Genetic Diversity Analysis of Pepper (Capsicum annuum) Landraces in North East Nigeria Using SSR Markers

Pepper (Capsicum annuum) landraces maintained by smallholder farmers in North East Nigeria represent an important reservoir of genetic diversity that remains largely uncharacterized using modern molecular tools. Understanding the genetic structure of these landraces is essential for rational conservation and utilization in breeding programs targeting improved yield, disease resistance, and quality traits. This study characterizes the genetic diversity of 45 pepper landrace accessions collected from Adamawa, Taraba, and Gombe states using 20 simple sequence repeat (SSR) markers. DNA extraction, PCR amplification, and fragment analysis were performed using standard molecular biology protocols. Genetic diversity statistics including polymorphic information content, expected heterozygosity, and Nei's gene diversity were computed. Population structure was analyzed using STRUCTURE software and UPGMA clustering. Results reveal substantial genetic diversity among the accessions, with mean expected heterozygosity of 0.68 and 19 of 20 SSR loci being highly polymorphic. Clustering analysis identified three genetically distinct population groups with partial correspondence to geographic origin, suggesting gene flow between communities. High-diversity accessions from Adamawa and Taraba states are recommended as priority material for ex situ conservation and inclusion in national pepper breeding programs. Keywords: genetic diversity, pepper, SSR markers, landraces, North East Nigeria