Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated castor (Ricinus communis L.) genotypes

Abstract

In the present study, 111 castor genotypes were differentiated by the DNA fingerprinting patterns using 37 SCoT primers. The selected primers amplified DNA fragments across the 111 genotypes studied with the number of amplified fragments varying from 3 (SCoT 14) to 10 (SCoT 30 and SCoT 44) and the amplicon size varied from 100 to 3000 bp. Of the 246 amplified bands, 186 were polymorphic with an average of 5.03 fragments per primer. The percentage of polymorphic bands ranged from 57.14 % (SCoT 34) to 100.00 % (SCoT 28 and SCoT 33) with an average of 77.50%. The polymorphic information content (PIC) values varied from 0.372 (SCoT 14) to 0.818 (SCoT 30) with an average of 0.677. A dendrogram was constructed from a genetic distance matrix based on profiles of the 37 SCoT primers using the unweighted pair-group method with the arithmetic average (UPGMA). According to analysis, the collection of 111 diverse accessions of castor was clustered into two main clusters (1 and 2). The first cluster were subdivided into two subclusters (1a and 1b). Subclaster 1a contained 11 genotypes of castor and subclaster 1b contained 6 genotypes of castor. Subclaster 2 were subdivided into two subclusters (2a and 2b). Subclaster 2a contained 44 castor genotypes and subclaster 2b contained 50 castor genotypes. Results showed the utility of SCoT markers for estimation of genetic diversity of castor genotypes leading to genotype identification.

Application of different molecular markers in biotechnology

“…Amplicons are evaluated by standard gel electrophoresis with agarose gels (Collard and Mackill, 2009). (Collard and Mackill, 2009) Similar to other molecular markers, SCoT could be successfully practised for genetic diversity (Vivodík et al, 2019;Vanijajiva et al, 2020;Xiao et al, 2020). In some studies, SCoT markers were combined with other molecular markers.…”

Polymorphism of Bolivian accessions of Arachis hypogaea L. revealed by allergen coding DNA markers

“…DNA markers from the different coding regions of plants' genomes can provide specific information on genomic polymorphism. For instance, start codon targeted markers have been applied for genetic diversity analysis of different plant species, such as chickpeas (Pakseresht et al 2013), potatoes (Gorji et al 2011), tomatoes (Shahlaei et al 2014), castor (Vivodík et al 2019), and wheat (Seyedimoradi et al 2016). In the case of A. hypogaea, start codon targeted (SCoT) markers were used for the purposes of functional genetic variation mapping (Xiong et al 2011), and this technique provided a level of polymorphism that ranged from 14.29% to 66.67%, and a high genetic similarity was obtained for the analysed peanut accessions.…”