Identification of AFLP markers associated with flowering time and ornamental traits in Chrysanthemum


1 Assistant Professor, Department of Horticultural Sciences, Ilam University, Ilam, Iran.

2 Professor, Department of Horticultural Sciences, University of Guilan, Rasht, Iran.

3 Assistant Professor, Department of Agronomy and Plant Breeding, University of Guilan, Rasht, Iran.


Flowering period and longevity play important roles in determining the quality of commercial flowers. Marker-trait associations for eight flowering and 12 ornamental traits have been studied using a GLM and MLM analysis with a set of 2099 AFLP polymorphic markers in Chrysanthemum. The GLM model identified 453 markers for phenotypic traits whereas the MLM association analysis model revealed a total of 197 significant marker-trait associations for the phenotypic traits. The strongest association was detected between AFLP markers with a bud diameter trait, which explained 68% of the variation. Among several polymorphic bands, 14 markers were associated with senescence, 10 with flower diameter and eight with stem length. This approach also led to the identification of seven markers with significant association to full bloom. Therefore, these markers can be used for the genetic improvement of the ornamental value of Chrysanthemum after further confirmation. The analysis of the results revealed a number of markers co-associated with different correlated phenotypic traits. The results revealed informative markers that have shown a significant correlation with several traits which could be useful for breeding programs and other analyses associated to future studies of Chrysanthemum.


Achleitner A., Tinker N. A., Zechner E., and Buerstmayr H. (2008). Genetic diversity among oat varieties of worldwide origin and associations of AFLP markers with quantitative traits. Theoretical and Applied Genetics, 117: 1041–1053.

Angiolini C., Bonari G., Frignani F., Iiriti G., Nannoni F., Protano G., and Landi M. (2015). Ecological patterns of morphological variation in italian populations of Romulea bulbocodium (Iridaceae). Flora, 214: 1–10.

Bradbury P. J., Zhang Z., Kron D. E., Casstevens T. M., Ramdoss Y., and Buckler E. S. (2007). TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics, 23: 2633–2635.

Breseghello F., and Sorrells M. E. (2006). Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics, 172: 1165–1177.

Carter A. H., Garland-Campbell K., and Kidwell K. K. (2011). Genetic mapping of quantitative trait loci associated with important agronomic traits in the spring wheat (Triticum aestivum L.) cross ‘Louise’ 9 ‘Penawawa’. Crop Science, 51: 84–95.

Chayanika S. (2012). Morphological and DNA marker - based genetic diversity assessment and tagging QTLs controlling economic traits in jasmine (Jasminum spp.). University of Agricultural Sciences, p.167.

Devlin B., and Risch N. (1995). A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics, 29: 311–322.

Evanno G., Regnaut S., and Goudet J. (2005). Detecting the number of clusters of individuals using the software structure: A simulation study. Molecular Ecology, 14: 2611–2620.

Fang W. M., Guo W. M., and Chen J. Y. (2009). Effects of grafting on the improvement of heat tolerance and antioxidant abilities in leaves of chrysanthemum. Acta Horticulturae Sinica, 36: 1327–1332.

Forcada C. F., Igartua N. O. E., Moreno M. A., and Gogorcena Y. (2013). Population structure and marker-trait associations for pomological traits in peach and nectarine cultivars. Tree Genetics and Genomes, 9: 331–349.

Gawenda I., Schroder-Lorenz A., and Debener T. (2012). Markers for ornamental traits in phalaenopsis orchids: Population structure, linkage disequilibrium and association mapping. Molecular Breeding, 30: 305–316.

Hedrick P. W. (1987). Gametic disequilibrium measures: Proceed with caution. Genetics, 117: 331–341.

IBM Corp. Released. (2012). IBM SPSS Statistics for Windows, Version 21.0. Armonk, NY: IBM Corp.

Kikuchi R., and Handa H. (2009). Photoperiodic control of flowering in barley. Breeding Science, 59: 546–552.

