Genetic Relationships of Pistacia Species and Cultivars by SCoT Markers

Document Type : Research Paper


1 Ph.D. Student, Department of Production Engineering and Breeding Genetics, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran.

2 Department of plant genetics and production engineering, Faculty of agriculture and natural resources, University of Mohaghegh Ardabili, Ardabil, Iran

3 Professor, Department of Genetics and Plant Production, Faculty of Agriculture, Valiasr University, Rafsanjan, Rafsanjan, Iran. email

4 Professor, Department of Plant Protection, Faculty of Agriculture, Valiasr University, Rafsanjan, Rafsanjan, Iran.

5 Research Assistant Professor, Pistachio Research Center, Horticultural sciences Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Rafsanjan, Iran


Pistachio is one of the most important agricultural products and iran has the richest germplasm of pistachio in the world. The presence of this genetic resources will be an appropriate opportunity for use in breeding purposes. Knowledge of genetic relationships among pistachio genotypes has important role in it’s breeding programs. Molecular markers are one of the powerful tools for studying plant phylogenetic relationships. Start Codon Targeted (SCoT) technique is one of the molecular systems that used to assess the genetic relationship among different plant species and cultivars. This study was performed in order to evaluate the genetic relationships between a numbers of Pistacia species and cultivars using SCoT molecular markers and to assess the usefulness of this markers in differentiating this genus.
Materials and methods
Plant materials of this study are included 29 genotypes of domestic and wild species of genus Pistacia. A total of 25 SCoT primers were used to evaluate the genetic relationships. Genomic DNA were extracted from leaf samples using CTAB method with minor modifications. The quantity and quality of the extracted DNA were measured by spectrophotometer and agarose gel electrophoresis. Cluster analysis based on Jaccard’s similarity matrix and complete linkage algorithm and Principal coordinate analysis were performed using NTSYSpc 2.02e software.
In total, 449 DNA fragments were amplified by primers out of which 433 bands (96/43%) were polymorphic. The average number of amplified fragments for each primer was 17.96 bands with a mean of 17.32 polymorphic bands per primer. A number of species-spicific marker were detected in some Genotypes. The average of polymorphism information content values varied from 0/18 to 0/38. Also, the values of marker indices ranged from 0/56 to 4/36. The range of similarity coefficients of genotypes varied between 25% to 68%. Cluster analysis divided Genotypes into two main cluster including vera (domestic) and wild species. Principal coordinate analysis separated vera cultivars and genotypes from wild species and confirmed the results of cluster analysis.
The results of this study demonstrated that SCoT molecular markers detected high polymorphism among pistachio species and cultivars and differentiated the studid genotypes. Therefore, SCoT Marker is a useful tool for studying phylogenetic relationships in genus Pistacia.


