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Genome-based fine mapping of the Tomato spotted wilt virus resistance gene, Tsw, in Capsicum
Byoung-Cheorl Kang,Ngoc Huy Hoang,Hee-Bum Yang,Won-Hee Kang,Bong Nam Chung 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07
Tsw, a single dominant resistant gene against Tomato spotted wilt virus (TSWV), has been mapped on chromosome 10 in Capsicum chinense species. Previously reported molecular markers linked to the Tsw gene are not transferable for all pepper breeding materials. To develop additional markers and do genome-based fine mapping of the Tsw gene, approaches of mapping comparison, pooled transcriptome analysis, and genome walking were applied. Eleven additional SNP molecular markers tightly linked to the Tsw gene were developed using tomato and pepper whole genome sequencing databases. Among them, four SNP markers, SNP7715-1, SNP68-1, SNP17918-1, and SNP1072-1, showed no recombination in two segregating populations of F2 ‘Telmo’ (210 individuals) and ‘SP’ (843 individuals). Three scaffold sequences from the C. annuum BAC database and two BAC clones from the BAC library of C. annuum ‘CM334’ covering the Tsw gene were identified by transcriptome analysis and genome walking. A pepper scaffold sequence covering three pepper scaffold sequences was identified from a final version of the C. annuum BAC database. The Tsw gene was delimited within 149 kb by alignment analysis of two BAC clone sequences and the pepper scaffold sequence. A total of 22 predicted genes were resided in the target region between SNP7715-1 and SNP1072-1 co-segregating markers. Among them, five predicted genes showing annotations of CC/TIR-NBS-LRR resistance proteins, mRNA-6, mRNA-7, mRNA-11, mRNA-12, and mRNA-13, were identified. The transcriptome analysis and gene expression study showed that the mRNA-13 was expressed in ‘PI152225’ but was absent in ‘Special’, demonstrating the mRNA-13 could be a strong candidate gene for the Tsw gene. This result will be favorable for cloning the Tsw gene and developing cultivars which carry the TSWV-resistance gene.
Genome-assisted marker development for disease resistance in pepper
Byoung-Cheorl Kang 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07
The last decade has witnessed tremendous progress in genome sequencing and explosion of genome sequence information. This remarkable advancement in genomics provides unprecedented opportunities for crop improvement. Pepper (Capsicum spp.) is an important vegetable crop worldwide. Pepper production is constantly challenged by various pathogens and developing cultivars harnessing multiple disease resistance genes are ever increasing. Molecular markers linked to disease resistance genes will expedite the gene pyramiding. Here, I introduce genome-assisted development of molecular markers linked to resistance genes, in pepper. Phytophthora capsici L. is one of the most destructive pathogens of pepper (Capsicum spp.). Resistance of Capsicum annuum against P. capsici is controlled by quantitative trait loci (QTL), including a major QTL on chromosome 5 that is the predominant contributor to resistance. Here, to maximize the effect of this QTL and study its underlying genes, an F2 population and recombinant inbred lines were inoculated with P. capsici strain JHAI1-7 zoospores at a low concentration (3 x 103 /mL). Resistance phenotype segregation ratios for the populations were close to 3:1 and 1:1 (resistant:susceptible), respectively, consistent with a single dominant gene model. Bulked segregant analysis (BSA) using Affymetrix GeneChips revealed a single position polymorphism (SPP) marker mapping to the major QTL. When this SPP marker (Phyto5SAR) together with other SNP markers located on chromosome 5 were used to confirm the position of the major QTL, Phyto5SAR showed the highest LOD value at the QTL. A scaffold sequence (scaffold194) containing Phyto5SAR was identified from the C. annuum genome database. The scaffold contained two putative NBS-LRR genes and one SAR 8.2A gene as candidates for contributing to Phytophthora resistance. Markers linked to these genes were developed and validated by testing 100 F1 commercial cultivars. Among the markers, Phyto5NBS1 showed about 90% accuracy in predicting resistance phenotypes to a low-virulence Phytophthora isolate. These results suggest that Phyto5NBS1 is a reliable marker for Phytophthora resistance and can be used for identification of a gene(s) underlying the major QTL on chromosome 5