Abstract
This experiment was conducted to assess genetic relationships among safflower genotypes from different geographical regions of Iran and other countries using newly developed simple sequence repeat (SSR) markers. By enrichment method, 32 primer pairs were designed of which 18 pairs were able to detect polymorphism in 105 safflower cultivars from Carthamus tinctorius, C. oxyacanthus, C. lanatus, C. glaucus, C. boissieri and C. dentatus. The selected SSR primers amplified a total of 59 alleles with an average of 3.27 alleles per locus among the cultivars and the average values of gene diversity, heterozygosity and PIC were 0.45, 0.37 and 0.39, respectively. Neighbour-joining cluster analysis based on Nei’s genetic distance categorized populations of Carthamus in six major clusters; all wild accessions were grouped differently from cultivated genotypes. Cluster analysis significantly distinguished C. oxyacanthus genotypes in different categories: centre (Arak), northeast (Azarbaiejan), east (Kermanshah) and southeast (Shiraz, Chaharmahal and Kohgiluyeh). The presence of C. boissieri and C. glaucus in one cluster appeared to be in close relationship between each other, indicating a common ancestor. The results revealed that C. dentatus discriminated from the species with \(n=10\) chromosomes, C. boissieri and C. glaucus assigned in to separate subsection. In summary, this study has shown that domesticated and wild genotypes were clustered into two major groups indicating these markers as appropriate tools to amassment genetic diversity and genome mapping.
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Ambreen H., Kumar S., Tottekkad Variath M., Joshi G., Bali S., Agarwal M. et al. 2015 Development of genomic microsatellite markers in Carthamus tinctorius L. (safflower) using next generation sequencing and assessment of their cross-species transferability and utility for diversity analysis. PLoS One 10, e0135443.
Arabnezhad H., Bahar M., Mohammadi H. R. and Latifian M. 2012 Development, characterization and use of microsatellite markers for germplasm analysis in date palm (Phoenix dactylifera L.). Sci. Hortic. 134, 150-156.
Chapman M. A., Hvala J., Strever J., Marvienko M., Kozik A., Michelmore R. W. et al. 2009 Development, polymorphism, and cross-taxon utility of EST-SSR markers from safflower (Carthamus tinctorius L.). Theor. Appl. Genet. 120, 85-91.
Derakhshan E., Majidi M. M., Sharafi Y. and Mirlohi A. 2014 Discrimination and genetic diversity of cultivated and wild safflowers (Carthamus spp.) using EST-microsatellites markers. Biochem. Syst. Ecol. 54, 130-136.
Estilai A. and Knowles P. F. 1976 Cytogenetic studies of Carthamus divaricatus with eleven pairs of chromosomes and its relationship to other Carthamus species. (Compositae). Am. J. Bot. 63, 771-782.
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.
Hamdan Y. A. S., Garcia-Moreno M. J., Redondo-NevadoVelasco J. and Perez-Vich B. 2011 Development and characterization of genomic microsatellite markers in safflower (Carthamus tinctorius L.). Plant Breed. 130, 237-241.
Hamilton M., Elaine B., Pincus L., Di Fiore A. and Fleischer R. C. 1999 Universal linker and ligation procedures for construction of genomic DNA libraries enriched for microsatellites. BioTechniques 27, 500-507.
Hanelt P. 1963 Monographische Ubersicht der Gattung Carthamus L. (Compositae). Feddes Repert. 67, 41-180.
Knowles P. F. 1958 Safflower. In Advances in agronomy, pp. 289-323. Academic Press, New York.
Lee G. A., Sung J. S., Lee S. Y., Chung J. W., Yi J. Y., Kim Y. G. and Lee M. C. 2014 Genetic assessment of safflower (Carthamus tinctorius L.) collection with microsatellite markers acquired via pyrosequencing method. Mol. Ecol. Resour. 14, 69-78.
López-González G. 1989 Acerca de la clasificación natural delgénero Carthamus L., s.l. Anales Jard. Bot. Madrid 47, 11-34.
