New phenotypes for new breeding goals in pigs

Animal board invited review: Heritability of nitrogen use efficiency in fattening pigs: Current state and possible directions

Pork, an important component of human nutrition worldwide, contributes considerably to anthropogenic nitrogen and greenhouse gas emissions. Reducing the environmental impact of pig production is therefore essential. This can be achieved through system-level strategies, such as optimising resource use, improving manure management and recycling leftovers from human food production, and at the individual animal level by maintaining pig health and fine-tuning dietary protein levels to individual requirements. Breeding, coupled with nutritional strategies, offers a lasting solution to improve nitrogen use efficiency (NUE) - the ratio of nitrogen retained in the body to nitrogen ingested. With a heritability as high as 0.54, incorporating NUE into breeding programmes appears promising. Nitrogen use efficiency involves multiple tissues and metabolic processes, and is influenced by the environment and individual animal characteristics, including its genetic background. Heritable genetic variation in NUE may therefore occur in many different processes, including the central nervous regulation of feed intake, the endocrine system, the gastrointestinal tract where digestion and absorption take place, and the composition of the gut microbiome. An animal's postabsorptive protein metabolism might also harbour important genetic variation, especially in the maintenance requirements of tissues and organs. Precise phenotyping, although challenging and costly, is essential for successful breeding. Various measurement techniques, such as imaging techniques and mechanistic models, are being explored for their potential in genetic analysis. Despite the difficulties in phenotyping, some studies have estimated the heritability and genetic correlations of NUE. These studies suggest that direct selection for NUE is more effective than indirect methods through feed efficiency. The complexity of NUE indicates a polygenic trait architecture, which has been confirmed by genome-wide association studies that have been unable to identify significant quantitative trait loci. Building sufficiently large reference populations to train genomic prediction models is an important next step. However, this will require the development of truly high-throughput phenotyping methods. In conclusion, breeding pigs with higher NUE is both feasible and necessary but will require increased efforts in high-throughput phenotyping and improved genome annotation.

The impact of slaughter weight and sex on the carbon footprint of pig feed intake

The impact of pork production on global livestock's greenhouse gas emissions is substantial. Understanding the factors influencing these emissions is crucial in achieving a more sustainable pig husbandry. In two independent experiments, the impact of slaughter weight on the carbon footprint (CFP) of pig feed intake (CFPFI) was evaluated for growing-finishing pigs of different sexes (entire males (EM), barrows (BA), immunocastrates (IC) and gilts (GI)). In experiment 1 118 animals were raised individually in experimental conditions. In experiment 2 384 animals were housed in group (four pigs per pen), in controlled commercial farm circumstances. All animals were fed ad libitum in a three-phase feeding regime and slaughtered at different BW, ranging from 110 to 148 kg (experiment 1) and from 99 to 138 kg (experiment 2). When only the fattening period was considered, the CFPFI was expressed per kg carcass growth. When the production of piglets was also taken into account, the CFPFI was calculated per kg carcass weight. For all sexes, the heavier the pig, the higher the CFPFI per kg carcass growth (P < 0.05, experiment 1; P < 0.001, experiment 2) and per kg carcass weight (P < 0.05, experiment 1; P < 0.01, experiment 2). In addition, BA had a significantly higher CFPFI per kg carcass growth and per kg carcass weight compared to EM and IC and to EM, IC and GI in respectively experiments 1 and 2 (P < 0.001). When performing a desk study with a soy-free (i.e. reduced CFP) feed in the third phase of experiment 2, slaughter weight no longer affected the CFPFI per kg carcass growth (P = 0.133) and per kg carcass weight (P = 0.856). A higher slaughter weight thus implies a lower sustainability, unless a sufficiently low-CFP feed is provided in the finisher phase.

Mutations on a conserved distal enhancer in the porcine C-reactive protein gene impair its expression in liver

C-reactive protein (CRP) is an evolutionary highly conserved protein. Like humans, CRP acts as a major acute phase protein in pigs. While CRP regulatory mechanisms have been extensively studied in humans, little is known about the molecular mechanisms that control pig CRP gene expression. The main goal of the present work was to study the regulatory mechanisms and identify functional genetic variants regulating CRP gene expression and CRP blood levels in pigs. The characterization of the porcine CRP proximal promoter region revealed a high level of conservation with both cow and human promoters, sharing binding sites for transcription factors required for CRP expression. Through genome-wide association studies and fine mapping, the most associated variants with both mRNA and protein CRP levels were localized in a genomic region 39.3 kb upstream of CRP. Further study of the region revealed a highly conserved putative enhancer that contains binding sites for several transcriptional regulators such as STAT3, NF-kB or C/EBP-β. Luciferase reporter assays showed the necessity of this enhancer-promoter interaction for the acute phase induction of CRP expression in liver, where differences in the enhancer sequences significantly modified CRP activity. The associated polymorphisms disrupted the putative binding sites for HNF4α and FOXA2 transcription factors. The high correlation between HNF4α and CRP expression levels suggest the participation of HNF4α in the regulatory mechanism of porcine CRP expression through the modification of its binding site in liver. Our findings determine, for the first time, the relevance of a distal regulatory element essential for the acute phase induction of porcine CRP in liver and identify functional polymorphisms that can be included in pig breeding programs to improve immunocompetence.

Comparing Visual-Only and Visual-Palpation Post-Mortem Lung Scoring Systems in Slaughtering Pigs

Respiratory diseases continue to pose significant challenges in pig production, and the assessment of lung lesions at the abattoir can provide valuable data for epidemiological investigations and disease surveillance. The evaluation of lung lesions at slaughter is a relatively simple, fast, and straightforward process but variations arising from different abattoirs, observers, and scoring methods can introduce uncertainty; moreover, the presence of multiple scoring systems complicates the comparisons of different studies, and currently, there are limited studies that compare these systems among each other. The objective of this study was to compare validated, simplified, and standardized schemes for assessing surface-related lung lesions in slaughtered pigs and analyze their reliability under field conditions. This study was conducted in a high-throughput abattoir in Italy, where two different scoring methods (Madec and Blaha) were benchmarked using 637 plucks. Statistical analysis revealed a good agreement between the two methods when severe or medium lesions were observed; however, their ability to accurately identify healthy lungs and minor injuries diverged significantly. These findings demonstrate that the Blaha method is more suitable for routine surveillance of swine respiratory diseases, whereas the Madec method can give more detailed and reliable results for the respiratory and welfare status of the animals at the farm level.

Integrative Analysis of Blood Transcriptomics and Metabolomics Reveals Molecular Regulation of Backfat Thickness in Qinchuan Cattle

A crucial goal of reducing backfat thickness (BFT) is to indirectly improve feed conversion efficiency. This phenotype has been reported in certain papers; however, the molecular mechanism has yet to be fully revealed. Two extreme BFT groups, consisting of four Qinchuan cattle, were chosen for this study. We performed metabolite and transcriptome analyses of blood from cattle with a high BFT (H-BFT with average = 1.19) and from those with a low BFT (L-BFT with average = 0.39). In total, 1106 differentially expressed genes (DEGs) and 86 differentially expressed metabolites (DEMs) were identified in the extreme trait. In addition, serum ceramide was strongly correlated with BFT and could be used as a potential biomarker. Moreover, the most notable finding was that the functional genes (SMPD3 and CERS1) and metabolite (sphingosine 1-phosphate (S1P)) were filtered out and significantly enriched in the processes related to the sphingolipid metabolism. This investigation contributed to a better understanding of the subcutaneous fat depots in cattle. In general, our results indicated that the sphingolipid metabolism, involving major metabolites (serum ceramide and S1P) and key genes (SMPD3 and CERS1), could regulate BFT through blood circulation.

