccan fig germplasm using inter simple sequence repeat and simple sequence repeat markers to establish a reference collection. Horticulture Science, 40 (1): 29-32.
Kumari, A., Sinha, S., Rashmi, K., Mandal, S. S., & Sahay, S. (2018). Genetic diversity analysis in maize (Zea mays L.) using SSR markers. Pharmacognosy and Phytochemistry S PP. 1116-1120. E- ISSN: 2278-4136 P-ISSN: 2349-8234.
Lansky E. P., Paavilainen, H. M., Pawlus, A. D., & Newman, R. A. (2008). Ficus spp. (fig): ethnobotany and potential as anticancer and anti-inflammatory agents. Journal of Ethnopharmacol, 119: 195-213.
Lazreg-Aref, H., Mars, M., Fekih, A., Aouni, M., & Said, K. (2012). Chemical composition and antibacterial activity of a hexane extract of Tunisian caprifig latex from the unripe fruit of Ficus carica. Pharmaceutical Biology, 50: 407-412.
Li, G. T., Ai, C. X., Zhang, L. S., Wei, H. R., & Liu, Q. Z. (2011). ISSR Analysis of Genetic Diversity among Seedling Walnut (Juglans spp.) Populations. Journal of Plant Genetic Resources, 12 (4): 640-645.
Liang, W., Dondini, L., Franceschi, P. D., Paris, R., Sansavini, S., & Tartarin, S. (2015). Genetic diversity, population structure and construction of a core collection of apple cultivars from Italian germpalsm. Plant Molecular Biology Reporter, 33 (3): 458-473.
Litt, M., & J. M. Luty. (1989). A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am. J. Hum. Genet, 44:397–401.
Malvolti, M. E., Pollegioni, P., Mapelli, S., & Cannata, F. (2010). Research of Juglans regia provenances by molecular, morphological and biochemical markers: a case study in Italy. Bioremediation, Biodiversity and Bioavailability, 4: 84-92.
Maniatis, T., Fritsch, E. F., & Sambrook, J. (2001). In vitro application of DNA by the Polymerase Chain Reaction, in Molecular Cold Spring Harbor Laboratory Press, New York, U.S.A., p. 691.
Neal, M.C. (1965). In Gardens of Hawai'i. Bernice P. Bishop Museum, Special Publication 40, Honolulu, HI.
Niu, J. X., Wang, L., Dai, Y. X., Li, R., Yang, X. K., & Lv., J. Q. (2007). Identification of AFLP Makers Linked to Early-Bearing Gene in Walnut. Molecular Plant Breeding, 5 (2): 266-268.
Perez-Jimenez, M. L. B., Dorado, G., Pujadas-Salva, A., Guzman, G., & Hernandez, P. (2012). Analysis of genetic diversity of southern Spain fig tree (Ficus carica L.) and reference materials as a tool for breeding and conservation. Hereditas, 149 (3): 108-113.
Rousset, F. (2008). Genepop’007: a complete reimplementation of the Genepop software for Windows and Linux. Mol. Ecol. Resources. 8: 103-106.
Saddoud, O., Barket, G., Chatti, K., Trifi, M., Marrakchi, M., Mars, M., & Salhi-Hannachi, A. (2011). Using morphological characters and simple sequence repeat (SSR) markers to characterize Tunisian fig (Ficua carica L.) cultivars. Acta Biologica Cracoviensia Series Botanica, 53: 7-14.
Shahbaz, S.E. (2010). Trees and shrubs. Afield guide to the trees and shrubs of Kurdistan region of Iraq . Duhok University Press. Iraq.pp601.
Takahashi, Y., Tanaka, R., Yamamoto, D., Noriyuki, S., & Kawata, M. (2018). Balanced genetic diversity improves population fitness. Proceeding Royal Society B, 285: 1-17.
Tautz, D., Trick, M., & Dover, G.A. (1986). Cryptic simplicity in DNA is a major source of genetic variation. Nature, 322: 652-656.
Teoman, S., Ipekl, M., Erturk, U., Tangu, N. A., Durgut, E., Barut, E., Ercisli, S., and Ipek, A. (2017). Assessment of Genetic Relationship among Male and Female Fig Genotypes Using Simple Sequence Repeat (SSR) Markers .Not Bot Horti Agrobo, 45 (1): 172-178.
