RNA-seq based SNP discovery in liver transcriptome of Polish Landrace pigs

Background: RNA-seq technology is most commonly used in quantitative measurement of gene expression levels and identification of non-annotated transcripts. It is also used for the coding SNPs (cSNPs) discoveries in an efficient and cost-effective way. The aim of this study was to identify the putative genetic cSNPs variants in liver transcriptome of Polish Landrace pigs fed with high and low (normal) omega-6 and omega-3 polyunsaturated fatty acids (PUFAs) diets.Methods: RNA-seq based NGS experiment was performed on Polish Landrace pigs fed with high and low PUFAs diets. Total RNA were isolated from liver tissues of low PUFAs (n=6) and high PUFAs dietary group (n=6) of Polish Landrace pigs. The RNA-seq libraries preparations were performed by mRNA enrichment, mRNA fragmentation, second strand cDNA synthesis, adaptor ligation, size selection and PCR amplification using the illumina TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego CA, USA), followed by NGS sequencing on MiSeq illumina platform. The quality control (QC) of raw RNA-seq data of liver transcriptome was performed using the Trimmomatic and FastQC tools. The paired-end mapping of the liver transcriptome RNA-seq data (n=12) was performed on the reference genome Sus scrofa v.10.2, followed by cSNPs discovery using GATK and SAMtools bioinformatics SNPs caller tools.Results: Two pooled paired-end libraries of 151bp liver transcriptome of Polish Landrace pigs were generated from MiSeq instrument and subsequent Fastq RNA-seq data were submitted to NCBI SRA database (https://www.ncbi.nlm.nih.gov/sra). Our study identified 25.3 million paired-end reads: representing 13,509,248 paired-end reads of high PUFAs dietary group and 11,815,696 paired-end reads of low PUFAs dietary group of Polish Landrace pigs liver transcriptome. The SNP discovery results revealed identification of 25909 homozygous and 23290 heterozygous cSNPs in the liver transcriptome of both dietary groups of Polish Landrace pigs. With regards to same or alternative SNPs alleles encoding amino acids regions, a total of 27141 synonymous cSNP and 5989 non-synonymous cSNPs were identified in liver transcriptome representing high PUFAs dietary group. However, a total of 15128 synonymous cSNPs and 3900 non-synonymous cSNPs were identified in liver transcriptome representing low PUFAs dietary groups of Polish Landrace pigs. The identification of single nucleotide variations (SNVs) representing substitutions of all four possibilities (A,T,G,C) were ranged 2872 to 6868 SNVs (high PUFAs) and 2574 to 3654 SNVs (low PUFAs) in the homozygous cSNPs and 2452 to 2678 SNVs (high PUFAs) and 2094 to 2230 SNVs (low PUFAs) in the heterozygous cSNPs of liver transcriptomes of Polish Landrace pigs, respectively.Conclusions: Study concluded that identification of cSNPs dataset representing the liver transcriptome of Polish Landrace pigs fed with a control diet (low) and pigs fed with a PUFAs diet (high) may be helpful to develop a new set of genetic markers for trait-associated studies (viz., growth and metabolic traits) specific to Polish Landrace pig breed. Such cSNP markers eventually can be utilized in the genetic improvement of the pig production traits using the genome-wide association studies (GWAS) and to finally implement on marker assisted selection (MAS) and genomics selection (GS) program in active breeding population of Polish Landrace pigs in Poland

The effect of varying gas headspace to meat ratio on the quality of pork loin stored in high O2 modified atmosphere

A comparison was made of the effect of different gas headspace to meat ratio on quality of pork loin (m. longissimus thoracis et lumborum) obtained from crossbred pigs (Polish Landrance x Duroc, n = 6) as a function of cold storage. Samples were stored in modified atmosphere packs (80% O₂:20% CO₂) with gas headspace to meat ratios (G/M) of 3:1, 1:1 and 1:3. Physicochemical and microbiological parameters were monitored for up to 12 days. The results indicated that the best properties of meat were obtained when stored pork loins with the gas headspace to meat ratio of 1:1. G/M = 1:3 contributed to the increase in the growth of microorganisms and G/M = 3:1 and led to unfavorable changes in meat color. Finally, chemical properties of pork loins were unaffected (P > 0.05) by varying the gas headspace to meat ratio

