Fur Seal Feces-Associated Circular DNA Virus Identified in Pigs in Anhui,China

Fur seal feces-associated circular DNA virus(FSfa CV) is an unclassified circular replication-associated protein(Rep)-encoding single-stranded(CRESS) DNA virus that has been detected in mammals(fur seals and pigs). The biology and epidemiology of the virus remain largely unknown. To investigate the virus diversity among pigs in Anhui Province,China, we pooled 600 nasal samples in 2017 and detected viruses using viral metagenomic methods. From the assembled contigs, 12 showed notably high nucleotide acid sequence similarities to the genome sequences of FSfa CVs. Based on these sequences, a full-length genome sequence of the virus was then obtained using overlapping PCR and sequencing, and the virus was designated as FSfa CV-CHN(Gen Bank No. MK462122). This virus shared 91.3% and 90.9% genome-wide nucleotide sequence similarities with the New Zealand fur seal strain FSfa CV-as50 and the Japanese pig strain FSfa CVJPN1, respectively. It also clustered with the two previously identified FSfa CVs in a unique branch in the phylogenetic tree based on the open reading frame 2(ORF2), Rep-coding gene, and the genome of the reference CRESS DNA viruses.Further epidemiological investigation using samples collected in 2018 showed that the overall positive rate for the virus was 56.4%(111/197) in Anhui Province. This is the first report of FSfa CVs identified in pigs in China, and further epidemiological studies are warranted to evaluate the influence of the virus on pigs.     

African Swine Fever Virus MGF-110-9L-deficient Mutant Has Attenuated Virulence in Pigs

African swine fever virus(ASFV) is the etiological agent of African swine fever(ASF), an often lethal disease in domestic and wild pigs. ASF represents a major threat to the swine industry worldwide. Currently, no commercial vaccine is available because of the complexity of ASFV or biosecurity concerns. Live attenuated viruses that are naturally isolated or genetically manipulated have demonstrated reliable protection against homologous ASFV strain challenge. In the present study, a mutant ASFV strain with the deletion of ASFV MGF-110-9 L(ASFV-D9 L) was generated from a highly virulent ASFV CN/GS/2018 parental strain, a genotype II ASFV. Relative to the parental ASFV isolate, deletion of the MGF-110-9 L gene significantly decreased the ability of ASFV-D9 L to replicate in vitro in primary swine macrophage cell cultures. The majority of animals inoculated intramuscularly with a low dose of ASFV-D9 L(10 HAD50) remained clinically normal during the 21-day observational period. Three of five ASFV-D9 L-infected animals displayed low viremia titers and low virus shedding and developed a strong virus-specific antibody response, indicating partial attenuation of the ASFV-D9 L strain in pigs. The findings imply the potential usefulness of the ASFV-D9 L strain for further development of ASF control measures.     

Evolution of viscera and muscle fractional protein synthesis rate in lean meat selected hybrids and castrated Duroc pigs fed under moderate crude protein restriction

Differences in producing performance and organoleptic meat characteristics among pig genotypes and/or producing types are widely known. These parameters are also subjected to the animal’s development, feeding and management. Detailed knowledge of the effects of production phase (PP), pig producing type (PT), dietary protein availability and their interactions on nutrient digestibility, nitrogen balance and protein metabolism is essential information to improve precision feeding techniques. The experiment was a 2 (PP) × 2 (PT) × 2 (diet) factorial design conducted with 32 male pigs, 16 entire F2 pigs progeny of Pietrain sires and Duroc × Landrace dams, and 16 castrated purebred Durocs belonging to two production phases (growing: 29.5 ± 3.19 v. fattening: 88.6 ± 6.26 kg BW), and assigned to one of two dietary CP levels, either standard (SP: 17% in growing and 15% in fattening) or low (LP: 15% in growing and 13% in fattening). Viscera and muscle fractional protein synthesis rates (FSRs; %/day) were conducted through a single infusion of 15% L-[ring-²H₅]-phenylalanine, with subsequent blood sampling from 12 to 40 min, and sample collection of liver, duodenum, biceps femoris and longissimus dorsi skeletal muscles after sacrifice. Fattening animals acquired a greater feed ingestion capacity, average daily gain (P < 0.01) and apparent ileal digestibility, whereas growing pigs showed higher FSRs in both viscera (duodenum and liver) and in longissimus dorsi. F2 pigs showed higher average daily gain, nitrogen retention rates and FSR in liver and longissimus dorsi (P < 0.01). Nevertheless, apparent ileal digestibility in all essential amino acids was lower in F2 compared with Duroc pigs (P < 0.05). Protein metabolism was barely influenced by dietary CP content, although animals fed LP registered the lowest apparent ileal digestibility for CP and also for most of the essential amino acids compared with SP-fed pigs. This information may reveal differences in amino acid requirements between both PTs, with Duroc pigs receiving excess of dietary amino acids.     

