Patterns of Genetic Diversity and Population Structure among Natural and Farmed Nile Tilapia (Oreochromis niloticus) Populations in Kenya

Nile tilapia (Oreochromis niloticus) is the cornerstone of Kenya's aquaculture industry, contributing approximately 80% of the country's farmed fish production. Sustaining genetic diversity within both cultured and wild populations is critical for long-term productivity, resilience, and conservation. This study assessed the genetic diversity and population structure of Nile tilapia populations sampled from selected natural water bodies and hatcheries across Kenya using eight polymorphic microsatellite markers. Genetic diversity indices revealed moderate to high levels of allelic variation within populations (mean Na = 5.46; mean He = 0.74), indicating substantial evolutionary and breeding potential. Analysis of Molecular Variance (AMOVA) showed that most genetic variation occurred within individuals and populations, while STRUCTURE analysis identified three major genetic clusters, demonstrating both gene flow and genetic differentiation among natural and farmed stocks. Farmed and wild populations shared genetic backgrounds but retained distinct population characteristics, suggesting varying levels of broodstock exchange and local adaptation. The findings highlight the importance of maintaining genetic diversity in breeding programs and underscore the need for structured genetic management of hatchery stocks. The observed diversity provides a valuable foundation for selective breeding initiatives targeting growth performance, disease resistance, and environmental adaptability. Furthermore, the results support the establishment of a national genetic management framework, routine genetic monitoring, and hatchery certification systems to safeguard genetic integrity and promote sustainable aquaculture development. This study provides critical baseline information for stock improvement, conservation planning, and the development of marker-assisted breeding strategies for Nile tilapia in Kenya and the wider African aquaculture sector.