Analysis of genetic structure in a large sample of pomegranate (Punica granatum L.) using fluorescent SSR markers

References

• Alcaraz-Mármol, F., Nuncio-Jáuregui, N., García-Sánchez, F., Martínez-Nicolás, J.J., & Hernández, F. (2017). Characterization of twenty pomegranate (Punica granatum L.) cultivars grown in Spain: Aptitudes for fresh consumption and processing. Scientia Horticulturae, 219, 152–160. doi:10.1016/j.scienta.2017.03.008
   Web of Science ®Google Scholar
• Aranzana, M.J., Kim, S., Zhao, K., Bakker, E., Horton, M., Jakob, K., … Nordborg, M. (2005). Genome-wide association mapping in Arabidopsis thaliana identifies previously known genes responsible for variation in flowering time and pathogen resistance. PLoS Genetics.
   PubMed Web of Science ®Google Scholar
• Cao, K., Zhou, Z., Wang, Q., Guo, J., Zhao, P., Zhu, G., … Wang, L. (2016). Genome-wide association study of 12 agronomic traits in peach. Nature Communications, 7, 13246. doi:10.1038/ncomms13246
   PubMed Web of Science ®Google Scholar
• Cook, J.P., McMullen, M.D., Holland, J.B., Tian, F., Bradbury, P., Ross-Ibarra, J., … Flint-Garcia, S.A. (2012). Genetic architecture of maize kernel composition in the nested association mapping and inbred association panels. Plant Physiology, 158, 824–834. doi:10.1104/pp.111.185033
   PubMed Web of Science ®Google Scholar
• Curro, S., Caruso, M., Distefano, G., Gentile, A., & La Malfa, S. (2010). New microsatellite loci for pomegranate, Punica granatum (Lythraceae). American Journal of Botany, 97, e58–e60. doi:10.3732/ajb.1000143
   PubMed Web of Science ®Google Scholar
• Ebrahimi, S., Sayedtabatabaei, B.E., & Sharifnabi, B. (2010). Microsatellite isolation and characterization in pomegranate (Punica granatum L.). Iranian Journal of Biotechnology, 8, 156–163.
   Google Scholar
• Evanno, G., Regnaut, S., & Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Molecular Ecology, 14, 2611–2620. doi:10.1111/mec.2005.14.issue-8
   PubMed Web of Science ®Google Scholar
• Excoffier, L., & Lischer, H.E. (2010). Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10, 564–567. doi:10.1111/men.2010.10.issue-3
   PubMed Web of Science ®Google Scholar
• Ganal, M.W., Altmann, T., & Röder, M.S. (2009). SNP identification in crop plants. Current Opinion in Plant Biology, 12, 211–217. doi:10.1016/j.pbi.2008.12.009
   PubMed Web of Science ®Google Scholar
• Hasnaoui, N., Buonamici, A., Sebastiani, F., Mars, M., Trifi, M., & Vendramin, G.G. (2010a). Development and characterization of SSR markers for pomegranate (Punica granatum L.) using an enriched library. Conservation Genetics Resources, 2, 283–285. doi:10.1007/s12686-010-9191-8
   Web of Science ®Google Scholar
• Hasnaoui, N., Mars, M., Chibani, J., & Trifi, M. (2010b). Molecular polymorphisms in Tunisian pomegranate (Punica granatum L.) as revealed by RAPD fingerprints. Diversity, 2, 107–114. doi:10.3390/d2010107
   Google Scholar
• Huang, X., Zhao, Y., Wei, X., Li, C., Wang, A., Zhao, Q., … Han, B. (2012). Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nature Genetics, 44, 32–39. doi:10.1038/ng.1018
   Web of Science ®Google Scholar
• Jbir, R., Hasnaoui, N., Mars, M., Marrakchi, M., & Trifi, M. (2008). Characterization of Tunisian pomegranate (Punica granatum L.) cultivars using amplified fragment length polymorphism analysis. Scientia Horticulturae, 115, 231–237. doi:10.1016/j.scienta.2007.09.002
   Web of Science ®Google Scholar
• Johanningsmeier, S.D., & Harris, G.K. (2011). Pomegranate as a functional food and nutraceutical source. Annual Review of Food Science and Technology, 2, 181–201. doi:10.1146/annurev-food-030810-153709
