Population genomic analysis reveals geographic structure and climatic diversification for Macrophomina phaseolina isolated from soybean and dry bean across the United States, Puerto Rico, and Colombia.

Macrophomina phaseolina causes charcoal rot, which can significantly reduce yield and seed quality of soybean and dry bean resulting from primarily environmental stressors. Although charcoal rot has been recognized as a warm climate-driven disease of increasing concern under global climate change, knowledge regarding population genetics and climatic variables contributing to the genetic diversity of M. phaseolina is limited. This study conducted genome sequencing for 95 M. phaseolina isolates from soybean and dry bean across the continental United States, Puerto Rico, and Colombia. Inference on the population structure using 76,981 single nucleotide polymorphisms (SNPs) revealed that the isolates exhibited a discrete genetic clustering at the continental level and a continuous genetic differentiation regionally. A majority of isolates from the United States (96%) grouped in a clade with a predominantly clonal genetic structure, while 88% of Puerto Rican and Colombian isolates from dry bean were assigned to a separate clade with higher genetic diversity. A redundancy analysis (RDA) was used to estimate the contributions of climate and spatial structure to genomic variation (11,421 unlinked SNPs). Climate significantly contributed to genomic variation at a continental level with temperature seasonality explaining the most variation while precipitation of warmest quarter explaining the most when spatial structure was accounted for. The loci significantly associated with multivariate climate were found closely to the genes related to fungal stress responses, including transmembrane transport, glycoside hydrolase activity and a heat-shock protein, which may mediate climatic adaptation for M. phaseolina. On the contrary, limited genome-wide differentiation among populations by hosts was observed. These findings highlight the importance of population genetics and identify candidate genes of M. phaseolina that can be used to elucidate the molecular mechanisms that underly climatic adaptation to the changing climate.

Understanding the complexity of disease-climate interactions for rice bacterial panicle blight under tropical conditions.

Bacterial panicle blight (BPB) caused by Burkholderia glumae is one of the main concerns for rice production in the Americas since bacterial infection can interfere with the grain-filling process and under severe conditions can result in high sterility. B. glumae has been detected in several rice-growing areas of Colombia and other countries of Central and Andean regions in Latin America, although evidence of its involvement in decreasing yield under these conditions is lacking. Analysis of different parameters in trials established in three rice-growing areas showed that, despite BPB presence, severity did not explain the sterility observed in fields. PCR tests for B. glumae confirmed low infection in all sites and genotypes, only 21.4% of the analyzed samples were positive for B. glumae. Climate parameters showed that Montería and Saldaña registered maximum temperature above 34°C, minimum temperature above 23°C, and Relative Humidity above 80%, conditions that favor the invasion model described for this pathogen in Asia. Our study found that in Colombia, minimum temperature above 23°C during 10 days after flowering is the condition that correlates with disease incidence. Therefore, this correlation, and the fact that Montería and Saldaña had a higher level of infected samples according to PCR tests, high minimum temperature, but not maximum temperature, seems to be determinant for B. glumae colonization under studied field conditions. This knowledge is a solid base line to design strategies for disease control, and is also a key element for breeders to develop strategies aimed to decrease the effect of B. glumae and high night-temperature on rice yield under tropical conditions.

VNTR Typing of the Bacterial Rice Pathogen Burkholderia glumae Reveals the Coexistence of Several Diverging Lineages in a Single Field in Colombia.

Burkholderia glumae is responsible for the panicle blight disease of rice. This disease is present worldwide and can result in significant drop in yields. To estimate the genetic diversity of the bacterial strains present in a rice paddy field in Colombia, we sampled 109 strains from infected panicles. To detect fine genetic relationships among related haplotypes, and to overcome a very low nucleotide diversity detected in previous studies, we designed primers to amplify and sequence several highly variable minisatellite loci, or variable number tandem repeats (VNTRs), as well as part of the Toxoflavin toxA gene in all strains. Results show that the toxA nucleotide diversity defined four lineages and was similar to that detected in several fields in Japan; data suggest that B. glumae has spread from Asia to America without major loss of genetic diversity, and that five VNTR loci discriminated the strains within the field revealing single and multi-infections of the rice panicles with a wide distribution of the haplotypes among the different plots. Even though disease levels vary considerably from year to year, the bacterial genetic diversity is maintained within a field. We do not detect any geographical structuring within the field, nor any effect of the rice cultivar on the observed diversity. The consequences on the origin and evolution of the bacteria are discussed.