Evaluation of genetic diversity of Estahban region fig genotypes based on morphological traits and SCoT molecular markers

Document Type : Research Paper


1 MSc Student, Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran

2 Associate Professor, Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran

3 Assistant Professor, Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran.

4 Assistant Professor, Fig Research Station, Fars Agricultural and Natural Resources Research and Education Center, AREEO, Estahban, Iran

5 Assistant Professor, Department of Plant Breeding, Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj, Iran.


Fig (Ficus carica) is a deciduous tree that is grown in arid and semi-arid regions. Figs, as an important crop, have undergone genetic erosion in recent decades due to living and non-living stresses. The aim of this study was to determine the genetic diversity of genotypes in Estahban using morphological traits and Start Codon Targeted (SCoT) molecular markers.
Materials and methods
In this study, 16 fig genotypes were evaluated in a completely randomized design with three replications based on their morphological traits. Also, their genomic DNA was extracted from leaves and the genotypic diversity of genotypes based on 10 SCoT primers was examined.
Variance analysis showed a significant difference between traits, and cluster analysis based on morphological traits placed the genotypes in five groups. Eight primers amplified a total of 50 polymorphic bands, and SCoT12 and SCoT11 produced the most bands with 13 and 9 polymorphic bands, respectively. The polymorphic information content (PIC) for the SCoT primers varied between 0.3423 and 0.3791 with an average of 0.3595. Cluster analysis by UPGMA and Gower similarity criterion based on SCoT data, 16 fig genotypes were placed in four groups. The grouping based on the Bayesian method placed the genotypes in nine groups, although the genotypes were not differentiated and were a mixture of all nine groups.
The results indicate that the use of SCoT marker has a high advantage and plays an important role in the differentiation of fig genotypes. In general, it can be said that SCoT molecular markers and morphological traits have shown high diversity among genotypes. In general, the results obtained from this study indicate the existence of high genetic diversity in the germplasm of Estahban fig cultivars, which can be used in breeding programs by protecting this rich germplasm source.


