Genotypic and Phenotypic Characterization of Lettuce Bacterial Pathogen Xanthomonas hortorum pv. vitians Populations Collected in Quebec, Canada

Abstract

Bacterial leaf spot of lettuce, caused by Xanthomonas hortorum pv. vitians, is an economically important disease worldwide. For instance, it caused around 4 million CAD in losses in only a few months during the winter of 1992 in Florida. Because only one pesticide is registered to control this disease in Canada, the development of lettuce cultivars tolerant to bacterial leaf spot remains the most promising approach to reduce the incidence and severity of the disease in lettuce fields. The lack of information about the genetic diversity of the pathogen, however, impairs breeding programs, especially when disease resistance is tested on newly developed lettuce germplasm lines. To evaluate the diversity of X. hortorum pv. vitians, a multilocus sequence analysis was performed on 694 isolates collected in Eastern Canada through the summers of 2014 to 2017 and two isolates in 1996 and 2007. All isolates tested were clustered into five phylogroups. Six pathotypes were identified following pathogenicity tests conducted in greenhouses, but when phylogroups were compared with pathotypes, no correlation could be drawn. However, in vitro production of xanthan and xanthomonadins was investigated, and isolates with higher production of xanthomonadins were generally causing less severe symptoms on the tolerant cultivar Little Gem. Whole-genome sequencing was undertaken for 95 isolates belonging to the pathotypes identified, and de novo assembly made with reads unmapped to the reference strain’s genome sequence resulted in 694 contigs ranging from 128 to 120,795 bp. Variant calling was performed prior to genome-wide association studies computed with single-nucleotide polymorphisms (SNPs), copy-number variants and gaps. Polymorphisms with significant p-values were only found on the cultivar Little Gem. Our results allowed molecular identification of isolates likely to cause bacterial leaf spot of lettuce, using two SNPs identified through genome-wide association study.

Harnessing the genomic diversity of Pseudomonas strains against lettuce bacterial pathogens

“…vitians B07-007, P. cichorii B12-019, and P. carotovorum B12-025. These strains were isolated from infected lettuce leaves in Southern Quebec, Canada (Affia, 2016;Hébert et al, 2021). Each pathogenic bacterium was initially grown for 48 h at 22.5 • C on yeast dextrose carbonate agar medium for X. hortorum pv.…”

“…Some of the main bacterial pathogens of lettuce include Xanthomonas hortorum pv. vitians ( Hébert et al, 2021 ), formerly known as X. campestris pv. vitians ( Vauterin et al, 1995 ; Morinière et al, 2020 ), Pseudomonas cichorii ( Pauwelyn et al, 2011 ), and Pectobacterium carotovorum ( Cariddi and Sanzani, 2013 ).…”

“…hortorum pv vitians is a hemibiotrophic organism mainly infecting plant species belonging to the Lactuca genus, especially lettuce, on which it induces bacterial leaf spot ( Toussaint et al, 2012 ; Morinière et al, 2022 ). This disease is characterized by the development of water-soaked and geometric lesions on leaves ( Subbarao et al, 2017 ; Hébert et al, 2021 ). These lesions can expand and coalesce, leading to the necrosis of entire leaves.…”

“…The current strategies to control these pathogens are often ineffective and rely primarily on preventive methods, as few curative options are available, if any ( Pauwelyn et al, 2011 ; Cariddi and Sanzani, 2013 ; Subbarao et al, 2017 ; Hébert et al, 2021 ). Prophylactic methods include the use of crop rotation, less susceptible cultivars, seed and equipment cleaning, well-drained soils, adequate spacing between the plants to improve air movement and reduce leaf wetness, and drip irrigation instead of sprinkler irrigation ( Agrios, 2005 ; Subbarao et al, 2017 ).…”

“…However, these compounds sometimes cause phytotoxicity and their widespread use favors resistance emergence, leading to restricted usage ( Carisse et al, 2000 ; Fatmi and Bolkan, 2017 ; Dia et al, 2022 ). A fungicide containing potassium salts of phosphorous acid is also used to control bacterial pathogens on lettuce ( Hébert et al, 2021 ). It favors resistance development in bacterial populations as well.…”