Effect of dietary organic and inorganic selenium supplementation on chemical, mineral and fatty acid composition of ostrich meat

This study evaluated the effect of dietary organic and inorganic selenium supplementation on chemical, mineral and fatty acid composition of ostrich meat. Forty ostriches were raised in two groups (OSe and IOSe, diets supplemented with an organic form and an inorganic form of selenium, respectively). The form of selenium had no influence on chemical composition of ostrich muscle. Although, there were no significant differences in total content of SFA, MUFA and PUFA, the content of LA and EPA was higher in the muscles of ostriches which were put on a diet supplemented with an organic form of selenium, what resulted in lower n-6/n-3 fatty acids ratio in OSe group (9.99) in comparison to IOSe group (11.70). The results of the study indicate that dietary organic selenium supplementation improves the quality of the ostrich meat as related to the health promoting properties (LA, EPA and selenium content) of meat

Quality control assessment of the RNA-Seq data generated from liver and pituitary transcriptome of Hereford bulls using StrandNGS software

Background: Quality control (QC) assessment is the most critical step in the high-throughput RNA-seq data analysis to characterize the in-depth understanding of genome and transcriptome assembling to a given reference genome. It provides not only a quick insight into the RNA-seq data quality to allow early identification of good or bad RNA-seq data samples, but also to verify the alignment QC checks for further essential high-throughput bioinformatics analysis such as, identification of novel genetic variants, differentially expressed genes (DEGs), gene network and metabolic pathways.Method: After isolation of total RNA from liver (n=15) and pituitary gland (n=15) tissues of young Hereford bulls, the pooled total RNA (n=30) were fragmented using GeneRead rRNA depletion kit (Qiagen, Hilden, Germany) and cDNA library preparation were preformed using ScriptSeqTM v2 RNA-Seq library preparation kit (Epicentre, illumina, USA), followed by high-throughput sequencing of combined liver and pituitary transcriptome using MiSeq reagent kit v2 (illumina, USA) to obtain high quality of paired-end RNA-seq reads of 251 base-pairs (bps). In this paper, the QC assessment of obtained RNA-seq raw data as well as post-alignment QC of processed RNA-seq data of combined liver and pituitary transcriptome (n=30) of Hereford bulls were performed using the strand NGS software v1.3 (Agilent; http://www.strand-ngs.com/) data analysis package. The reads were aligned with Bowtie using default settings against both Bull and Cow genome assembly.Results: Using two runs of MiSeq platform, a total of over 60 million paired-end RNA-seq reads were successfully obtained and submitted to NCBI SRA resources (https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=312148). Library complexity plot results revealed 72.02% of duplicate reads with a low library complexity value of 0.28. The pre-alignment QC analysis of raw RNA-seq data revealed the sequence read lengths ranged from 35-251 bp size with more than 50% of all reads with length over 200bp and 10% of reads below 100bp.Conclusion: By testing the RNA-seq methodology on Illumina platform, two MiSeq sequencing runs yielded significantly high quality of 30 million sequencing reads per single MiSeq run. Our initial pre-alignment and post-alignment analysis of RNA-seq data analysis revealed that mapping of the Hereford liver and pituitary gland transcriptome to reference Bos taurus genome was successfully performed, however, more than 50% of all reads with length over 200bp were recovered. Therefore, obtained results concludes that liver and pituitary transcriptome sequencing with rRNA depletion method is less effective than mRNA RNA-seq method

RNA-seq based SNP discovery in gluteus medius muscle of Polish Landrace pigs

BackgroundSingle nucleotide polymorphisms (SNPs) are the well-known molecular markers in genetics and breeding studies applied to veterinary sciences and livestock production. Advancement of next generation sequencing (NGS) provides a high-throughput means of potential putative SNP discovery. The aim of the study was to identify the putative genetic variants in gluteus medius muscle transcriptome of Polish Landrace pigs.MethodsRNA-seq based NGS experiment was performed on Polish Landrace pigs fed with omega-6 and omega-3 polyunsaturated fatty acids (PUFAs) and normal diets. Isolation of total RNA from gluteus medius muscle was performed on low PUFAs (n=6) and High PUFAs dietary group of Polish Landrace pigs. The RNA-seq libraries were constructed 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 of raw RNA-seq data was performed using the Trimmomatic and FastQC tools. High QC paired-end RNA-seq data of gluteus medius muscle transcriptome were mapped to the reference genome Sus scrofa v.10.2. Finally, the SNPs discovery was performed using GATK and SAMtools bioinformatics SNPs caller tools.ResultsThe Fastq RNA-seq data generated from two pooled paired-end libraries (151bp) of gluteus medius muscle tissue of Polish Landrace pigs were submitted to NCBI SRA database (https://www.ncbi.nlm.nih.gov/sra). Study identified a total of 50.5 million paired-end reads (32.5 million low PUFAs dietary group and 18 million reads high PUFAs dietary group) of gluteus medius muscle transcriptome of Polish Landrace pigs. SNP discovery identified a total of 35436 homozygous and 28644 heterozygous cSNPs in gluteus medius muscle transcriptomes representing both dietary groups of Polish Landrace pig. Moreover, a total of 25187 and 5488 cSNP were identified as synonymous SNPs, and 18005 and 4780 cSNP were identified as nonsynonymous SNPs. Finally, single nucleotide variation (SNV) representing substitutions of all four possibilities (A,T,G,C) were identified ranging 2935 to 3227 SNVs (high PUFAs) and 3528 to 3882 SNVs (low PUFAs) for the heterozygous cSNPs and 2712 to 4058 (high PUFAs) and 4169 to 5692 SNVs (low PUFAs) for the heterozygous SNPs in gluteus medius muscle transcriptomes of Polish Landrace pigs.ConclusionsStudy concluded that identification of cSNPs dataset representing the gluteus medius muscle 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 specific to Polish Landrace pig breed. Such cSNP markers eventually can be utilized in 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

