Exploring the Genetic Landscape of Sesame: Whole Genome Sequencing Reveals Distinct Egyptian Lineages and SNP Variability

Sesame Population Genomics Analysis This repository contains the data and scripts used for the analysis described in “Whole Genome Sequencing Reveals Distinct Egyptian Lineages and SNP Variability in Sesame (Sesamum indicum L.)”. We analyzed 24 sesame genotypes (5 Egyptian and 19 international) using whole-genome resequencing and transcriptomic profiling. After filtering more than 6 million variants, we identified 26,449 high-quality SNPs and detected three major population clusters. Egyptian genotypes formed a distinct and genetically pure group. Main Findings Total variants: 6,106,085 High-quality SNPs: 26,449 Population clusters: 3 Missense variants: ~51% Distinct group: Egyptian sesame lines Here’s your text converted into clear, concise bullet points — perfect for slides, summaries, or README highlights: 🧬 Study Summary Sesame (Sesamum indicum L.) is one of the earliest cultivated oil crops, valued for its high oil content, rich flavor, and nutty aroma. Whole-genome resequencing was performed on: Five Egyptian sesame genotypes: Shandaweel 3, Toshky 1, and three *gamma-irradiated mutant lines. 19 publicly available sesame genomes from the NCBI SRA for comparative analysis. Total variants identified: 6,106,085 nucleotide variants. Filtered high-quality SNPs: 26,449 SNPs with MAF > 0.05. 🧩 Variant Distribution Highest SNP counts: Si01 → 4,144 SNPs Si12 → 3,721 SNPs Si13 → 3,151 SNPs Lowest SNP counts: Si09 → 241 SNPs Si02 → 359 SNPs 🌿 Genetic Diversity High heterozygosity and PIC: Chromosomes Si04, Si07, Si13 showed Ho = 0.816–0.849 and PIC = 0.347–0.353. Population structure analysis: Identified three distinct genetic clusters. Egyptian cultivars formed a pure, separate cluster. Chinese cultivars overlapped with USA and South Korea, suggesting historical seed exchange. Phylogenetic analysis confirmed country-based clustering, with Egyptian genotypes forming a unique lineage. ⚙️ Functional Insights SNP effect analysis: 51% (938 SNPs) were missense mutations, potentially impacting protein function. Key affected genes: AXR1 – growth regulation CYP73A5 – stress resilience CERK1 – pathogen defense 🔬 Multi-Omics Integration Integrated RNA-seq data with genomic variants to assess gene expression relationships. Identified stress adaptation networks involving: Membrane stabilizers: UGT80B1, CalS10 Signaling regulators: PUB9, CNGC15b Hormonal integrators: ARF2, DLO1 Redox managers: cysteine synthase, ascorbate oxidase 🌍 Conclusions Geographic origin significantly influences sesame’s genetic diversity. Egyptian genotypes represent a distinct genetic lineage. The results provide valuable insights for breeding programs aimed at improving adaptability and stress resilience in sesame.