Association between cathepsin L (CTSL) and cathepsin S (CTSS) polymorphisms and meat production and carcass traits in Italian Large White pigs

Quantitative proteomic analysis of trachea in fatting pig exposed to ammonia

Ammonia (NH₃) is considered as the main pollutant in livestock houses and air environment, and its adverse effects on animal and human health have attracted widespread attention. However, trachea proteomics respond to NH₃ is lacking, which is crucial to understanding how NH₃ induces respiratory damage. In this study, we performed labeled quantitative proteomic (TMT-MS) analysis in the trachea of fatting pigs exposed to NH₃ for 30 days. The proteomic results were then validated by Immunohistochemistry (IHC) and Parallel Reaction Monitoring (PRM). The results showed that a total of 126 differentially abundant proteins (DAPs) were identified (fold change <0.83 or > 1.2 and P < 0.05), including 70 differentially up-regulated proteins (DUPs) and 56 differentially down-regulated proteins (DDPs). These proteins were mainly located in intracellular regions and involved in immune response, metabolism and protein synthesis. The results of DAPs (EHHADH, RPL28, SLC25A6, TUBB6, CD14, CTSS, RPS11, RPL19, SLC25A5, RPS8, FABP3, RPL21, RPL34, RPL32, PDIA3, FBP1, HSPH1, SAR1A and SEC24C) verified by IHC and PRM were consistent with the proteomic results. The results of this study provided a basis and a novel insight for understanding the mechanism of NH₃-induced tracheal injury. SIGNIFICANCE: Ammonia (NH₃) is considered as the main pollutant in livestock houses and air environment, and its adverse effects on animal and human health have attracted widespread attention. However, trachea proteomics respond to NH₃ is lacking, which is crucial to understanding how NH₃ induces respiratory damage. Therefore, in this study, labeled quantitative proteomics (TMT-MS) was used to detect trachea tissue samples from finishing pigs in NH₃ exposure group and control group, and PRM method was used to further verify the highly abundant proteins in NH₃ exposure samples, so as to identify new diagnostic markers for NH₃ poisoning. The results of this study provided a basis and a novel insight for understanding the molecular pathological mechanism of NH₃-induced tracheal injury.

Polymorphisms of the porcine cathepsins, growth hormone-releasing hormone and leptin receptor genes and their association with meat quality traits in Ukrainian Large White breed

Cathepsins, growth hormone-releasing hormone (GHRH) and leptin receptor (LEPR) genes have been receiving increasing attention as potential markers for meat quality and pig performance traits. This study investigated the allele variants in four cathepsin genes (CTSB, CTSK, CTSL, CTSS), GHRH and LEPR in pure-bred Ukrainian Large White pigs and evaluated effects of the allele variants on meat quality characteristics. The study was conducted on 72 pigs. Genotyping was performed using PCR-RFLP technique. Meat quality characteristics analysed were intramuscular fat content, tenderness, total water content, ultimate pH, crude protein and ashes. A medium level of heterozygosity values was established for GHRH and LEPR genes which corresponded to very high levels of informativeness indexes. Cathepsins CTSL, CTSB and CTSK had a low level of heterozygosity, and CTSS did not segregate in this breed. Association studies established that intramuscular fat content and tenderness were affected by the allele variance in GHRH and LEPR but not by CTSB and CTSL genes. The GHRH results could be particularly relevant for the production of lean prime cuts as the A allele is associated with both, a lower meat fat content and better tenderness values, which are two attributes highly regarded by consumers. Results of this study suggest that selective breeding towards GHRH/AA genotype would be particularly useful for improving meat quality characteristics in the production systems involving lean Large White lines, which typically have less than 2 % intramuscular fat content.

Feed intake, average daily gain, feed efficiency, and real-time ultrasound traits in Duroc pigs: II. Genomewide association

Efficient use of feed resources has become a clear challenge for the U.S. pork industry as feed costs continue to be the largest variable expense. The availability of the Illumina Porcine60K BeadChip has greatly facilitated whole-genome association studies to identify chromosomal regions harboring genes influencing those traits. The current study aimed at identifying genomic regions associated with variation in feed efficiency and several production traits in a Duroc terminal sire population, including ADFI, ADG, feed conversion ratio, residual feed intake (RFI), real-time ultrasound back fat thickness (BF), ultrasound muscle depth, intramuscular fat content (IMF), birth weight (BW at birth), and weaning weight (BW at weaning). Single trait association analyses were performed using Bayes B models with 35,140 SNP on 18 autosomes after quality control. Significance of nonoverlapping 1-Mb length windows (n = 2,380) were tested across 3 QTL inference methods: posterior distribution of windows variances from Monte Carlo Markov Chain, naive Bayes factor, and nonparametric bootstrapping. Genes within the informative QTL regions for the traits were annotated. A region ranging from166 to 140 Mb (4-Mb length) on SSC 1, approximately 8 Mb upstream of the MC4R gene, was significantly associated with ADFI, ADG, and BF, where SOCS6 and DOK6 are proposed as the most likely candidate genes. Another region affecting BW at weaning was identified on SSC 4 (84-85 Mb), harboring genes previously found to influence both human and cattle height: PLAG1, CHCHD7, RDHE2 (or SDR16C5), MOS, RPS20, LYN, and PENK. No QTL were identified for RFI, IMF, and BW at birth. In conclusion, we have identified several genomic regions associated with traits affecting nutrient utilization that could be considered for future genomic prediction to improve feed utilization.