Trichopoulou, A., Vasilopoulou, E., Georga, K., Soukara, S., & Dilis, V. (2006). Traditional foods: why and how to sustain them. Trends Food Science Technology, 17: 498-504.
Urrestarazu, J., Miranda, C., Santesteban, L. G., & Royo, J. B. (2012). Genetic diversity and structure of local apple cultivars from northeastern Spain assessed by microsatellite markers. Tree Genetics and Genomes, 8: 1163-1180.
Vignes, H., Hossa, M., Beaune, D., Fevre, D., Anstett, M. C., Borges, R. M., Kjellberg, F., & Chevallier, M. H. (2006). Development and characterization of microsatellite markers for a monoecious Ficus species, Ficus insipida, and cross-species amplification among different sections of Ficus. Molecular Ecology Notes, 6: 792-795.
Weigand F., Baum, M., & Udupa, S. (1993). DNA molecular marker technics, technical manual, No. 20 International Center for Agricultural Research in the Dry Areas (ICARDA). Aleppo, Syria.
Zavodna, M., Arens, P., Van, P. J., & Vosman, B. (2005). Development and characterization of microsatellite markers for two dioecious Ficus species. Molecular Ecology Notes, 5: 355-357.
Zhang, Q., Gao, Y. J., Saghai-Maroof, M. A., Yang, S. H., & Li, J. X. (1995). Molecular diveryence and hybrid performance in rice. Molecular Breeding, 1: 133-142.
AL-Nema, Q. S., & AL-Mallah, M. K. (2020). Electrofusion of Mesophyll Protoplasts From Two Varieties of Sugar Beet, (Beta vulgaris L.). Journal of Life and Bio-sciences Research, 1 (1): 22-25
Baraket, G., Abdelkrim, A., Mars, M., & Hannachi, A. S. (2011). Comparative Assessment of SSR and AFLP Markers for Evaluation of Genetic Diversity and Conservation of Fig, Ficus carica L. Plant Mol Biol Rep, 29: 171–184.
Botstein, D., White, R. L., Skolnick, M. H., & Davis, R.W. (1980). Construction of a genetic map in man using restriction fragment length polymorphisms. American Journal of Human Genetic, 32: 314-331.
California Rare Fruit Growers, Inc. (1996). Fig Fruit Facts. The Fullerton Arboretum, CSUF, Fullerton, CA. Available: http://www.crfg.org/pubs/ff/fig.html.
Cervera, M. T., Remington, D., Frigerio, J. M., Storme , V., Ivens, B., Boerjan, W., & Plomion, C. (2000). Improved AFLP analysis of tree species. Canadian Journal of Forest Research, 30 (10): 1608-1616.
Chatti, K. G. B. A. A., Saddoud, O., Mars, M., Trifi, M., & Salhihannachi, A. (2010). Development of molecular toolls for characterization and genetic diversity analysis in Tunisian fig (Ficus carica L.) cultivars. Biochemical Genetics, 48 (9-10): 789-806.
Cooper, G. (1995). Analysis of genetic variation and sperm competition in Dragon flies. D. Phil. Thesis, Oxford University.
Dehgan, B. (1998). Landscape Plants for Subtropical Climates. University Press of Florida, Gainesville, FL.
Esselman E. J., Crawford, D. J., Brauner, S., Stuessy, Anderson, T. F., G. J., & Silva, O. M. (2000). RAPD marker diversity within and divergence among species of Dendroseris (Asteraceae: Lactuceae). American Journal of Botany, 87: 591–596.
FAO, The FAO Statistical Database-Agriculture. (2009). http://www.fao.org/economic/the-statistics-division-ess/publitions studies/statistical-yearbook/fao-statistical-year book-2009/en/.
Flaishman, M., Rodov, V., & Stover, E. (2008). The Fig: Botany, Horticulture, and Breeding, Horticultural Reviews, 34: 113-197.
