One century of genetic changes in pigs and the future needs

Significance of successive feeding of sources of n-3 fatty acids to broiler breeders and their progeny on growth performance, intestinal lesion scores, lymphoid organs weight and plasma immunoglobulin A in broiler chickens challenged with Eimeria

The study examined the effects of successive feeding of sources of n-3 PUFA to broiler breeders (BB) and their progeny in broiler chickens challenged with Eimeria. The BB were fed: 1) control (CON), corn-soybean meal diet, 2) CON + 1 % microalgae (DMA), as a source of DHA and 3) CON + 2.50% co-extruded full fat flaxseed (FFF), as a source of ALA. Eggs were hatched at 34, 44, and 54 wk of age. Posthatch treatments (BB-progeny) were: CON-CON, DMA-CON, FFF-CON, DMA-DMA and FFF-FFF with diets formulated for starter (d 1-10) and grower/finisher (d 11-42) phases. All chicks were orally challenged with Eimeria (E. acervulina and E. maxima) on d 10. Relative to CON, DMA and FFF increased concentration of n-3 PUFA by ≥ 2-fold in hatching eggs and progeny diets. There were no (P > 0.05) interactions between treatment and BB age on d 0 to 10 growth. In general, BB age affected (P < 0.05) growth performance throughout the study. In the starter phase, successive exposure to DHA and ALA improved FCR over CON-CON (P < 0.01). The interaction between treatment and BB age in grower/finisher was such that DHA exposure to younger BB resulted in poor growth performance (P < 0.05) relative to exposure to older BB. In contrast, exposure to ALA had similar (P > 0.05) growth performance irrespective of BB age. Moreover, successive exposure to ALA resulted in higher BWG, breast weight and lower FCR compared to successive exposure to DHA (P < 0.05). There were no (P > 0.05) interactions between treatment and BB age on the intestinal lesion scores, lymphoid organ weights and concentration of plasma immunoglobulin A (IgA). Successive exposure to DHA resulted in higher (P = 0.006) jejunal lesion scores than CON-CON birds. The results showed that successive exposure of DHA and ALA improved FCR relative to non-exposed birds in the starter phase. However, responses in the grower/finisher phase depended on n-3 PUFA type, with birds on successive ALA exposure supporting better growth and breast yield than birds on successive DHA exposure.

Effects of dietary-reduced nitrogen (N) and phosphorus (P) on N and P balance, retention and nutrient digestibility of contemporary fattening pigs fed ad libitum

The reduction of nitrogen (N) and phosphorus (P) in fattening pigs' diets is one possible approach to lower N and P excretion in livestock farming relative to N and P intake. Due to the implementation of the European Nitrates Directive and the consecutive amendments to the German fertiliser legislation since 2017, N- and P-reduced diets for fattening pigs are becoming more and more important and are increasingly used in practice. To investigate the effects of such diets on N and P balance and retention as well as on nutrient digestibility of contemporary fattening pigs, a balance experiment was performed with eight barrows (average live weight = 61.5 ± 2.1 kg) which were surgically fitted with a simple T-cannula at the terminal ileum. The pigs received a control diet meeting nutrient requirements (CON) and an N- and P-reduced diet (NPred) ad libitum (n = 4/diet) in a 3-phased feeding regimen (3 weeks/phase). In the last week of each phase, faeces and urine were collected quantitatively for 5 days followed by a 2 × 12 hours collection of ileal digesta. Daily feed intake, live weight gain and feed-to-gain ratio did not differ between CON and NPred. NPred-fed pigs consumed 10.5% (p = 0.006) and excreted 28.3% (p = 0.028) less N than CON-fed pigs. Phosphorus excretion was lowered by 15.1% in NPred-fed pigs (p = 0.012). N and P retention did not differ between CON and NPred, but were elevated in comparison to other studies. N and P efficiency, expressed as nutrient retention divided by nutrient intake, was higher in NPred - than CON-fed pigs (N: 68 vs 60%, P: 54.2 vs 49.3%). Apparent post-ileal digestibility coefficient (DCpost-ileal) and apparent total tract digestibility coefficient (DCtotal) of crude protein were higher in NPred - than CON-fed pigs (p < 0.013), but apparent precaecal digestibility coefficient (DCpc) of crude protein was unaffected by diet. DCpc, DCpost-ileal and DCtotal of P were similar for CON- and NPred-fed pigs. NPred-fed pigs showed an elevated DCpc and DCtotal of organic matter, N-free-extractives and starch compared to CON-fed pigs. DCpc of calcium was also higher in NPred-fed pigs. In conclusion, the results suggest that N- and P-reduced feeding of fattening pigs remains an effective strategy to lower the N and P release into the environment. Furthermore, results indicate that N- and P-reduced feeding leads to a higher N and P efficiency in contemporary fattening pigs.