Progress and opportunities through use of genomics in animal production

The rearing of farmed animals is a vital component of global food production systems, but its impact on the environment, human health, animal welfare, and biodiversity is being increasingly challenged. Developments in genetic and genomic technologies have had a key role in improving the productivity of farmed animals for decades. Advances in genome sequencing, annotation, and editing offer a means not only to continue that trend, but also, when combined with advanced data collection, analytics, cloud computing, appropriate infrastructure, and regulation, to take precision livestock farming (PLF) and conservation to an advanced level. Such an approach could generate substantial additional benefits in terms of reducing use of resources, health treatments, and environmental impact, while also improving animal health and welfare.

Traits Defining Sow Lifetime Maternal Performance

Simple Summary

In pig production, the ability of a sow to produce and rear a high number of viable piglets that meet weight targets for a desired age at slaughter is the ultimate goal. To achieve this, both management and breeding programs have to be tailored and continuously optimized. Reproductive characteristics, maternal attributes, and the ability to maintain body condition are highly variable, both within sows and amongst sows. For individual sows, maternal performance alters with age, and the environmental factors have a large impact on sow performance. This study demonstrated that the sow influences the number of high-quality slaughter pigs produced, which is not solely related to variation in litter size. Accounting for the sow’s influence on the number of tail-enders in breeding programs could assist with producing more high-quality slaughter pigs.

Abstract

Declining sow performance with increasing parity or an increase in the number of poor- quality pigs potentially impacts on farm productivity. This study investigated the phenotypic and genetic background of the sow’s influence on (i) the number of pigs not meeting the industry standards (tail-enders) and (ii) changes in performance with parity. Data were available for 3592 sows and their litters (13,976 litters) from a pig production system in NSW, Australia. The mean, standard deviation (SD), and slope for trait values over time were estimated for the sow characteristic traits: number of born-alive (NBA) and stillborn (SB) piglets and body condition of sow recorded with a caliper (CAL), along with maternal effects on piglet performance, represented by: average piglet birth weight (APBW), number of weaned piglets (WEAN), and tail-enders (TEND). Traits were analyzed in ASReml 4.2, by using an animal model. The number of tail-enders produced by a sow is a heritable trait, with a heritability estimate of 0.14 ± 0.04. Sow characteristics and maternal effects on piglet performance expressed by mean and slope had similar heritability estimates, ranging from 0.10 ± 0.03 to 0.38 ± 0.05, whereas estimates for SD traits were generally not different from zero. The latter suggests individual variability in sow characteristics or maternal performance between parities is largely not genetic in origin. This study demonstrated that more attention is required to identify contributions to the problem of tail-enders, and that slope traits could potentially be useful in the breeding program to maximize lifetime performance.

Identifying selection signatures for litter size in Guangxi Bama Xiang pigs

Litter size is an important economic trait in pig production. However, the genetic mechanisms underlying varying litter size in Guangxi Bama Xiang pigs remain unknown. To identify selection signatures for litter size in Guangxi Bama Xiang pigs, we obtained 297 Illumina PorcineSNP50 BeadChip array data and the average born number (ABN) from parity one to nine in Guangxi Bama Xiang pigs. Fixation index (Fst) methods were used to identify the selection signature of the litter size, and three phenotypic gradient differential population pairs (according to the ABN) in individuals were used to reduce the false positives of signature selections. Single nucleotide polymorphisms (SNPs) were identified in the VEGFA promoter and exons. The general linear model was used to analyse the differences in distinct genotypes after they were typed using three-round multiplex PCR technology. Finally, the transcriptome factor and CpG island in the VEGFA promoter were predicted. A total of 328, 328 and 317 significant loci were identified in the 1st, 2nd and 3rd population pairs, respectively. After removing the false positives, 25 SNPs were defined as the selection signatures in relation to litter size. Ten (VEGFA, USP49, USP25, SRPK1, SLC26A8, RPL10A, PPARD, MAPK14, HMGA1 and CHRDL2) out of 52 genes in the selection regions were annotated as the candidate genes of litter size, respectively, VEGFA. There were no SNPs in the VEGFA exon region, but we obtained three SNPs (rs786889605, rs343769603 and rs323942424) in the VEGFA promoter regions. The ABN in CC was significantly higher than that in TT in rs786889605, and the ABN in TT was significantly lower than that in GG in rs323942424. Meanwhile, the mutation of the VEGFA promoter result in the loss of Sp1 and NF-1 and the formation of Oct-1. In summary, we obtained ten candidate genes, and two mutations in the VEGFA promoter that could be important potential molecular biomarkers for litter size in Bama Xiang pigs.

Welfare of pigs on farm

This scientific opinion focuses on the welfare of pigs on farm, and is based on literature and expert opinion. All pig categories were assessed: gilts and dry sows, farrowing and lactating sows, suckling piglets, weaners, rearing pigs and boars. The most relevant husbandry systems used in Europe are described. For each system, highly relevant welfare consequences were identified, as well as related animal-based measures (ABMs), and hazards leading to the welfare consequences. Moreover, measures to prevent or correct the hazards and/or mitigate the welfare consequences are recommended. Recommendations are also provided on quantitative or qualitative criteria to answer specific questions on the welfare of pigs related to tail biting and related to the European Citizen's Initiative 'End the Cage Age'. For example, the AHAW Panel recommends how to mitigate group stress when dry sows and gilts are grouped immediately after weaning or in early pregnancy. Results of a comparative qualitative assessment suggested that long-stemmed or long-cut straw, hay or haylage is the most suitable material for nest-building. A period of time will be needed for staff and animals to adapt to housing lactating sows and their piglets in farrowing pens (as opposed to crates) before achieving stable welfare outcomes. The panel recommends a minimum available space to the lactating sow to ensure piglet welfare (measured by live-born piglet mortality). Among the main risk factors for tail biting are space allowance, types of flooring, air quality, health status and diet composition, while weaning age was not associated directly with tail biting in later life. The relationship between the availability of space and growth rate, lying behaviour and tail biting in rearing pigs is quantified and presented. Finally, the panel suggests a set of ABMs to use at slaughter for monitoring on-farm welfare of cull sows and rearing pigs.

Effective Selection for Lower Mortality in Organic Pigs through Selection for Total Number Born and Number of Dead Piglets

Simple Summary

Breeders use breeding goals to guide genetic gain in a population in a desired direction. Breeding goals consist of economically interesting traits, in which each trait receives an economic value. For example, to increase the size of a piglet litter, breeders use a breeding goal that includes the trait “number of live piglets in a litter” for a specific day after birth. While the litter size is selected using the trait “number of live piglets,” it is composed of two traits: “total number born” and “number of dead piglets.” The current study used simulations to illustrate that selection for litter size could be improved by selecting for the latter two traits rather than the former. This approach corrects for the fact that these two traits are genetically related to each other, but they also have genetic differences. Further, splitting one trait into two traits allows breeders to focus on the specific elements of a trait. For example, organic pig breeders could select for better piglet welfare by splitting “number of live piglets” into two traits, giving a negative economic value to the number of dead piglets.

