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

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

doi:10.3389/fpls.2021.809959

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

Front Plant Sci. 2022 Jan 26:12:809959. doi: 10.3389/fpls.2021.809959. eCollection 2021.

Authors

Alebel Mekuriaw Abebe¹, Chang-Sik Oh², Hyoung Tae Kim¹, Giwon Choi¹, Eunyoung Seo³, Inhwa Yeam⁴, Je Min Lee¹

Affiliations

¹ Department of Horticultural Science, Kyungpook National University, Daegu, South Korea.
² Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, South Korea.
³ Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States.
⁴ Department of Horticulture and Breeding, Andong National University, Andong, South Korea.

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.

Keywords: DNA marker; QTL-seq; bacterial canker; candidate genes; tomato.