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

Document Type : Research Paper

Authors

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

Abstract

Objective
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.
 
Results
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.
 
Conclusions
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.

Keywords


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.
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