Estimates of Water Consumption of Growing Pigs under Practical Conditions Based on Climate and Performance Data

The water consumption of fattening pigs was recorded under practical conditions and compared with calculated water consumption. The experiment was carried out in the summer of 2020 with 79 fattening pigs. Data loggers were used to record the climate data, such as temperature and relative humidity. These data were used to calculate the temperature-humidity index (THI). It was found that there were sometimes considerable discrepancies between the measured and the calculated water consumption. One possible reason for this discrepancy could be the age of the existing water requirement equations, as in recent decades there has been a clear breeding development and thus a strong increase in pig performance. Based on these deviations, six new water consumption equations were established, which considered the variables body weight (BW), temperature, THI and feed consumption. It was found that the THI and BW should be included in one equation as predictor variables and the evaluation also showed good results. Its use, in practice, should also be considered. Overall, it became apparent that there is still a need for further research to make water consumption equations more precise. This would require a larger database.

Identification of transcriptional regulatory variants in pig duodenum, liver, and muscle tissues

BACKGROUND

In humans and livestock species, genome-wide association studies (GWAS) have been applied to study the association between variants distributed across the genome and a phenotype of interest. To discover genetic polymorphisms affecting the duodenum, liver, and muscle transcriptomes of 300 pigs from 3 different breeds (Duroc, Landrace, and Large White), we performed expression GWAS between 25,315,878 polymorphisms and the expression of 13,891 genes in duodenum, 12,748 genes in liver, and 11,617 genes in muscle.

RESULTS

More than 9.68 × 1011 association tests were performed, yielding 14,096,080 significantly associated variants, which were grouped in 26,414 expression quantitative trait locus (eQTL) regions. Over 56% of the variants were within 1 Mb of their associated gene. In addition to the 100-kb region upstream of the transcription start site, we identified the importance of the 100-kb region downstream of the 3'UTR for gene regulation, as most of the cis-regulatory variants were located within these 2 regions. We also observed 39,874 hotspot regulatory polymorphisms associated with the expression of 10 or more genes that could modify the protein structure or the expression of a regulator gene. In addition, 2 motifs (5'-GATCCNGYGTTGCYG-3' and a poly(A) sequence) were enriched across the 3 tissues within the neighboring sequences of the most significant single-nucleotide polymorphisms in each cis-eQTL region.

CONCLUSIONS

The 14 million significant associations obtained in this study are publicly available and have enabled the identification of expression-associated cis-, trans-, and hotspot regulatory variants within and across tissues, thus shedding light on the molecular mechanisms of regulatory variations that shape end-trait phenotypes.

Fine Mapping of a Major Backfat QTL Reveals a Causal Regulatory Variant Affecting the CCND2 Gene

