Genome-wide differential expression profiling of ovarian circRNAs associated with litter size in pigs

In this study, porcine ovaries with smaller or larger litter size (SLS or LLS) were subjected to high-throughput RNA-sequencing. In total, 38,722 circRNAs were identified, of which 1,291 circRNAs were commonly expressed in all samples. There were 56 circRNAs significantly down-regulated and 54 circRNAs up-regulated in LLS pig. Besides, 411 miRNAs were identified, and of these 17 were significantly down-regulated and 16 miRNAs were up-regulated when comparing sows with LLS and SLS, respectively. In addition, we identified a total of 3,556 lncRNA candidates, of which 96 lncRNAs were up-regulated and 206 lncRNAs were down-regulated when comparing LLS to SLS. 16,428 genes were detected, and 2,392 unigenes were significantly differently expressed at the LLS and SLS ovarian samples. In addition, a competitive endogenous RNA (ceRNA) network was constructed. Our study indicates that non-coding RNAs may play roles in modulating porcine litter size. Overall design: For RNA-seq, 3 ovaries were sampled from each group small and large litter size (8.48±0.53 piglets/litter in small litter size, and 16.19±0.43 piglets/litter in large litter size).