Abstract

Selection for the number of living pigs on day 11 (L11) aims to reduce piglet mortality and increase litter size simultaneously. This approach could be sub-optimal, especially for organic pig breeding. This study evaluated the effect of selecting for a trait by separating it into two traits. Genetic parameters for L11, the total number born (TNB), and the number of dead piglets at day 11 (D11) were estimated using data obtained from an organic pig population in Denmark. Based on these estimates, two alternative breeding schemes were simulated. Specifically, selection was made using: (1) a breeding goal with L11 only versus (2) a breeding goal with TNB and D11. Different weightings for TNB and D11 were tested. The simulations showed that selection using the first breeding scheme (L11) produced lower annual genetic gain (0.201) compared to the second (TNB and D11; 0.207). A sensitivity analysis showed that the second scheme performed better because it exploited differences in heritability, and accounted for genetic correlations between the two traits. When the second breeding scheme placed more emphasis on D11, D11 declined, whereas genetic gain for L11 remained high (0.190). In conclusion, selection for L11 could be optimized by separating it into two correlated traits with different heritability, reducing piglet mortality and enhancing L11.

A high-throughput study of visceral organs in CT-scanned pigs

It has been debated whether intensive selection for growth and carcass yield in pig breeding programmes can affect the size of internal organs, and thereby reduce the animal’s ability to handle stress and increase the risk of sudden deaths. To explore the respiratory and circulatory system in pigs, a deep learning based computational pipeline was built to extract the size of lungs and hearts from CT-scan images. This pipeline was applied on CT images from 11,000 boar selection candidates acquired during the last decade. Further, heart and lung volumes were analysed genetically and correlated with production traits. Both heart and lung volumes were heritable, with h² estimated to 0.35 and 0.34, respectively, in Landrace, and 0.28 and 0.4 in Duroc. Both volumes were positively correlated with lean meat percentage, and lung volume was negatively genetically correlated with growth (r_g = − 0.48 ± 0.07 for Landrace and r_g = − 0.44 ± 0.07 for Duroc). The main findings suggest that the current pig breeding programs could, as an indirect response to selection, affect the size of hearts- and lungs. The presented methods can be used to monitor the development of internal organs in the future.

Genome-Wide Association Studies, Runs of Homozygosity Analysis, and Copy Number Variation Detection to Identify Reproduction-Related Genes in Bama Xiang Pigs

Litter size and teat number are economically important traits in the porcine industry. However, the genetic mechanisms influencing these traits remain unknown. In this study, we analyzed the genetic basis of litter size and teat number in Bama Xiang pigs and evaluated the genomic inbreeding coefficients of this breed. We conducted a genome-wide association study to identify runs of homozygosity (ROH), and copy number variation (CNV) using the novel Illumina PorcineSNP50 BeadChip array in Bama Xiang pigs and annotated the related genes in significant single nucleotide polymorphisms and common copy number variation region (CCNVR). We calculated the ROH-based genomic inbreeding coefficients (FROH) and the Spearman coefficient between FROH and reproduction traits. We completed a mixed linear model association analysis to identify the effect of high-frequency copy number variation (HCNVR; over 5%) on Bama Xiang pig reproductive traits using TASSEL software. Across eight chromosomes, we identified 29 significant single nucleotide polymorphisms, and 12 genes were considered important candidates for litter-size traits based on their vital roles in sperm structure, spermatogenesis, sperm function, ovarian or follicular function, and male/female infertility. We identified 9,322 ROHs; the litter-size traits had a significant negative correlation to FROH. A total of 3,317 CNVs, 24 CCNVR, and 50 HCNVR were identified using cnvPartition and PennCNV. Eleven genes related to reproduction were identified in CCNVRs, including seven genes related to the testis and sperm function in CCNVR1 (chr1 from 311585283 to 315307620). Two candidate genes (NEURL1 and SH3PXD2A) related to reproduction traits were identified in HCNVR34. The result suggests that these genes may improve the litter size of Bama Xiang by marker-assisted selection. However, attention should be paid to deter inbreeding in Bama Xiang pigs to conserve their genetic diversity.

The application of new breeding technology based on gene editing in pig industry

Genome/gene-editing (GE) techniques, characterized by a low technological barrier, high efficiency, and broad application among organisms, are now being employed not only in medical science but also in agriculture/veterinary science. Different engineered CRISPR/Cas9s have been identified to expand the application of this technology. In pig production, GE is a precise new breeding technology (NBT), and promising outcomes in improving economic traits, such as growth, lean or healthy meat production, animal welfare, and disease resistance, have already been documented and reviewed. These promising achievements in porcine gene editing, including the Myostatin gene knockout (KO) in indigenous breeds to improve lean meat production, the uncoupling protein 1 (UCP1) gene knock-in to enhance piglet thermogenesis and survival under cold stress, the generation of GGTA1 and CMP-N-glycolylneuraminic acid hydroxylase (CMAH) gene double KO (dKO) pigs to produce healthy red meat, and the KO or deletion of exon 7 of the CD163 gene to confer resistance to porcine reproductive and respiratory syndrome virus infection, are described in the present article. Other related approaches for such purposes are also discussed. The current trend of global regulations or legislation for GE organisms is that they are exempted from classification as genetically modified organisms (GMOs) if no exogenes are integrated into the genome, according to product-based and not process-based methods. Moreover, an updated case study in the EU showed that current GMO legislation is not fit for purpose in term of NBTs, which contribute to the objectives of the EU’s Green Deal and biodiversity strategies and even meet the United Nations’ sustainable development goals for a more resilient and sustainable agri-food system. The GE pigs generated via NBT will be exempted from classification as GMOs, and their global valorization and commercialization can be foreseen.

The Genetics of Thermoregulation in Pigs: A Review

Heat stress (HS) affects pig performance, health and welfare, resulting in a financial burden to the pig industry. Pigs have a limited number of functional sweat glands and their thermoregulatory mechanisms used to maintain body temperature, are challenged by HS to maintain body temperature. The genetic selection of genotypes tolerant to HS is a promising long-term (adaptation) option that could be combined with other measures at the production system level. This review summarizes the current knowledge on the genetics of thermoregulation in pigs. It also discusses the different phenotypes that can be used in genetic studies, as well as the variability in thermoregulation between pig breeds and the inheritance of traits related to thermoregulation. This review also considers on-going challenges to face for improving heat tolerance in pigs.

A Co-Association Network Analysis Reveals Putative Regulators for Health-Related Traits in Pigs

In recent years, the increase in awareness of antimicrobial resistance together with the societal demand of healthier meat products have driven attention to health-related traits in livestock production. Previous studies have reported medium to high heritabilities for these traits and described genomic regions associated with them. Despite its genetic component, health- and immunity-related traits are complex and its study by association analysis with genomic markers may be missing some information. To analyse multiple phenotypes and gene-by-gene interactions, systems biology approaches, such as the association weight matrix (AWM), allows combining genome wide association study results with network inference algorithms. The present study aimed to identify gene networks, key regulators and candidate genes associated to immunocompetence in pigs by integrating multiple health-related traits, enriched for innate immune phenotypes, using the AWM approach. The co-association network analysis unveiled a network comprised of 3,636 nodes (genes) and 451,407 edges (interactions), including a total of 246 regulators. From these, five genes (ARNT2, BRMS1L, MED12L, SUPT3H and TRIM25) were selected as key regulators as they were associated with the maximum number of genes with the minimum overlapping (1,827 genes in total). The five regulators were involved in pathways related to immunity such as lymphocyte differentiation and activation, platelet activation and degranulation, megakaryocyte differentiation, FcγR-mediated phagocytosis and response to nitric oxide, among others, but also in immunometabolism. Furthermore, we identified genes co-associated with the key regulators previously reported as candidate genes (e.g., ANGPT1, CD4, CD36, DOCK1, PDE4B, PRKCE, PTPRC and SH2B3) for immunity traits in humans and pigs, but also new candidate ones (e.g., ACSL3, CXADR, HBB, MMP12, PTPN6, WLS) that were not previously described. The co-association analysis revealed new regulators associated with health-related traits in pigs. This approach also identified gene-by-gene interactions and candidate genes involved in pathways related to cell fate and metabolic and immune functions. Our results shed new light in the regulatory mechanisms involved in pig immunity and reinforce the use of the pig as biomedical model.

