Identification of Differentially Expressed Genes in Porcine Ovaries at Proestrus and Estrus Stages Using RNA-Seq Technique

Abstract

Estrus is an important factor for the fecundity of sows, and it is involved in ovulation and hormone secretion in ovaries. To better understand the molecular mechanisms of porcine estrus, the expression patterns of ovarian mRNA at proestrus and estrus stages were analyzed using RNA sequencing technology. A total of 2,167 differentially expressed genes (DEGs) were identified (P ≤ 0.05, |log₂ Ratio| ≥ 1), of which 784 were upregulated and 1,383 were downregulated in the estrus compared with the proestrus group. Gene Ontology (GO) enrichment indicated that these DEGs were mainly involved in the cellular process, single-organism process, cell and cell part, and binding and metabolic process. In addition, a pathway analysis showed that these DEGs were significantly enriched in 33 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including cell adhesion molecules, ECM-receptor interaction, and cytokine-cytokine receptor interaction. Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) confirmed the differential expression of 10 selected DEGs. Many of the novel candidate genes identified in this study will be valuable for understanding the molecular mechanisms of the sow estrous cycle.

Figure 1

Distribution of DEGs. (a) The number of downregulated and upregulated DEGs in the estrus compared to the proestrus group. (b) Volcano plot displaying DEGs. The y-axis displays the value of −log10 (P value); the x-axis shows the log₂ fold change value. The upregulated genes are displayed by the red dots; downregulated genes are displayed by the green dots; and the black dots represent genes with no significant changes.

Figure 2

GO analysis of the DEGs. Genes were classified into biological process, cellular component, and molecular function. The left y-axis shows the percentage of genes in each category. The right y-axis indicates the number of genes in each category. The solid columns indicate DEGs, and slash columns indicate the background genes.

Figure 3

Top 30 significant enriched KEGG pathways.

Figure 4

Validation of DEGs by qRT-PCR. White columns represent the expression level of the DEGs obtained by qRT-PCR, and gray columns represent the RNA-Seq results.