Ber Supply data
Description
The supplementary data consist of Variation in the leaf relative water content and rate of water loss, reducing sugar, non reducing sugar and total content. And also PCR-RAPD amplicons of ber varieties.
Files
Steps to reproduce
DNA extraction DNA extraction was performed from tender leaves of each genotype using the Cetyltrimethylammonium bromide (CTAB) method with minor modifications. DNA quality and concentration were assessed using spectrophotometry (A260/A280 ratio) and agarose gel electrophoresis to ensure suitability for PCR amplification. Amplification studies For diversity studies thirty labelled RAPD primers were used (Table 2). Amplification studies were carried out using a thermocycler (Perkin Elmer 480; USA) where, PCR plates were filled with reaction mixture (10 microlitres ) containing Taq 2x Master Mix (JumpStart Taq ReadyMix, Sigma Aldrich, USA), 50 ng of genomic DNA, RAPD primer (5 pmol/ml). Amplification profile consisted 1 cycle at 95°C 4min-1; 35 cycles at 94°C min-1, 33°C 2 min-1 and 72°C 2 min-1; 1 cycle at 72°C 30 min-1.; hold at 4°C/∞. The PCR product was examined on agarose gel (1. 6%) and was prepared thoroughly to analyze the obtained PCR product with a 100 Kb ladder (Geneii) and then a close-up shot was taken over under the gel documentation system (UVI Tech England). Reproducibility and Reliability Due to RAPD’s sensitivity to experimental conditions three independent replicates per primer per genotype were performed 17. Three replications of one sample per primer have been carried out to ensure that DNA of the same genotype was used as a control in each amplification cycle. Consequently, the final analysis only considered DNA fragments that were distinguished, reproducible, and distinct in all genotypes. RAPD markers were employed for preliminary assessment of genetic diversity due to their ease of use, economy, and expedited processing, which allows screening of multiple genotypes. Data analysis Each RAPD primer pair is considered a single genetic marker. The RAPD profile data were individually scored for each fragment in every genotype for each primer combination. The scores were recorded as 1 to represent the presence of a fragment and 0 to represent the lack of a fragment. This information was used to create a binary qualitative data matrix. Jaccard's similarity coefficient was calculated using the matrix. The similarity matrices underwent cluster analysis using the un-weighted pair group approach. The arithmetic mean (UPGMA) used the sequential agglomerative hierarchical and nested (SAHN) cluster analysis module to generate a dendrogram. To assess the appropriateness of RAPD markers for evaluating the genetic profiles of Ziziphus genotypes markers were evaluated based on four parameters: (I) Polymorphic information content (PIC), (II) Number of monomorphic bands, and (III) Number of polymorphic bands. (4IV Count of distinct bands and (V) Total count of bands. The calculations were performed using the NTSYS-pc version 2.1 program.
Institutions
- Vellore Institute of Technology UniversityTamil Nadu, Vellore