Association Between ATP Citrate Lyase (ACLY) Gene Polymorphism and Fattening, Slaughter and Pork Quality Traits in Polish Pigs

The primary aim of this study was to estimate the relationship between ATP citrate lyase (ACLY) gene polymorphism (c.*523 T>C) and fattening and pork quality traits. Investigations were carried out on 526 pigs represented by three breeds: Polish Landrace (n=269), Polish Large White (n=189) and Puławska (n=68). ACLY genotypes were determined by PCR–RFLP method. It was demonstrated that the analyzed polymorphism had significant influence (P<0.05 and P≤0.01) on several economically important traits in pigs, e.g. average daily gain, average backfat thickness, lean meat percentage. The results obtained allow for application of c.*523 T>C polymorphism in breeding programs to improve the pig population in terms of fattening and slaughter traits. However, this breeding program may have a slight negative effect on meat texture parameters.

Long-term, multidomain analyses to identify the breed and allelic effects in MSTN-edited pigs to overcome lameness and sustainably improve nutritional meat production

Beef and mutton production has been aided by breeding to integrate allelic diversity for myostatin (MSTN), but a lack of diversity in the MSTN germplasm has limited similar advances in pig farming. Moreover, insurmountable challenges with congenital lameness and a dearth of data about the impacts of feed conversion, reproduction, and meat quality in MSTN-edited pigs have also currently blocked progress. Here, in a largest-to-date evaluation of multiple MSTN-edited pig populations, we demonstrated a practical alternative edit-site-based solution that overcomes the major production obstacle of hindlimb weakness. We also provide long-term and multidomain datasets for multiple breeds that illustrate how MSTN-editing can sustainably increase the yields of breed-specific lean meat and the levels of desirable lipids without deleteriously affecting feed-conversion rates or litter size. Apart from establishing a new benchmark for the data scale and quality of genome-edited animal production, our study specifically illustrates how gene-editing site selection profoundly impacts the phenotypic outcomes in diverse genetic backgrounds.

Genetic Analysis of Major Production and Reproduction Traits of Korean Duroc, Landrace and Yorkshire Pigs

The study aimed to investigate the genetic parameters of the production and reproduction traits of Korean Duroc, Landrace, and Yorkshire pigs. Three production traits, namely average daily gain (ADG), age at 105 kg body weight (DAYS105) and backfat thickness (BFT), and three reproduction traits, namely age at first farrowing (AFF), total number of piglets born (TNB) and number of piglets born alive (NBA), were analyzed. The reproduction dataset was based on first-parity gilts only. However, the production dataset comprised pigs of both sexes. Genetic parameters were estimated from individual datasets using a multiple-trait animal model in AIREMLF90 software. The heritability values of ADG, DAYS105 and BFT were 0.34-0.36, 0.41-0.44 and 0.38-0.48, respectively, across breeds. Heritability values for AFF, TNB and NBA were 0.07-0.14, 0.09-0.11 and 0.09-0.10, respectively. Strong genetic correlations existed between ADG and DAYS105 (-0.97) and between TNB and NBA (0.90 to 0.96). In line with breeding goals, all productive traits in Duroc pigs, and all reproduction traits except AFF in Landrace and Yorkshire pigs, also showed noticeable improvements in recent years. In conclusion, we believe that our findings on economic traits would greatly assist future pig breeding decisions in Korea.

Revealing New Candidate Genes for Teat Number Relevant Traits in Duroc Pigs Using Genome-Wide Association Studies

Simple Summary

Number of teats is very important for lactating sows. We conducted genome-wide association studies (GWAS) and estimated the genetic parameters for traits related to teat number. Results showed that there were nine and 22 SNPs exceeding genome-wide significance and suggestive significance levels, respectively. Eighteen genes annotated near them were concentrated on chromosomes 7 and 10. Among them, three new candidate genes were located on the genomic regions around the significant SNPs. Our findings provide new insight into investigating the complex genetic mechanism of traits related to teat number in pigs.

Abstract

The number of teats is related to the nursing ability of sows. In the present study, we conducted genome-wide association studies (GWAS) for traits related to teat number in Duroc pig population. Two mixed models, one for counted and another for binary phenotypic traits, were employed to analyze seven traits: the right (RTN), left (LTN), and total (TTN) teat numbers; maximum teat number on a side (MAX); left minus right side teat number (LR); the absolute value of LR (ALR); and the presence of symmetry between left and right teat numbers (SLR). We identified 11, 1, 4, 13, and 9 significant SNPs associated with traits RTN, LTN, MAX, TTN, and SLR, respectively. One significant SNP (MARC0038565) was found to be simultaneous associated with RTN, LTN, MAX and TTN. Two annotated genes (VRTN and SYNDIG1L) were located in genomic region around this SNP. Three significant SNPs were shown to be associated with TTN, RTN and MAX traits. Seven significant SNPs were simultaneously detected in two traits of TTN and RTN. Other two SNPs were only identified in TTN. These 13 SNPs were clustered in the genomic region between 96.10—98.09 Mb on chromosome 7. Moreover, nine significant SNPs were shown to be significantly associated with SLR. In total, four and 22 SNPs surpassed genome-wide significance and suggestive significance levels, respectively. Among candidate genes annotated, eight genes have documented association with the teat number relevant traits. Out of them, DPF3 genes on Sus scrofa chromosome (SSC) 7 and the NRP1 gene on SSC 10 were new candidate genes identified in this study. Our findings demonstrate the genetic mechanism of teat number relevant traits and provide a reference to further improve reproductive performances in practical pig breeding programs.

Endocrine Fertility Parameters-Genomic Background and their Genetic Relationship to Boar Taint in German Landrace and Large White

The surgical castration of young male piglets without anesthesia is no longer allowed in Germany from 2021. One alternative is breeding against boar taint, but shared synthesis pathways of androstenone (AND) and several endocrine fertility parameters (EFP) indicate a risk of decreasing fertility. The objective of this study was to investigate the genetic background between AND, skatole (SKA), and six EFP in purebred Landrace (LR) and Large White (LW) populations. The animals were clustered according to their genetic relatedness because of their different origins. Estimated heritabilities (h²) of AND and SKA ranged between 0.52 and 0.34 in LR and LW. For EFP, h² differed between the breeds except for follicle-stimulating hormone (FSH) (h²: 0.28-0.37). Both of the breeds showed unfavorable relationships between AND and testosterone, 17-β estradiol, and FSH. The genetic relationships (r_g) between SKA and EFP differed between the breeds. A genome-wide association analysis revealed 48 significant associations and confirmed a region for SKA on S us S crofa chromosome (SSC) 14. For EFP, the results differed between the clusters. In conclusion, r_g partly confirmed physiologically expected antagonisms between AND and EFP. Particular attention should be spent on fertility traits that are based on EFP when breeding against boar taint to balance the genetic progress in both of the trait complexes.

