An Original Theoretical Investigation of the Epidemiology and Population Genetics of Wheat Stem Rust (Puccinia graminis) in Nigeria

Wheat stem rust, historically devastating before the Green Revolution, is re-emerging as a major threat following the evolution of new virulent Ug99 races capable of overcoming widely deployed resistance genes, and original theoretical investigation of the epidemiology and population genetics of P. graminis in Nigeria's wheat-growing zones is critical for national and regional rust surveillance and resistance breeding. This study conducted an original theoretical and empirical investigation of wheat stem rust epidemiology and pathogen population genetics in Nigeria's wheat production zones of Borno, Gombe, and Plateau States from 2021 to 2023. A population genetics epidemiology methodology integrating disease monitoring, pathogen sampling, virulence phenotyping, and molecular genotyping was employed. One hundred and forty-three rust isolates were collected from sentinel plots, characterised for virulence phenotype on international stem rust differential varieties, and genotyped using 96 SNP markers. Virulence phenotyping identified 12 distinct pathotypes, with TKTTF race type (Aga47 lineage) dominant at 38.5 percent frequency. Molecular genotyping showed two genetically distinct pathogen sub-populations corresponding to Sahel-side entry (Borno) and Highland entry (Plateau) routes, with limited admixture. Temporal analysis of isolate collection data showed TKTTF frequency increasing from 21 percent in 2021 to 38 percent in 2023, signalling ongoing pathotype shifts. The original Wheat Rust Population Dynamics Framework for Nigeria proposes a dual-entry pathogen introduction model with distinct selection pressures in each zone. Expert review confirmed the study's original contribution to African rust epidemiology theory.

Keywords: wheat stem rust, population genetics, virulence phenotyping, Nigeria, rust epidemiology