Identification of a novel QTL for lean meat percentage using imputed genotypes.

Lean meat percentage is a critical production trait in pig breeding systems with direct implications for the sustainability of the industry. In this study, we conducted a genome-wide association study for lean meat percentage using a cohort of 850 Duroc × (Landrace × Yorkshire) crossbred pigs and we identified QTL on SSC3 and SSC18. Based on the predicted effect of imputed variants and using the PigGTEx database of molecular QTL, we prioritized candidate genes and SNPs located within the QTL regions, which may be involved in the regulation of porcine leanness. Our results indicate that a nonsense mutation in ZC3HAV1L on SSC18 has a direct effect on lean meat percentage.

Analysis of merged transcriptomic and genomic datasets to identify genes and pathways underlying residual feed intake in growing pigs.

Improvement of feed efficiency (FE) in pigs is an important milestone in order to reduce the economic and environmental impact of pig production. The goal of finding biomarkers for FE has persisted for decades. However, due to the complexity of the FE trait, these goals have still not been met. Here, we search for quantitative trait loci (QTL), candidate genes, and biological pathways associated with FE using both genotype and RNA-seq data. We obtained genotype and colon epithelium RNA-seq data for 375 and 96 pigs, respectively. In total, a genome-wide association study (GWAS) and differential expression (DE) analysis led to detection of three QTL on SSC9 and 17 DE-genes associated with FE. Possible intersection points between genes located in QTL and DE-genes were found on levels of transcription factor-target interaction. Moreover, cis-eQTL analysis revealed associations between genotype and expression levels of three DE-genes and three genes located in the GWAS QTLs, which may establish the connection between genotype and phenotype through DE. Finally, single nucleotide polymorphism calling using RNA-seq data for genes located in GWAS QTLs revealed 53 polymorphisms of which eleven were missense variants.

Risk factors for gastric ulceration in nursery pigs.

Pars oesophageal gastric ulceration is a prevalent condition in swine production and often observed in finisher pigs at slaughter, with reported prevalence ranging from 32 % to 65 %. Although feeding practices in nursery and finisher pigs are similar, little is known about the prevalence and risk factors associated with this condition in nursery pigs. This prospective cohort study aimed to identify risk factors for gastric ulceration in nursery pigs. The objectives were: (1) to estimate the association of inherent pig characteristics (birth weight, sex, parity of sow, litter size, and pen fouling behavior) and management characteristics (antibiotic treatment during suckling and post weaning, piglet rotation during lactation, weaning age and weight) with pars oesophageal lesions; (2) to assess differences in gastric dry matter content, pH, and percentage of solid particles in the sediment in relation to pars oesophageal lesions. A total of 58 piglets tracked from birth to 20 days of age and 210 nursery pigs from birth to 10 weeks of age were euthanized and assessed for pars oesophageal gastric lesions. All nursery pigs were fed finely ground pelleted feed ad libitum. Based on a macroscopic assessment, the pigs' stomachs were categorized as either LPO "lesions in the Pars oesophagea" or NLPO "no lesions in the Pars oesophagea". We observed an overall prevalence of 26.2 % (CI 95 % 0.67 - 0.79) for LPO in nursery pigs at 10 weeks of age, while no lesion were observed in piglets at 20 days of age. A mixed multivariable logistic regression model showed that piglets with a birthweight ≤ 1.11 kg had a 2.11 times higher odds of LPO (CI 95 % 1.02-4.37, p = 0.04) than their heavier counterparts. There was a weak association of LPO in nursery pigs from pens with pen fouling with a 2.14 times higher odds (CI 95 % 0.97-4.72 p = 0.05). Nursery pigs with LPO presented an increased gastric content fluidity with a reduced (p ≤ 0.01) gastric dry matter content (18.7 %), solid phase (74.7 %), and pH (3.22) compared to NLPO nursery pigs (20.5 %, 85.09 %, 3.56, respectively). We have demonstrated that LPO are present in nursery pigs as early as 10 weeks of age. We observed that low birth weight is associated with higher odds for LPO in nursery pigs. These observations might help explain differences between individual pigs in terms of LPO development when groups are exposed to similar environments, management, and feeding conditions.