Selection for feed efficiency using the social effects animal model in growing Duroc pigs: evaluation by simulation

BACKGROUND

Traits recorded on animals that are raised in groups can be analysed with the social effects animal model (SAM). For multiple traits, this model specifies the genetic correlation structure more completely than the animal model (AM). Our hypothesis was that by using the SAM for genetic evaluation of average daily gain (ADG) and backfat thickness (BF), a high rate of improvement in feed conversion ratio (FCR) might be achieved, since unfavourable genetic correlations between ADG and BF reported in a Duroc pig line could be partially avoided. We estimated genetic and non-genetic correlations between BF, ADG and FCR on 1144 pigs using Bayesian methods considering the SAM; and responses to selection indexes that combine estimates of indirect (IGE) and direct (DGE) genetic effects for ADG and BF by stochastic simulation.

RESULTS

Estimates of the ratio of the variance of DGE to the phenotypic variance were 0.31, 0.39 and 0.25 and those of the total genetic variance to the phenotypic variance were 0.63, 0.74 and 0.93 for ADG, BF and FCR, respectively. In spite of this, when the SAM was used to generate data and for the genetic evaluations, the average economic response was worse than that obtained when BV predictions from the AM were considered. The achieved economic response was due to a direct reduction in BF and not to an improvement in FCR.

CONCLUSIONS

Our results show that although social genetic effects play an important role in the traits studied, their proper consideration in pig breeding programs to improve FCR indirectly is still difficult. The correlations between IGE and DGE that could help to overcome the unfavourable genetic correlations between DGE did not reach sufficiently high magnitudes; also, the genetic parameters estimates from the SAM have large errors. These two factors penalize the average response under the SAM compared to the AM.

Omics Application in Animal Science-A Special Emphasis on Stress Response and Damaging Behaviour in Pigs

Increasing stress resilience of livestock is important for ethical and profitable meat and dairy production. Susceptibility to stress can entail damaging behaviours, a common problem in pig production. Breeding animals with increased stress resilience is difficult for various reasons. First, studies on neuroendocrine and behavioural stress responses in farm animals are scarce, as it is difficult to record adequate phenotypes under field conditions. Second, damaging behaviours and stress susceptibility are complex traits, and their biology is not yet well understood. Dissecting complex traits into biologically better defined, heritable and easily measurable proxy traits and developing biomarkers will facilitate recording these traits in large numbers. High-throughput molecular technologies (“omics”) study the entirety of molecules and their interactions in a single analysis step. They can help to decipher the contributions of different physiological systems and identify candidate molecules that are representative of different physiological pathways. Here, we provide a general overview of different omics approaches and we give examples of how these techniques could be applied to discover biomarkers. We discuss the genetic dissection of the stress response by different omics techniques and we provide examples and outline potential applications of omics tools to understand and prevent outbreaks of damaging behaviours.

The puzzling mitochondrial phylogeography of the black soldier fly (Hermetia illucens), the commercially most important insect protein species

BACKGROUND

The black soldier fly (Diptera: Stratiomyidae, Hermetia illucens) is renowned for its bioconversion ability of organic matter, and is the worldwide most widely used source of insect protein. Despite varying extensively in morphology, it is widely assumed that all black soldier flies belong to the same species, Hermetia illucens. We here screened about 600 field-collected and cultured flies from 39 countries and six biogeographic regions to test this assumption based on data for three genes (mitochondrial COI, nuclear ITS2 & 28S rDNA) and in order to gain insights into the phylogeography of the species.

RESULTS

Our study reveals a surprisingly high level of intraspecific genetic diversity for the mitochondrial barcoding gene COI (divergences up to 4.9%). This level of variability is often associated with the presence of multiple species, but tested nuclear markers (ITS2 and 28S rDNA) were invariant and fly strain hybridization experiments under laboratory conditions revealed reproductive compatibility. COI haplotype diversity is not only very high in all biogeographic regions (56 distinct haplotypes in total), but also in breeding facilities and research centers from six continents (10 haplotypes: divergences up to 4.3%). The high genetic diversity in fly-breeding facilities is mostly likely due to many independent acquisitions of cultures via sharing and/or establishing new colonies from field-collected flies. However, explaining some of the observed diversity in several biogeographic regions is difficult given that the origin of the species is considered to be New World (32 distinct haplotypes) and one would expect severely reduced genetic diversity in the putatively non-native populations in the remaining biogeographic regions. However, distinct, private haplotypes are known from the Australasian (N = 1), Oriental (N = 4), and the Eastern Palearctic (N = 4) populations. We reviewed museum specimen records and conclude that the evidence for introductions is strong for the Western Palearctic and Afrotropical regions which lack distinct, private haplotypes.

CONCLUSIONS

Based on the results of this paper, we urge the black soldier fly community to apply molecular characterization (genotyping) of the fly strains used in artificial fly-breeding and share these data in research publications as well as when sharing cultures. In addition, fast-evolving nuclear markers should be used to reconstruct the recent invasion history of the species.

Performance Results and Concentrations of Biochemical Indices and Mineral Elements in Blood Serum of Fatteners Fed Diets Containing Mixtures of Raw Seeds of Pea (Pisum sativum L.) or Blue Lupin (Lupinus angustifolius L.)

Two experiments were conducted with fatteners (♀ (Landrace × Yorkshire) × ♂ duroc), 50 animals each (10 pigs per group). The fatteners from the control group (C) were administered feed mixtures with genetically modified soybean meal (SBM-GM) used as the only protein source; whereas these from experimental groups (E1-E4) received feed mixtures in which the SBM-GM was replaced with increasing amounts of raw seeds of pea (Experiment I) or blue lupin (Experiment II): E1-5.0%, E2-10.0%, E3-15.0%, and E4-17.5%. Once the fattening period was completed, production results were determined, and selected blood serum indices were assayed to establish the effect of the nutritional factor on body homeostasis and health status of the animals. Pigs from all groups revealed a similar growth rate and meatiness (p > 0.05). In Experiment I serum analyses showed lower (p < 0.001) concentrations of: cholesterol in E1, E3 and E4; creatinine in E1 and E4 and urea in E3 and E4, compared to the C. In Experiment II, lower (p < 0.001) concentrations of aspartate aminotransferase, alanine-aminotransferase, total protein, and Mg were determined in the serum of fatteners from E1-E4 compared to the C. Even though values of all analyzed blood markers differed among the groups, in most cases they fitted within reference values for the species, which indicates the maintenance of body homeostasis. Study results show that there are no contraindications to the use of pea and blue lupin seeds as alternative feed materials to SBM-GM in pig fattening.