Kim S., and Xing E. P. (2009). Statistical estimation of correlated genome associations to a quantitative trait network. Public Library of Science Genetics, 5, e1000587.

Klie M., Menz I., Linde M., and Debener T. (2013). Lack of structure in the gene pool of the highly polyploidy ornamental chrysanthemum. Molecular Breeding, 32: 339–348.

Koyama M. L., Levesley A., Koebner R. M. D., Flowers T. J., and Yeo A. R. (2001). Quantitative trait loci for component physiological traits determining salt tolerance in rice. Plant Physiology, 125: 406–422.

Liu M., Zhang S., Liang H., and Zhen Z. (2008). AFLP analysis on the genetic diversity of some chrysanthemum species. Journal of Agricultural University of Hebei, 31: 48–59.

Mannai Y. E., Shehzad T., and Okuno K. (2011). Variation in flowering time in sorghum core collection and mapping of QTLs controlling flowering time by association analysis. Genetic Resources and Crop Evolution, 58: 983–989.

Martin C., Uberhuaga E., and Perez C. (2002). Application of RAPD markers in the characterisation of chrysanthemum varieties and assessment of somaclonal variation. Euphytica, 127: 247–253.

Mazzucato A., Papa R., Bitocchi E., Mosconi P., Nanni L., Negri V., Picarella M.E., Siligato F., Soressi G.P., Tiranti B., and Veronesi F. (2008). Genetic diversity, structure and marker-trait associations in a collection of Italian tomato (Solanum lycopersicum L.) landraces. Theoretical and Applied Genetics, 116: 657–669.

Misra S., Mandal T., and Vanlalruati Das S. K. (2013). Correlation and path coefficient analysis for yield contributing parameters in spray chrysanthemum. Journal of Horticulture Letters, 3: 14–16.

Nakano Y., Higuchi Y., Sumitomo K., and Hisamatsu T. (2013). Flowering retardation by high temperature in chrysanthemums: involvement of FLOWERING LOCUS T-like 3 gene repression. Journal of Experimental Botany, 64: 909–920.

Nishi N., Muta T., Ito Y., Nakamura M., and Tsukiboshi T. (2009). Ray speck of chrysanthemum caused by Stemphylium lycopersici in Japan. Journal of General Plant Pathology, 75: 80–82.

Nordborg M., and Tavare S. (2002). Linkage disequilibrium: what history has to tell us? Trends in Genetics, 18: 83–90.

Portis E., Mauro R. P., Barchi L., Acquadro A., Mauromicale G., and Lanteri S. (2014). Mapping yield-associated QTL in globe artichoke. Molecular Breeding, 34: 615–630.

Pritchard J., Stephens M., and Donnelly P. (2000). Inference of population structure using multi locus genotype data. Genetics, 155: 945–959.

Rakshit A., Rakshit S., Singh J., Chopra S. K., Balyan H. S., Gupta P. K., and Bhat S. R. (2010). Association of AFLP and SSR markers with agronomic and fiber quality traits in Gossypium hirsutum L. Journal of Genetics, 89: 155–162.

Roein Z., Hassanpour Asil M., Sabouri A., and Dadras A. R. (2014). Genetic structure of chrysanthemum genotypes from Iran assessed by AFLP markers and phenotypic traits. Plant Systematics and Evolution, 300: 493–503.

Rostoks N., Ramsay L., MacKenzie K., Cardle L., Bhat P. R., Roose M. L., Svensson J. T., Stein N., Varshney R. K., Marshall D. F., Graner A., Close T. J., and Waugh R. (2006). Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. Proceedings of the National Academy of Sciences, 103: 18656–18661.

Saghai-Maroof M. A., Soliman K. M., Jorgensen R. A., and Allard R. W. (1984). Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proceedings of the National Academy of Sciences, 81: 8014–8018.

Saïdou A. A., Clotault J., Couderc M., Mariac C., Devos K. M., Thuillet A. C., Amoukou I. A., and Vigouroux Y. (2014). Association mapping, patterns of linkage disequilibrium and selection in the vicinity of the PHYTOCHROME C gene in pearl millet. Theoretical and Applied Genetics, 127: 19–32.