Backfat is an important trait in pork production, and it has been included in the breeding objectives of genetic companies for decades. Although adipose tissue is a good energy storage, excessive fat results in reduced efficiency and economical losses. A large QTL for backfat thickness on chromosome 5 is still segregating in different commercial pig breeds. We fine mapped this QTL region using a genome-wide association analysis (GWAS) with 133,358 genotyped animals from five commercial populations (Landrace, Pietrain, Large White, Synthetic, and Duroc) imputed to the porcine 660K SNP chip. The lead SNP was located at 5:66103958 (G/A) within the third intron of the CCND2 gene, with the G allele associated with more backfat, while the A allele is associated with less backfat. We further phased the QTL region to discover a core haplotype of five SNPs associated with low backfat across three breeds. Linkage disequilibrium analysis using whole-genome sequence data revealed three candidate causal variants within intronic regions and downstream of the CCND2 gene, including the lead SNP. We evaluated the association of the lead SNP with the expression of the genes in the QTL region (including CCND2) in a large cohort of 100 crossbred samples, sequenced in four different tissues (lung, spleen, liver, muscle). Results show that the A allele increases the expression of CCND2 in an additive way in three out of four tissues. Our findings indicate that the causal variant for this QTL region is a regulatory variant within the third intron of the CCND2 gene affecting the expression of CCND2.

Identification of circRNA-associated ceRNA networks using longissimus thoracis of pigs of different breeds and growth stages

Background

Long-term artificial selection for growth rate and lean meat rate has eventually led to meat quality deterioration. Muscle fiber type is a key factor that markedly affects meat quality. circRNAs have been reported to participate in diverse biological activities, including myofiber growth and development; thus, we herein compared porcine circRNA transcriptome between oxidative and glycolytic muscle tissues.

Results

Longissimus thoracis muscle tissues were obtained from Lantang and Landrace pigs at birth (LT1D and LW1D, respectively) and 90 postnatal days (LT90D and LW90D, respectively). Hematoxylin and eosin staining and quantitative real-time PCR revealed that all structural traits of the muscle showed large variations between different breeds and growth stages. In total, 329 known miRNAs and 42,081 transcript candidates were identified; 6,962 differentially expressed transcripts were found to play a key role in myogenesis by gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses. In addition, 3,352 circRNAs were identified using five predicting algorithms, and 104 circRNA candidates were differentially expressed. Integrated analysis of differentially expressed miRNAs, mRNAs, and circRNAs led to the identification of 777, 855, and 22 convincing ceRNA interactions in LT1D vs. LT90D, LW1D vs. LW90D, and LT90D vs. LW90D, respectively. Finally, we identified a circRNA candidate circKANSL1L, which showed high homology between mice and pigs, and it was found to inhibit the proliferation of C₂C₁₂ cells but promote their differentiation.

Conclusions

We identified genome-wide circRNAs in 0- and 90-day-old Lantang and Landrace pigs by RNA-seq and found that circRNAs were abundant, differentially expressed, and associated with myogenesis. Our results should serve as a reference for future studies on pork quality.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08515-7.

Role of microRNAs in myogenesis and their effects on meat quality in pig - A review

The demand for food is increasing day by day because of the increasing global population. Therefore, meat, the easiest and largely available source of protein, needs to be produced in large amounts with good quality. The pork industry is a significant shareholder in fulfilling the global meat demands. Notably, myogenesis- development of muscles during embryogenesis- is a complex mechanism which culminates in meat production. But the molecular mechanisms which govern the myogenesis are less known. The involvement of miRNAs in myogenesis and meat quality, which depends on factors such as myofiber composition and intramuscular fat contents which determine the meat color, flavor, juiciness, and water holding capacity, are being extrapolated to increase both the quantity and quality of pork. Various kinds of microRNAs (miRNAs), miR-1, miR-21, miR22, miR-27, miR-34, miR-127, miR-133, miR-143, miR-155, miR-199, miR-206, miR-208, miR-378, and miR-432 play important roles in pig skeletal muscle development. Further, the quality of meat also depends upon myofiber which is developed through the expression of different kinds of miRNAs at different stages. This review will focus on the mechanism of myogenesis, the role of miRNAs in myogenesis, and meat quality with a focus on the pig.

