Gene genealogies reveal recent population expansion of cotton root rot incitant, Macrophomina phaseolina (Tassi) Goid in North-Western India

Cotton root rot, incited by Macrophomina phaseolina is one of the most devastating fungal disease of the crop. The present study marks the inception of comprehensive population genetic analysis of M. phaseolina across the North Western cotton belt of India, encompassing 55 geographically distinct isolates of the pathogen collected from four states of India: Haryana, Punjab, Rajasthan, and Gujarat. The isolates were subjected to ITS and EF-1α region sequencing. All four M. phaseolina populations display haplotype and nucleotide diversity patterns indicative of historical bottlenecks followed by rapid population expansion, as evidenced by high haplotype diversity (0.714) coupled with low nucleotide diversity (0.0025). The star-like structure observed in the median-joining network also support the assumption of a departure from neutrality in the context of a constant population size, hence providing an evidence of population expansion. M. phaseolina populations in different geographical locations appear to form a largely panmictic or weakly structured metapopulation rather than being strongly subdivided as evident from low levels of genetic differentiation. Neutrality tests on M. phaseolina showed significant deviations from neutrality, with strongly negative Tajima's D, Fu and Li's D∗, and F∗ values, indicating recent positive selection or population expansion. Mismatch distribution analysis further supported a recent demographic expansion in the population. The results of hierarchical AMOVA analysis implied a lack of clear genetic boundaries between different populations of M. phaseolina, as supported by the low percentage of variation between populations compared to within-population differences.