Integrated Transcriptomic and Metabolomic Profiling Identifies Candidate Genes and Pathways Associated With Pedicel Abscission Susceptibility in Capsicum annuum

Abstract

Pedicel abscission susceptibility in Capsicum annuum affects fruit retention and harvesting efficiency, making it a key agronomic trait in pepper breeding. In this study, two germplasm lines (LC-8 and LC-17) exhibiting distinct abscission characteristics were analyzed to explore the molecular basis underlying this trait. Although phenotypic differences have been documented, the molecular mechanisms regulating abscission susceptibility remain largely unclear. We performed a comprehensive analysis integrating morphological observations with transcriptomic and metabolomic profiling. Anatomical analysis revealed differential lignification patterns in the abscission zone (AZ), suggesting structural specialization. Transcriptome profiling identified 4635-7519 differentially expressed genes (DEGs), with KEGG enrichment highlighting phenylpropanoid biosynthesis and plant hormone signal transduction as core regulatory pathways. Metabolomic profiling detected 966 metabolites, including significantly altered flavonoids (e.g., apigenin O-hexosyl-O-pentoside, naringenin O-malonylhexoside) and phytohormones (e.g., abscisic acid, GA_7-1). Integrated multi-omics analysis revealed that key genes and metabolites involved in lignin biosynthesis and hormone signaling displayed distinct expression and accumulation patterns between the two lines. These findings suggest that these metabolic pathways play central roles in modulating pedicel abscission susceptibility. This study lays a theoretical foundation for regulating abscission and supports the breeding of pepper cultivars optimized for mechanical harvesting.

Keywords: Capsicum annuum; metabolomic; pedicel abscission; susceptibility; transcriptomic.

FIGURE 1

Comparative analysis of abscission zone (AZ) traits in pepper germplasm lines LC‐8 and LC‐17. (a) Phenotypic characterization of AZ detachment: LC‐8 fruit‐end AZ (A1) shows high susceptibility to pedicel abscission, whereas the pedicel‐stem junction (A2) exhibits reduced susceptibility to abscission. In contrast, LC‐17 displays an inverse pattern, with retained fruit‐end AZ (B1: Reduced pedicel abscission susceptibility) and detached shoot‐end AZ (B2: Increased susceptibility to abscission at the pedicel‐stem junction). (b) Safranin O‐fast green‐stained paraffin sections of AZs. LC‐8 A1 displays lignified cells (red) in the abscission layer (AL), contrasting with weakly lignified A2. LC‐17 B2 shows enhanced lignification compared to B1. (c) Fluorol yellow 088 staining reveals suberin accumulation (yellow fluorescence) in AZs.

FIGURE 2

Gene expression analysis. (a) Box figure of FPKM. Horizontal is sample ID and ordinate is log₁₀ ^FPKM; (b) Pearson correlation between samples; (c) principal component analysis; (d) the number of DEGs in different comparison groups.

FIGURE 3

The top 20 enriched KEGG pathways of the DEGs in each comparison: (a) A1 versus A2; (b) A1 versus B1; (c) A1 versus B2; (d) A2 versus B1; (e) A2 versus B2; (f) B1 versus B2.

FIGURE 4

Orthogonal partial least‐squares discriminant (OPLS‐DA) analysis. (a, c, e, g, i, k) Were score plots of the OPLS‐DA model; (b, d, f, h, g, l) were overfitting analyses of the OPLS‐DA model (two hundred permutations). (a, b) A1 versus A2; (c, d) A1 versus B1; (e, f) A1 versus B2; (g, h) A2 versus B1; (i, j) A2 versus B2; (k, l) B1 versus B2.

FIGURE 5

Metabolite analysis of four tissues. (a) Relative content stacked histogram of different metabolite categories. (b) DiffExp metabolites statistics of different tissue types.

FIGURE 6

The top 25 differential expression metabolite box line diagram. To intuitively demonstrate the differences in metabolite levels between groups, boxplots were drawn for the top 25 representative metabolites with the smallest p‐values identified from univariate statistical analysis. Each box represents one experimental group: A1 (green), A2 (red), B1 (blue), and B2 (purple). Statistical significance was assessed using Student's t‐test, and metabolites with **** indicate p < 0.0001. Each boxplot is based on n = 3 biological replicates per group.

FIGURE 7

The pvalue_heatmap of KEGG pathways significantly enriched in DEGs and DAMs: (a) A1 versus A2; (b) A1 versus B1; (c) A1 versus B2; (d) A2 versus B1; (e) A2 versus B2; (f) B1 versus B2.

FIGURE 8

Heatmap of DEGs and DAMs involved in lignin synthesis pathways.

FIGURE 9

Heatmap of DEGs and DAMs involved in plant hormone signal transduction: a:Auxin; b:Cytokinine; c:Gibberellin; d:Abscisic acid; e:Jasmonic acid; f:Salicylic acid; g:Ethylene.

FIGURE 10

Gene expression validation was conducted using quantitative reverse transcription polymerase chain reaction (qRT‐PCR) analysis. The data presented represent the mean expression values derived from both transcriptomic and qRT‐PCR datasets. Error bars indicate the standard error of the mean (SEM).