Comparative assessment of ISSR, DAMD and SCoT markers for evaluation of genetic diversity and conservation of landrace chickpea (Cicer arietinum L.) genotypes collected from north-west of Iran

Abstract

Morphological traits and three molecular markers techniques: start codon targeted (SCoT), inter-simple sequence repeat (ISSR) and directly amplified minisatellite DNA (DAMD) markers were compared for fingerprinting of 40 landraces chickpea genotypes collected from different geographical locations of north-west of Iran. Variance analysis of ten measured morphological traits showed significant differences existed between genotypes. Cluster analysis based on morphological traits, divided genotypes in three distinct clusters. Average polymorphism information content (PIC) for ISSR, DAMD and SCoT markers was 0.216, 0.232 and 0.232, respectively, and this revealed that SCoT markers were more informative, followed by ISSRs marker, than other markers for the assessment of diversity amongst genotypes. Cluster analysis for three different molecular types revealed that genotypes taken for the analysis can be divided in three and four distinct clusters. Accessions from same geographical regions mostly showed more genetic similarities than those from origins far isolated apart. These results suggest that efficiency of SCOT, DAMD and ISSR markers was relatively the same in fingerprinting of genotypes but SCOT and DAMD analysis are more effective in fingerprinting of chickpea genotypes. To our knowledge, this is the first detailed report of a comparison of performance among two targeted DNA region molecular markers (SCoT and DAMD) and the ISSR technique on a set of samples of chickpea. Overall, our results indicate that SCOT, ISSR and DAMD fingerprinting could be used to detect polymorphism for genotypes of chickpea.

Geographical diversity pattern in Iranian landrace durum wheat (Triticum turgidum) accessions using start codon targeted polymorphism and conserved DNA-derived polymorphism markers

“…Although the polymorphism rate for the markers was relatively similar, we anticipate that the source of detected diversity differs, as the markers target different regions of the genome (Pakseresht et al 2013).…”

“…Several authors also reported that these marker techniques were able to provide more reliable diversity information compare to RAPD or ISSR techniques (Amirmoradi et al 2012;Li et al 2013;Poczai et al 2013) and are useful as tools for studying the genetic diversity of different plant germplasm. There have been previous reports on clustering of genotypes using gene-based molecular markers in potato (Gorji et al 2011), chickpea (Pakseresht et al 2013;Hajibarat et al 2015), ramie (Satia et al 2015), and wheat (Hamidi et al 2014). In comparison with those studies, we found that the average polymorphism rate for SCoT and CDDP markers in Iranian durum wheat landraces were relatively high.…”

“…It is expected that when such diverse genotypes are involved in breeding programmes, as a result of reshuffling of the alleles due to recombination, there are better chances for the appearance of transgressive segregation with beneficial traits that can be selected to extract high yielding lines with desirable trait combination (Sofalian et al 2008;Pakseresht et al 2013). For the first time, we demonstrated the capability of SCoT and CDDP in estimaion not only for determining the polymorphism rate, but also for the management of genetic diversity in Iranian durum wheat landraces and their uses in applied breeding programmes, particularly for the development of a core collection.…”

“…The SCoT primers are based on conserved regions flanking the initiation codon sequences of genes and CDDPs are short primers to generate useful genetic markers across functional domains of well-characterised plant genes (Collard, Mackill 2009a;Collard, Mackill 2009b). These marker techniques has been successfully employed in genetic diversity analysis of several plants, such as chickpea (Pakseresht et al 2013), wheat (Hamidi et al 2014), ramie (Satya et al 2015) and jojoba (Heikrujam et al 2015). The aim of the present study was to investigate the gentic diversity in Iranian landrace durum wheat accessions and examine the relationships of geographical sources of these accessions with their genetic diversity pattern.…”

Recent advances in the identification and the study of composition and activities of medicinal plants

“…The effectiveness of start codon targeted, directly amplified minisatellite DNA and ISSR markers was quite similar in finger printing of genotypes and might be employed to identify polymorphism for genotypes of chick pea (Cicer arietinum) [18].…”