Influence of frozen storage on the fatty acid composition of ostrich meat enriched with linseed and rapeseed

CITATION: Horbanczuk, J. O. et al. 2015. Influence of frozen storage on the fatty acid composition of ostrich meat enriched with linseed and rapeseed. South African Journal of Animal Science, 45(2):129-136, doi:10.4314/sajas.v45i2.3.The original publication is available at http://www.sasas.co.za/journalsThe aim of the study was to evaluate the effect of the duration (24 hours, 60 days and 120 days) of frozen storage (−20 ºC) on the fatty acid composition of meat from ostriches supplemented with linseed and rapeseed. The study was carried out on muscles of 40 ostriches raised on five dietary groups: control with no supplementation (C), with 4% linseed (L4); 8% linseed (L8); and 5% rapeseed (R5); or 10% rapeseed (R10) in the diet. As the frozen storage period increased, the fatty acid profile of the ostrich meat in all the “enriched” groups changed, especially treatments L4 and L8. There was a decrease in the polyunsaturated fatty acid content (especially from 61 to 120 days of storage) including linolenic, arachidonic and docosahexaenoic acids. However, storage did not influence the fatty acid profile of ostrich meat up to 60 days. These results suggest that freezing is an acceptable method for preserving ostrich meat (up to 60 days), causing only a small decrease in the fatty acids of ostrich meat enriched with n-3 fatty acids. However, further research on prolonged frozen storage is recommended.http://www.sasas.co.za/influence-frozen-storage-fatty-acid-composition-ostrich-meat-enriched-linseed-and-rapeseedPublisher's versio

The physical traits and fatty acids profile of ostrich meat enriched in n3 fatty acids as influenced by duration of refrigerated storage and type of packaging

The aim of the study was to evaluate physical traits and fatty acids profile of ostrich meat enriched in n3 fatty acids as affected by refrigerated storage (for 14 days) and type of packaging (VAC vs. skin-packaging - SP). During refrigerated storage time drip loss after 7 days was significantly (P<0.001) higher in VAC as compared to SP samples. No significant differences in the SFA content in meat during storage in both types of packaging types recorded. Although there were no significant differences (P=0.067), a tendency for higher MUFA values was observed during storage in VAC packed meat. A significant decrease (P<0.05) in the content of PUFA after 7 and 14 days of storage was also observed in VAC packed meat as compared to fresh meat, whereas, when skin packaging was used, no differences in the PUFA concentration were found. Considering this, the SP can be recommended packaging for ostrich meat industry

The effect of slaughter weight on the carcass characteristics of pork with sex type as co-variable

A study was conducted with 192 pigs of three sex types with treatments according to slaughter weight (65 kg to 144 kg). The main statistical differences observed were for slaughter weight with significant (P < 0.05) and highly significant (P < 0.01) differences describing more than 10% of variance observed for all characteristics (liveweight, warm carcass weight, dressing percentage, eye muscle area, subcutaneous fat thickness, intramuscular fat area, subcutaneous fat:eye muscle area, intramuscular fat:eye muscle area, fat thickness, muscle depth, carcass length, ham circumference, ham length and chest depth) measured. Sex differences (P < 0.05) were also observed for dressing percentage, fat measurements and muscle depth measured between the 5th and 6th lumbar vertebrae. Sex type differences, in all instances, accounted for 10% or less variance except for subcutaneous fat:eye muscle area ratio (18.47%). It was shown that although significant sex type differences (P < 0.05) existed; slaughter weight had the largest effect on carcass characteristics in the given circumstances accounting for most of the observed variance

The effect of dietary oil seeds on the fatty acid profile and metabolism in ostrich liver

The study was carried out on 40 ostriches randomly allocated into five groups and each group was randomly assigned to a different dietary treatment. Experimental diets were made on the basis of a control diet, where a part of the gross energy was replaced with energy from linseed (4 or 8% -treatment L4 and L8, respectively) or rapeseed (5 or 10% - treatment R5 and R10, respectively). The ostriches were slaughtered at 12 months of age and within 30 minutes after slaughter liver samples (50 g) were taken. The results indicate that the linseed supplementation, especially 4%, to the ostrich diet improves the nutritional value of ostrich liver by decreasing the n-6/n-3 ratio and by increasing the PUFA/SFA ratio. It makes ostrich liver more valuable for the production of meat products e.g. pates. The rapeseed supplementation to the ostrich diet has no influence on the fatty acid profile of ostrich liver compared to the control diet. Dietary supplementation by linseed changes the fatty acid metabolism in ostrich liver