Identification of inheritance and genetic loci responsible for wrinkled fruit surface phenotype in chili pepper () by quantitative trait locus analysis.

UNLABELLED

The phenotypes of chili pepper () fruit are sometimes characterized by having either smooth or wrinkled surfaces, both of which are commercially important. However, as the inheritance patterns and responsible loci have not yet been identified, it is difficult to control fruit surface traits in conventional chili pepper breeding. To obtain new insights into these aspects, we attempted to clarify the genetic regulation mechanisms responsible for the wrinkled surface of fruit from the Japanese chili pepper 'Shishito' (. ). First, we investigated the segregation patterns of fruit-surface wrinkling in F progeny obtained from crosses between the . cultivars 'Shishito' and 'Takanotsume', the latter of which has a smooth fruit surface. The F progeny exhibited a continuous variation in the level of wrinkling, indicating that the wrinkled surface in 'Shishito' was a quantitative trait. To identify the responsible loci, we performed quantitative trait locus (QTL) analysis of the F progeny using restriction site-associated DNA sequencing data obtained in our previous study. The results showed that two significant QTLs ( and ) were newly detected on chromosome 11 and 12, which explained 17.5 and 66.0% of the genetic variance, respectively. We then investigated the genetic effects of these QTLs using molecular markers. The findings showed that the levels of wrinkling in the F progeny could mostly be explained by the independent additive effects of the 'Shishito' allele in . This locus was therefore considered to be a useful genomic region for controlling fruit surface traits in the chili pepper.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s11032-024-01528-y.