Identification of Ovarian Circular RNAs and Differential Expression Analysis between MeiShan and Large White Pigs

SIMPLE SUMMARY: Chinese MeiShan pigs make up one of the oldest Chinese pig breeds. Compared with Large White pigs, MeiShans are hyper-productive and prolific, however, the expression and function of circular RNAs (circRNAs) in these two breeds of pig are not yet fully understood. We performed RNA-seq analysis of porcine ovaries from three MeiShan sows and three Large White sows, identifying 85 differentially expressed circRNAs (p < 0.05). In MeiShan pigs, 37 circRNAs were significantly up-regulated and 48 circRNAs were down-regulated. We verified that circular RNA scinderin (circSCIN) can target and sponge miR-133 and miR-148a/b, two miRNAs that affect estrogen secretion. This study highlights the circRNA profiling of ovaries and helps investigators to understand the differences in reproductive efficiency between MeiShan and Large White pigs. ABSTRACT: MeiShan and Large White pigs differ in their female fecundity. However, the mechanisms behind the gene expression and regulation that cause these differences remain unclear. In this study, we profiled circRNAs and identified 5,879 circRNAs from the ovaries of MeiShan and Large White pigs. Eighty-five circRNAs were differentially expressed between the two pig breeds. Of these, 37 were up-regulated and 48 were down-regulated in MeiShan pigs. Gene ontology enrichment analysis suggested that the differentially expressed circRNA were involved in the hormone-mediated signaling pathway. We verified that circSCIN and its parent gene, scinderin (SCIN), were differentially expressed by reverse transcription and quantitative PCR (RT-qPCR). Luciferase assays demonstrated that circSCIN can target and sponge miR-133 and miR-148a/b. The identification of differentially expressed circRNAs (DECs) and their regulatory functions increased our understanding of the differences in reproductive efficiency between MeiShan and Large White pigs.