Interaction of CP levels in maternal and nursery diets,and its effect on performance,protein digestibility,and serum urea levels in piglets

Reduced protein levels in nursery diets have been associated with a lower risk of postweaning diarrhea, but the interaction with CP levels in maternal diet on the performance of the offspring remains unclear. The objective of this study was to determine the effect of protein content in sow gestation and piglet nursery diets on the performance of the piglets until slaughter. This was studied in a 2 × 2 factorial trial (35 sows, 209 piglets), with higher or lower (H or L) dietary CP in sow diets (168 vs 122 g CP/kg) during late gestation. A standard lactation feed was provided for all sows (160 g CP/kg). For both sow treatments, half of the litters received a higher or lower CP in the piglet nursery diet (210 vs 166 g CP/kg). This resulted in four possible treatment combinations: HH, HL, LH and LL, with sow treatment as first and piglet treatment as second letter. For each phase, all diets were iso-energetic and had a similar level of essential amino acids. P_s*p is the p-value for the interaction effect between sow and piglet treatment. In the nursery phase (3.5–9 weeks of age), a tendency toward interaction between piglet and sow treatments with feed efficiency (P_s*p = 0.08) was observed with HH having the highest gain:feed ratio (G:F) (0.74 ± 0.01), LH the lowest (0.70 ± 0.01) and the other two groups intermediate. In the growing-finishing phase, an interaction was observed between the piglet and sow diets with decreased G:F for LH (P_s*p = 0.04) and a tendency toward interaction with increased daily feed intake for LH (P_s*p = 0.07). The sow diet showed a tendency toward a long-lasting effect on the dressing percentage and meat thickness of the offspring, which was higher for the progeny of H sows (P_s < 0.01 and P_s = 0.02, respectively). At 23 weeks, serum urea concentrations tended to be lower for the HH and LL groups (P_s*p = 0.07). Fecal consistency scores were higher at day 10–day 14 after weaning for piglets from L sows (P_s = 0.03 and P_s < 0.01, respectively). At day 7 after weaning, fecal consistency score was higher for piglets fed the higher protein diet (P_p < 0.01). At 8 weeks of age, the apparent total tract digestibility of CP (ATTD_CP) interacted between piglet and sow diet (P_s*p = 0.02), with HH showing the highest digestibility values. In conclusion, the protein levels in sow late-gestation and piglet nursery diets interacted with feed efficiency, ATTD_CP and serum urea concentrations in the nursery phase.     

Genome-wide association study reveals a quantitative trait locus and two candidate genes on Sus scrofa chromosome 5 affecting intramuscular fat content in Suhuai pigs

Intramuscular fat content (IFC) is an essential quantitative trait of meat, affecting multiple meat quality indicators. A certain amount of IFC could not only improve the sensory score of pork but also increase the flavour, tenderness, juiciness and shelf-life. To dissect the genetic determinants of IFC, two methods, including genome-wide efficient mixed-model analysis (GEMMA) and linkage disequilibrium adjusted kinships (LDAKs), were used to carry out genome-wide association studies for IFC in Suhuai pig population. A total of 14 and 18 significant single nucleotide polymorphisms (SNPs) were identified by GEMMA and LDAK, respectively. The results of these two methods were highly consistent and all 14 significant SNPs in GEMMA were detected by LDAK. Seven of the 18 SNPs reached the genome-wide significance level (P < 9.85E−07) while 11 cases reached the suggestive significance level (P < 1.77E−05). These significant SNPs were mainly distributed on Sus scrofa chromosome (SSC) 5, 3, and 7. Moreover, one locus resides in a 2.27 Mb (71.37–73.64 Mb) region on SSC5 harbouring 13 significant SNPs associated with IFC, and the lead SNP (rs81302978) also locates in this region. Linkage disequilibrium (LD) analysis showed that there were four pairs of complete LD (r² = 1) among these 13 SNPs, and the remaining 9 SNPs with incomplete LD (r² ≠ 1) were selected for subsequent analyses of IFC. Association analyses showed that 7 out of 9 SNPs were significantly associated with IFC (P < 0.05) in 330 Suhuai pigs, and the other 2 SNPs tended to reach a significant association level with IFC (P < 0.1). The phenotypic variance explained (PVE) range of these 9 SNPs was 0.92–3.55%. Meanwhile, the lead SNP was also significantly associated (rs81302978) with IFC (P < 0.05) in 378 commercial hybrid pigs (Pietrain × Duroc) × (Landrace × Yorkshire) (PDLY), and the PVE was 1.38%. Besides, two lipid metabolism-relevant candidate genes, the leucine rich repeat kinase 2 (LRRK2) and PDZ domain containing ring finger 4 (PDZRN4) were identified in the 2.27 Mb region on SSC5. In conclusion, our results may provide a set of markers useful for genetic improvement of IFC in pigs and will advance the genome selection process of IFC on pig breeding programmes.     