Genomics of Heat Tolerance in Reproductive Performance Investigated in Four Independent Maternal Lines of Pigs

Improving swine climatic resilience through genomic selection has the potential to minimize welfare issues and increase the industry profitability. The main objective of this study was to investigate the genetic and genomic determinism of tolerance to heat stress in four independent purebred populations of swine. Three female reproductive traits were investigated: total number of piglets born (TNB), number of piglets born alive (NBA) and average birth weight (ABW). More than 80,000 phenotypic and 12,000 genotyped individuals were included in this study. Genomic random-regression models were fitted regressing the phenotypes of interest on a set of 95 environmental covariates extracted from public weather station records. The models yielded estimates of (genomic) reactions norms for individual pigs, as indicator of heat tolerance. Heat tolerance is a heritable trait, although the heritabilities are larger under comfortable than heat-stress conditions (larger than 0.05 vs. 0.02 for TNB; 0.10 vs. 0.05 for NBA; larger than 0.20 vs. 0.10 for ABW). TNB showed the lowest genetic correlation (-38%) between divergent climatic conditions, being the trait with the strongest impact of genotype by environment interaction, while NBA and ABW showed values slightly negative or equal to zero reporting a milder impact of the genotype by environment interaction. After estimating genetic parameters, a genome-wide association study was performed based on the single-step GBLUP method. Heat tolerance was observed to be a highly polygenic trait. Multiple and non-overlapping genomic regions were identified for each trait based on the genomic breeding values for reproductive performance under comfortable or heat stress conditions. Relevant regions were found on chromosomes (SSC) 1, 3, 5, 6, 9, 11, and 12, although there were important regions across all autosomal chromosomes. The genomic region located on SSC9 appears to be of particular interest since it was identified for two traits (TNB and NBA) and in two independent populations. Heat tolerance based on reproductive performance indicators is a heritable trait and genetic progress for heat tolerance can be achieved through genetic or genomic selection. Various genomic regions and candidate genes with important biological functions were identified, which will be of great value for future functional genomic studies.

Role of Feed Processing on Gut Health and Function in Pigs and Poultry: Conundrum of Optimal Particle Size and Hydrothermal Regimens

The aim is to give an overview of available literature data on the role of feed processing on gut health and function with specific focus on particle size and hydrothermal processing. In addition, influence of feed processing on efficacy of exogenous feed enzymes will be discussed. The current feed processing technologies are such that ingredient choices and diet form are refined to improve feed intake and nutrient utilization efficiency. Finer feed particle size enables optimal nutrient utilization and enhances animal performance due to increased surface area allowing better contact with digestive enzymes. Moreover, adequate diminution of feed ingredients is beneficial to feed manufacturing processes such as mixing and hydrothermal treatments including pelleting, extrusion, and expansion. However, emerging trends in consumer and regulatory demands for restriction or cessation of animal production practices such as use of antimicrobial growth promoters are challenging current approaches to feed processing. There is limit as to the fineness of the particle size, as very fine particles negatively affect gut health due to higher incidences of stomach ulceration in pigs and gizzard dysfunction in poultry. Coarse particle size increases stomach and hindgut acidification which may be beneficial in controlling proliferation of enteric pathogens such as salmonella and E. coli. Optimal particle size could be designed in the grinding process using roller or hammer mill. However, since most commercial pigs and poultry diets are subjected to hydrothermal processes, additional reduction of feed particle size is inevitable. The need to achieve high physical quality and to reduce potential levels of feed-borne pathogens such as Salmonella has led to the application of relatively high conditioning temperatures during conventional hydrothermal processes, a practice that does not favor high nutrient utilization and stability of heat sensitive feed additives such as feed enzymes. Therefore, with evolving pig and poultry production practices, the regimens for feed processing will no longer be appreciated only in terms of optimizing nutrients utilization, but also in terms of impact on feed hygienic status, efficacy of feed additives, animal health, and food safety.

Population size may shape the accumulation of functional mutations following domestication

BACKGROUND

Population genetics theory predicts an important role of differences in the effective population size (N e ) among species on shaping the accumulation of functional mutations by regulating the selection efficiency. However, this correlation has never been tested in domesticated animals.

