Comparison of two different electrophoretic methods in studying the genetic diversity among plantains (Musa spp.) using ISSR markers

Abstract

Inter simple sequence repeat markers were employed for the genotyping of 16 plantain ecotypes. Two different electrophoretic systems namely conventional gel electrophoresis (CVGE) and fully automated high‐resolution CGE were used to evaluate the genetic diversity. Comparative analysis indicated that all parameters related to marker informativeness were higher in CGE except polymorphic information content. But genetic diversity parameters like effective number of alleles, Nei's gene diversity (1973) and Shannon's information index showed higher values (1.52 ± 0.12, 0.34 ± 0.05 and 0.52 ± 0.05, respectively) in CVGE as against CGE (1.29 ± 0.04, 0.22 ± 0.02 and 0.38 ± 0.03, respectively) system. The unweighed pair group method with arithmetic averages was used to obtain the dendrogram for both analyses. The results of dendrogram and principal component analysis were found to be consistent in both systems except for some minor disagreements. The clone‐specific bands could be used in the identification and development of SCAR markers. Inter simple sequence repeat markers used in this study provided sufficient polymorphism and reproducible banding pattern for evaluating the genetic diversity of different plantain ecotypes. Lack of accuracy and consistency of the CVGE warrants the employment of high‐throughput CGE for diversity analysis as it provided better separation of bands with higher resolution.

Trait-based description of the agronomic and usage potential of a range of plantain varieties from Cameroon

“…One group of plantain plants of this variety thus showed significantly higher cycle length, emitted leaf number and pseudostem circumference at flowering values. This difference should be further investigated using tailored molecular marker methods (Lamare and Rao, 2015;Marimuthu Somasundaram et al, 2019).…”

Automated ISSR Fingerprinting is a Cost-effective way to assess Genetic Diversity and Taxonomic Differentiation – a Case Study on the Encephalartos eugene-maraisii Species Complex

“…ISSRs have proven valuable in a wide range of applications including hybridisation and taxonomic studies [21,25], phylogeny reconstruction [28], population genetic studies [29][30][31][32], demographics [33] the investigation of the mating systems and reproduction of plants [34], sex determination [35,36], distinguishing ecotypes [37], as well as studies on crops and crop relatives and medicinal plants [38][39][40][41] and identifying markers for traits such as toxin production or phenotypes [35,36,42]. Of particular relevance to our study, this method has also been applied to rare and endangered or endemic species (Xue et al 2004 [46].…”

“…This modification of the primers and use of slightly more costly automated detection systems provides greater sensitivity and resolution of bands coupled with the ability to accurately size much larger ISSR fragments, resulting in larger datasets and more accurate fragment sizing potentially able to differentiate fragments with as li le difference as a single nucleotide [48,49]. Owing to the higher sensitivity of the automated process, much larger datasets are produced, but possibly with lower marker informativeness [37]. However, despite being available since approximately 2004 (e.g Schrader and Graves 2004), the advantage of obtaining larger datasets and ensuring band sizes are comparable, this approach has not been widely used.…”

Molecular Genetic Diversity of Prunus armeniaca L. (Rosaceae) Genotypes by RAPD, ISSR-PCR, and Chloroplast DNA (cpDNA) trnL-F Sequences

“…RAPD markers offer many advantages such as higher polymorphism frequency, fast results, simplicity, low amount DNA requirement, and no prior knowledge of DNA sequence (Ruzi-Chután et al, 2019). ISSR is one of the simplest and most widely used PCR-based marker techniques that amplifies DNA segments between two identical microsatellite repeat regions (Marimuthu Somasundaram et al, 2019). However, among molecular markers, ISSR markers have some advantages comparing to low reproducibility of RAPD markers, high cost of the AFLP markers and the limitations of the complex SSR markers (Ramzan et al, 2018).…”