Population Genomic Characterization of Cercospora janseana on Rice in the Southern United States
Semester of Graduation
Master of Science (MS)
Plant Pathology & Crop Physiology
Cercospora janseana is the causative agent of narrow brown leaf spot (NBLS). Effort had been undertaken since the 1940’s to control this disease through resistance breeding in the Southern United States. However, a severe epidemic of NBLS in 2006 inspired renewed focus on managing this disease. One tool for managing this disease has been identified among resistant cultivars, the CRSP-2.1 resistance locus to NBLS. One thing limiting the investment and deployment of CRSP-2.1, and other unknown resistance genes, is the historical observation that resistance to NBLS rapidly breaks-down in the field. Together, the rapid breakdown of resistance to NBLS and the recent epidemic of the disease generates the desire to understand and characterize the pathogen populations that are causing disease. To do this, we sampled C. janseana exhibiting NBLS from necrotic, foliar lesions on rice. Beaumont, Texas and Crowley, Louisiana were sampled in 2019 and 2020 with the inclusion of a ratoon (second) crop from Crowley in 2020. A population genetic approach was utilized to characterize population structure and diversity of C. janseana in the southern United States. A reference genome was developed and whole genome resequencing was conducted on 136 isolates among the sampling populations. Two lineages of C. janseana were identified, with the lineage NA1 being dominant (85%) among all sampling populations. Members from both lineages were identified in each state and year sampled. Migration between states appeared high as FST values were moderately low between sampling populations and was only high between lineages (0.63). Modes-of-reproduction were determined among lineages as the teleomorph had been reported but has not been recently observed. NA1 has strong signatures of recent or ongoing sexual reproduction based on linkage decay, index of association, and pairwise-homoplasy index results. NA2 showed strong signatures of clonality.
Searight, Jacob, "Population Genomic Characterization of Cercospora janseana on Rice in the Southern United States" (2022). LSU Master's Theses. 5686.