RESULTS

Here, we synthesized 62 whole genome data in eight domesticated species (cat, dog, pig, goat, sheep, chicken, cattle and horse) and compared domesticates with their wild (or ancient) relatives. Genes with significantly different selection pressures (revealed by nonsynonymous/synonymous substitution rate ratios, Ka/Ks or ω) between domesticated (Dω) and wild animals (Wω) were determined by likelihood-ratio tests. Species-level effective population sizes (N e ) were evaluated by the pairwise sequentially Markovian coalescent (PSMC) model, and Dω/Wω were calculated for each species to evaluate the changes in accumulation of functional mutations after domestication relative to pre-domestication period. Correlation analysis revealed that the most recent (~ 10.000 years ago) N e (s) are positively correlated with Dω/Wω. This result is consistent with the corollary of the nearly neutral theory, that higher N e could boost the efficiency of positive selection, which might facilitate the overall accumulation of functional mutations. In addition, we also evaluated the accumulation of radical and conservative mutations during the domestication transition as: Dradical/Wradical and Dconservative/Wconservative, respectively. Surprisingly, only Dradical/Wradical ratio exhibited a positive correlation with N e (p < 0.05), suggesting that domestication process might magnify the accumulation of radical mutations in species with larger N e .

CONCLUSIONS

Our results confirm the classical population genetics theory prediction and highlight the important role of species' N e in shaping the patterns of accumulation of functional mutations, especially radical mutations, in domesticated animals. The results aid our understanding of the mechanisms underlying the accumulation of functional mutations after domestication, which is critical for understanding the phenotypic diversification associated with this process.

Invited review: Measurable biomarkers linked to meat quality from different pig production systems

Abstract. Biological processes underlie all livestock traits, including post-mortem meat quality traits. Biomarkers are molecular components of the biological processes showing differential expression associated with the phenotype of the trait. The phenotypes of the meat quality traits are determined by the animal's genotype interacting with the environment affecting the expression of the genome. The omics technologies enable measuring the expression of the genome at all levels: transcriptome, proteome, and metabolome. Associations between the phenotype of the traits and expressions measured with the omics techniques are a first step in developing biomarkers. Biomarkers enable the monitoring, diagnosis, and prediction of changes in meat quality related to external (environmental, e.g. feed and animal management conditions) stimuli and interactions with the genotype. In this paper we review the development of biomarkers for meat quality of pigs in diverse pig breeds, environments, and pork production chains.

Plasma proteome profiles associated with diet-induced metabolic syndrome and the early onset of metabolic syndrome in a pig model

Obesity and related diabetes are important health threatening multifactorial metabolic diseases and it has been suggested that 25% of all diabetic patients are unaware of their patho-physiological condition. Biomarkers for monitoring and control are available, but early stage predictive biomarkers enabling prevention of these diseases are still lacking. We used the pig as a model to study metabolic disease because humans and pigs share a multitude of metabolic similarities. Diabetes was chemically induced and control and diabetic pigs were either fed a high unsaturated fat (Mediterranean) diet or a high saturated fat/cholesterol/sugar (cafeteria) diet. Physiological parameters related to fat metabolism and diabetes were measured. Diabetic pigs' plasma proteome profiles differed more between the two diets than control pigs plasma proteome profiles. The expression levels of several proteins correlated well with (patho)physiological parameters related to the fat metabolism (cholesterol, VLDL, LDL, NEFA) and diabetes (Glucose) and to the diet fed to the animals. Studying only the control pigs as a model for metabolic syndrome when fed the two diets showed correlations to the same parameters but now more focused on insulin, glucose and abdominal fat depot parameters. We conclude that proteomic profiles can be used as a biomarker to identify pigs with developing metabolic syndrome (prediabetes) and diabetes when fed a cafeteria diet. It could be developed into a potential biomarkers for the early recognition of metabolic diseases.

