Deep sequencing of a QTL-rich region spanning 128-136Mbp of pig chromosome 15

The present study shows the characterization of the chromosome 15 (SSC15) region that is highly rich in quantitative traits loci (QTLs) associated with pork quality, growth performance, fat and meat carcass contents. The analytic method that was utilized included targeted enrichment DNA sequencing and RNA hybridisation probes. The research included two pig breeds (Puławska and Polish Landrace) that are significantly different in terms of carcass and meat quality features. Filtered sequences were aligned to the Sscrofa10.2 assembly genome with the STAR aligner and GATK HaplotypeCaller was used for identified gene variants in SSC15 region. In Puławska pigs, which were characterized by high meat quality, mutations were predominantly observed in non-coding regions such as introns and intergenic regions. The highest over 50% frequencies of alternate alleles were identified in the introns of TNS1, VIL1 and USP37 genes. In the upstream gene regions of the Polish Landrace pigs, were observed more mutations than in the upstream gene regions of Puławska. The present study showed interesting gene variant panel that could be analyzed in the further association studies in order to understand the impact on important productive pig traits.