Ethyl-N-dodecanoyl-l-arginate hydrochloride combats pathogens with low-resistance generation by membrane attack and modifies gut microbiota structure

Ethyl-N-dodecanoyl-l-arginate hydrochloride (LAE, ethyl lauroyl arginate HCl) is a cationic surfactant used as a food preservative with broad-spectrum antibacterial activities. However, its resistance development, influences on gut microbiome and molecular target are unclear. In this study, bacteria were stimulated by LAE for 30 days to test the bacterial resistance. Several infected animal models were used to evaluate the antibacterial effect of LAE in vivo. Mice were orally treated with LAE to test its effect on animal growth. The influence of LAE on mice gut microbiome was analysed by 16S rDNA sequencing. The results indicated that Escherichia coli did not develop resistance to LAE. LAE significantly combats bacterial infection in mice, ducklings and piglets. Moreover, LAE promotes mouse weight gain without changing body composition or reducing animal vitality, and induces lower hepatotoxicity than ampicillin. In the mouse gut microbiome assessment and characterization, LAE modifies host gut microbiota structure. Mechanistically, LAE specifically binds to acidic phospholipids including phosphatidylserine, depolarizes the membrane and disrupts the bacterial membrane followed by bacterial growth inhibition. This study investigates the molecular mechanism of LAE as well as its antibacterial functions in poultry and livestock. Our data suggest LAE is a potential antibacterial agent in animal health.

Investigating the potential for genetic improvement of nitrogen and phosphorus efficiency in a Swiss large white pig population using chemical analysis

Pig production contributes to environmental pollution through excretion of phosphorus and nitrogenous compounds. European pig production requires annual imports of currently 36 million tons of soya bean, because domestic plant protein sources often do not meet the required protein quality. Most of the mineral phosphate sources are also imported. It is therefore desirable to improve nutrient deposition efficiency through selective breeding, that is to realise similar growth rates and carcass compositions as currently achieved but with a lower intake of dietary crude protein or phosphate. For a preliminary evaluation of the potential of selecting for increased nutrient deposition efficiency, we estimated genetic parameters for nitrogen and phosphorus efficiencies in a Swiss Large White pig population including 294 individuals. Nutrient efficiency phenotypes were obtained from wet‐chemistry analyses of pigs of various live weights. Heritability of nitrogen efficiency was estimated at 41%. Heritability of phosphorus efficiency was very low (0.3%), but positive genetic correlations with nitrogen efficiency suggest that breeding for nitrogen efficiency would positively affect phosphorus efficiency. Further studies are needed to improve the quality of estimates and to obtain accurate high‐throughput measures of nutrient efficiency to be implemented on farms.

Whole-genome resequencing analysis of 20 Micro-pigs

BACKGROUND

Miniature pigs have been increasingly used as mammalian model animals for biomedical research because of their similarity to human beings in terms of their metabolic features and proportional organ sizes. However, despite their importance, there is a severe lack of genome-wide studies on miniature pigs.

OBJECTIVE

In this study, we performed whole-genome sequencing analysis of 20 Micro-pigs obtained from Medi Kinetics to elucidate their genomic characteristics.

RESULTS

Approximately 595 gigabase pairs (Gb) of sequence reads were generated to be mapped to the swine reference genome assembly (Sus scrofa 10.2); on average, the sequence reads covered 99.15% of the reference genome at an average of 9.6-fold coverage. We detected a total of 19,518,548 SNPs, of which 8.7% were found to be novel. With further annotation of all of the SNPs, we retrieved 144,507 nonsynonymous SNPs (nsSNPs); of these, 5968 were found in all 20 individuals used in this study. SIFT prediction for these SNPs identified that 812 nsSNPs in 402 genes were deleterious. Among these 402 genes, we identified some genes that could potentially affect traits of interest in Micro-pigs, such as RHEB and FRAS1. Furthermore, we performed runs of homozygosity analysis to locate potential selection signatures in the genome, detecting several loci that might be involved in phenotypic characteristics in Micro-pigs, such as MSTN, GDF5, and GDF11.

CONCLUSION

In this study, we identified numerous nsSNPs that could be used as candidate genetic markers with involvement in traits of interest. Furthermore, we detected putative selection footprints that might be associated with recent selection applied to miniature pigs.

Assessment of Piglet Vitality by Farmers-Validation of A Scoring Scheme and Estimation of Associated Genetic Parameters

Simple Summary

The aim of animal breeding is to improve desirable traits in animals over generations by selecting those animals with the best performance for producing offspring. Sows have been bred for bearing and raising large litters. However, piglets in large litters are often underweight at birth and have a higher risk of dying before weaning. Therefore, breeding for large litters presents an animal welfare issue and focus should be put on new traits, such as piglet vitality. To select the best performing sows, breeders need a scheme to assess piglet vitality on a routine basis. In this study, 23 farmers used a four-point scoring scheme for piglet vitality (1 = low vitality to 4 = high vitality) to assess 3171 litters. To validate the new scoring scheme, i.e., to see if it assesses what it is supposed to assess, the vitality scores were compared to the piglet mortality rate of the respective litters. The results show that litters assessed with low vitality scores had the highest mortality rate and vice versa. Furthermore, genetic analysis showed that the trait is hereditary. Therefore, including piglet vitality into breeding programs may contribute to animal welfare improvement.

Abstract

Maternal breeds for sows have been bred for high prolificacy during recent decades. Although large litters may be beneficial for economic efficiency, pre-weaning mortality is increased. Thus, focus should instead be put on new traits such as piglet vitality (PV). Until now, no validated scoring scheme for piglet vitality exists, which is feasible to be applied for routine on-farm trait recording. The objective of this study was to validate a four-point vitality scoring scheme (1 = low vitality to 4 = high vitality) applied by farmers based on pre-weaning mortality and to estimate genetic parameters. A linear mixed model was fitted for piglet vitality for 3172 litters from Large White and Landrace sows on 23 farms and correlations were calculated for vitality score and piglet mortality. A subsample of 2900 records was used for genetic analysis. Pre-weaning mortality differed significantly between all vitality score categories except for 1 and 2, ranging between 7.98% (category 4) and 29.1% (category 1). PV was genetically negatively correlated to litter size (−0.68) and mortality rate (−0.65), whereas litter size was positively correlated with mortality rate (0.59). Including PV into breeding programs may, thus, improve animal welfare.

Antimicrobial Effects on Swine Gastrointestinal Microbiota and Their Accompanying Antibiotic Resistome

Antimicrobials are the most commonly prescribed drugs in the swine industry. While antimicrobials are an effective treatment for serious bacterial infections, their use has been associated with major adverse effects on health. It has been shown that antimicrobials have substantial direct and indirect impacts on the swine gastrointestinal (GI) microbiota and their accompanying antimicrobial resistome. Antimicrobials have also been associated with a significant public health concern through selection of resistant opportunistic pathogens and increased emergence of antimicrobial resistance genes (ARGs). Since the mutualistic microbiota play a crucial role in host immune regulation and in providing colonization resistance against potential pathogens, the detrimental impacts of antimicrobial treatment on the microbiota structure and its metabolic activity may lead to further health complications later in life. In this review, we present an overview of antimicrobial use in the swine industry and their role in the emergence of antimicrobial resistance. Additionally, we review our current understanding of GI microbiota and their role in swine health. Finally, we investigate the effects of antimicrobial administration on the swine GI microbiota and their accompanying antibiotic resistome. The presented data is crucial for the development of robust non-antibiotic alternative strategies to restore the GI microbiota functionality and guarantee effective continued use of antimicrobials in the livestock production system.