عسکری ناهید، باقی‌زاده امین، محمدآبادی محمدرضا (1389). مطالعه تنوع ژنتیکی در چهار جمعیت بز کرکی راینی با استفاده از نشانگرهای ISSR. مجله ژنتیک نوین 5، 56-49.
محمدی‌فر آمنه، فقیه ایمانی سیدعلی، محمدآبادی محمدرضا، سفلایی محمد (1392) تأثیر ژن TGFb3 بر ارزش های فنوتیپی و ارثی صفات وزن بدن در مرغ بومی استان فارس. مجله بیو تکنولوژی کشاورزی  5(4)، 136-125.
محمدی‌فر آمنه، محمدآبادی محمدرضا (1390). کاربرد نشانگرهای ریزماهواره برای مطالعه ژنوم گوسفند کرمانی. مجله علوم دامی ایران 42 (4) 344-337.
Abdelsalam NR, Awad RM, Ali HM et al. (2019) Morphological, pomological, and specific molecular marker resources for genetic diversity analyses in fig (Ficus carica L.). HortScience 54, 1299-1309.
Akbulut M, Ercisli S, Karlidag H (2009) RAPD-based study of genetic variation and relationships among wild fig genotypes in Turkey. Genet Mol Res 8, 1109-1115.
Ali-Shtayeh MS, Jamous RM, Zaitoun SYA et al. (2014) Genetic diversity of the Palestinian fig (Ficus carica L.) collection by pomological traits and RAPD markers. Am J Plant Sci 2014.
Amiryousefi A, Hyvönen J, Poczai P (2018) iMEC: Online marker efficiency calculator. Appl Plant Sci 6, Article number e01159, 01154 pages.
Aradhya MK, Stover E, Velasco D et al. (2010) Genetic structure and differentiation in cultivated fig (Ficus carica L.). Genetica 138, 681-694.
Arnon DI (1949) Copper enzymes in isolated chloroplasts. Polyphenoloxidase in Beta vulgaris. Plant Physiol 24, 1.
Askari N, Baghizadeh A, Mohammadabadi M (2008) Analysis of the genetic structure of Iranian indigenous Raeni Cashmere goat populations using microsatellite markers. Biotechnol 2, 1-4.
Askari N, Baghizadeh A, Mohammadabadi MR (2010) Study of genetic diversity in four populations of Raeini cashmere goat using ISSR markers. Mod Genet J 5, 49-56 (In Persian).
Beck N, Lord E (1988) Breeding system in Ficus carica, the common fig. II. Pollination events. Am J Bot 75, 1913-1922.
Behera TK, Gaikward AB, Singh AK et al. (2008) Relative efficiency of DNA markers (RAPD, ISSR and AFLP) in detecting genetic diversity of bitter gourd (Momordica charantia L.). J Sci Food Agric 88, 733-737.
Benettayeb Z, Bencheikh M, Setti B et al. (2017) Genetic diversity of Algerian fig (Ficus carica L.) cultivars based on morphological and quality traits. Indian J Hortic 74, 311-316.
Botstein D, White RL, Skolnick M et al. (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics 32, 314– 331.
Chatti K, Baraket G, Abdelkrim AB et al. (2010) Development of molecular tools for characterization and genetic diversity analysis in Tunisian fig (Ficus carica) cultivars. Biochem Genet 48, 789-806.
Dalklccedil Z, Mestav HO, Kocata H (2011) Genetic diversity of male fig (Ficus carica caprificus L.) genotypes with random amplified polymorphic DNA (RAPD) markers. Afr J Biotechnol 10, 519-526.
Datwyler SL, Weiblen GD (2004) On the origin of the fig: phylogenetic relationships of Moraceae from ndhF sequences. Am J Bot 91, 767-777.
De Masi L, Castaldo D, Galano G et al. (2005) Genotyping of fig (Ficus carica L) via RAPD markers. J Sci Food Agric 85, 2235-2242.
Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA minipreparation: version II. Plant Mol Biol Rep 1, 19-21.
Doolatian L, Khodayari H, Mohammadi A (2017) The genetic diversity survey of the Ficus l. genus in Iran using inter simple sequence repeats markers. Plant Genet Res 4, 51-62.
Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4, 359-361.
Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14, 2611-2620.
FAOSTAT (2020) Statistical databases. In: Food and Agriculture Organization of the United Nations, http://wwwfaoorg/faostat/en/#data/QC, (Accessed March, 2022).
Fateh A, Ali F (2010) Assessment of genetic diversity among some southern Tunisian fig (Ficus carica L.) cultivars based on morphological descriptors. Jordan J Agric Sci 5, 1-16.
Ganopoulos I, Kalivas A, Kavroulakis N et al. (2015) Genetic diversity of Barbary fig (Opuntia ficus-indica) collection in Greece with ISSR molecular markers. Plant Gene 2, 29-33.
Ghasemi M, Baghizadeh A, Abadi M (2010) Determination of genetic polymorphism in Kerman Holstein and Jersey cattle population using ISSR markers. Aust J Basic Appl Sci 4, 5758-5760.
Gheitarani B, Erfani-Moghadam J, Fazeli A (2020) Evaluation of genetic diversity among some common fig using RAPD and ISSR molecular markers. Plant Genet Res 6, 43-54.
Ghorbani A, Hasanpour H, Ercisli S (2019) Variation on biochemical, phytochemical and genetic diversity of fig (Ficus carica) from East Azerbaijan province. J Iran Plant EcophysiolRes 13, 16-28.
Golkar P, Mokhtari N (2018) Molecular diversity assessment of a world collection of safflower genotypes by SRAP and SCoT molecular markers. Physiol Mol Biol Plants 24, 1261-1271.
Hadia HA, El-Mokadem HE, El-Tayeb H (2008) Phylogenetic relationship of four Ficus species using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. J Appl Sci Res 4, 507-514.
Hammer Ø, Harper D, Ryan P (2001) PAST: Paleontological statistics software package for education and data analysis. Palaeontologia Electronica 4, 9pp.
