Study of differentially expressed short-RNAs in swine backfat between fat and lean animals and target prediction of genes regulating fat traits

Short noncoding RNAs (sRNAs) are one of the major categories of transcripts modulating the expression of messenger RNAs (mRNAs) in almost all tissues. In pigs, the number of papers describing the micro-RNAs (miRNAs) expressed in backfat tissue is limited. and only a few of them are included in the present release of miRBase (Release 21, June 2014). Nevertheless, the identification of the molecular mechanisms regulating the aptitude of fat deposition in pigs can lead to the detection of key genes and markers for the genetic improvement of the fat trait in pigs. We analyzed by RNA-seq the sRNAs differentially expressed (DE) in backfat tissue between two groups of Italian Large White (ILW) pigs divergent for backfat deposition. We detected 31 DE sRNAs, 14 up-regulated and 17 down-regulated in fat pigs compared with lean pigs. MiRanda v.3.3a software was used to predict the putative target mRNA of the DE sRNAs. For the target prediction we used the porcine differentially expressed mRNAs detected on the same samples (Zambonelli et al., 2016, Animal Genetics doi: 10.1111/age.12413) used for the identification of the DE sRNAs. Using this approach we detected on the whole 40 DE transcripts targeted by 30 DE sRNAs with a total of 193 interactions. This result shows a strong relationships between the two categories of transcripts opening new possibilities to understand the patterns of regulation of differentially expressed coding genes in pigs with different aptitude for backfat deposition. The target DE mRNAs and the sRNAs were localized on porcine genome and were used to detect some co-localization with QTL region available in pigQTLdb identified as responsible of fat traits. On the whole, our findings add new data useful to elucidate the complex mechanism regulating fat deposition on pigs that can be used to implement innovative strategies based on genomic markers.