# Integrated RNA-Seq and Metabolomics Analyses of Biological Processes and Metabolic Pathways Involved in Seed Development in Arachis hypogaea L

## TL;DR

This study combines RNA-Seq and metabolomics to explore seed development in peanuts, identifying genes and metabolic pathways linked to yield and quality traits.

## Contribution

The study integrates transcriptomic and metabolomic data to uncover cultivar-specific genes and metabolic processes in peanut seed development.

## Key findings

- JNH3 and SLH cultivars show distinct patterns of differentially expressed genes and metabolites in flowers and aerial pegs.
- JNH3 is associated with pollen germination and phenylalanine metabolism, while SLH is linked to protein degradation and DNA repair.
- Significant differences in lipid profiles were observed between JNH3 and SLH flowers.

## Abstract

In peanut cultivation, fertility and seed development are essential for fruit quality and yield, while pod number per plant, seed number per pod, kernel weight, and seed size are indicators of peanut yield. In this study, metabolomic and RNA-seq analyses were conducted on the flowers and aerial pegs (aerpegs) of two peanut cultivars JNH3 (Jinonghei) and SLH (Silihong), respectively. Compared with SLH, JNH3 had 3840 up-regulated flower-specific differentially expressed genes (DEGs) and 5890 up-regulated aerpeg-specific DEGs. Compared with the JNH3 aerpegs, there were 4079 up-regulated variety-specific DEGs and 18 up-regulated differentially accumulated metabolites (DAMs) of JNH3 flowers, while there were 3732 up-regulated variety-specific DEGs and 48 up-regulated DAMs in SLH flowers. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the DEGs of JNH3 were associated with pollen germination and phenylalanine metabolism in flower and aerpeg tissues, respectively. In contrast, the DEGs of SLH were associated with protein degradation, amino acid metabolism, and DNA repair. However, there were significant differences in the lipids and lipid-like molecules between JNH3 flowers and SLH flowers. This investigation provides candidate genes and an experimental basis for the further improvement of high-quality and high-yield peanut varieties.