Leveraging Available Resources and Stakeholder Involvement for Improved Productivity of African Livestock in the Era of Genomic Breeding

The African continent is home to diverse populations of livestock breeds adapted to harsh environmental conditions with more than 70% under traditional systems of management. Animal productivity is less than optimal in most cases and is faced with numerous challenges including limited access to adequate nutrition and disease management, poor institutional capacities and lack of adequate government policies and funding to develop the livestock sector. Africa is home to about 1.3 billion people and with increasing demand for animal proteins by an ever growing human population, the current state of livestock productivity creates a significant yield gap for animal products. Although a greater section of the population, especially those living in rural areas depend largely on livestock for their livelihoods; the potential of the sector remains underutilized and therefore unable to contribute significantly to economic development and social wellbeing of the people. With current advances in livestock management practices, breeding technologies and health management, and with inclusion of all stakeholders, African livestock populations can be sustainably developed to close the animal protein gap that exists in the continent. In particular, advances in gene technologies, and application of genomic breeding in many Western countries has resulted in tremendous gains in traits like milk production with the potential that, implementation of genomic selection and other improved practices (nutrition, healthcare, etc.) can lead to rapid improvement in traits of economic importance in African livestock populations. The African livestock populations in the context of this review are limited to cattle, goat, pig, poultry, and sheep, which are mainly exploited for meat, milk, and eggs. This review examines the current state of livestock productivity in Africa, the main challenges faced by the sector, the role of various stakeholders and discusses in-depth strategies that can enable the application of genomic technologies for rapid improvement of livestock traits of economic importance.

Invited review: Piglet survival: benefits of the immunocompetence

Piglet mortality has a negative impact on animal welfare and public acceptance. Moreover, the number of weaned piglets per sow mainly determines the profitability of piglet production. Increased litter sizes are associated with lower birth weights and piglet survival. Decreased survival rates and performance of piglets make the control of diseases and infections within pig production even more crucial. Consequently, selection for immunocompetence becomes an important key aspect within modern breeding programmes. However, the phenotypic recording of immune traits is difficult and expensive to realize within farm routines. Even though immune traits show genetic variability, only few examples exist on their respective suitability within a breeding programme and their relationships to economically important production traits. The analysis of immune traits for an evaluation of immunocompetence to gain a generally improved immune response is promising. Generally, in-depth knowledge of the genetic background of the immune system is needed to gain helpful insights about its possible incorporation into breeding programmes. Possible physiological drawbacks for enhanced immunocompetence must be considered with regards to the allocation theory and possible trade-offs between the immune system and performance. This review aims to discuss the relationships between the immunocompetence of the pig, piglet survival as well as the potential of these traits to be included into a breeding strategy for improved robustness.

Genetic Parameters for Resistance to Non-specific Diseases and Production Traits Measured in Challenging and Selection Environments; Application to a Rabbit Case

Breeding for disease resistance is a challenging but increasingly necessary objective to overcome the issues with the reduced use of antibiotics and growing concern for animal welfare while limiting economic losses. However, implementing such strategies is a complex process because animals face numerous diseases, and the environments on selection farms differ from those on commercial farms. We evaluated whether selection for resistance to non-specific diseases based on a single visual record in selection (S) and challenging (Ch) environments is possible. Records from 23,773 purebred rabbits born between 2012 and 2016 were used in this study. After weaning (at 32 days of age), 17,712 rabbits were raised in the S environment and 6,061 sibs were raised in the Ch environment. Clinical signs of disease were recorded for all animals at the end of the test, at a single time point, at 70 or 80 days of age. The causes of mortality occurring before the end of the test were also recorded. Three disease traits were analyzed: signs of respiratory disease, signs of digestive disease, and a composite trait (Resist) taking into account signs of digestive, respiratory and various infectious diseases. This latter composite trait is proposed to capture the global resistance to disease. All disease traits were binary, with 0 being the absence of symptoms. Two production traits were also recorded: the number of kits born alive (4,121 litters) and the weaning weight (13,090 rabbits). Disease traits were analyzed with animal threshold models, assuming that traits are different in the two environments. Bivariate analyses were carried out using linear animal models. The heritabilities of the disease traits ranged from 0.04 ± 0.01 to 0.11 ± 0.03. The genetic correlations between disease traits in both environments were below unity (≤ 0.84), indicating genotype by environment interactions. Most of the genetic correlations between disease and production traits were not significantly different from zero, except between the weaning weight and Resist_S, with a favorable correlation of -0.34 ± 0.12. Given these genetic parameters, for the same level of exposure of rabbits to pathogens, the expected response to selection is a reduction of disease incidence of 4-6% per generation.

A genome scan for selection signatures in Taihu pig breeds using next-generation sequencing

Taihu pig breeds are the most prolific breeds of swine in the world, and they also have superior economic traits, including high resistance to disease, superior meat quality, high resistance to crude feed and a docile temperament. The formation of these phenotypic characteristics is largely a result of long-term artificial or natural selection. Therefore, exploring selection signatures in the genomes of the Taihu pigs will help us to identify porcine genes related to productivity traits, disease and behaviour. In this study, we used both intra-population (Relative Extend Haplotype Homozygosity Test (REHH)) and inter-population (the Cross-Population Extend Haplotype Homozygosity Test (XPEHH); F-STATISTICS, F ST ) methods to detect genomic regions that might be under selection process in Taihu pig breeds. As a result, we found 282 (REHH) and 112 (XPEHH) selection signature candidate regions corresponding to 159.78 Mb (6.15%) and 62.29 Mb (2.40%) genomic regions, respectively. Further investigations of the selection candidate regions revealed that many genes under these genomic regions were related to reproductive traits (such as the TLR9 gene), coat colour (such as the KIT gene) and fat metabolism (such as the CPT1A and MAML3 genes). Furthermore, gene enrichment analyses showed that genes under the selection candidate regions were significantly over-represented in pathways related to diseases, such as autoimmune thyroid and asthma diseases. In conclusion, several candidate genes potentially under positive selection were involved in characteristics of Taihu pig. These results will further allow us to better understand the mechanisms of selection in pig breeding.

Human-Mediated Introgression of Haplotypes in a Modern Dairy Cattle Breed

Domestic animals can serve as model systems of adaptive introgression and their genomic signatures. In part, their usefulness as model systems is due to their well-known histories. Different breeding strategies such as introgression and artificial selection have generated numerous desirable phenotypes and superior performance in domestic animals. The modern Danish Red Dairy Cattle is studied as an example of an introgressed population. It originates from crossing the traditional Danish Red Dairy Cattle with the Holstein and Brown Swiss breeds, both known for high milk production. This crossing happened, among other things due to changes in the production system, to raise milk production and overall performance. The genomes of modern Danish Red Dairy Cattle are heavily influenced by regions introgressed from the Holstein and Brown Swiss breeds and under subsequent selection in the admixed population. The introgressed proportion of the genome was found to be highly variable across the genome. Haplotypes introgressed from Holstein and Brown Swiss contained or overlapped known genes affecting milk production, as well as protein and fat content (CD14, ZNF215, BCL2L12, and THRSP for Holstein origin and ITPR2, BCAT1, LAP3, and MED28 for Brown Swiss origin). Genomic regions with high introgression signals also contained genes and enriched QTL associated with calving traits, body confirmation, feed efficiency, carcass, and fertility traits. These introgressed signals with relative identity-by-descent scores larger than the median showing Holstein or Brown Swiss introgression are mostly significantly correlated with the corresponding test statistics from signatures of selection analyses in modern Danish Red Dairy Cattle. Meanwhile, the putative significant introgressed signals have a significant dependency with the putative significant signals from signatures of selection analyses. Artificial selection has played an important role in the genomic footprints of introgression in the genome of modern Danish Red Dairy Cattle. Our study on a modern cattle breed contributes to an understanding of genomic consequences of selective introgression by demonstrating the extent to which adaptive effects contribute to shape the specific genomic consequences of introgression.

