Transcript variants of a region on SSC15 rich in QTLs associated with meat quality in pigs

A high meat percentage in the porcine carcass has been achieved as a result of selection, but it has contributed to a deterioration of pork quality. The level of intramuscular fat has significantly declined, the pork has lost its tenderness and drip loss in meat has substantially increased, which has led to a deterioration of meat flavour and its technological suitability. The recovery of good pork quality could be supported by the development of genetic markers enabling faster breeding progress. This study presents a method by using RNA-seq data that identifies new variants for a chromosome region rich in QTLs for pork quality and selects gene candidates for these traits. This work included two pig breeds: the Polish Landrace (PL) and Puławska (PUL), which differ in meat quality and fat content. The transcriptome profile was estimated for semimembranosus and longissimus dorsi muscles. Into variant calling analysis, transcripts of both muscles encoded by genes located in a region between microsatellites SW964 and SW906 (43-135.9 Mbp) in SSC15 were included. In total, 439 transcripts were searched, 2,800 gene variants were identified and 6 mutations with a high effect belonging to the frameshift variants were found (ENSSSCG00000015976, ENSSSCG00000027516, WRN and XIRP2). Moreover, several interesting significant missense variants in PDLIM3, PLCD4 and SARAF genes were detected. These genes are recommended as candidates for meat quality; however they require further investigation in an association study.