AUTHOR=Abebe Alebel Mekuriaw , Oh Chang-Sik , Kim Hyoung Tae , Choi Giwon , Seo Eunyoung , Yeam Inhwa , Lee Je Min 

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

JOURNAL=Frontiers in Plant Science

VOLUME=12

YEAR=2022

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2021.809959

DOI=10.3389/fpls.2021.809959

ISSN=1664-462X

ABSTRACT=<p>Bacterial canker caused by <italic>Clavibacter michiganensis</italic> (<italic>Cm</italic>) 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. <italic>Solanum lycopersicum</italic> “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<sub>2</sub> individuals derived from a cross between <italic>S. lycopersicum</italic> “E6203” (susceptible) and “Hawaii 7998,” and a genomic region (37.24–41.15 Mb) associated with bacterial canker resistance on chromosome 6 (<italic>Rcm6</italic>) was found. To dissect the <italic>Rcm6</italic> 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 <italic>Rcm6</italic> as a resistance locus and the Rcm6-9 efficiency, subsequent analysis using F<sub>2</sub> and F<sub>3</sub> 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 <italic>Rcm6</italic>. 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 <italic>Cm</italic> infection. The DNA markers and candidate genes will facilitate marker-assisted breeding and provide genetic insight of bacterial canker resistance in tomato.</p>