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Warmblood fragile foal syndrome (WFFS) is an autosomal recessive disorder caused by a single nucleotide variant in the procollagen-lysine-2-oxoglutarate-5-dioxygenase 1 gene (PLOD1:c.2032G&gt, A, p.Gly678Arg). Homozygosity for the PLOD1 variant causes an Ehler-Danlos-like syndrome, which has to date only been reported in warmblood breeds but the WFFS allele has been also detected in the Thoroughbred. To investigate the breed distribution of the WFFS allele, 4081 horses belonging to 38 different breeds were screened. In total, 4.9% of the horses representing 21 breeds carried the WFFS allele. The affected breeds were mainly warmbloods, with carrier frequency as high as 17% in the Hanoverian and Danish Warmblood. The WFFS allele was not detected in most non-warmblood breeds. Exceptions include WFFS carriers in the Thoroughbred (17/716), Haflinger (2/48), American Sport Pony (1/12), and Knabstrupper (3/46). The origin of the WFFS allele remains unknown. The Arabian breed and specifically the stallion Bairactar Or. Ar. (1813), whose offspring were reported to have a similar phenotype in the 19th century, were hypothesized as the origin. DNA from a museum sample of Bairactar Or. Ar. showed that he did not carry the mutated allele. This result, together with the genotypes of 302 Arabians, all homozygous for the reference allele, does not support an Arabian origin of the WFFS allele. Our extensive survey shows the WFFS allele to be of moderate frequency and concern in warmbloods and also in breeds where it may not be expected.

Additional file 2: File S2. Primers and probes used in the qPCR analysis.

Additional file 1: File S1. Overall statistics and read annotations obtained for each library.

Objective The aim of the present study was to identify genetic variants based on RNA-seq data, obtained via transcriptome sequencing of muscle tissue of pigs differing in muscle histological structure, and to verify the variants’ effect on histological microstructure and production traits in a larger pig population. Methods RNA-seq data was used to identify the panel of single nucleotide polymorphisms (SNPs) significantly related with percentage and diameter of each fiber type (I, IIA, IIB). Detected polymorphisms were mapped to quantitative trait loci (QTLs) regions. Next, the association study was performed on 944 animals representing five breeds (Landrace, Large White, Pietrain, Duroc, and native Puławska breed) in order to evaluate the relationship of selected SNPs and histological characteristics, meat quality and carcasses traits. Results Mapping of detected genetic variants to QTL regions showed that chromosome 14 was the most overrepresented with the identification of four QTLs related to percentage of fiber types I and IIA. The association study performed on a 293 longissimus muscle samples confirmed a significant positive effect of transforming acidic coiled-coil-containing protein 2 (TACC2) polymorphisms on fiber diameter, while SNP within forkhead box O1 (FOXO1) locus was associated with decrease of diameter of fiber types IIA and IIB. Moreover, subsequent general linear model analysis showed significant relationship of FOXO1, delta 4-desaturase, sphingolipid 1 (DEGS1), and troponin T2 (TNNT2) genes with loin ‘eye’ area, FOXO1 with loin weight, as well as FOXO1 and TACC2 with lean meat percentage. Furthermore, the intramuscular fat content was positively associated (p

Fatty acid composition is one of the main factors affecting health benefits of food. Stearoyl-CoA desaturase 1 (SCD), acetyl-CoA carboxylase alpha (ACACA) and lipoprotein lipase (LPL) have been considered as the rate-limiting enzymes in the biosynthesis of different fatty acids critical in lipid metabolism. The aim of our study was the analysis of differences in expression profiles of three ovine genes related to lipid metabolism (LPL, ACACA, SCD) depending on feeding system and tissue type. The gene expression measurement was performed using a real-time PCR method on 60 old-type Polish Merino Sheep, which were divided into three feeding groups (I – complete pellet mixture, n = 12; II – complete mixture with addition of fresh grass, n = 24; III – complete mixture with addition of fresh red clover, n = 24). From all lambs, tissue samples – subcutaneous fat, perirenal fat and liver – were collected immediately after slaughter and LPL, ACACA and SCD expression was estimated based on two endogenous controls (RPS2 – ribosomal protein S2; ATP5G2 – H(+)-transporting ATP synthase). Our research indicated that supplementation of diet with an addition of fresh grass or red clover significantly (P SCD, ACACA and LPL genes in fat tissue compared to standard complete pelleted mixture. On the other hand, the highest expression of ACACA was detected in liver tissue collected from sheep fed a diet with an addition of fresh red clover (P SCD gene was detected in animals fed with grass supplementation (P SCD transcript abundance was detected in perirenal fat, while LPL and ACACA expression was the highest in both perirenal and subcutaneous fat. The ability of nutrigenomic regulation of transcription of analyzed genes confirmed that these genes play a critical role in regulation of lipid metabolism processes in sheep and could be associated with fatty acid profiles in milk and meat.

Table S1. The dam lines classification with matrilineal founders and number of generations. (DOC 62 kb)

Comparison of selected phenotypic traits for the studied pig breeds. (DOCX 19 kb)

Breed characteristics. (DOCX 12 kb)

The fold-change values obtained from comparisons between subsequent training periods using RNA-seq and qPCR methods. (DOC 38 kb)

Primer sequences used in real-time qPCR validation. (DOC 40 kb)

The training procedure and points of sample collection. (DOC 212 kb)

Identified gene orthologues with differential expression between analysed training periods. (DOC 112 kb)

Although they are the most common neoplasms in equids, sarcoids are not fully characterized at the molecular level. Therefore, the objective of this study was to characterize the landscape of structural rearrangements, such as copy number variation (CNV) and copy neutral loss of heterozygosity (cnLOH), in the genomes of sarcoid tumor cells. This information will not only broaden our understanding of the characteristics of this genome but will also improve the general knowledge of this tumor and the mechanisms involved in its generation. To this end, Equine SNP64K Illumina microarrays were applied along with bioinformatics tools dedicated for signal intensity analysis. The analysis revealed increased instability of the genome of sarcoid cells compared with unaltered skin tissue samples, which was manifested by the prevalence of CNV and cnLOH events. Many of the identified CNVs overlapped with the other research results, but the simultaneously observed variability in the number and sizes of detected aberrations indicated a need for further studies and the development of more reliable bioinformatics algorithms. The functional analysis of genes co-localized with the identified aberrations revealed that these genes are engaged in vital cellular processes. In addition, a number of these genes directly contribute to neoplastic transformation. Furthermore, large numbers of cnLOH events identified in the sarcoids suggested that they may play no less significant roles than CNVs in the carcinogenesis of this tumor. Thus, our results indicate the importance of cnLOH and CNV in equine sarcoid oncogenesis and present a direction of future research.

The basic NGS data statistics for the analysed samples. (DOC 71 kb)