QTL-Seq Analysis for Identification of Resistance Loci to Bacterial Canker in Tomato

Bacterial canker caused by Clavibacter michiganensis (Cm) is one of the most economically important vascular diseases causing unilateral leaf wilting, stem canker, a bird's-eye lesion on fruit, and whole plant wilting in tomato. There is no commercially available cultivar with bacterial canker resistance, and genomics-assisted breeding can accelerate the development of cultivars with enhanced resistance. Solanum lycopersicum Hawaii 7998 was found to show bacterial canker resistance. A Quantitative trait loci (QTL)-seq was performed to identify the resistance loci using 909 F-2 individuals derived from a cross between S. lycopersicum E6203 (susceptible) and Hawaii 7998, and a genomic region (37.24-41.15 Mb) associated with bacterial canker resistance on chromosome 6 (Rcm6) was found. To dissect the Rcm6 region, 12 markers were developed and several markers were associated with the resistance phenotypes. Among the markers, the Rcm6-9 genotype completely matched with the phenotype in the 47 cultivars. To further validate the Rcm6 as a resistance locus and the Rcm6-9 efficiency, subsequent analysis using F-2 and F-3 progenies was conducted. The progeny individuals with homozygous resistance allele at the Rcm6-9 showed significantly lower disease severity than those possessing homozygous susceptibility alleles. Genomes of five susceptible and two resistant cultivars were analyzed and previously known R-genes were selected to find candidate genes for Rcm6. Nucleotide-binding leucine-rich repeat, receptor-like kinase, and receptor-like protein were identified to have putative functional mutations and show differential expression upon the Cm infection. The DNA markers and candidate genes will facilitate marker-assisted breeding and provide genetic insight of bacterial canker resistance in tomato.

Automated summary

Bacterial canker caused by Clavibacter michiganensis is a major vascular disease in tomato which currently lacks commercially available resistant cultivars. Through QTL-seq, a genomic region associated with bacterial canker resistance (Rcm6) was identified on chromosome 6 in the resistant cultivar Solanum lycopersicum Hawaii 7998. Further analysis revealed the Rcm6-9 genotype as an effective resistance allele with potential candidate genes for bacterial canker resistance.