Comparison of prenatal muscle tissue expression profiles of two pig breeds differing in muscle characteristics1

The objective of this study was to compare purebred Duroc and Pietrain prenatal muscle tissue transcriptome expression levels at different stages of prenatal development to gain insight into the differences in muscle tissue development in these pig breeds. Commercial western pig breeds have been selected for muscle growth for the past 2 decades. Pig breeds differ for their muscle phenotypes (i.e., myofiber numbers and myofiber types). Duroc and Pietrain pig breeds are extremes; Duroc pigs have redder muscle fiber types with more intramuscular fat, and Pietrain pigs have faster-growing and whiter muscle fiber types. Pietrain pigs are more muscular than Duroc pigs, whereas Duroc pigs are fatter than Pietrain pigs. The genomic background underlying these breed-specific differences is poorly known. Myogenesis is a complex exclusive prenatal process involving proliferation and differentiation (i.e., fusion) of precursor cells called myoblasts. We investigated the difference in the prenatal muscle-specific transcriptome profiles of Duroc and Pietrain pigs using microarray technology. The microarray contained more than 500 genes affecting myogenesis, energy metabolism, muscle structural genes, and other genes from a porcine muscle cDNA library. The results indicated that the expression of the myogenesis-related genes was greater in early Duroc embryos than in early Pietrain embryos (14 to 49 d of gestation), whereas the opposite was found in late embryos (63 to 91 d of gestation). These findings suggest that the myogenesis process is more intense in early Duroc embryos than in Pietrain embryos but that myogenesis is more intense in late Pietrain fetuses than in Duroc fetuses. Transcriptomes of muscle structural genes followed that pattern. The energy metabolism genes were expressed at a higher level in prenatal Pietrain pigs than in prenatal Duroc pigs, except for d 35, when the opposite situation was found. Fatty acid metabolism genes were expressed at a higher level in early (14 to 49 d of gestation) Duroc embryos than in Pietrain embryos. Better understanding of the genomic regulation of tissue formation leads to improved knowledge of the genome under selection and may lead to directed breed-specific changes in the future.

Transcriptome expression profiles in prenatal pigs in relation to myogenesis

Myogenesis, the formation of muscle fibers, is a complex process. Pigs have been selected for efficient muscle growth for the past decades making them interesting to study myogenesis. We studied expression profiles of genes known to affect myogenesis, muscle structural proteins, and energy metabolism in prenatal pigs from 14 to 91 days of gestation. Primary and secondary muscle fiber formation takes place during days 30-60 and 54-90 of gestation, respectively. Differential expression and expression levels of the genes were studied using microarray technology. Gene activation and repression profiles were studied counting the number of spots with detectable signal. The number of spots for muscle tissue structural protein genes showing upregulated expression increased constantly from day 14 until day 91 of gestation indicating continued activation of genes during this period. The mRNA expression level of the genes showed a peak around day 35 of gestation. The expression levels of genes affecting myogenic differentiation (stimulating and inhibiting) showed a peak at day 35 of gestation. The number of spots for differentiation-stimulating genes showing differential expression reaches a first peak around day 35 of gestation and a nadir at day 49 of gestation while the number of spots for differentiation-inhibiting genes reaches a nadir at day 35 of gestation. Myogenic differentiation seems less a matter of the expression level of genes affecting differentiation, but depends on the balance between the number of significantly activated genes for stimulating and inhibiting differentiation. Genes stimulating myoblast proliferation showed a small peak expression prior to day 35 of gestation indicating myoblast proliferation before differentiation. The number of spots and the expression levels of genes for glycolysis and ATP-metabolism are at a nadir around days 35 and 49-63 of gestation suggesting that the energy metabolism is low during fusion of myoblasts into multinucleated muscle fibers.

Genomics for food safety and sustainable animal production

There is a growing concern in society about the safety of animal-derived food, the health and welfare of farm animals and the sustainability of current animal production systems. Along farm animal, breeding genomics may contribute to a solution for these concerns. The use of genomic analysis tools, to achieve genetic progress in typical out-bred populations of farm animals, seems to be more difficult compared to 'model' organisms or plants. However, identification of positional candidate genes may be accelerated by linkage disequilibrium (LD) mapping. Recording of sustainable traits requires a large financial and logistic input and the economic advantages for the market are not as clear as for traditional selection traits. Examples show that the major genes causing variability for similar traits in different species are rarely the same. Therefore, for breeding purposes genomic analysis of the species of interest is needed. The fundamental knowledge obtained on the genetic architecture of complex traits will open new perspectives for the use of DNA tests in selection schemes. For food safety and traceability, DNA-based techniques evolve for monitoring and early warning systems.