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.

Fig. 1

Difference between smooth and wrinkled fruit surfaces of chili peppers. (a) ‘Cherry Bomb’, (b) ‘Prick Den’, (c) ‘Gogosari’, (d) ‘Jalapeno’, and (e) ‘Takanotsume’ represent smooth fruit surfaces, while (f) ‘Ise sweet pepper’, (g) ‘Shimizumori Namba’, (h) ‘Passila’, (i) ‘Hishino Nanban’, and (j) ‘Shishito’ represent wrinkled fruit surfaces. Black horizontal bars in each figure indicate the scale of 2 cm

Fig. 2

Images of level of wrinkling on fruit surface observed in (a) parental varieties ‘Shishito’ and ‘Takanotsume’, (b) F₁ progeny, and (c) F₂ population. Numbers under varieties and progeny names represent the level of wrinkling evaluated using a four-point ordinal scale (smooth = 0, slightly wrinkled = 1, moderately wrinkle = 2, extremely wrinkled = 3). The arrows indicate examples of visual characteristics used as the criteria to determine the level of wrinkling: creases, grooves, roughness, and shrinkage

Fig. 3

Frequency distribution of level of wrinkling on fruit surface in 160 F₂ progeny (‘Shishito’ × ‘Takanotsume’) grown in 2020 and 2021. The values in ‘Takanotsume’ (TK), F₁ progeny, and ‘Shishito’ (SH) are represented by the annotated arrows. The level of wrinkling was assessed based on a four-point ordinal scale, as shown in Fig. 2, and the mean value of five fruits was used as the representative value in each individual. The different symbol of parentheses in x-axis represent whether the interval include the boundary values or not; the symbols ‘[’ and ‘)’ mean the interval include and exclude the close boundary values, respectively

Fig. 4

Correlations between level of wrinkling on fruit surface and five fruit-related traits in F₂ progeny (‘Shishito’ × ‘Takanotsume’) cultivated in 2020. Scatter plots exhibit (a) FL: fruit length, (b) FWD: fruit width, (c) FWT: fruit weight, (d) SFS: presence of sunken fruit shape at the distal end, (e) CAP: Capsaicinoid content in F₂ individuals. For each trait, the mean values of the five fruits were used as representative values for each individual. SFS was evaluated as 0 (absent) and 1 (present), as shown in Fig. S1. Pearson’s correlation coefficient is shown as r. **: p < 0.01

Fig. 5

Logarithm of odds (LOD) score plot of twelve pepper chromosomes for fruit surface trait in F₂ population in 2020 (n = 104). Two QTLs, Wr11 and Wr12, were identified on chromosomes 11 and 12. The dashed line represents the LOD threshold, which was calculated using a 1,000 permutation test at a significance level of p < 0.05

Fig. 6

Genotypic effects of Wr11 and Wr12 on fruit surface trait in F₂ population in 2020 and 2021. The genotypes were identified using two markers in each locus, and non-recombinant plants in each locus were selected. The boxplots show the level of wrinkling on the fruit surface in three genotypes of each locus. Red circles indicate the mean values. TK, H, and SH denote the homozygous allele of ‘Takanotsume’, the heterozygous allele, and the homozygous allele of ‘Shishito’, respectively. Different letters indicate significant differences at p < 0.05 as estimated by the Tukey–Kramer test. The letter "n" denotes the number of F₂ individuals investigated at each locus and in each year

Fig. 7

Effects of genotypic combination of Wr11 and Wr12 on fruit surface trait in F₂ population in 2020 and 2021. The genotypes were identified using two markers in each locus, and the non-recombinant progenies in both loci were selected. The boxplots show the level of wrinkling on the fruit surface for nine genotypic combination genotypes of each locus. Red circles indicate the mean values. TK, H, and SH denote the homozygous allele of ‘Takanotsume’, the heterozygous allele, and the homozygous allele of ‘Shishito’, respectively. Different letters indicate significant differences at p < 0.05 as estimated by the Tukey–Kramer test. The letter "n" denotes the number of F₂ individuals investigated at both loci and in each year