Identification of a molecular marker tightly linked to bacterial wilt resistance in tomato by genome-wide SNP analysis

Abstract

Genotyping of disease resistance to bacterial wilt in tomato by a genome-wide SNP analysis Bacterial wilt caused by Ralstonia pseudosolanacearum is one of the destructive diseases in tomato. The previous studies have identified Bwr-6 (chromosome 6) and Bwr-12 (chromosome 12) loci as the major quantitative trait loci (QTLs) contributing to resistance against bacterial wilt in tomato cultivar 'Hawaii7996'. However, the genetic identities of two QTLs have not been uncovered yet. In this study, using whole-genome resequencing, we analyzed genome-wide single-nucleotide polymorphisms (SNPs) that can distinguish a resistant group, including seven tomato varieties resistant to bacterial wilt, from a susceptible group, including two susceptible to the same disease. In total, 5259 non-synonymous SNPs were found between the two groups. Among them, only 265 SNPs were located in the coding DNA sequences, and the majority of these SNPs were located on chromosomes 6 and 12. The genes that both carry SNP(s) and are near Bwr-6 and Bwr-12 were selected. In particular, four genes in chromosome 12 encode putative leucine-rich repeat (LRR) receptor-like proteins. SNPs within these four genes were used to develop SNP markers, and each SNP marker was validated by a high-resolution melting method. Consequently, one SNP marker, including a functional SNP in a gene, Solyc12g009690.1, could efficiently distinguish tomato varieties resistant to bacterial wilt from susceptible varieties. These results indicate that Solyc12g009690.1, the gene encoding a putative LRR receptor-like protein, might be tightly linked to Bwr-12, and the SNP marker developed in this study will be useful for selection of tomato cultivars resistant to bacterial wilt.

Construction of a single nucleotide polymorphism marker based QTL map and validation of resistance loci to bacterial wilt caused by Ralstonia solanacearum species complex in tomato

“…Previous reports showed that Bwr-12 is confined to phylotype I defense response (Carmeille et al 2006a, b;Wang et al 2000Wang et al , 2013. Recently it was reported by Kim et al (2018) that genes encoding leucine-rich repeat (LRR) receptor-like proteins are located in the Bwr-12 region and may be associated with resistance. A dense genetic map with markers flanking and within QTL regions will help to improve the efficiency to breed tomato resistant to BW.…”

Construction of a Single-Nucleotide Polymorphism Marker Based Quantitative Trait Loci Map and Validation of Resistance Loci to Bacterial Wilt <em>(Ralstonia solanacearum)</em> in Tomato

“…Mean values of NILs, the susceptible parent and controls showed different sensitivity patterns depending of the bacterial strain and season. Under higher temperatures (21-30°C) the plant defense response against BW seems to be lower [61][62], while Pss4 and Pss1632 or other tropical strains such as of K60 and GMI1000 have reduced virulence in cooler conditions (18-25°C) [3,[63][64]. Consequently, the percentage of wilted NILs was significantly higher in the relative warm conditions of the autumn trial than in the cool spring trial.…”

Development of diagnostic molecular markers for marker-assisted breeding against bacterial wilt in tomato

“…Non-synonymous SNPs between resistant and susceptible groups of tomato cultivars near Bwr-6 within 15 candidate genes (18 SNPs) were previously identified by whole-genome resequencing ( Kim et al 2018 ). Each candidate gene contained one non-synonymous SNP except two genes, Solyc06g051110.1 and Solyc06g051140.2 , which have two and three SNPs, respectively.…”

“…Although two QTL, Bwr-6 and Bwr-12 , were repeatedly confirmed as major contributors to bacterial wilt resistance in Hawaii 7996, the genetic nature of these critical QTL remained unidentified. We have previously conducted whole-genome resequencing of two susceptible cultivars (Heinz 1706 and BWS-3) and seven resistant cultivars (Hawaii 7996, Hawaii 7998, 10-BA-3-33, 10-BA-4-24, BWR-1, BWR-22, and BWR-23) of tomato and identified genome-wide single nucleotide polymorphisms (SNPs) in resistant and susceptible groups of cultivars ( Kim et al 2018 ). The highest number of polymorphic SNPs in coding regions were found on chromosome 12 (168 SNPs) followed by chromosome 6 (53 SNPs).…”

“…These SNPs might be associated with resistance to bacterial wilt. Based on the SNP information generated by re-sequencing, an HRM marker (KHU-1) that is tightly linked to Bwr-12 was developed; however, no tightly linked SNP-based molecular marker was developed to trace Bwr-6 resistance due to the large interval (~12.7 Mbp) ( Kim et al 2018 ).…”