Chili pepper fruits possess considerable economic value owing to their diverse applications as spices, vegetables, and ornamental plants (Moscone et al. 2006). The specific use influences the desired fruit traits in different varieties. Consequently, characteristics such as fruit size, shape, color, and pungency have been primary targets in long-term cultivation and breeding efforts (Devi et al. 2021). Recent advances in next-generation sequencing techniques have facilitated the identification of loci responsible for these traits (Lee et al. 2020). However, despite being a critical factor in appearance, few studies on the heredity and genetic regulation of fruit surface morphology in chili peppers have been conducted to date.
To obtain new insights, we focused on the wrinkled fruit surface of the ‘Shishito’ cultivar. In the present study, we investigated the genetic factors that affect the inheritance of fruit surface traits using the F2 population: ‘Shishito’ × ‘Takanotsume’ (smooth fruit surface). As a result, we observed a continuous range of variations in the level of wrinkling in F2 progeny over two years of cultivation (Figs. 1c and 2). We identified two loci associated with this trait (Wr11 and Wr12), which together accounted for approximately 70% of the total GVE (Table 1). These results suggested that the wrinkled surface in the ‘Shishito’ fruit was a quantitative trait under the control of several loci including Wr11 and Wr12. When focusing on the genotypic effects of Wr11 and Wr12, our analysis revealed that the accumulation of the ‘Shishito’ allele of Wr12 broadly and gradually increased the level of wrinkling in the F2 progeny, regardless of the Wr11 genotypes (Figs. 5 and 6). Observing the genotypic effects of Wr11 was difficult under most Wr12 genotypes, except for those that were homozygous for the ‘Shishito’ allele. The differences in the level of wrinkling of the F2 progeny could thus mostly be explained by independent additive effects of the Wr12 genotype. However, under the Shishito homozygous condition, the Wr11 genotypes affected the level of wrinkling. We concluded that the extremely wrinkled surface phenotype (wrinkling level = 3) observed in ‘Shishito’ resulted from the combined genotypic effects of both Wr12 and Wr11. Elucidating the presence of epistasis between these two loci was challenging and it is possible that the genotypic effects of Wr11 were suppressed by the Wr12 genotypes, suggesting a potential epistatic interaction. Alternately, if there was no epistasis (i.e., Wr11 functioned independently of Wr12), the genotypic effect of Wr11 might have been too subtle to detect under the TK and H genotypes of Wr12. Further studies should be undertaken to more accurately clarify this mechanism.
In related research, a genetic study focusing on the fruit surface grooves in melon (Cucumis melo) identified the locus responsible on chromosome 11 (Zhao et al. 2019). Subsequently, the gene MELO3C019694 encoding an AGAMOUS MADS-box transcription factor, was identified as being responsible for this trait (Du et al. 2022). Previous studies highlighted the diverse regulatory roles of MADS-box family in fruit maturation, fruit skin development, and embryonic development in tomatoes (Busi et al. 2003; Hileman et al. 2006). Conversely, research on the genetics of the wrinkled surface of chili pepper fruits is limited. One study by Lee (2018) used GWAS analysis to identify genomic regions controlling 13 agronomic traits, including the surface texture, in a C. annuum population. Similar to Wr11, that study also identified the locus on chromosome 11 as being associated with the level of wrinkling of the fruit surface. This locus was strongly linked with five candidate genes, one of which was the bidirectional sugar transporter SWEET12 gene (Lee 2018). This gene is one of three sucrose transporters ––SWEET11, 12, and 15–– mutations of which have been shown to result in significant seed defects. These defects include a delay in embryonic development, a decrease in seed weight, and a loss of starch and lipid content, culminating in a "wrinkled" seed phenotype (Chen et al. 2015). However, in the present study, we found that the loci for these genes (located at 131.5 Mbp on chromosome 11) are located approximately 80.5 Mbp away from the Wr11 region. Thus, Wr11 was not detected in that previous study, suggesting the presence of another gene responsible for the trait. Furthermore, we discovered another locus, Wr12, on chromosome 12, which was not identified in previous studies. This discovery provides novel insights into the genetic mechanisms that regulate fruit surface wrinkling in chili peppers. Notably, given its significant genotypic effect as described above, Wr12 appears to be a promising target for controlling fruit surface phenotype (smooth or wrinkled) in chili pepper breeding through marker-assist selection. However, the genomic region of Wr12 encompasses over 400 genes (data not shown), necessitating further mapping to identify the gene responsible.
In exploring further breeding possibilities concerning fruit surface traits, we also examined their relationship with other fruit-related traits. The present results showed that there was no significant correlation between wrinkling of the fruit surface and CAP, FL, and FWT. However, significant and positive correlations were observed between the level of wrinkling and FWD and SFS (Fig. 3b, d). These findings partially contradicted those of Lee (2018), who reported a positive correlation between wrinkling of the fruit surface and FL, and negative correlations between wrinkling of the fruit surface and FWT and FWD. The discrepancies might be attributed to differences in the genetic populations used for analysis. Notably, our study observed a tendency for wrinkled fruit surfaces to exhibit increased SFS. This pattern can be explained by a tight genetic linkage between two genes controlling fruit surface and SFS, or alternatively, by a single gene influencing wrinkle levels that also affects the morphological characteristics of the distal end of the fruits. Regardless, these findings underscore the importance of considering the strong co-segregation between fruit surface traits and SFS in breeding cultivars with wrinkled surfaces, such as ‘Shishito’.
In conclusion, the present study was the report to identify the novel genetic factors responsible for wrinkled surface traits and firstly clarify their inheritance patterns in Japanese chili peppers. Importantly, we clarified that one of the key loci (Wr12) is strongly associated with the intensity of fruit surface wrinkling. Given its marked genotypic effects, it is highly likely that the responsible genes at this locus will be identified in future studies through fine mapping. Consequently, this Wr12 is expected to be a useful locus for chili pepper breeding programs targeting the modification of fruit surface traits.