Migration Drives the Replacement of Xanthomonas perforans Races in the Absence of Widely Deployed Resistance

Abstract

Changes in Xanthomonas race and species composition causing bacterial spot of tomato have occurred throughout the world and are often associated with epidemics. Knowledge of bacterial population structure is key for resistance discovery and deployment. We surveyed Xanthomonas spp. composition from processing tomato fields in the Midwestern United States over a 4-year period between 2017 and 2020, compared these to strains collected previously, and found that X. perforans is currently the most prevalent species. We characterized 564 X. perforans isolates for sequence variation in avrXv3 to distinguish between race T3 and T4 and validated race designation using hypersensitive response (HR) assays for 106 isolates. Race T4 accounted for over 95% of X. perforans isolates collected in the Midwest between 2017 and 2020. Whole genome sequencing, Average Nucleotide Identity (ANI) analysis, core genome alignment and single nucleotide polymorphism (SNP) detection relative to a reference strain, and phylogenomic analysis suggest that the majority of Midwestern X. perforans strains collected between 2017 and 2020 were nearly identical, with greater than 99.99% ANI to X. perforans isolates collected from Collier County, Florida in 2012. These isolates shared a common SNP variant resulting an a premature stop codon in avrXv3. One sequenced isolate was identified with a deletion of avrXv3 and shared 99.99% ANI with a strain collected in Collier Co., Florida in 2006. A population shift to X. perforans T4 occurred in the absence of widely deployed resistance, with only 7% of tomato varieties tested having the resistant allele at the Xv3/Rx-4 locus. The persistence of nearly identical strains over multiple years suggests that migration led to the establishment of an endemic population. Our findings validate a genomics-based framework to track shifts in X. perforans populations due to migration, mutation, drift, or selection based on comparisons to 146 genomes.

Marker-assisted Selection to Combine Alleles for Four Disease Resistance Genes of Tomato Collocated on Chromosome 11

“…In the spray-inoculated trial, the recombinant plants behaved similarly, with severity scores (1.6) comparable to those of the resistant control H7981. Achieving broadspectrum resistance to bacterial spot is challenging because of the complex genetic control of resistance and rapidly shifting pathogen populations (Bernal et al 2022;Rotondo et al 2022). Combinations of bacterial spot resistance genes and QTL (Bernal et al 2020;Sim et al 2015), such as QTL-11 and Xv3/Rx4 present in parent line OH08-7663, aim to combat rapid shifts in pathogenicity or virulence.…”

Intercontinental dissemination and diversification ofXanthomonas perforansin tomato production

“…The X. perforans strains we examined from the USA were assigned to core gene clusters 1, 2, 3, 4, 5, 6, and 8, suggesting repeated emergence of genetically distinct lineages in tomato production systems. The release of new varieties of plants that carry disease resistance genes can have dramatic effects on pathogen population structure due to selection to overcome host resistance 65,66 , and we have previously reported on the loss of function of effector AvrXv3 (XopAF) in X. perforans populations, which has occurred across lineages 12,36,59 . We hypothesize that changes in prevalence and distribution of lineages are not exclusively due to selection on the pathogen population but rather are associated with the multinational structure of tomato breeding and seed production, in which parental lines and geographic locations of seed production change over time 67 .…”

“…Examination of Type III effector content at a global scale puts variation previously observed in Florida into a larger context. XopAF was present in strains collected in the 1990s (cluster 1), but absent or non-functional in most strains from Florida, Indiana Ohio, and North Carolina, USA 8,10,12,36,59 . Here, we found that xopAF was intact in many strains from seed production areas, suggesting strong selection for loss of function in commercial fruit production.…”

“…A plausible hypothesis for new outbreaks of X. perforans is pathogen movement with seeds and planting materials 28 .The success of X. perforans as a pathogen, and its replacement of X. euvesicatoria on tomato, has been attributed to its production of bacteriocins against competing bacterial spot species, rapid genome evolution via recombination affecting the chromosome, and introduction of genes via horizontal gene transfer that contribute to fitness in tomato fields [29][30][31][32][33][34][35] . Distinct genetic lineages of X. perforans, each with unique patterns of allelic variation among core genes (genes present in all strains), were identified in fresh market and processing tomato production fields in the United States 30,33,34,36,37 . Additional lineages of X. perforans have been found in Nigeria, Iran, Italy, and the Southwest Indian Ocean islands 27,31,38 .…”

Mitigation of water scarcity with sustained growth of Rice by plant growth promoting bacteria

“…Rhizosphere soil was studied for the re-isolation of inoculated bacteria by viable count at 15 DAS (Bernal et al, 2022). Identification of re-isolated drought-tolerant PGP bacteria was done by comparing their morphology and PGP attributes (drought tolerance, IAA production, and P solubilization) to the pure colonies of inoculated bacteria as described by Yasmin et al (2016).…”