SCoT molecular markers are efficient in genetic fingerprinting of pomegranate (Punica granatum L.) cultivars
DOI:
https://doi.org/10.36253/caryologia-1567Keywords:
AMOVA, DAPC, genetic diversity, POMEGRANATE, SCoTAbstract
The pomegranate is an economically important fruit plant species which has been utilized since ancient time as a source of food and medicine by mankind. This plant although is cultivated in certain geographical regions, but its fruits are imported and sold throughout the world. Iran is the center of origin for pomegranate and contains huge number of known cultivars. However, genetic studied on these cultivars are very limited and much detailed information has to be produced for better hybridization and breeding tasks in the country. A fingerprinting study was performed on 178 Punica trees in 47 known cultivars by using SCoT molecular markers. We obtained 61 SCoT bands/ loci which were used for genetic diversity analyses and grouping of the cultivars. A low genetic variability was obtained within and among Punica cultivars, but as revealed by AMOVA, this was quiet enough to produce significant genetic difference among them. DAPC analysis revealed a trace of genetic admixture among the cultivars either due to gene flow or as a result of common ancestral shared alleles. Discriminating SCoT loci may be used in germplasm evaluation of Punica. The genetic difference of these cultivars can be utilized for hybridization and breeding programs.
Downloads
References
Abdel-Lateif K.S and Hewedy O.A (2018) Genetic diversity among Egyptian wheat cultivars using SCoT and ISSR markers. SABRAO Journal of Breeding and Genetics, 50(1): 36-45.
Ahmed A.H (2018) Molecular Identification and Fingerprinting of Some Pomegranate Cultivars Grown in Egypt Using ISSR and SCoT Analyses. Journal of Horticultural Science & Ornamental Plants 10 (3): 179-188.
Beghè D, Fabbri A, Petruccelli R, Marieschi M, Torelli A, Ganino T (2019) Morphological and molecular characteriza-tion of ancient pomegranate (Punica granatum L.) accessions in Northern Italy. Adv. Hort. Sci., 33(4): 581592. DOI: 10.13128/ahsc7908.Chem. 9
Collard BCY, Mackill DJ (2009) Start codon targeted (SCoT) polymorphism: a simple novel DNA marker technique for generating gene-targeted markers in plants. Plant Mol Biol Rep 27:86–93.
Dora S.A, Mansour M, Aboulila A.A, Abdel- Wahab (2017) Genetic diversity and relationships among some barley genotypes for net blotch disease resistance using RAPD, SCoT and SSR markers. Egyptian Journal of Genetics and Cy-tology, 46: 139-165.
Fischer U. A., Carle R., Kammerer D. R (2010) Identification and quantification of phenolic compounds from pome-granate (Punica granatum L.) peel, mesocarp, aril and differently produced juices by HPLC-DAD?ESI/MSn. Food Chem. 2011, 127, 807?821. https://doi.org/10.1016/j.foodchem. 12.156
Gorji A.M., Poczai P, Polgar Z and Taller J (2011) Efficiency of arbitrarily amplified dominant markers (SCoT, ISSR and RAPD) for diagnostic fingerprinting in tetraploid potato. Am. J. Potato Res., 88: 226-237.
Graham S. A, Thorne & Reveal (1998) "Validation of subfamily names in Lythraceae". Taxon. Taxon, Vol. 47, No. 2. 47 (2): 435 436. doi:10.2307/1223775. JSTOR 1223775
Gundogdu M, Yilmaz H (2012) Organic acid, phenolic profile and antioxidant capacities of pomegranate (Punica gran-atum L.) cultivars and selected genotypes Sci. Hortic. (Amsterdam) 143, 38?42. https://doi.org/ 10.1016/j.scienta.2012.05.029.
Guo, D.L., Zhang, J.Y and Liu, C.H. (2012) Genetic diversity in some grape varieties revealed by SCoTanalyses. Mol. Biol. Rep., 39: 5307-5313.
Hammer Ø, Harper, D. A, & Ryan, P. D (2001) PAST: Paleontological statistics software package for education and data analysis. Palaeontologia electronica, 4(1), 9.
Hasnaoui N, Mars, M, Chibani, J, Trifi, M (2010a) Molecular Polymorphisms in Tunisian Pomegranate (Punica gran-atum L.) as Revealed by RAPD Fingerprints. Diversity 2: 107-114.
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
Jombart T (2008) adegenet: a R package for the multivariate analysis of genetic markers. Genetics and population analy-sis Vol. 24 no. 11 2008, pages 1403–1405 doi:10.1093/bioinformatics/btn129
Jombart T, Devillard S, Balloux, F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. Jombart et al. BMC Genetics 11:94.
Khadivi A, Mirheidari F, Moradi Y, Paryan S (2020) Morphological variability of wild pomegranate (Punica granatum L.) accessions from natural habitats in the Northern parts of Iran. Scientia Horticulturae 264:109165.
Krizman M., Jakse J, Baricevic D, Javornik B, Mirko P (2006) Robust CTAB-activated charcoal protocol for plant DNA extraction. Acta agri Slov 87: 427 – 433.
Li Y, Guo C, Yang J, Wei J, Xu J, Cheng, S (2006) Evaluation of antioxidant properties of pomegranate peel extract in comparison with pomegranate pulp extract. Food Chemistry, Volume 96, Issue 2,Pages 254-260. https://doi.org/10.1016/j.foodchem.2005.02.033
Luo C, He X, Chen H, Ou S, Gao, M (2010) Analysis of diversity and relationships among mango cultivars using Start Codon Targeted (SCoT) markers Biochemical Systematics and Ecology, 38: 1176-1184.
