The viral disease induced by Tomato yellow leaf curl virus (TYLCV) reduces tomato (Solanum lycopersicum) yield significantly in tropical and subtropical regions. A number of loci, including Ty-1 to Ty-5, conferring resistance to TYLCV have been described and introgressed into modern tomato cultivars. The availability of molecular markers linked to these genes would expedite the introgression of TYLCV resistance into commercial cultivars. In the present study, we developed gene-based markers linked to the Ty-3 gene using a segregating population derived from a cross between the TYLCV-resistant line S. lycopersicum ‘A45’ and the susceptible line S. lycopersicum ‘A39’. Agrobacterium-mediated screening was used to test TYLCV resistance of plants in the segregating population, and the resistance was evaluated by a visual scoring method and polymerase chain reaction analysis. By comparing sequences of the Ty-3 genes of the resistant and susceptible lines, two high-resolution melting (HRM) markers (Ty3-HRM1 and Ty3-HRM2) and one sequence characterized amplified region (SCAR) marker (Ty3-SCAR1) were developed. The HRM markers were based on single nucleotide polymorphisms at the 13th exon and the 15th intron, whereas the SCAR marker was based on a 246-bp deletion in the 16th intron. These gene-based markers will be useful tools for marker-assisted selection in breeding programs to improve TYLCV resistance of tomato.

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Capsinoids are the class of secondary metabolites identified in non-pungent peppers exhibiting the same bioactive properties as capsaicinoid. Previously, it has been demonstrated that capsinoid production is controlled by the capsaicin synthase (CS) gene and the putative-aminotransferase (pAMT) gene. In this study, we report that C. chinense ‘SNU11-001’ containing high levels of capsinoid has an early stop codon in pAMT resulted from 403 bp and 8 bp insertions deletion in the third and sixth exons. In order to know whether CS expression is correlated with the level of capsinoid, CS and pAMT expressions were determined using SNU11-001 and four Capsicum accessions with different pungency level. RT-PCR analysis showed higher transcription levels of CS in pungent accessions but no clear differences in pAMT expression. To investigate the effect of the substitution of the pAMT allele of C. chinense ‘Habanero’ with the dysfunctional pAMT allele of SNU11-001, an F₂ population was constructed by a cross between aforementioned parental lines. Molecular markers were developed to distinguish CS and pAMT genotypes of SNU11-001 and Habanero and F₂ plants were genotyped. All F₂ plants having the pAMT genotype of SNU11-001 contained high levels of capsinoid while very low levels of capsaicinoid. There was no significant difference in levels of capsinoid among the F₂ plants regardless of CS genotypes. This may be due to strong CS expression of both parental lines. In conclusion, our results show that it is possible to develop a new Habanero cultivar with high capsinoid content by introducing a dysfunctional pAMT allele.

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