Shao Q. S., Guo Q. S., Deng Y. M., and Guo H. P. (2010). A comparative analysis of genetic diversity in medicinal Chrysanthemum morifolium based on morphology, ISSR and SRAP markers. Biochemical Systematics and Ecology, 38: 1160–1169.

Sun C. Q., Chen F. D., Teng N. J., Liu Z. L., Fang W. M., and Hou X. L. (2010). Interspecific hybrids between Chrysanthemum grandiflorum (Ramat.) Kitamura and C. indicum (L.) Des Moul and their drought tolerance evaluation. Euphytica, 174: 51–60.

Teixeira da Silva J. A. (2004). Ornamental chrysanthemums: improvement by biotechnology. Plant Cell, Tissue and Organ Culture, 79: 1–18.

Vos P., Hogers R., Bleeker M., Reijans M., Delee T. V., Hornes M., Friters A., Pot J., Paleman J., Kuiper M., and Zabeau M. (1995). AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research, 23: 4407–4414.

Wang X. G., Wang H. B., Chen F. D., Jiang J. F., Fang W. M., Liao Y., and Teng N. J. (2014). Factors affecting quantity of pollen dispersal of spray cut chrysanthemum (Chrysanthemum morifolium). BMC Plant Biology, 14: 5.

Yagi M., Yamamoto T., Isobe S., Tabata S., Hirakawa H., Yamaguchi H., Tanase K., and Onozaki T. (2014). Identification of tightly linked SSR markers for flower type in carnation (Dianthus caryophyllus L.). Euphytica, 198: 175–183.

Yan W. G., Li Y., Agrama H. A., Luo D., Gao F., Lu X., and Ren G. (2009). Association mapping of stigma and spikelet characteristics in rice (Oryza sativa L.). Molecular Breeding, 24: 277–292.

Yu J., and Buckler E. S. (2006). Genetic association mapping and genome organization of maize. Current Opinion in Biotechnology, 17: 155–160.

Yu J., Pressoir G., Briggs W. H., Bi I. V., Yamasaki M., Doebley J. F., McMullen M. D., Gaut B. S., Nielsen D. M., Holland J. B., Kresovich S., and Buckler E. S. (2006). A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature Genetics, 38: 203–208.

Yu S., Zhang F., Wang X., Zhao X., Zhang D., Yu Y., and Xu J. (2010). Genetic diversity and marker‐trait associations in a collection of Pak‐choi (Brassica rapa L. ssp. chinensis Makino) accessions. Genes Genome, 32: 419–428.

Zhang F., Chen S., Chen F., Fang W., Deng Y., Chang Q., and Liu P. (2011). Genetic analysis and associated SRAP markers for flowering traits of chrysanthemum (Chrysanthemum morifolium). Euphytica, 177: 15–24.

Zhang F., Chen S., Chen F., Fang W., and Li F. (2010). A preliminary genetic linkage map of chrysanthemum (Chrysanthemum morifolium) cultivars using RAPD, ISSR and AFLP markers. Scientia Horticulturae, 125: 422–428.

Zhang F., Jiang J., Chen S., Chen F., and Fang W. (2012). Mapping single-locus and epistatic quantitative trait loci for plant architectural traits in chrysanthemum. Molecular Breeding, 30: 1027–1036.

Zhao J., Paulo M. J., Jamar D., Lou P., van Eeuwijk F., Bonnema G., Vreugdenhil D., and Koornneef M. (2007). Association mapping of leaf traits, flowering time, and phytate content in Brassica rapa. Genome, 50: 963–973.

Zhao W.G., Chung J. W., Kwon S. W., Lee J. H., Ma K. H., and Park Y. J. (2013). Association analysis of physicochemical traits on eating quality in rice (Oryza sativa L.). Euphytica, 191: 9–21.