   PubMed Web of Science ®Google Scholar
• Koohidehkordi, M., Sayedtabatabaei, B.E., Yamchi, A., & Daneshshahraki, A. (2007). Microsatellite markers in pomegranate. Acta Horticulturae, 760, 179–184. doi:10.17660/ActaHortic.2007.760.23
   Google Scholar
• Kumar, L.S. (1999). DNA markers in plant improvement: An overview. Biotechnology Advances, 17, 143–182. doi:10.1016/S0734-9750(98)00018-4
   PubMed Web of Science ®Google Scholar
• Liu, K., & Muse, S.V. (2005). PowerMarker: An integrated analysis environment for genetic marker analysis. Bioinformatics, 21, 2128–2129. doi:10.1093/bioinformatics/bti282
   PubMed Web of Science ®Google Scholar
• Melgarejo, P., Martínez, J.J., Hernández, F., Martínez, R., Legua, P., Oncina, R., & Martínez-Murcia, A. (2009). Cultivar identification using 18S–28S rDNA intergenic spacer-RFLP in pomegranate (Punica granatum L.). Scientia Horticulturae, 120, 500–503. doi:10.1016/j.scienta.2008.12.013
   Web of Science ®Google Scholar
• Micheletti, D., Dettori, M.T., Micali, S., Aramini, V., Pacheco, I., Da Silva Linge, C., … Han, Y. (2015). Whole-genome analysis of diversity and SNP-major gene association in peach germplasm. PloS One, 10, e0136803. doi:10.1371/journal.pone.0136803
   PubMed Web of Science ®Google Scholar
• Moslemi, M., Zahravi, M., & Khaniki, G.B. (2010). Genetic diversity and population genetic structure of pomegranate (Punica granatum L.) in Iran using AFLP markers. Scientia Horticulturae, 126, 441–447. doi:10.1016/j.scienta.2010.08.007
   Web of Science ®Google Scholar
• Narzary, D., Mahar, K.S., Rana, T.S., & Ranade, S.A. (2009). Analysis of genetic diversity among wild pomegranates in Western Himalayas, using PCR methods. Scientia Horticulturae, 121, 237–242. doi:10.1016/j.scienta.2009.01.035
   Web of Science ®Google Scholar
• Norouzi, M., Talebi, M., & Sayed-Tabatabaei, B.-E. (2012). Chloroplast microsatellite diversity and population genetic structure of Iranian pomegranate (Punica granatum L.) genotypes. Scientia Horticulturae, 137, 114–120. doi:10.1016/j.scienta.2012.01.034
   Web of Science ®Google Scholar
• Ono, N.N., Britton, M.T., Fass, J.N., Nicolet, C.M., Lin, D., & Tian, L. (2011). Exploring the transcriptome landscape of pomegranate fruit peel for natural product biosynthetic gene and SSR marker discovery. Journal of Integrative Plant Biology, 53, 800–813. doi:10.1111/j.1744-7909.2011.01073.x
   PubMed Web of Science ®Google Scholar
• Parvaresh, M., Talebi, M., & Sayed-Tabatabaei, B.-E. (2012). Molecular diversity and genetic relationship of pomegranate (Punica granatum L.) genotypes using microsatellite markers. Scientia Horticulturae, 138, 244–252. doi:10.1016/j.scienta.2012.02.038
   Web of Science ®Google Scholar
• Patel, C., Dadhaniya, P., Hingorani, L., & Soni, M.G. (2008). Safety assessment of pomegranate fruit extract: Acute and subchronic toxicity studies. Food & Chemical Toxicology, 46, 2728–2735. doi:10.1016/j.fct.2008.04.035
   PubMed Web of Science ®Google Scholar
• Pirseyedi, S.M., Valizadehghan, S., Mardi, M., Ghaffari, M.R., Mahmoodi, P., Zahravi, M., … Nekoui, S.M. (2010). Isolation and characterization of novel microsatellite markers in pomegranate (Punica granatum L.). International Journal of Molecular Sciences, 11, 2010–2016. doi:10.3390/ijms11052010
   PubMed Web of Science ®Google Scholar
• Porebski, S., Bailey, L.G., & Baum, B.R. (1997). Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Molecular Biology Reporter, 15, 8–15. doi:10.1007/BF02772108
   Web of Science ®Google Scholar
• Pritchard, J.K., Stephens, M., & Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155, 945–959.