Luo X, Li H, Wu Z, Yao W, Zhao P, Cao D, Yu H, Li K, Poudel K, Zhao D, Zhang F, Xia X, Chen L, WangQ, Jing D, Cao S (2020) The pomegranate (Punica granatumL.) draft genomedissects genetic divergence between soft- andhard-seeded cultivars.
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
Nandakumar N, Singh A, Sharma, R et al. (2004) Molecular fingerprinting of hybrids and assessment of genetic purity of hybrid seeds in rice using microsatellite markers. Euphytica 136, 257–264. https://doi.org/10.1023/B:EUPH.0000032706.92360.c6
Narzary D, Rana TS, Ranade SA (2010) Genetic diversity in inter-simple sequence repeat profiles across natural popula-tions of Indian pomegranate (Punica granatum L.). Plant Biol 12: 806-813.
Noormohammadi Z, Fasihee A, Homaee-Rashidpoor S, Sheidai M, Ghasemzadeh Baraki S, Mazooji A, Tabatabaee- Ar-dakani S-Z (2012) The Comparison of RAPD, ISSR and SSR markers for genetic variation analysis among Iranian pom-egranates. Australian Journal of Crop
Nybom H, Weising K, Rotter, B (2014) DNA fingerprinting in botany: past, present, future. Investig Genet 5, 1. https://doi.org/10.1186/2041-2223-5-1
Patel C, Dadhaniya P, Hingorani, L, Soni M.G (2008) Safety assessmentof pomegranate fruit extract: acute and subchron-ic toxicity studies.FoodChem. Toxicol.46, 2728-2735.
Patil P.G, Singh N.V, Parashuram S et al. (2020) Genome-wide characterization and development of simple sequence re-peat markers for genetic studies in pomegranate (Punica granatum L.). Trees 34, 987–998. https://doi.org/10.1007/s00468-020-01975-y
Patil PG, Singh NV, Bohra A, Raghavendra KP, Mane R, Mundewadikar DM, Babu KD Sharma J (2021) Comprehen-sive Characterization and Validation of Chromosome-Specific Highly Polymorphic SSR Markers From Pomegranate (Punica granatum L.) cv. Tunisia Genome. Front. Plant Sci. 12:645055. doi: 10.3389/fpls.2021.645055
Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and re-search. Mol Ecol Notes 6:288–295
Poets, A, Silverstein, K, Pardey, P, Hearne, S, Stevenson, J (2020) DNA Fingerprinting for Crop Varietal Identification: Fit-for-Purpose Protocols, their Costs and Analytical Implications.
Saboori S, Noormohammadi Z, Sheidai M, Marashi S. S (2021) Date Palm (Phoenix dactylifera L.) Cultivar Relation-ships Based on Chloroplast Genotyping. Iran J Sci Technol Trans Sci. https://doi.org/10.1007/s40995-021-01085-5(01234).
Saboori S, Noormohammadi Z, Sheidai M, Marashi, S. S (2020) Insight into Date Palm Diversity: Genetic and Morpho-logical Investigations. Plant Molecular Biology Reporter (2021b) 39:137–145. https://doi.org/10.1007/s11105-020-01241-y.
Sepahian,N, Noormohammadi Z, Sheidai M, Zamanizadeh H.-R (2021) Authentication, genetic fingerprinting and as-sessing relatedness of rice (Oryza Sativa) genotypes by SSR molecular markers. Caryologia 74(1): 13-22. doi: 10.36253/caryologia-550.
Shahsavari Sh, Noormohammadi Z, Sheida M, Vazifeshenas M.R., Farahani F (2021b) A bioinformatic insight into the genetic diversity within pomegranate cultivars: from nuclear to chloroplast genes. Genet Resour Crop Evol. https://doi.org/10.1007/s10722-021-01297-z
Shahsavari Sh, Noormohammadi Z, Sheidai M, Farahani F, Vazifeshenas M.R (2021a) Genetic structure, clonality and diversity in commercial pomegranate (Punica granatum L.) cultivars. Genet Resour Crop Evol. https://doi.org/10.1007/s10722-021-01167-8
Sheidai, M, Noormohammadi, Z, Saneghi, A, Shahryari, ZH (2007) RAPD analysis of eleven Iranian pomegranate (Punica granatum L.) cultivars. Acta Biol Szeged 51(1): 61-64.
Vazifeshenas M, Hakimnia M, Goldeney A, Tehrani Far, A tailor, M (2012) Investigation and Comparison of Conven-tional Pomegranate Breeding Methods. International conference of Pomegranate Ferdows. Page 234-239.
Zarei, A and Sahraroo, A (2018) Molecular characterization of pomegranate (Punica granatum L.) accessio.ns from Fars Province of Iran using microsatellite markers. Horticulture, Environment, and Biotechnology volume 59, pages239–249. https://doi.org/10.1007/s13580-018-0019-x.
Downloads
Published
How to Cite
Issue
Section
License
Copyright (c) 2022 Shiva Shahsavari, Zahra Noormohammadi, Masoud Sheidai, Farah Farahani, Mohammad Reza Vazifeshenas
This work is licensed under a Creative Commons Attribution 4.0 International License.
- Copyright on any open access article in a journal published byCaryologia is retained by the author(s).
- Authors grant Caryologia a license to publish the article and identify itself as the original publisher.
- Authors also grant any third party the right to use the article freely as long as its integrity is maintained and its original authors, citation details and publisher are identified.
- The Creative Commons Attribution License 4.0 formalizes these and other terms and conditions of publishing articles.
- In accordance with our Open Data policy, the Creative Commons CC0 1.0 Public Domain Dedication waiver applies to all published data in Caryologia open access articles.
