Molecular Marker Based Assessment of Wheat Biodiversity for Conservation and Sustainable Breeding

Background Wheat ( Triticum aestivum L.) is a vital cereal crop, providing a substantial share of dietary calories and protein. However, climate variability, including heat stress, drought, and irregular rainfall, poses serious challenges to wheat production, particularly in regions already experiencing food insecurity. Enhancing genetic diversity and stress tolerance is crucial for sustaining wheat yields under changing environmental conditions. However, intensive breeding for high-yielding cultivars has led to a reduced genetic base, limiting adaptability and resilience. Objectives This study aims to assess the genetic diversity of 40 wheat genotypes collected from diverse agro-climatic zones using a combination of molecular marker systems: simple sequence repeats (SSR), inter-simple sequence repeats (ISSR), and amplified fragment length polymorphism coupled with capillary electrophoresis (AFLP-CE). The goal is to characterize genetic relationships, detect polymorphisms, and provide insights to support conservation and sustainable breeding strategies. Methods Genotypic differentiation was analyzed using a combination of SSR, ISSR markers, and high-resolution fragment analysis of AFLP-CE to ensure comprehensive genome-wide polymorphism detection. The genetic relationships among wheat genotypes were inferred through similarity matrix analysis and hierarchical clustering, facilitating a robust framework for classification and selection. Results The integrated marker approach revealed substantial genetic variability among the studied wheat genotypes, reflecting diverse ecological adaptations. AFLP-CE enhanced the resolution of rare and informative polymorphisms, improving genotype discrimination. These results highlight the richness of genetic resources that can be harnessed to improve stress tolerance and yield stability. Conclusion This study underscores the effectiveness of combining SSR, ISSR, and AFLP-CE for the complete evaluation of wheat biodiversity. The findings support conservation and targeted breeding strategies for improved resilience and sustainable yield under climate variability.