<b>Genetic diversity of Ocimum species through biochemical technique and UPGMA cluster analysis</b>
Creators: name: Kumar Bompalli, Lenin
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 310806
subject: Plant physiology
classificationCode: 310802
subject: Plant biochemistry
classificationCode: 300105
subject: Genetically modified field crops and pasture
classificationCode: 300106
subject: Genetically modified horticulture plants
classificationCode: 300107
subject: Genetically modified trees
classificationCode: 310113
subject: Synthetic biology
classificationCode: 310109
subject: Proteomics and intermolecular interactions (excl. medical proteomics)
classificationCode: 310108
subject: Protein trafficking

description: Studying the genetic diversity of Ocimum species involves biochemical techniques and UPGMA (Unweighted Pair Group Method with Arithmetic Mean) cluster analysis. Here’s a structured approach to how this can be done:Biochemical Techniques for Genetic Diversity Analysis:<b>DNA Extraction</b>: Start by isolating genomic DNA from various Ocimum species. This can be done using methods such as CTAB (cetyltrimethylammonium bromide) extraction, which is effective for plants and yields high-quality DNA suitable for downstream analysis.<b>PCR (Polymerase Chain Reaction)</b>: Use PCR to amplify specific genetic markers. For assessing genetic diversity, regions such as the Internal Transcribed Spacer (ITS) of rDNA, chloroplast DNA regions (like trnL-trnF intergenic spacer), or other suitable markers (e.g., SSRs - Simple Sequence Repeats) can be targeted. These markers are chosen for their variability and ability to differentiate between closely related species or varieties.<b>Gel Electrophoresis</b>: Separate and visualize the PCR products using agarose gel electrophoresis. This step helps confirm the presence and size of the amplified DNA fragments.<b>Sequencing (Optional)</b>: For detailed analysis, sequencing of PCR products can provide nucleotide-level information, especially useful for resolving relationships between closely related species.<b>Biochemical Profiling (Metabolomics)</b>: Another approach involves analyzing the biochemical composition of Ocimum species. This can be done using techniques like HPLC (High-Performance Liquid Chromatography) or GC-MS (Gas Chromatography-Mass Spectrometry) to identify and quantify secondary metabolites such as essential oils, flavonoids, and phenolics. Variations in these compounds can reflect genetic differences among species.UPGMA Cluster Analysis:After obtaining biochemical data or DNA sequence data, UPGMA cluster analysis can be employed:<b>Data Preparation</b>: Convert the biochemical or molecular data into a matrix format where each species is represented by its profile (presence/absence or quantity of specific markers or compounds).<b>Distance Matrix Calculation</b>: Compute pairwise distances between species based on their biochemical profiles or genetic distances derived from sequence data. Common distance measures include Euclidean distance for biochemical data or genetic distances (such as Jaccard distance for presence/absence data or nucleotide distances for sequence data).<b>Cluster Construction</b>: Use the UPGMA algorithm to construct a hierarchical clustering tree (dendrogram). UPGMA starts with each species as its own cluster and iteratively merges the closest clusters based on the calculated distances until all species are in a single cluster.<b>Visualization and Interpretation</b>: Visualize the dendrogram to interpret the genetic relationships among Ocimum species. Species that cluster together at lower branches of the dendrogram share more similarity in their biochemical or genetic profiles, indicating closer genetic relatedness.<br>