Mining Genes Related to Single Fruit Weight of Peach (Prunus persica) Based on WGCNA and GSEA

Abstract

Single fruit weight is an important goal of crop production and horticultural species domestication, but its genetic mechanism is still unclear. In this study, the fruits of different peach fruit types in their first rapid development period were used as materials. First, the differentially expressed genes were analyzed by RNA-seq data. Secondly, weighted gene co-expression network analysis (WGCNA) was used to calculate the correlation between genes and modules, the genes with different expression patterns were divided into 17 modules, the modules were correlated with the phenotype of single fruit, and a highly correlated blue module was obtained. Then, the possible differentially expressed genes and signal pathways among different fruit types were compared by gene set enrichment analysis (GSEA) and 43 significant pathways were obtained. Finally, 54 genes found to be repeatedly expressed in 3 of the methods were screened, and 11 genes involved in plant hormone signal transduction were selected for subsequent analysis according to their functional annotations. Combined with the changing trend of phenotype, three genes (Prupe.7G234800, Prupe.8G079200 and Prupe.8G082100) were obtained as candidate genes for single fruit weight traits. All three genes are involved in auxin signal transduction, with auxin playing an important role in plant growth and development. This discovery provides a new perspective for revealing the genetic law of single fruit weight in peach.

Exploring the PpEXPs Family in Peach: Insights into Their Role in Fruit Texture Development through Identification and Transcriptional Analysis

“…WGCNA has been used to identify the coexpression modules related to volatile organic compounds (VOCs) in Osmanthus fragrans [57]. It has been reported that three genes (Prupe.7G234800, Prupe.8G079200 and Prupe.8G082100) were obtained as candidate genes for single fruit weight traits based on the WGCNA in peaches [58]. ERF has been demonstrated to activate the expression of genes involved in fruit softening, such as PG [59], PME [60], and EXP [61].…”

“…The PpEXP protein showed divergent lengths (241-288 amino acids, aa), molecular weights (26.12-31.56 kDa) and isoelectric points (4.69 to 9.83) (Table 1). Phylogenetic analysis showed that 26 PpEXPs were grouped into four subfamilies based on the full length protein sequences, including expansins from Arabidopsis (35) and rice (58). EXPA, as the largest subfamily, contained 79 genes, including 20 PpEXPAs, 25 AtEXPAs and 34 OsEXPAs (Figure 1).…”