A genome-wide association scan in pig identifies novel regions associated with feed efficiency trait

Feed conversion ratio (FCR) is an economically important trait in pigs, and feed accounts for a significant proportion of the costs involved in pig production. In this study we used a high-density SNP chip panel, Porcine SNP60 BeadChip, to identify the association between FCR and SNP markers and to study the genetic architecture of the trait. After quality control, a total of 30,847 SNP that could be mapped to the 18 porcine autosomes (SSC) using the pig genome assembly 10.2 were used in the analyses. Deregressed estimated breeding value was used as the response variable. A total of 3,071 Duroc pigs had both FCR data and genotype data. The linkage disequilibrium (r(2)) between adjacent markers was 0.56. Two association mapping approaches were used: a linear mixed model (LMM) based on single-locus regression analysis and a Bayesian variable selection approach (BVS). A total of 79 significant (P < 0.0001) SNP associations on 6 chromosomes were identified by LMM analyses. Out of these, 10 SNP crossed the genome-wide significance threshold. These 10 SNP were all located on SSC 4 and 14. In the BVS analysis, a total of 44 SNP located on 12 chromosomes had posterior probability more than or equal to 0.05 (i.e., Bayes factor ≥ 10). Thirteen SNP were identified by both LMM and BVS. These 13 SNP were located on 4 chromosomes: SSC 4, 7, 8, and 14. Hypoxia inducible factor 1, alpha subunit inhibitor (HIF1AN) and ladybird homeobox 1 (LBX1) are 2 possible candidate genes affecting FCR on SSC 4 and 14, respectively. The study provides a list of SNP associated with FCR and also offers valuable information on the genetic architecture and candidate genes for this trait.

Factors in pig production that impact the quality of dry-cured ham: a review

This study reviews the factors of pig production that impact the quality of dry-cured ham. When processing is standardized, the quality of the final dry-cured product is primarily determined by the quality of the meat before curing (green ham). This has been defined as the aptitude for seasoning and is determined by the green ham weight, adipose tissue quantity and quality, meat physico-chemical properties and the absence of visual defects. Various ante-mortem factors including pig age and weight, genetic type, diet, feeding strategy and slaughter conditions determine green ham properties such as the dynamics of water loss, salt intake and, as a consequence, proteolysis and lipolysis. Muscle conditions (pH, salt concentration, water content and availability, temperature) influence enzymatic activity and development of characteristic texture and flavor. Generally, hams of older and heavier pigs present better seasoning aptitude because of higher adiposity. Adiposity is also positively correlated with fat saturation, which is desired to avoid rancidity and oiliness. The fatty acid profile of tissue lipids can be manipulated by diet composition. Feeding strategy affects tissue accretion and protein turnover, thus directly impacting proteolysis. With respect to the impact of pig genotype on dry-cured ham quality, local breeds are generally considered more suitable for producing quality dry hams; however, the majority of dry-cured hams on the market today are from modern pig breeds raised in conventional systems, providing lean hams. The importance of all these factors of pig production is discussed and synthesized, with an emphasis on the main difficulties encountered in dry-cured ham production.

Dietary factors impact on the association between CTSS variants and obesity related traits

Background/Aims

Cathepsin S, a protein coded by the CTSS gene, is implicated in adipose tissue biology–this protein enhances adipose tissue development. Our hypothesis is that common variants in CTSS play a role in body weight regulation and in the development of obesity and that these effects are influenced by dietary factors–increased by high protein, glycemic index and energy diets.

Methods

Four tag SNPs (rs7511673, rs11576175, rs10888390 and rs1136774) were selected to capture all common variation in the CTSS region. Association between these four SNPs and several adiposity measurements (BMI, waist circumference, waist for given BMI and being a weight gainer–experiencing the greatest degree of unexplained annual weight gain during follow-up or not) given, where applicable, both as baseline values and gain during the study period (6–8 years) were tested in 11,091 European individuals (linear or logistic regression models). We also examined the interaction between the CTSS variants and dietary factors–energy density, protein content (in grams or in % of total energy intake) and glycemic index–on these four adiposity phenotypes.

Results

We found several associations between CTSS polymorphisms and anthropometric traits including baseline BMI (rs11576175 (SNP N°2), p = 0.02, β = −0.2446), and waist change over time (rs7511673 (SNP N°1), p = 0.01, β = −0.0433 and rs10888390 (SNP N°3), p = 0.04, β = −0.0342). In interaction with the percentage of proteins contained in the diet, rs11576175 (SNP N°2) was also associated with the risk of being a weight gainer (p_interaction = 0.01, OR = 1.0526)–the risk of being a weight gainer increased with the percentage of proteins contained in the diet.

Conclusion

CTSS variants seem to be nominally associated to obesity related traits and this association may be modified by dietary protein intake.

Association between polymorphisms in cathepsin and cystatin genes with meat production and carcass traits in Italian Duroc pigs: confirmation of the effects of a cathepsin L (CTSL) gene marker

We genotyped single nucleotide polymorphisms (SNPs) in 5 cathepsin or cystatin genes (cathepsin F, CTSF; cathepsin L, CTSL; cathepsin S, CTSS; cathepsin Z, CTSZ; cystatin B, CSTB) in two groups of Italian Duroc pigs: the first group (n. 100) was chosen using a selective genotyping approach with extreme estimated breeding value (EBV) for visible intermuscular fat (VIF); the second group (n. 218) was made of performance-tested Duroc pigs not selected by any criteria. CTSL marker showed a tendency towards association (P<0.10) with VIF (first group) and back fat thickness (BFT) and average daily gain (ADG; second group). In the second group, the CTSL polymorphism was associated with weight of lean cuts (LC; P<0.05). Additive effects for all mentioned traits in the second group was significant (P<0.05). The results we obtained in the Italian Duroc pigs confirmed the results and the direction of the effects already reported for the Italian Large White breed.