Utilization of a set of high-polymorphism DAMD markers for genetic analysis of a cucumber germplasm collection

Abstract

Eighteen minisatellite core sequences, derived from rice, human and phage M13, were used as primers in a PCR technique, known as directed amplification of minisatellite-region DNA (DAMD), to genotype 19 cucumber (Cucumis sativus L.) accessions from a wide collection. All the primers amplified polymorphic bands across the accessions. Out of 165 bands scored, 129 were polymorphic with 78.2% polymorphism. The average of polymorphism information content of the primers was 0.844, revealing a high discrimination power in cucumber. Based on Jaccard's similarity indices and matrix generated by the DAMD markers, a dendrogram was constructed using the unweighted pair group method using arithmetic averages and allowed for separation of the 19 accessions into four distinct groups which demonstrated genetic relationship among the different types of germplasms. Sequencing of six polymorphic amplicons resulted in the identification of only one minisatellite locus, which indicated that variation in minisatellite number was not always the factor underlying DAMD polymorphism.

A comparative assessment of morphological and molecular diversity among Sechium edule (Jacq.) Sw. accessions in India

“…Eight primers showed 100% polymorphism, i.e., URP2F, URP25F, URP38F, HVR (-), OGRBO1, M13, 14C2 and HBV5. Four primers were found to have 100% polymorphism as compared to studies conducted by Hu et al (2010) using DAMD markers for cucumber collections. Avendano-Arrazate et al (2012) reported high degree of polymorphism in Mexican accessions of S. edule but such studies was limited to the use of isozyme systems.…”

“…The samples were then stored at -20°C and aliquots were maintained at 4°C. A total of 12 DAMD primers were used to screen and amplify the genomic DNA of 36 accessions of S. edule (Hu et al 2010). PCR amplification was performed in 25 ll of the reaction mixture containing 25 ng sample DNA, 1 mM dNTP, 10 pM primer and 2 units Taq polymerase with 2.5 ll of PCR buffer containing 15 mM MgCl 2 per reaction.…”

“…The temperature profile was as follows: 94°C for 4 min, followed by 40 cycles at 94°C for 1 min, annealing temperature (50-61°C) for 1 min, 72°C for 1 min and 72°C for 5 min final extension. The PCR products were separated by electrophoresis through 1.2% agarose gel and the profiles were analyzed (Hu et al 2010). The presence and absence of bands were recorded; the binary data generated was used to estimate the level of polymorphism using UPGMA.…”

“…DAMD markers are advantageous as they are highly polymorphic. Cucumber (Hu et al 2010), Capsicum spp. (Ince et al 2009), grapevine cultivars (Seyedimoradi et al 2012) and mulberry species (Bhattacharya and Ranade 2001) have been evaluated successfully for its diversity studies, but no information is available to compare the morphological and genetic studies of S. edule species in India.…”

Phenetic and genetic diversity in Indian Luffa (Cucurbitaceae) inferred from morphometric, ISSR and DAMD markers

“…Among the Single Primer Amplification Reaction (SPAR) markers, Inter Simple Sequence Repeats (ISSR: Zietkiewicz et al 1994) and Directed Amplification of Minisatellite DNA (DAMD: Heath et al 1993) are highly efficient and reproducible PCR-based techniques that have been widely used in the estimation of genetic diversity in several plant groups (Idress and Irshad 2014). ISSR and/or DAMD markers have been successfully used in the assessment of genetic diversity in several cucurbits (Paris et al 2003;Verma et al 2007;Behera et al 2008;Sikdar et al 2010;Hu et al 2011;Bhawna et al 2014;Singh et al 2015;Payel et al 2015). We report here an expanded analysis on the extent and pattern of genetic diversity, relationships and mating system in the cultivated and wild genotypes of Indian Luffa using ISSR and DAMD markers.…”