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The chromosome region on SCC15 in pigs between microsatellites SW1683 and SW906 (79.3–89.3 cM) is rich in quantitative traits loci (QTLs) associated with meat quality such as juiciness, meat color, pH, cooking and drip loss, firmness, shear force, thawing loss and an intramuscular fat. The goal of the study was to identify the genetic markers on chromosome 15 in pigs, which could be helpful in breeding programs leading to faster breeding progress focusing on the improvement of meat quality. The study was conducted on 16 pigs of two breeds: Polish Landrace (n= 8) and Puławska (n= 8) differing in meat quality traits and as a method the targeted-enrichment strategy for next generation sequencing was used. The enrichment technique applied in this approach was RNA hybrid capture (1x tiling). DNA was isolated by Wizard® Genomic DNA Purification Kit (Promega) from whole blood stabilized by EDTA. 200 ng of total DNA was used to prepare the DNA library by SureSelectXT Custom 3–5.9 and SureSelectXT Reagents (Agilent) according to a protocol (Index A1-H2). The quality and quantity of DNA libraries were measured by TapeStation 2200 (Agilent) and Qubit Fluorometer (Invitrogen). The final concentration of the DNA libraries was normalized to 10 nM, diluted to 2 nM and pooled altogether according to a cluster generation protocol, loaded into a v3 Illumina flowcell (16 samples) and clustered by cBot (Illumina) using a TruSeq SR Cluster Kit v3-cBot-HS. Pair-end sequencing, with a read length of 75 bp in two technical replicates was performed on the HiScanSQ System using TruSeq SBS Kit v3-HS chemistry (Illumina). To process the raw data FastQC tool, Flexbar (quality score ≥ 20, size reads ≥ 36 bp). Filtered sequences were aligned to the pig genome (Sscrofa10.2 assembly) with BWA aligner, and SAMtools/Picard tools and GATK were used to base quality score recalibration, INDEL realignment, duplicate removal, and performed SNP and INDEL with GATK Best Practices approach. The alignment statistics were obtained with Qualimap. An average 80% reads per sample to chromosome 15 were aligned. Moreover, a high coverage was obtained for 10 unmapped contigs: JH118564.1, GL893143.2, JH118558.1, JH118457.1, GL893450.2, GL893465.2, GL892871.2, GL894011.1, JH118559.1, GL892452.1, in which are encoded a few novel genes and two known BCS1L and IGFBP2. In further analysis will be performed the analysis of polymorphic variant for SSC15 regions rich in QTLs associated with meat quality in pigs to identify the candidate genes.

The Arabians are commonly believed to be one of the oldest and the most influential horse breeds in the world and have been widely used to improve several horse breeds. Since the eighteenth century they have a very special place in Polish horse breeding. The origin of founding mares traces back to 1800 and since then the breeding is documented as pure breed. That is why Polish population are excellent example of a closed population, strongly affected by selection. The race track performance is considered as one of the selection criteria of Arabian horses which favorably influences the development of young horses. On the other hand racing training is considered to be aggravating for a developing organism, thus the aim of presented research is identification of the transcriptomic signatures of musculoskeletal fatigue in the blood of Arabian horses under a racing training regime. The RNA-seq analysis of blood has been performed for 6 2,5 y.o. horses. Total of 12 samples has been collected in two periods: I–unbroken and II–after heavy canters. The RNA sequencing was performed in 75 single-end cycles on HiScanSQ platform (Illumina). The cDNA libraries were prepared by using TruSeq RNA Kit v2 kit (Illumina) and their quality and quantity were estimated using Qubit 2.0 (Invitrogen) and TapeStation 2200 (Agilent). Validation of obtained results was performed by the real-time PCR method. The differentially expressed genes (DEG) were determined using Deseq2 software. Between two investigated training periods we detected the high number of significant differentially expressed genes (FDR < 0.05; fold change < 1.5): 2544 DEGs. Apart from a large number of transcripts corresponding to the general biological processes, the pathways indicating musculoskeletal fatigue have been observed. The identified pathways regarding regulation of proteoglycans, regulation of actin cytoskeleton, thyroid hormone signaling pathways together with training mediated activation of transcriptional response of muscle burden (ATPase gene family–e.g., ATP5, ubiquinone gene family–e.g., NDUFA3, hyaluronic maintain pathways–e.g., CD44) demonstrate the impact of the racing training regime on musculoskeletal system in young developing horses.