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

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

doi:10.3389/fpls.2021.809959

Abstract

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 F2 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 F2 and F3 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.

Highlights

Bacterial canker of tomato (Solanum lycopersicum) is a destructive disease caused by a Gram-positive actinomycete Clavibacter michiganensis (Cm) and was first detected in 1909, United States (Smith, 1910; Nandi et al, 2018)
The F2 population derived from a cross between “E6203” and “Hawaii 7998”, and the parents were inoculated with Cm strain LMG 7333
The Quantitative trait loci (QTL) analysis was conducted in a few resistant accessions of wild species for bacterial canker resistance

Summary

Introduction

Bacterial canker of tomato (Solanum lycopersicum) is a destructive disease caused by a Gram-positive actinomycete Clavibacter michiganensis (Cm) and was first detected in 1909, United States (Smith, 1910; Nandi et al, 2018). The yield losses caused by the bacterial canker range from 46 to 93% and result in a significant decrease in fruit weight during the highest disease incidence under field condition (Chang et al, 1992; Poysa, 1993). The Cm multiplies extensively within the xylem lumen and fills it with bacterial aggregates (Chalupowicz et al, 2012; Peritore-Galve et al, 2020). It secretes extracellular cell wall degrading enzymes, such as cellulase, polygalacturonase, pectate lyase, and xylanase to degrade xylem vessels and the adjacent parenchyma cells leading to induction of disease symptom (Gartemann et al, 2008; Hwang et al, 2019). A wide range of tomato germplasm collections was evaluated to find new resistance sources to bacterial canker (Poysa, 1993; Sotirova et al, 1994; Sandbrink et al, 1995; Francis et al, 2001; Sen et al, 2013)

Methods

Results

Conclusion