Liu K. and Muse S. V. 2005 PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21, 2128-2129.
Majidi M. M. and Zadhoush S. 2014 Molecular and morphological variation in a world-wide collection of safflower. Crop Sci. 54, 2109-2119.
Mokhtari N., Rahim malek M., Talebi M. and Khorrami M. 2013 Assessment of genetic diversity among and within Carthamus species using sequence-related amplified polymorphism (SRAP) markers. Plant Syst. Evol. 299, 1285-1294.
Murray M. G. and Thompson W. F. 1980 Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 8, 4321-4325.
Oliviera E. J., Padua J. G., Zucchi M. I., Venkovsky R. and Carneiro Vieira M. L. 2006 Origin, evolution and genome distribution of microsatellite. Genet. Mol. Biol. 29, 294-307.
Pritchard J. K., Stephens M. and Donnelly P. 2000a Inference of population structure using multilocus genotype data. Genetics 155, 945–959.
Rousset F. 2008 Genepop’007: a complete re-implementation of the genepop software for Windows and Linux. Mol. Ecol. Resour. 8, 103–106.
Rozen S. and Skaletsky H. J. 2000 Primer 3 on the WWW for general users and for biologist programmers. In Bioinformatics methods and protocols, methods in molecular biology. (ed. S. Krawetz Misener), pp. 365-386. Humana, New Jersey, USA.
Sabzalian M. R., Mirlohi A., Saeidi G. and Rabbani M. T. 2009 Genetic variation among populations of wild safflower, Carthamus oxyacanthus analyzed by agro-morphological traits and ISSR markers. Genet. Resour. Crop Evol. 56, 1057-1064.
Sehgal D., Raina S. N., Devarumath R. M., Sasanuma T. and SasakumaT. 2009 Nuclear DNA assay in solving issues related to ancestry of the domesticated diploid safflower (Carthamus tinctorius L.) and the polyploid (Carthamus) taxa, and phylogenetic and genomic relationships in the genus Carthamus L. (Asteraceae). Mol. Phylogen. Evol. 53, 631-644.
Talebi M., Mokhtari N., Rahim malek M. and Sahhafi S. R. 2013 Molecular characterization of Carthamus tinctorius and C. oxyacanthus germplasm using sequence related amplified polymorphism (SRAP) markers. Plant Omics 5, 136-142.
Vilatersana R., Garnatje T., Susanna A. and Garcia-Jacas N. 2005 Taxonomic problems in Carthamus (Asteraceae), RAPD markers and sectional classification. Bot. J. Linn. Soc. 147, 375-383.
Wright S. 1978 Evolution and genetics of populations: variability within and among natural populations. University of Chicago Press, Chicago.
Xie W., Zhang X., Cai H., Liu W. and Peng Y. 2010 Genetic diversity analysis and transferability of cereal EST-SSR markers to orchardgrass (Dactylis glomerata L.). Bioch. Syst. Ecol. 38, 740-749.
Yang Y. X., Wu W., Zheng Y. L., Chen L., Liu R. J. and Huang C. Y. 2007 Genetic diversity and relationships among safflower (Carthamus tinctorius L.) analyzed by inter-simple sequence repeats (ISSRs). Genet. Resour. Crop Evol. 54, 1043-1051.
Yeh F. C., Yang R., Boyle T. J., Ye Z. and Xiyan J. M. 2000 POPGENE 32, Microsoft Window-based freeware for population genetic analysis, version 1.32. Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton, Canada.
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We thank Prof. Mohammad Mahdi Majidi, Genetic and Plant Breeding, College of Agriculture, Isfahan University of Technology for supplying seed samples.
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Mokhtari, N., Sayed-Tabatabaei, B.E., Bahar, M. et al. Assessment of genetic diversity and population genetic structure of Carthamus species and Iranian cultivar collection using developed SSR markers. J Genet 97 (Suppl 1), 67–78 (2018). https://doi.org/10.1007/s12041-018-0956-2
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DOI: https://doi.org/10.1007/s12041-018-0956-2