Fornari, B., Malvolti, M. E., Taurchini, D., Fineschi, S., Beritognolo, I., McCaglia, E., & Cannata, F. (2001). Isozyme and organellar DNA analysis of genetic diversity in natural/ naturalized European and Asiatic walnut (Juglans regia) populations. Acta Hort, 544: 167-178.
Ganopoulos, I. A., Xanthopulou, A., Molassiotis, E., Karagiannis, T., Moysiadis, P., Katsaris, F., Aravanopoulos, A., Tsaftaris, A., Kalivas, A., & Madesis, P. (2015). Mediterranean basin (Ficus carica L.) from genetic diversity and structure to authentication of protected designation of origin cultivar using microsatellite markers. Trees, 29 (6): 1959-1971.
Giraldo, E., Lopez-corrales, M., & Jose Ignacio Hormaza, J. I. (2010). Optimization of the management of an ex-situ germplasm bank in common fig with SSR. American Journal of Horticulture Science, 133: 69-77.
Goldstein, D.B., & Schlotterer, C. (1999). Microsatellites, evolution and applications. Oxford University Press, New York.
Govindaraij, M., Vetriventhan, M., & Srinivasan, M. (2015). Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives. Genetics Research International, 2015, 1-14. Article ID 431487.
Guasmi, F., Ferchichi, A., Farés, K., & Touil, L. (2006). Identification and differentiation of Ficus carica L. cultivars using inter simple sequence repeat markers. Afr. J. Biotechnol, 5: 1370-1374.
Gupta, P.K., Varshney, R.K., Sharma, P.C., & Ramesh, B. (1999). Molecular markers and their applications in wheat breeding. Plant Breed, 118: 369-390.
Gregory T. R. (2008). Understanding Evolutionary Trees. Evo Edu Outreach, 1(2): 121-137.
Ikegami, H., Nogata, H., Hirashima, K., Mitsuo Awamura, M., & Nakahara, T. (2009). Analysis of genetic diversity among European and Asian fig varieties (Ficus carica L.) using ISSR, RAPD, and SSR markers. Genetic Resources and Crop Evolution, 56: 201-209.
Jarne, P., & Lagoda, P. (1996). Microsatellites, from molecules to populations and back. Trends Ecol. Evol, 11: 424-429.
Khadari, B., Ater, M., Mamouni, A., Roger, J. P., & Kjellberg, F. (2004). Molecular characterization of Moroccan fig germplasm using inter simple sequence repeat and simple sequence repeat markers to establish a reference collection. Horticulture Science, 40 (1): 29-32.
Kumari, A., Sinha, S., Rashmi, K., Mandal, S. S., & Sahay, S. (2018). Genetic diversity analysis in maize (Zea mays L.) using SSR markers. Pharmacognosy and Phytochemistry S PP. 1116-1120. E- ISSN: 2278-4136 P-ISSN: 2349-8234.
Lansky E. P., Paavilainen, H. M., Pawlus, A. D., & Newman, R. A. (2008). Ficus spp. (fig): ethnobotany and potential as anticancer and anti-inflammatory agents. Journal of Ethnopharmacol, 119: 195-213.
Lazreg-Aref, H., Mars, M., Fekih, A., Aouni, M., & Said, K. (2012). Chemical composition and antibacterial activity of a hexane extract of Tunisian caprifig latex from the unripe fruit of Ficus carica. Pharmaceutical Biology, 50: 407-412.
Li, G. T., Ai, C. X., Zhang, L. S., Wei, H. R., & Liu, Q. Z. (2011). ISSR Analysis of Genetic Diversity among Seedling Walnut (Juglans spp.) Populations. Journal of Plant Genetic Resources, 12 (4): 640-645.
Liang, W., Dondini, L., Franceschi, P. D., Paris, R., Sansavini, S., & Tartarin, S. (2015). Genetic diversity, population structure and construction of a core collection of apple cultivars from Italian germpalsm. Plant Molecular Biology Reporter, 33 (3): 458-473.
Litt, M., & J. M. Luty. (1989). A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am. J. Hum. Genet, 44:397–401.
Malvolti, M. E., Pollegioni, P., Mapelli, S., & Cannata, F. (2010). Research of Juglans regia provenances by molecular, morphological and biochemical markers: a case study in Italy. Bioremediation, Biodiversity and Bioavailability, 4: 84-92.
