Study on the genetic diversity of tomato’s cultivars via SCoT marker

Document Type : Research Paper


1 Department of Crop Production and Genetics, College of Agriculture, Razi University, Kermanshah, Iran

2 Department of Plant Production and Genetics- College of Agriculture, Razi University, Kermanshah, Iran


This study was conducted to investigate the application of the start codon targeted (SCoT) markers in the genetic diversity of tomato. In addition, the genetic diversity in important cultivars of tomato, which have been previously cultivated, are being cultivated, or are hoped to be cultivated in Iran were assessed.
Materials and Methods
Ninety nine 99 tomato cultivars were investigated for SCoT polymorphism. DNA isolation and SCoT analysis were carried out using the fresh leaf samples. Thirty-six SCoT primers were initially screened for analysis and fifteen primers were considered for the further analysis.
The cultivars produced 207 amplicons while the 206 were polymorphic. Amplicon size varied from 250 to 3200 base pair (bp). The average of polymorphism and the mean of polymorphic information content were 99.52 and 0.30, respectively. Also, Jaccard's similarity coefficient was applied and the mean Jaccard genetic similarity coefficient was 0.52. According to Jaccard's coefficient, the lowest similarity (0.17) has been observed for cultivars 34 and 97 while the highest similarity (0.84) were detected between cultivars 86 and 87. In addition, the cluster analysis was conducted based on Jaccard similarity coefficient and centroid method which classified cultivars into three clusters. Besides, the principal coordinate analysis was considered. Accordingly, the cultivars divided into four groups and the first three components explained 58.82% of the molecular variation. The results of the principal coordinate analysis were largely consistent with the results of the cluster analysis. Having high polymorphic information content, marker index, effective multiplex ratio, and resolution power, SCoT12 and SCoT23 primers were properly effective in differentiating the cultivars.
This study showed that SCoT molecular markers are appropriate for investigating the genetic diversity amongst tomato genotypes and generate a high level of polymorphism. Thus, these markers have considerable efficiency in differentiating tomato genotypes. In addition, this investigation indicated that SCoT12 and SCoT23 primers were suitably effective in differentiating the cultivars. Furthermore, our resech claimed that tomato cultivars that are used in Iran do not have high genetic diversity while for more precise conclusion; it is suggested to practice more SCoT primers along with other markers.


