Remapping the precise genomic positions of two loci (Shql3 and Shql7) associated with the reduction of pungency in chili pepper (Capsicum annuum)

The pungency level in chili peppers (Capsicum spp.) is a crucial trait determined by the capsaicinoid content, which significantly impacts their utility.
In a previous study, our research group successfully identified two genetic loci, Shql3 and Shql7, through QTL analysis in F₂ progenies derived from C. annuum cultivars, ‘Shishito’ (quite low pungency) and ‘Takanotsume’ (high pungency). These loci demonstrated the potential to reduce pungency and were seen as valuable tools for finely adjusting pungency levels in chili pepper breeding programs.
However, the precise physical positions of these loci remained elusive due to limitations in marker density and population size.
Therefore, we tried to narrow down the responsible genomic regions.
In this study, we designed high resolution melting (HRM) markers encompassing the two loci and constructed linkage maps for the F₂ progenies (n=160) across two years of cultivation.
Through QTL mapping regarding capsaicinoid content, we successfully determined their responsible genomic regions (approximately 5 Mbp range). This information holds the potential to facilitate the establishment of marker-assisted selection methods for controlling pungent levels in future breeding.
Whereas we also comprehensively analyzed the transcriptome and genomic variants between the parental strains using RNA-seq and whole-genome resequencing data.
Despite these efforts, we were unable to pinpoint the responsible gene expression patterns and mutations.
Therefore, it became evident that further fine mapping is necessary to unveil the underlying genetic mechanisms governing pungency in chili peppers.

IV Asian Horticultural Congress – AHC2023

F. Kondo, K. Umeda, K. Nemoto, K. Matsushima

chili pepper, capsaicinoid, QTL analysis

https://doi.org/10.17660/ActaHortic.2024.1404.91