Analyzing Differentially Expressed Genes and Pathways Associated with Pistil Abortion in Japanese Apricot via RNA-Seq

Abstract

Reproduction is a critical stage in the flower development process, and its failure causes serious problems affecting fruit quality and yield. Pistil abortion is one of the main factors in unsuccessful reproduction and occurs in many fruit plants. In Japanese apricot, the problem of pistil abortion is very common and affects fruit quality and plant yield; however, its molecular mechanism is not clearly understood. Therefore, in the current study, we used RNA-Seq to identify the differentially expressed genes (DEGs) and pathways actively involved in pistil abortion. A total of 3882 differentially expressed genes were found after cutoff and pairwise comparison analysis. According to KEGG pathway analysis, plant hormone signaling transduction and metabolic pathways were found most significantly enriched in this study. A total of 60 transcription factor families such as MADS-box, NAC and TCP showed their role in this process. RT-qPCR assays confirmed that the expression levels were consistent with RNA-Seq results. This study provides an alternative to be considered for further studies and understanding of pistil abortion processes in Japanese apricot, and it provides a reference related to this issue for other deciduous fruit crops.

Keywords: Japanese apricot; RNA-Seq; hormone signaling; metabolic pathways; pistil abortion.

Figure 1

An overview of differentially expressed genes (DEGs) involved in normal and abortive pistils of Japanese apricot. (A) Heatmap showing the differential expression pattern of the DEGs. The color scale shows the gene expression values (log2fc). (B) Up- and down-regulation of differentially expressed genes. (C) Volcano plot showing the differentially expressed genes. The x-axis represents the log2 fold change conversion of the values, and the y-axis represents the significance value after –log10 conversion. Red shows up-regulated DEGs, blue shows down-regulated DEGs, while grey represents no DEGs.

Figure 2

Gene Ontology (GO) analysis between normal pistil (NP) and abortive pistil (AP) showing the abundance of differentially expressed enriched GO terms.

Figure 3

KEGG pathway enrichment analysis (A) DEGs related to significant enrichment analysis were involved in different processes (B) Bubble plot showing top20 most enriched pathways (C) Regulation (up/down) trend of the DEGs involved in different pathways.

Figure 4

Analysis of transcription factors (TFs) between normal and abortive pistils of Japanese apricot. (A) Distribution of important TF families and their percentage of genes in each TF family. (B) Average expression profiles of genes involved in each TF family in normal and abortive pistils. The bar represents the scale of expression of each gene as indicated by blue (lower expression) and dark yellow (higher expression).

Figure 5

Expression profiles of the DEGs involved in plant hormones and signaling transduction pathway (A) Heatmap shows the expression of DEGs in normal and abortive pistils associated with different hormones like auxin, gibberellin, cytokinin, abscisic acid and ethylene. The bar represents the expression level of each gene as indicated by blue (lower expression) and dark yellow (higher expression). (B) Endogenous hormone contents between normal and abortive pistils. Three independent samples were collected for hormone measurement.

Figure 6

Validation of RNA-Seq data. (A) Verification of the expression level of the selected DEGs from RNA-Seq data through RT-qPCR. Error bars indicate the standard error as mean + SD. The x-axis represents the relative expression level, and the y-axis represents NP (normal pistils) and AP (abortive pistils). (B) Correlation coefficient of gene expression obtained from RT-qPCR analysis. *** shows highly significant level of the data.