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

Abstract

The phenotypes of chili pepper (Capsicum annuum) 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' (C. annuum). First, we investigated the segregation patterns of fruit-surface wrinkling in F₂ progeny obtained from crosses between the C. annuum cultivars 'Shishito' and 'Takanotsume', the latter of which has a smooth fruit surface. The F₂ 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 F₂ progeny using restriction site-associated DNA sequencing data obtained in our previous study. The results showed that two significant QTLs (Wr11 and Wr12) 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 F₂ progeny could mostly be explained by the independent additive effects of the 'Shishito' allele in Wr12. 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.

Keywords: Chili pepper; Fruit surface; QTL analysis; RAD-seq; Wrinkle.