Quality of pork loin stored under different light intensity

El objetivo de este experimento fue estudiar la influencia de la intensidad de luz en la superficie del lomo de cerdo, en particular en sus propiedades fisicoquímicas y microbiológicas como función del almacenamiento en frío. Se envasaron las porciones de carne en paquetes de atmosfera modificada (MAP: 80% de O2 y 20% de CO2) y se almacenaron en la oscuridad o se colocaron bajo fluorescentes (1000 lx y 2000 lx respectivamente) durante 12 días. Los resultados indicaron que en el último día de almacenamiento el lomo de cerdo almacenado con luz presentaba una apariencia más descolorida, una mayor pérdida por goteo y menos ternura (P < 0,05). Además, el exceso de intensidad de luz aceleró el crecimiento de microorganismos y conllevó a un aumento de la proporción de n-6/n-3 (P < 0,05). Finalmente, los paquetes de MAP almacenados bajo 2000 lx se caracterizaron por tener el menor contenido de oxígeno y el mayor contenido de dióxido de carbono. Considerando los aspectos examinados, se recomienda almacenar el lomo de cerdo en la oscuridad y en caso de no ser posible, hacerlo con la menor intensidad de luz posible.The objective of the experiment was to study the influence of the intensity of light at the pork loins surface on their physicochemical and microbiological properties as a function of cold storage. Meat slices were packed in modified atmosphere packs (MAP: 80% O2 and 20% CO2) and stored in the darkness or displayed under fluorescent light (1000 lx and 2000 lx, respectively) for 12 days. Results indicated that on the last day of storage pork loins stored under light were more discolored, had greater drip loss, and were less tender (P < 0.05). Moreover, excessive light intensity (LI) accelerated microorganism growth and led to an increase of n-6/n-3 ratio (P < 0.05). Finally, MAP packages stored under 2000 lx were characterized by the lowest oxygen and the highest carbon dioxide content. Considering the above, it is recommended to store pork loins in the dark and if it is not possible in the low LI

Omega-3 alpha-linolenic fatty acid affects the level of telomere binding protein trf1 in porcine skeletal muscle

Omega-3 fatty acids are health-promoting nutrients that contribute to the amelioration of age-related diseases. Recent studies have reported the role of these fatty acids in the aging process, explicitly impacting telomere biology. The shelterin protein complex, located at the extremities of chromosomes, ensures telomere protection and length regulation. Here, we analyzed the impact of dietary omega-3 alpha-linolenic fatty acid from linseed oil on skeletal muscle telomere biology using an animal model of female pigs. Fifteen animals were supplemented with linseed oil for nine weeks and an equal number of individuals were fed with a control diet. Linseed-oil-supplemented animals showed an increased level of alpha-linolenic acid in skeletal muscles compared to control animals. There was no difference between groups in the telomere length measured in leukocytes and muscles. However, muscles of the linseed-oil-supplemented pigs showed lower levels of the shelterin TRF1 protein compared to the control group. Our results suggest that omega-3 linolenic acid counteracts the elevation of TRF1 levels, which increase with age and due to the presence of reactive oxygen species in muscle. The observed effect may be due to attenuation of oxidative stress.</p

Effect of dietary linseed and rapeseed supplementation on fatty acids profiles in the ostriches. Part 2. Fat

The aim of the study was to determine the effect of linseed and rapeseed dietary supplementation on the fatty acids profiles of two ostrich fat depots: breast and subcutaneous (above the leg). The study was carried out on 40 ostriches raised in five groups - control (C) or with 4% (L4) or 8% (L8) linseed, or 5% (R5) or 10% (R10) rapeseed in the diet, from hatching to 12 months of age. Fat samples of breast (BF) and leg fat (LF) were taken for fatty acids analysis. Generally ostrich fat has high contents of PUFA (BF - 23.9, LF - 20.2 g/100 g FAME), especially linoleic acid (BF - 16.4, LF - 12.5 g/100 g FAME) and linolenic acid (BF - 5.7 and LF - 6.2 g/100 g FAME). Ostrich BF had a higher content of n-6 FA and total PUFA and lower n-3 FA than the LF. Both fat depots had desired PUFA/SFA ratios above 0.4, but not desirable n-6/n-3 ratios. BF had significantly higher (0.69) PUFA/SFA ratio than LF (0.55). Both L4 and L8 caused higher total PUFA content (27.8, 25.6 g/100 g

Effects of Three-Month Feeding High Fat Diets with Different Fatty Acid Composition on Myocardial Proteome in Mice

Westernized diet is characterized by a high content of saturated fatty acids (SFA) and a low level of omega-3 polyunsaturated fatty acids (PUFA), often accompanied by an imbalance in the omega-6/omega-3 PUFA ratio. Since increased intake of SFA and n-6 PUFA is considered as a cardiovascular disease risk factor, this study was conducted to determine whether a three-month dietary supplementation of high-fat diets (HFDs) with saturated fatty acids and a significant proportion of various n-6 and n-3 PUFA ratios would affect the architecture and protein expression patterns of the murine heart. Therefore, three HFD (n = 6) feeding groups: rich in SFA, dominated by PUFA with the n-6/n-3–14:1, and n-6/n-3–5:1, ratios were compared to animals fed standard mouse chow. For this purpose, we performed two-dimensional electrophoresis with MALDI-ToF mass spectrometry-based identification of differentially expressed cardiac proteins, and a histological examination of cardiac morphology. The results indicated that mice fed with all HFDs developed signs of hypertrophy and cardiac fibrosis. Animals fed SFA-rich HFD manifested the most severe cardiac hypertrophy and fibrosis lesions, whereas less pronounced changes were observed in the group of animals that ingested the highest amount of omega-3 FA. In general, all HFDs, regardless of FA composition, evoked a comparable pattern of cardiac protein changes and affected the following biological processes: lipid metabolism and FA β-oxidation, glycolysis, TCA cycle, respiratory chain, myocardium contractility, oxidative stress and PUFA eicosanoid metabolism. However, it should be noted that three proteins, namely IDH3A, LDHB, and AK1, were affected differently by various FA contents. High expression of these myocardial proteins found in the group of animals fed a HFD with the highest n-3 PUFA content could be closely related to the observed development of hypertrophy