خدادادی شیرین، دشتی حسین، صابری ریسه روح اله، ملک‌زاده خلیل، تاج‌آبادی پور علی (1400) تنوع ژنتیکی ارقام و ژنوتیپ‌های پسته از نظر مقاومت به بیماری پوسیدگی طوقه و ریشه (Phytophthora drechsleri) و ارتباط آن با مارکرهای مولکولی SCoT. مجله ژنتیک نوین. 16 (3)، 248-235.
محمدی سید ابوالقاسم (1385) تجزیه‌وتحلیل داده‌های مولکولی از دیده گاه بررسی تنوع ژنتیکی. نهمین کنگره علوم زراعت و اصلاح نباتات ایران. دانشگاه تهران، پردیس ابوریحان. 119-96.
محمدی فر آمنه، فقیه ایمانی سید علی، محمدآبادی محمدرضا، سفلایی محمد (1392) تأثیر ژن TGFb3 بر ارزش‌های فنوتیپی و ارثی صفات وزن بدن در مرغ بومی استان فارس. مجله بیوتکنولوژی کشاورزی 5(4)، 136-125.
کریمی حمیدرضا (1389) فیلوژنی گونه‌های جنس پسته. نشر پلک، تهران. ص 78-31.
Ahmadi Afzadi M, Seyed Tabatabaei BE, Mohammadi SA, Tajabadipour A (2007) Comparison of genetic diversity in species and cultivars of pistachio (Pistacia sp. L.) based on Amplified Fragment Length Polymorphism (AFLP) markers. Iran J Biotech 5, 147–152.
Arabnezhad H, Bahar M, Tajabadipour A (2011) Evaluation of genetic relationships among Iranian pistachios using microsatellite markers developed from Pistacia khinjuk Stocks. Sci Hort 128(3), 249-254.
Baghizadeh A, Noroozi Sh, JalaliJavaran M (2010) Study on genetic diversity of some Iranian pistachio (Pistacia vera L.) cultivars using random amplified polymorphic DNA (RAPD), inter sequence repeat (ISSR) and simple sequence repeat (SSR) markers: A comparative study. African J Biotech 9(45), 7632-7640.
Collard BC, Mackill DJ (2009) Start codon targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Mol Bio Rep 27(1), 86-93.
Dempewolf H, Baute G, Anderson J et al. (2017) Past and future use of wild relatives in crop breeding. Crop Sci 57(3), 1070-1082.
Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull J 19, 11-15.
Gajera HP, Bambharolia RP, Domadiya RK et al. (2014) Molecular characterization and genetic variability studies associated with fruit quality of indigenous mango (Mangifera indica L.) cultivars. Plant Syst Evol 300(5), 1011-1020.
Ghaemmaghami L, Attar F, Rahiminejad MR (2013) Distinctness and inter relationships of Pistacia L. species in Iran as evidenced by retroelement insertional polymorphisms (IRAP method), Iran J Bot 19(1), 78–85.
Golan-Goldhirsh A, Barazani O, Wang ZS et al. (2004) Genetic relationships among Mediterranean Pistacia species evaluated by RAPD and AFLP markers. Plant Syst Evol 246(1), 9-18.
Gower JC (1966) Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika 53(3-4), 325-338.
Guney M, Kafkas S, Zarifikhosroshahi M et al. (2021) Genetic diversity and relationships of terebinth (Pistacia terebinthus L.) genotypes growing wild in Turkey. Agro 11(4), 671-681.
He SA, Yi TS, Pei SJ, Huang H (2015) Crop plants and their wild relatives. The Plants of China: A Companion to the Flora of China. Cambridge University Press, Cambridge, United Kingdom 23, 283-308.
Ibrahim SD, Adawy SS, Atia MAM et al. (2016) Genetic diversity, variety identification and gene detection in some Egyptian grape varieties by SSR and SCoT markers. Plant Omics J 9(5), 311-318.
Iranjo P, NabatiAhmadi D, Sorkheh K et al. (2016) Genetic diversity and phylogenetic relationships between and within wild Pistacia species populations and implications for its conservation. J For Res 27(3), 685-697.
Kafkas S, Kafkas E, Perl-Treves R (2002) Morphological diversity and a germplasm survey of three wild Pistacia species in Turkey. Genet Resour Crop Evol 49(3), 261-270.
Kafkas S (2006) Phylogenetic analysis of the genus Pistacia by AFLP markers. Plant Sys Evol 262(1), 113-124.
Karimi HR, Kafkas S (2011) Genetic relationships among Pistacia species studied by SAMPL markers. Plant Syst Evol 297(3), 207-212.
Karimi HR (2010) Phylogeny of the Pistacia species. Pelk Publication,Tehran, pp. 31-78 (In Persian).
Karimi HR, Kafkas S, Zamani, Z Ebadi et al. (2009) Genetic relationships among Pistacia species using AFLP markers. Plant Syst Evol 279(1), 21-28.
Karimi HR, Zamani Z, Ebadi A, Fatahi R (2012) Genetic relationships among pistacia species studied by morphological characteristics and RAPD marker. Int J Nuts & Related Sci 3(1), 49-56.
Katsiotis A, Hagidimitriou M, Drossou A et al. (2003) Genetic relationships among species and cultivars of Pistacia using RAPDs and AFLPs. Euphytica 132(3), 279-286.
Khodadadi Sh, Dashti H, Saberi R, Malekzadeh Kh, Tajabadipour A (2021) Genetic diversity of pistachio cultivars and genotypes in terms of resistance to crown and root rot (Phytophthora drechsleri) and its relationship with SCoT molecular markers. New Genet 16(3), 235-248 (In Persian).