احمدی کریم، عبادزاده حمیدرضا، عبدشاه هلدا، کاظمیان آرزو، رفیعی مریم (1397) آمارنامه کشاورزی سال زراعی 96- 1395. وزارت جهاد کشاورزی، معاونت برنامه ریزی و اقتصادی، مرکز فناوری اطلاعات و ارتباطات، تهران 35- 31.
پورابوقداره علیرضا، اطمینان علیرضا، شوشتری لیا، ملکی تبریزی ندا (1398) ارزیابی مقایسه‌ای نشانگرهای CBDP و SCoT در بررسی تنوع ژنتیکی در توده‌های مختلف Aegilops. مجله بیوتکنولوژی کشاورزی 11(4)، 174-153.
شازده‌احمدی مرضیه، خرازی مهین (1394) استفاده از نشانگر مولکولی ISSR در بررسی تنوع ژنتیکی برخی از ژنوتیپ‌های توتون. مجله پژوهش‌های ژنتیک گیاهی 2(2)، 46- 33.
کردرستمی مجتبی، رحیمی مهدی، صفائی چائی‌کار صنم، سراجی علی، آزادی رضا (1398) بررسی کارآیی نشانگرهای مولکولی در ارزیابی تنوع ژنتیکی کلون‌های مختلف چای ایران. مجله بیوتکنولوژی کشاورزی 11(2)، 100- 79.
نبی‌پور مریم، فارسی محمد، نعمتی حسین، ملک‌زاده سعید (1390) بررسی تنوع ژنتیکی ژنوتیپ‌های گوجه‌فرنگی با استفاده از نشانگر‌های مولکولی AFLP و ارتباط آن با هتروزیس. نشریه پژوهش‌های زراعی ایران 10(6)، 360- 354.
نقوی محمدرضا، قره‌یاضی بهزاد، حسینی سالکده قاسم (1388) نشانگرهای مولکولی. انتشارات دانشگاه تهران 6- 5.
Ahmadi K, Ebadzadeh HR, Abdshah H, Kazemian A, Rafiei M (2018) Agriculture statistical center of iran. Ministry of Agriculture Jihad, Deputy of Planning and Economics, Information and Communication Technology Center, Tehran, pp. 31-35. (In Persian).
Amirmoradi B, Talebi R, Karami E (2012) Comparison of genetic variation and differentiation among annual Cicer species using start codon targeted (SCoT) polymorphism, DAMD-PCR, and ISSR markers. Plant Syst Evol 298, 1679-1688.
Areshchenkova T, Ganal MW (2002) Comparative analysis of polymorphism and chromosomal location of tomato microsatellite markers isolated from different sources. Theor Appl Genet 104, 229-235.
Bhattacharyya P, Kumaria S, Kumar Sh, Tandon P (2013) Start Codon Targeted (SCoT) marker reveals genetic diversity of Dendrobium nobile Lindl., an endangered medicinal orchid species. Gene 529, 21–26.
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.
Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA mini preparation version II. Plant Mol Biol Rep 1, 19-21.
Etminan A, Pour-Aboughadareh A, Mohammadi R et al. (2016) Applicability of start codon targeted (SCoT) and inter-simple sequence repeat (ISSR) markers for genetic diversity analysis in durum wheat genotypes. Biotechnol Biotechnol Equip 30, 1075-1081.
Feng SG, He RF, Jiang MY et al. (2016) Genetic diversity and relationships of medicinal Chrysanthemum morifolium revealed by start codon targeted (SCoT) markers. Sci Hortic 201, 118-123.
Foolad MR (2007) Genome mapping and molecular breeding of tomato. Int J Plant Genom 2007, 1-52.
Foolad MR, Sharma A (2004) Molecular markers as selection tools in tomato breeding. In International Symposium on Tomato Diseases 695, 225-240.
Fowler C, Mooney PR (1990) Shattering: food, politics, and the loss of genetic diversity. University of Arizana Press.
Gorji AM, Poczai P, Polgar Z, Taller J (2011) Efficiency of arbitrarily amplified dominant markers (SCOT, ISSR and RAPD) for diagnostic fingerprinting in tetraploid potato. Am J Pot Res 88, 226–237.
Govindaraj M, Vetriventhan M, Srinivasan M (2015) Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives. Genet Res Int 2015, 1-14.
Gue DL, Zhang JY, Liu ChH (2012) Genetic diversity in some grape varieties revealed by SCoT analyses. Mol Biol Rep 39, 5307–5313.
Heidari P, Etminan A, Azizinezhad R, Khosroshahli M (2017) Genomic variation studies in durum wheat (Triticum turgidum ssp. durum) using CBDP, SCoT and ISSR markers. Indian J Genet Plant Breed 77, 379-386.
Heikrujam M, Kumar J, Agrawal V (2015) Genetic diversity analysis among male and female jojoba genotypes employing gene targeted molecular markers, start codon targeted (SCoT) polymorphism and CAAT box-derived polymorphism (CBDP) markers. Meta Gene 5, 90-97.
Kordrostami M, Rahimi M, Safaei Chaeikar S et al. (2019) Investigation the efficiency of molecular markers to assess genetic diversity of Iranian tea clones. Agric Biotech J 11, 79-100. (In Persian).
Lopez-Raez JA, Charnikhova T, Mulder P et al. (2008) Susceptibility of the tomato mutant high pigment-2 dg (hp-2dg) to Orobanche spp. infection. J Agric Food Chem 56, 6326-6332.
Luo C, He XH, Chen H et al. (2010) Analysis of diversity and relationships among mango cultivars using start codon targeted (SCoT) markers. Biochem Syst Ecol 38, 1176-1184.‏
Luo C, He XH, Chen H et al. (2012) Genetic relationship and diversity of Mangifera indica L.: revealed through SCoT analysis. Genet Resour Crop Ev 59, 1505-1515.
Miller JC, Tanksley SD (1990) RFLP analysis of phylogenetic relationships and genetic variation in the genus Lycopersicon. Theor Appl Genet 80, 437- 448.
Mohammadi SA, Prasanna BM (2003) Analysis of genetic diversity in crop plants—salient statistical tools and considerations. Crop Sci 43, 1235-1248.
Nabipour M, Farsi M, Nemmati H, Malekzadeh S (2011) Study of genetic diversity of tomato genotypes using AFLP molecular markers and its relationship with heterosis. Iranian Journal of Field Crops Research 10, 354-360. (In Persian).
Naghavi MR, Ghareyazie B, Hosseini Salekdeh Gh (2009) Molecular markers (3 st edn). University of Tehran Press, pp. 5-6. (In Persian).
Nair AGH, Vidya P, Mohan C (2016) Analysis of genetic variability in sweet potato accessions using Start Codon Targeted (SCoT) polymorphism. Int J Biote and Biochem 12, 111-121.
Pour-Aboughadareh A, Etminan A, Shooshtari L, Maleki-Tabrizi N (2019) Comparative Assessment of SCoT and CBDP Markers for Investigation of Genetic Diversity Existing in Different Aegilops Species. Agric Biotech J 11, 153-174. (In Persian).
Powell W, Morgante M, Andre C et al. (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2, 225-238.‏
Que Y, Pan Y, Lu Y et al. (2014) Genetic analysis of diversity within a chinese local sugarcane germplasm based on Start Codon Targeted polymorphism. Biomed Res Int 2014, 1-10.
Rao VR, Hodgkin T (2002) Genetic diversity and conservation and utilization of plant genetic resources. Plant Cell Tiss Org 68, 1-19.
Rajesh, MK, Sabana AA, Rachana KE et al. (2015) Genetic relationship and diversity among coconut (Cocos nucifera L.) accessions revealed through SCoT analysis. 3 Biotech 5,  999 –1006.
Shazdehahmadi M, Kharrazi M (2016) Application of ISSR molecular markers for genetic diversity study of some tobacco genotypes. Plant Genetic Researches 2, 33-46. (In Persian).
Shibata D (2005) Genome sequencing and functional genomics approaches in tomato. J Gen Plant Pathol 71, 1-7.
Singh AK, Rana MK, Singh S et al. (2014) CAAT box-derived polymorphism (CBDP): a novel
promoter-targeted molecular marker for plants. J Plant Biochem Biot 23, 175–183.
Sinha SK, Srivastava HS, Tripath RD (1993) Influence of some growth regulators and cations on inhibition of chlorophill biosynthesis by lead in maize. Bull Environ Contam Toxicol 51, 241-246.
Sorkheh K, Amirbakhtiar N, Ercisli S (2016) Potential Start Codon Targeted (SCoT) and Interretrotransposon Amplified Polymorphism (IRAP) markers for evaluation of genetic diversity and conservation of wild pistacia species population. Biochem Genet 54, 368-387.
Staub JE, Serquen FC, Gupta M (1996) Genetic markers, map construction, and their application in plant breeding. Hort Science 31, 729-741.
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, 659.