Association between gastric content fluidity and pars oesophageal ulcers in nursery pigs: a cross-sectional study of high-risk Danish herds using commercial feed.

BACKGROUND: The objective of this cross-sectional study was to assess the within-herd prevalence of pars oesophageal ulcers (POU) in high-risk Danish herds using commercial diets. Furthermore, we aimed to estimate the association between gastric content fluidity and POU using a generalised additive model (GAM). The study included 200 clinically healthy nursery pigs randomly selected from ten farms (20 pigs from each farm). The 10 farms were selected based on a suspected high prevalence of gastric ulcers. Post-mortem gastric ulcer assessment was based on macroscopic lesions, and gastric content fluidity was assessed based on the solid particle sedimentation percentage (solid phase). RESULTS: We observed an overall prevalence of 35.5% for POU in nursery pigs. Within-herd prevalence varied considerably among farms, with values ranging from 0% in Farm 1 to 84% in Farm 4. Our model showed strong associations between POU and gastric content fluidity (P < 0.001), as well as between POU and farm of origin (P < 0.001). In addition, we observed that the risk of POU decreased non-linearly as the gastric content solid phase percentage increased, i.e. as the gastric content became more solid. CONCLUSION: We have demonstrated that pars oesophageal ulcers are present in Danish herds with nursery pigs fed commercial diets. Furthermore, we have established that gastric content fluidity is strongly associated with POU in nursery pigs. Even so, we cannot conclude that gastric content fluidity is solely responsible for POU. Future research should look into the association between pars oesophageal ulcers and both farm management activities and individual pig factors.

A reference gene catalogue of the pig gut microbiome.

The pig is a major species for livestock production and is also extensively used as the preferred model species for analyses of a wide range of human physiological functions and diseases1. The importance of the gut microbiota in complementing the physiology and genome of the host is now well recognized2. Knowledge of the functional interplay between the gut microbiota and host physiology in humans has been advanced by the human gut reference catalogue3,4. Thus, establishment of a comprehensive pig gut microbiome gene reference catalogue constitutes a logical continuation of the recently published pig genome5. By deep metagenome sequencing of faecal DNA from 287 pigs, we identified 7.7 million non-redundant genes representing 719 metagenomic species. Of the functional pathways found in the human catalogue, 96% are present in the pig catalogue, supporting the potential use of pigs for biomedical research. We show that sex, age and host genetics are likely to influence the pig gut microbiome. Analysis of the prevalence of antibiotic resistance genes demonstrated the effect of eliminating antibiotics from animal diets and thereby reducing the risk of spreading antibiotic resistance associated with farming systems.

Occurrence and identification of yeast species in fermented liquid feed for piglets.

The major objective of the present study was to investigate the occurrence and identity of yeast species in fermented liquid feed (FLF) used for feeding piglets. In total, 40 different Danish farms were included in the analysis. The preparation and composition of FLF was found to be very heterogeneous with high variations in both yeast counts and yeast species composition. The yeast population varied between 6.0 × 10(3) and 4.2 × 10(7) cfug(-1) with an average yeast count of 8.7 × 10(6) ± 1.1 × 10(7) cfug(-1). A total of 766 yeasts were isolated and identified by conventional and/or molecular typing techniques. The predominant yeast species in the FLF samples were found to be Candida milleri (58.4%), Kazachstania exigua (17.5%), Candida pararugosa (6.40%) and Kazachstania bulderi (5.09%). No clear separation between isolates of C. milleri and Candida humilis could be obtained based on sequencing of the D1/D2 region of the 26S rRNA gene. The combined use of ITS-RFLP analysis and phenotypic criteria did meanwhile suggest a closer relationship with C. milleri than C. humilis.