Luo C, He XH, Hu Y et al. (2014) Oligo-dT anchored cDNA–SCoT: a novel differential display method for analyzing differential gene expression in response to several stress treatments in mango (Mangifera indica L.). Genet 548(2), 182-189.
Mahjbi A, Baraket G, Oueslati A, Salhi-Hannachi A (2015) Start Codon Targeted (SCoT) markers provide new insights into the genetic diversity analysis and characterization of Tunisian Citrus species. Biochem Syst Ecol 61, 390-398.
Mais AS, Faory H, Nakar M et al. (2014) Genetic relationships among some Pistacia species (Anacardiaceae) in Syria. Middle-East J Sci Res 21(9), 1487-1497.
Malekzadeh KH, Mahmoodnia Meimand M, Farzad Amirebrahimi F (2018) Analysis of genetic diversity among male and female pistachio genotypes using start codon targeted (SCoT) makers. J Plant Mol Breed 6(2), 10-18.
Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27, 209-220.
Michel D (2017) Iran’s impending water crisis. In Water, Security and US Foreign Policy, Routledge, pp. 168-188.
Mirzaei S, Bahar M, Sharifnabi B (2005) A phylogenetic study of Iranian wild pistachio species and some cultivars using RAPD markers. In IV International Symposium on Pistachios and Almonds 726, 39-44.
Mohammadabadi MR (2017) Inter-Simple Sequence Repeat loci Associations with Predicted Breeding Values of Body Weight in Kermani Sheep. Genet 3rd Millennium 14 (4), 4383-4390.
Mohammadifar A, Faghih Imani SA, Mohammadabadi MR, Soflaei M (2014) The effect of TGFb3 gene on phenotypic and breeding values of body weight traits in Fars native fowls. Agric Biotechnol J 5 (4), 125-136.
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 (3), 85-90.
Mohammadabadi MR, Esfandyarpoor E, Mousapour A (2017) Using Inter Simple Sequence Repeat Multi-Loci Markers for Studying Genetic Diversity in Kermani Sheep. J Res Develop 5 (2), e154.
Mohammadi SA (2003) Analysis of molecular data from the perspective of genetic diversity. 9th Iranian Congress of Agricultural Sciences and Plant Breeding. Tehran University, AbuRiha Cmpuse. 96-119.
Mohammadi SA, Prasanna, BM (2003) Analysis of genetic diversity in crop plants: Salient statistical tools and considerations. Crop Sci 43, 1235-1248.
Mulpuri S, Muddanuru T, Francis G (2013) Start codon targeted (SCoT) polymorphism in toxic and non-toxic accessions of Jatropha curcas L. and development of a codominant SCAR marker. Plant Sci 207, 117-127.
Pazouki L, Mardi M, Salehi Shanjani P (2010) Genetic diversity and relationships among Pistacia species and cultivars. Conserv Genet 11(1), 311-318.
Powell W, Morgante M, Andre C (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2(3), 225-238.
Pourian MR, Bakhshi D, Aalami A, Hokmabadi H (2019) Assessment of genetic relationship among cultivated and wild pistachios (Pistacia vera L.) using molecular markers. J Hort Res 27(1), 37-46.
Rohlf FJ (1998) NTSYSpc numerical taxonomy and multivariate analysis system version 2.02. Exeter Software, Setauket, NewYork.
Sankhla AK, Malik CP, Parashar M (2015) A review on start codon targeted (SCoT) marker. J Plant Sci Res 31(2), 153-160.
Salehi Shanjani P, Mardi M, Pazouki L (2009) Analysis of the molecular variation between and within cultivated and wild Pistacia species using AFLPs. Tree Genet Genomes 5(3), 447-458.
Talebi M, Akbari M, Zamani M, Seyed Tabatabaei BE (2016) Molecular polymorphism in Pistacia vera L. using non-coding regions of chloroplast DNA. J Genet Eng Biotech 14(1), 31-37.
Wu JM, Li YR, Yang LT et al. (2013) cDNA-SCoT: a novel rapid method for analysis of gene differential expression in sugarcane and other plants. Aust J Crop Sci 7(5), 659-664.
Xiong F, Zhong R, Han Z et al. (2011) Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated peanut (Arachis hypogaea L.) genotypes. Mol biol Rep 38(5), 3487-3494.
Xiong FQ, Tang RH, Chen ZL et al. (2009) SCoT: a novel gene targeted marker technique based on the translation start codon. Mol Plant Breed 7(3), 635-638.
Yang HB, Kang WH, Nahm SH, Kang BC (2015) Methods for developing molecular markers. In Current technologies in plant molecular breeding, Springer Dordrecht, pp. 15-50.
Zarei A, Erfani-Moghadam J (2021) SCoT markers provide insight into the genetic diversity, population structure and phylogenetic relationships among three Pistacia species of Iran. Genet Resour Crop Evol 68, 625-1643.
Zohary M (1952) A monographical study of the genus Pistacia. Palestine J Bot Jerusalem Ser 5(4), 187-228.