Early social contact alters the community structure and functions of the faecal microbiome in suckling-growing piglets

Social contact during suckling, in an enriched social environment, can reduce the aggressive behaviours of piglets during regrouping at weaning, and improve their production performance and welfare. The aim of this study was to determine the possible impact of suckling social contact on gut microbes. We performed 16S rRNA sequencing to measure the faecal microbial structure and function in piglets experiencing social contact. Eighteen-litter piglets were allocated to two treatments: an early continuous social contact (CSC) group where piglets from adjacent pens shared a mutual pen starting at 14 days postpartum and a control (CON) group where piglets had no contact with individuals from adjacent pens during the suckling period. The piglets were regrouped at 36 days of age. The litter weights at 35 and 63 days of age were measured. Faecal samples were randomly collected at 16, 35, 42, and 63 days of age and faecal DNA was determined. The results showed that the litter weight of piglets in the CSC group was significantly decreased at 63 days compared with the CON group. Continuous social contact also significantly decreased the microbial richness at 16 and 35 days of age (P < 0.05). Firmicutes was the most abundant bacterial phylum in both groups at all detected time-points and the abundance increased with social contact. At the genus level, Lactobacillus was the most abundant bacterium after weaning and the abundance increased in the piglets with social contact. Compared with the faecal microbiota of control piglets, a total of 22 genera at 16 days, 20 genera at 35 days, 12 genera at 42 days, and 27 genera at 63 days in the faeces of CSC piglets were observed to be significantly different in abundance (linear discriminant analysis score > 3, P < 0.05). Furthermore, functional analysis of the microbial composition showed that the changes induced by early CSC mainly altered the relative abundance of metabolic and related pathways. The social contact notably had an effect on the abundance of microbial pathways for amino acid and carbohydrate metabolism. In conclusion, CSC changed the microbial composition in the faeces of piglets, which might have a negative effect on nutrient metabolism for the suckling-growing piglets. Our study provided new insight into the influence of social contact on the suckling-growing piglets.     

A comprehensive landscape genomics approach for seed sourcing strategies in landscapes under varying degrees of habitat disturbance

As most ecosystems around the world are threatened by anthropogenic degradation and climate change, there is an increasing urgency to implement restoration strategies aiming at ensuring ecosystem self‐sustainability and resilience. An initial step towards that goal relies on selecting the most suitable seed sources for a successful revegetation, which can be extremely challenging in highly degraded landscapes. The most common seed sourcing strategy is to select local seeds because it is assumed that plants experience strong adaptations to their natal sites. An alternative strategy is the selection of climate‐adapted genotypes to future conditions. While considering future climatic projections is important to account for spatial shifts in climate to inform assisted gene flow and translocations, to restore highly degraded landscapes we need a comprehensive approach that first accounts for species adaptations to current at‐site environmental conditions. In this issue of Molecular Ecology Resources, Carvalho et al. present a novel landscape genomics framework to identify the most appropriate seed sourcing strategy for moderately and highly degraded sites by integrating genotype, phenotype and environmental data in a spatially explicit context for two native plant species with potential to help restore iron‐rich Amazonian savannas. This framework is amenable to be applicable and adapted to a broad range of restoration initiatives, as the dichotomy between focusing on the current or future climatic conditions should depend on the goals and environmental circumstances of each restoration site.     

The Fat Mass and Obesity-Associated (FTO) Gene is Associated with Intramuscular Fat Content and Growth Rate in the Pig

The association of the FTO gene with obesity has been implicated in various human populations. The FTO gene is also most likely involved in the regulation of energy balance and feed intake. Here, the FTO gene was studied as a candidate gene for fatness and growth rate traits in pigs. The amino acid sequence of the FTO gene showed high conservation among human, pig, and other important domestic animals. Twelve variants including ten SNPs and two indels were detected, and then five SNPs within different genomic regions were genotyped in the ISU Berkshire × Yorkshire pig resource family. The linkage disequilibrium analyses revealed that most of these FTO variants were not in strong LD with each other. The SNPs c.46–139A > T within intron 1 and a synonymous mutation c.594C > G (Ala198Ala) within exon 3 had significant (P < 0.01) associations with average daily gain on test and total lipid percentage in muscle, respectively. Five major haplotypes were identified and the subsequent association analyses suggested that haplotype 2 (-CTTGG-) was the most favorable for increased growth rate, while haplotype 1 (-CTACG-) was unfavorably associated with intramuscular fatness traits.