Hoehn E, Gasser F, Guggenbühl B et al. (2003) Efficacy of instrumental measurements for determination of minimum requirements of firmness, soluble solids, and acidity of several apple varieties in comparison to consumer expectations. Postharvest Biol Technol 27, 27-37.
Hssaini L, Hanine H, Razouk R et al. (2020) Assessment of genetic diversity in Moroccan fig (Ficus carica L.) collection by combining morphological and physicochemical descriptors. Genet Resour Crop Evol 67, 457-474.
Ikegami H, Nogata H, Hirashima K et al. (2009) Analysis of genetic diversity among European and Asian fig varieties (Ficus carica L.) using ISSR, RAPD, and SSR markers. Genet Resour Crop Evol 56, 201-209.
Jiang L, Shen Z, Zheng H et al. (2013) Noninvasive evaluation of fructose, glucose, and sucrose‎ contents in fig fruits during development using‎ chlorophyll fluorescence and chemometrics. J Agric Sci Technol 15, 333-342.
Khadari B, Lashermes P, Kjellberg F (1995) RAPD fingerprints for identification and genetic characterization of fig (Ficus carica L.) genotypes. J Genet Breed 49, 77-85.
Kumar H (1991) Cytogenetics of safflower. In: Developments in Plant Genetics and Breeding. Elsevier. pp. 251-277.
Li J, Pei G, Pang H et al. (2006) A new method for RAPD primers selection based on primer bias in nucleotide sequence data. J Biotechnol 126, 415-423.
Liu BH (1998) Statistical genomics: Linkage, mapping and QTL analysis. CRC Press, Boca Raton, Florida, USA.
Luo C, He X-h, Chen H et al. (2011) Genetic diversity of mango cultivars estimated using SCoT and ISSR markers. Biochem Syst Ecol 39, 676-684.
Mohammadabadi M (2017) Inter-simple sequence repeat loci associations with predicted breeding values of body weight in Kermani sheep. Genet Third Millenn 14, 4383-4390.
Mohammadabadi M, Bordbar F, Jensen J et al. (2021) Key genes regulating skeletal muscle development and growth in farm animals. Animals 11, e835.
Mohammadabadi M, Esfandyarpoor E, Mousapour A (2017) Using inter simple sequence repeat multi-loci markers for studying genetic diversity in Kermani sheep. J Res Dev 5, e154.
Mohammadifar A, Faqih Imani SA, Mohammad Abadi MR et al. (2014) The effect of TGF 3 gene on phenotypic and breeding values of body weight traits in Fars native fowls. Agric Biotechnol J 5, 125-136 (In Persian).
Mohammadifar A, Mohammadabadi M (2012) Application of microsatellite markers for a study of Kermani sheep genome. Iran J Anim Sci 42, 337-344 (In Persian).
Mohammadifar A, Mohammadabadi M (2018) Melanocortin-3 receptor (mc3r) gene association with growth and egg production traits in Fars indigenous chicken. Malays Appl Biol 47, 85-90.
Nadeem MA, Nawaz MA, Shahid MQ et al. (2018) DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnol Biotechnol Equip 32, 261-285.
Nei M (1972) Genetic distance between populations. The American Naturalist 106, 283-292.
Piya S, Nepal MP, Butler JL et al. (2014) Genetic diversity and population structure of sickleweed (Falcaria vulgaris; Apiaceae) in the upper Midwest USA. Biol Invasions 16, 2115-2125.
Powell W, Morgante M, Andre C et al. (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Molecular Breeding 2, 225-238.
Price A, Hendry G (1991) Iron‐catalysed oxygen radical formation and its possible contribution to drought damage in nine native grasses and three cereals. Plant Cell Environ 14, 477-484.
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155, 945-959.
Rout GR, Aparajita S (2009) Genetic relationships among 23 Ficus accessions using inter-simple sequence repeat markers. J Crop Sci Biotechnol 12, 91-96.
Sadder M, Ateyyeh A (2006) Molecular assessment of polymorphism among local Jordanian genotypes of the common fig (Ficus carica L.). Sci Hortic 107, 347-351.
Saddoud O, Chatti K, Salhi‐Hannachi A et al. (2007) Genetic diversity of Tunisian figs (Ficus carica L.) as revealed by nuclear microsatellites. Hereditas 144, 149-157.
Saddoud O, Salhi-Hannachi A, Chatti K et al. (2005) Tunisian fig (Ficus carica L.) genetic diversity and cultivar characterization using microsatellite markers. Fruits 60, 143-153.
Shannon CE (2001) A mathematical theory of communication. ACM SIGMOBILE Mobile Computing and Communications Review 5, 3-55.
Talebi R, Nosrati S, Etminan A et al. (2018) Genetic diversity and population structure analysis of landrace and improved safflower (Cartamus tinctorious L.) germplasm using arbitrary functional gene-based molecular markers. Biotechnol Biotechnol Equip 32, 1183-1194.
Teoman S, Meryem I, Erturk U et al. (2017) Assessment of genetic relationship among male and female fig genotypes using simple sequence repeat (SSR) markers. Not Bot Horti Agrobot Cluj Napoca 45, 172-178.
Tessier C, David J, This P et al. (1999) Optimization of the choice of molecular markers for varietal identification in Vitis vinifera L. Theoretical and Applied Genetics 98, 171– 177.
Yeh FC (1999) POPGENE (version 1.3. 1). Microsoft Window-Bases Freeware for Population Genetic Analysis. http://www ualberta ca/~ fyeh/.
Zeynel D, Gonca G, nver-Dalklccedil et al. (2011) Genetic diversity of male fig (Ficus carica caprificus L.) genotypes with random amplified polymorphic DNA (RAPD) markers. Afr J Biotechnol 10, 519-526.