   PubMed Web of Science ®Google Scholar
• Rahimi, T., Sayed Tabatabaei, B.E., Sharifnabi, B., & Ghobadi, C. (2006). Genetic relationships between Iranian pomegranate (Punica granatum L.) cultivars, using Amplified Fragment Length Polymorphism (AFLP) marker. Iranian Journal of Agricultural Sciences, 36, 1373–1379.
   Google Scholar
• Soleimani, M.H., Talebi, M., & Sayedtabatabaei, B.E. (2012). Use of SRAP markers to assess genetic diversity and population structure of wild, cultivated, and ornamental pomegranates (Punica granatum L.) in different regions of Iran. Plant Systematics & Evolution, 298, 1141–1149. doi:10.1007/s00606-012-0626-4
   Web of Science ®Google Scholar
• Soriano, J.M., Zuriaga, E., Rubio, P., Llácer, G., Infante, R., & Badenes, M.L. (2011). Development and characterization of microsatellite markers in pomegranate (Punica granatum L.). Molecular Breeding, 27, 119–128. doi:10.1007/s11032-010-9511-4
   Web of Science ®Google Scholar
• Talebi, M., Bahar, M., Sharifnabi, B., & Yamchi, A. (2011). Evaluation of genetic diversity among Iranian pomegranate (Punica granatum L.) cultivars, using ISSR and RAPD markers. Taxonomy and Biosystematics, 8, 35–44.
   Google Scholar
• Yang, N., Lu, Y., Yang, X., Huang, J., Zhou, Y., Ali, F., … Yan, J. (2014). Genome wide association studies using a new nonparametric model reveal the genetic architecture of 17 agronomic traits in an enlarged maize association panel. PLoS Genetics, 10, e1004573. doi:10.1371/journal.pgen.1004573
   PubMed Web of Science ®Google Scholar
• Yano, K., Yamamoto, E., Aya, K., Takeuchi, H., Lo, P.-C., Hu, L., … Matsuoka, M. (2016). Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice. Nature Genetics, 48, 927–934. doi:10.1038/ng.3596
   PubMed Web of Science ®Google Scholar
• Yuan, Z., Yin, Y., Qu, J., Zhu, L., & Li, Y. (2007). Population genetic diversity in Chinese pomegranate (Punica granatum L.) cultivars revealed by fluorescent-AFLP markers. Journal of Genetics and Genomics, 34, 1061–1071. doi:10.1016/S1673-8527(07)60121-0
   PubMedGoogle Scholar
• Zamani, Z., Sarkhosh, A., Fatahi, R., & Ebadi, A. (2007). Genetic relationships among pomegranate genotypes studied by fruit characteristics and RAPD markers. The Journal of Horticultural Science and Biotechnology, 82, 11–18. doi:10.1080/14620316.2007.11512192
   Web of Science ®Google Scholar
• Zhang, Z., Ersoz, E., Lai, C.-Q., Todhunter, R.J., Tiwari, H.K., Gore, M.A., … Buckler, E.S. (2010). Mixed linear model approach adapted for genome-wide association studies. Nature Genetics, 42, 355–360. doi:10.1038/ng.546
   PubMed Web of Science ®Google Scholar