Genetic diversity and population structure analysis of Nigerian sesame (Sesamum indicum L.) based on the ITS2 molecular marker

Sesame (Sesamum indicum L.) is a vital oilseed crop in Nigeria, yet the genetic diversity across its major production belts remains insufficiently characterized. This study evaluated the intraspecific genetic variation and eco-geographic population structure of 29 Nigerian sesame accessions collected from 16 states across four distinct agro-ecological zones: Southern Guinea Savanna (SGS), Northern Guinea Savanna (NGS), Sudan Savanna (SS), and Lowland Rainforest/Derived Savanna (RF/DS). Sanger sequencing of the nuclear ribosomal internal transcribed spacer 2 (ITS2) region yielded an average length of 601.4 bp, with a high mean GC content of 67.62%. BLAST analysis confirmed species identity, with 98.36%–100% sequence identity across all accessions. Sequence analysis identified 10 distinct haplotypes and 11 polymorphic sites, demonstrating moderate haplotype diversity (Hd = 0.692) and low overall nucleotide diversity (π = 0.0056). A predominant haplotype (H2), shared by 16 accessions, underscored a conserved core genetic lineage. Neighbor Joining phylogenetic analysis resolved a well-supported split (100% bootstrap value) separating the conserved H2-dominated clade from a divergent group containing haplotypes H3–H10. Analysis of Molecular Variance (AMOVA) revealed significant genetic differentiation among agro-ecological zones (FST = 0.642), with 64.2% of the total molecular variation partitioned among zones. Although the SGS and SS populations displayed extensive gene flow (FST = 0.024, Nm ≈ 10.17), the NGS zone harbored the highest haplotype diversity (Hd = 0.933), while the RF/DS zone exhibited the highest nucleotide diversity (π = 0.0118). These findings indicate that while major Nigerian sesame production zones depend mainly on a narrow genetic lineage, divergent germplasm from the Northern Guinea Savanna and Lowland Rainforest/Derived Savanna provides essential genetic variation for conservation strategies and breeding programmes.

Alege Gbenga Olorunshola is a Professor of Applied Genetics and Plant Breeding, affiliated with the Federal University Lokoja, Nigeria. Alege’s core research areas are plant biotechnology, crop population genetics, and germplasm conservation. He has contributed to research on genetic diversity and molecular characterization of economically important plants such as sesame including the use of protein profiling and DNA-based molecular markers such as Random Amplified Polymorphic DNA (RAPD). Through his research Prof. Alege actively promotes plant germplasm conservation, crop improvement strategies, and sustainable agricultural development in Sub-Saharan Africa.