Maniatis, T., Fritsch, E. F., & Sambrook, J. (2001). In vitro application of DNA by the Polymerase Chain Reaction, in Molecular Cold Spring Harbor Laboratory Press, New York, U.S.A., p. 691.
Neal, M.C. (1965). In Gardens of Hawai'i. Bernice P. Bishop Museum, Special Publication 40, Honolulu, HI.
Niu, J. X., Wang, L., Dai, Y. X., Li, R., Yang, X. K., & Lv., J. Q. (2007). Identification of AFLP Makers Linked to Early-Bearing Gene in Walnut. Molecular Plant Breeding, 5 (2): 266-268.
Perez-Jimenez, M. L. B., Dorado, G., Pujadas-Salva, A., Guzman, G., & Hernandez, P. (2012). Analysis of genetic diversity of southern Spain fig tree (Ficus carica L.) and reference materials as a tool for breeding and conservation. Hereditas, 149 (3): 108-113.
Rousset, F. (2008). Genepop’007: a complete reimplementation of the Genepop software for Windows and Linux. Mol. Ecol. Resources. 8: 103-106.
Saddoud, O., Barket, G., Chatti, K., Trifi, M., Marrakchi, M., Mars, M., & Salhi-Hannachi, A. (2011). Using morphological characters and simple sequence repeat (SSR) markers to characterize Tunisian fig (Ficua carica L.) cultivars. Acta Biologica Cracoviensia Series Botanica, 53: 7-14.
Shahbaz, S.E. (2010). Trees and shrubs. Afield guide to the trees and shrubs of Kurdistan region of Iraq . Duhok University Press. Iraq.pp601.
Takahashi, Y., Tanaka, R., Yamamoto, D., Noriyuki, S., & Kawata, M. (2018). Balanced genetic diversity improves population fitness. Proceeding Royal Society B, 285: 1-17.
Tautz, D., Trick, M., & Dover, G.A. (1986). Cryptic simplicity in DNA is a major source of genetic variation. Nature, 322: 652-656.
Teoman, S., Ipekl, M., Erturk, U., Tangu, N. A., Durgut, E., Barut, E., Ercisli, S., and Ipek, A. (2017). Assessment of Genetic Relationship among Male and Female Fig Genotypes Using Simple Sequence Repeat (SSR) Markers .Not Bot Horti Agrobo, 45 (1): 172-178.
Trichopoulou, A., Vasilopoulou, E., Georga, K., Soukara, S., & Dilis, V. (2006). Traditional foods: why and how to sustain them. Trends Food Science Technology, 17: 498-504.
Urrestarazu, J., Miranda, C., Santesteban, L. G., & Royo, J. B. (2012). Genetic diversity and structure of local apple cultivars from northeastern Spain assessed by microsatellite markers. Tree Genetics and Genomes, 8: 1163-1180.
Vignes, H., Hossa, M., Beaune, D., Fevre, D., Anstett, M. C., Borges, R. M., Kjellberg, F., & Chevallier, M. H. (2006). Development and characterization of microsatellite markers for a monoecious Ficus species, Ficus insipida, and cross-species amplification among different sections of Ficus. Molecular Ecology Notes, 6: 792-795.
Weigand F., Baum, M., & Udupa, S. (1993). DNA molecular marker technics, technical manual, No. 20 International Center for Agricultural Research in the Dry Areas (ICARDA). Aleppo, Syria.
Zavodna, M., Arens, P., Van, P. J., & Vosman, B. (2005). Development and characterization of microsatellite markers for two dioecious Ficus species. Molecular Ecology Notes, 5: 355-357.
Zhang, Q., Gao, Y. J., Saghai-Maroof, M. A., Yang, S. H., & Li, J. X. (1995). Molecular diveryence and hybrid performance in rice. Molecular Breeding, 1: 133-142.
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2020-12-30
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Hussein, A. E., & Jubrael, J. M. (2020). SSR Markers in Genetic Diversity Assessment of Fig Ficus carica L. Populations in Kurdistan Region – Iraq. Science Journal of University of Zakho, 8(4), 123–130. https://doi.org/10.25271/sjuoz.2020.8.4.758
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