Dataset Information

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

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.

SUBMITTER: Abebe AM

PROVIDER: S-EPMC8826648 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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

Abebe Alebel Mekuriaw AM Oh Chang-Sik CS Kim Hyoung Tae HT Choi Giwon G Seo Eunyoung E Yeam Inhwa I Lee Je Min JM

Frontiers in plant science 20220126

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 r ...[more]

PMID: 35154207

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Project description:BackgroundHigh temperature is one of the major abiotic stresses in tomato and greatly reduces fruit yield and quality. Identifying high-temperature stress-responsive (HSR) genes and breeding heat-tolerant varieties is an effective way to address this issue. However, there are few reports on the fine mapping of heat-tolerance quantitative trait locus (QTL) and the identification of HSR genes in tomato. Here, we applied three heat tolerance-related physiological indexes, namely, relative electrical conductivity (REC), chlorophyll content (CC) and maximum photochemical quantum efficiency (Fv/Fm) of PSII (photosystem II), as well as the phenotypic index, the heat injury index (HII), and conventional QTL analysis combined with QTL-seq technology to comprehensively detect heat-tolerance QTLs in tomato seedlings. In addition, we integrated the QTL mapping results with RNA-seq to identify key HSR genes within the major QTLs.ResultsA total of five major QTLs were detected: qHII-1-1, qHII-1-2, qHII-1-3, qHII-2-1 and qCC-1-5 (qREC-1-3). qHII-1-1, qHII-1-2 and qHII-1-3 were located, respectively, in the intervals of 1.43, 1.17 and 1.19 Mb on chromosome 1, while the interval of qHII-2-1 was located in the intervals of 1.87 Mb on chromosome 2. The locations observed with conventional QTL mapping and QTL-seq were consistent. qCC-1-5 and qREC-1-3 for CC and REC, respectively, were located at the same position by conventional QTL mapping. Although qCC-1-5 was not detected in QTL-seq analysis, its phenotypic variation (16.48%) and positive additive effect (0.22) were the highest among all heat tolerance QTLs. To investigate the genes involved in heat tolerance within the major QTLs in tomato, RNA-seq analysis was performed, and four candidate genes (SlCathB2, SlGST, SlUBC5, and SlARG1) associated with heat tolerance were finally detected within the major QTLs by DEG analysis, qRT-PCR screening and biological function analysis.ConclusionsIn conclusion, this study demonstrated that the combination of conventional QTL mapping, QTL-seq analysis and RNA-seq can rapidly identify candidate genes within major QTLs for a complex trait of interest to replace the fine-mapping process, thus greatly shortening the breeding process and improving breeding efficiency. The results have important applications for the fine mapping and identification of HSR genes and breeding for improved thermotolerance.

Project description:BackgroundPod shatter resistance is an important trait in Brassica species, significantly impacting the yield and profitability of growers. Identifying genomic regions and understanding genes underlying shatter resistance is a major objective of breeding programs. Brassica rapa, commonly known as rape or field mustard, is an ancestral species of Brassica napus and Brassica juncea - the most widely oilseed crops grown worldwide. In this study, we performed diversity analysis of B. rapa accessions, bulked segregant analysis based quantitative trait locus-sequencing (QTL-seq), and traditional quantitative trait locus (QTL) mapping in an F2 population to identify genomic regions associated with pod shatter resistance in B. rapa.ResultsA considerable genetic variation for pod shatter resistance, measured as rupture energy (RE), varied from 0.63 to 3.49 mJ(½) was revealed among 90 accessions of B. rapa. Cluster analysis based on 10,324 DArTseq markers showed that pod shatter-resistant accessions originated from diverse sources. We further investigated the genetic and anatomical bases of variation in pod shatter resistance from two contrasting parental lines, ATC90153 (maternal parent with high RE) and ATC91215 (paternal parent with low RE). Bulked segregant resequencing analysis of parental lines and two pooled samples, prepared from 10 resistant and 10 sensitive lines to pod shatter, identified three genomic regions for shatter resistance on chromosomes A06 and A09. Traditional QTL analysis validated marker-pod shatter resistance associations on chromosomes A06 and A09 in the same F2 population using a linkage map based on 23,274 DArTseq markers. Physical positions of significantly associated markers and the priori pod dehiscence genes on the B. rapa reference genome sequence suggested BEE1/PEROXIDASE/TCP8 on A06 and ADPG1/SHP1/MYB116 genes on A09 as potential candidates for pod shatter resistance. Sequence comparison of parental lines identified sequence variants (194 SNPs and 74 InDELs on A06, and two SNPs and two InDELs on A09) in the promoter and downstream regions of B. rapa genes within the QTL.ConclusionsWe identified QTLs and priori candidate genes associated with variation in pod shatter resistance on chromosomes A06 and A09 in B. rapa. This study provides potential gene targets to understand molecular mechanisms and improve pod shatter resistance in Brassica crops.

Dataset Information

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

Publications

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

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