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.

Tsw, a single dominant resistant gene against Tomato spotted wilt virus (TSWV), has been mapped on chromosome 10 in Capsicum. Previously found molecular markers linked to the Tsw gene are not transferable for all pepper breeding materials. To develop segregating populations for the Tsw, commercial F1 cultivar C. annuum ‘Telmo’ was self-pollinated. An F2 population was obtained from the self-pollination of F1 plants deriving from a cross between C. annuum ‘Special’ and C. chinense ‘PI152225’. Twelve additional molecular markers linked to the Tsw gene were developed using tomato and pepper genome sequence database. A tomato scaffold sequence of 7841 kb in size covering the corresponding region of the Tsw locus was identified based on the sequence of Tsw-linked marker. Analyzing the tomato scaffold sequence, two sequences of pepper scaffold and contig at down and up site of the Tsw locus, respectively, were located. Three SNP markers linked to the Tsw locus (HRM1, HRM2, and HRM3) were developed using the pepper scaffold sequence of 419 kb in size. All three markers showed 2 recombinants (1.0 cM) out of 198 individuals of F2 ‘Telmo’ population. When analyzing these SNP markers in an F2 population deriving from C. annuum ‘Special’ and C. chinense ‘PI152225’, we detected 5 recombinants (0.76 cM) out of 659 individuals. HRM4, a SNP marker linked to the Tsw gene, was developed with a 99 kb pepper contig sequence. It showed 7 recombinants (3.5 cM) out of 198 individuals of F2 ‘Telmo’ population. We found 5 recombinants (0.76 cM) out of 659 individuals when HRM4 was analyzed in F2 population derived from C. annuum ‘Special’ and C. chinense ‘PI152225’. To narrow down the molecular markers linked to the Tsw locus, four SNP markers, HRM5, HRM6, HRM7, and HRM8, were developed with the pepper scaffold sequence. All of them showed 5 recombinants (0.76 cM) out of 659 individuals of F2 ‘SP’ population. Four other SNP markers, HRM9, HRM10, HRM11, and HRM12, were developed using the pepper contig sequence. HRM9 showed 5 recombinants (0.76 cM), HRM10 showed 4 recombinants (0.61 cM), and HRM11 and HRM12 showed 3 recombinants (0.46 cM) out of 659 individuals of F2 ‘SP’ population. The SNP markers developed in this study will be useful for fine mapping of the Tsw gene and for developing cultivars which carry TSWV-resistance gene.