Objecthood, Agency and Mutualism in Valenced Farm Animal Environments

Genetic selection of farm animals for productivity, and intensification of farming practices have yielded substantial improvements in efficiency; however, the capacity of animals to cope with environmental challenges has diminished. Understanding how the animal and environment interact is central to efforts to improve the health, fitness, and welfare of animals through breeding and management strategies. The review examines aspects of the environment that are sensed by the animal. The predictive brain model of sensory perception and motor action (the Bayesian brain model) and its recent extension to account for anticipatory, predictive control of physiological activities is described. Afferent sensory input from the immune system, and induction of predictive immune functions by the efferent nervous system are also in accord with the Bayesian brain model. In this model, expected sensory input (from external, physiological and immunological environments) is reconciled with actual sensory input through behavioural, physiological and immune actions, and through updating future expectations. Sustained discrepancy between expected and actual sensory inputs occurs when environmental encounters cannot be predicted and controlled resulting in stress and negative affective states. Through these processes, from the animal's perspective, aspects of the environment acquire a negative or positive character: that is the environment becomes valenced. In a homeostatic manner, affective experience guides the animal towards synchronisation and a greater degree of mutualism with its environment. A better understanding of the dynamic among environmental valence, animal affect and mutualism may provide a better understanding of genetic and phenotypic links between temperament, immune function, metabolic performance, affective state, and resilience in farm animals, and provide further opportunities to improve their welfare.

Artificial selection on introduced Asian haplotypes shaped the genetic architecture in European commercial pigs

Early pig farmers in Europe imported Asian pigs to cross with their local breeds in order to improve traits of commercial interest. Current genomics techniques enabled genome-wide identification of these Asian introgressed haplotypes in modern European pig breeds. We propose that the Asian variants are still present because they affect phenotypes that were important for ancient traditional, as well as recent, commercial pig breeding. Genome-wide introgression levels were only weakly correlated with gene content and recombination frequency. However, regions with an excess or absence of Asian haplotypes (AS) contained genes that were previously identified as phenotypically important such as FASN, ME1, and KIT. Therefore, the Asian alleles are thought to have an effect on phenotypes that were historically under selection. We aimed to estimate the effect of AS in introgressed regions in Large White pigs on the traits of backfat (BF) and litter size. The majority of regions we tested that retained Asian deoxyribonucleic acid (DNA) showed significantly increased BF from the Asian alleles. Our results suggest that the introgression in Large White pigs has been strongly determined by the selective pressure acting upon the introgressed AS. We therefore conclude that human-driven hybridization and selection contributed to the genomic architecture of these commercial pigs.

Genetic analysis of teat number in pigs reveals some developmental pathways independent of vertebra number and several loci which only affect a specific side

Background

Number of functional teats is an important trait in commercial swine production. As litter size increases, the number of teats must also increase to supply nutrition to all piglets. Therefore, a genome-wide association analysis was conducted to identify genomic regions that affect this trait in a commercial swine population. Genotypic data from the Illumina Porcine SNP60v1 BeadChip were available for 2951 animals with total teat number (TTN) records. A subset of these animals (n = 1828) had number of teats on each side recorded. From this information, the following traits were derived: number of teats on the left (LTN) and right side (RTN), maximum number of teats on a side (MAX), difference between LTN and RTN (L − R) and absolute value of L − R (DIF). Bayes C option of GENSEL (version 4.61) and 1-Mb windows were implemented. Identified regions that explained more than 1.5% of the genomic variation were tested in a larger group of animals (n = 5453) to estimate additive genetic effects.

Results

Marker heritabilities were highest for TTN (0.233), intermediate for individual side counts (0.088 to 0.115) and virtually nil for difference traits (0.002 for L − R and 0.006 for DIF). Each copy of the VRTN mutant allele increased teat count by 0.35 (TTN), 0.16 (LTN and RTN) and 0.19 (MAX). 15, 18, 13 and 18 one-Mb windows were detected that explained more than 1.0% of the genomic variation for TTN, LTN, RTN, and MAX, respectively. These regions cumulatively accounted for over 50% of the genomic variation of LTN, RTN and MAX, but only 30% of that of TTN. Sus scrofa chromosome SSC10:52 Mb was associated with all four count traits, while SSC10:60 and SSC14:54 Mb were associated with three count traits. Thirty-three SNPs accounted for nearly 39% of the additive genetic variation in the validation dataset. No effect of piglet sex or percentage of males in litter was detected, but birth weight was positively correlated with TTN.

Conclusions

Teat number is a heritable trait and use of genetic markers would expedite selection progress. Exploiting genetic variation associated with teat counts on each side would enhance selection focused on total teat counts. These results confirm QTL on SSC4, seven and ten and identify a novel QTL on SSC14.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-016-0282-1) contains supplementary material, which is available to authorized users.

Prenatal Mammary Gland Development in the Mouse: Research Models and Techniques for Its Study from Past to Present

Mammary gland development starts during prenatal life, when at designated positions along the ventrolateral boundary of the embryonic or fetal trunk, surface ectodermal cells coalesce to form primordia for mammary glands, instead of differentiating into epidermis. With the wealth of genetically engineered mice available as research models, our understanding of the prenatal phase of mammary development has recently greatly advanced. This understanding includes the recognition of molecular and mechanistic parallels between prenatal and postnatal mammary morphogenesis and even tumorigenesis, much of which can moreover be extrapolated to human. This makes the murine embryonic mammary gland a useful model for a myriad of questions pertaining to normal and pathological breast development. Hence, unless indicated otherwise, this review describes embryonic mammary gland development in mouse only, and lists mouse models that have been examined for defects in embryonic mammary development. Techniques that originated in the field of developmental biology, such as explant culture and tissue recombination, were adapted specifically to research on the embryonic mammary gland. Detailed protocols for these techniques have recently been published elsewhere. This review describes how the development and adaptation of these techniques moved the field forward from insights on (comparative) morphogenesis of the embryonic mammary gland to the understanding of tissue and molecular interactions and their regulation of morphogenesis and functional development of the embryonic mammary gland. It is here furthermore illustrated how generic molecular biology and biochemistry techniques can be combined with these older, developmental biology techniques, to address relevant research questions. As such, this review should provide a solid starting point for those wishing to familiarize themselves with this fascinating and important subdomain of mammary gland biology, and guide them in designing a relevant research strategy.

Variance component estimates for alternative litter size traits in swine

Litter size at d 5 (LS5) has been shown to be an effective trait to increase total number born (TNB) while simultaneously decreasing preweaning mortality. The objective of this study was to determine the optimal litter size day for selection (i.e., other than d 5). Traits included TNB, number born alive (NBA), litter size at d 2, 5, 10, 30 (LS2, LS5, LS10, LS30, respectively), litter size at weaning (LSW), number weaned (NW), piglet mortality at d 30 (MortD30), and average piglet birth weight (BirthWt). Litter size traits were assigned to biological litters and treated as a trait of the sow. In contrast, NW was the number of piglets weaned by the nurse dam. Bivariate animal models included farm, year-season, and parity as fixed effects. Number born alive was fit as a covariate for BirthWt. Random effects included additive genetics and the permanent environment of the sow. Variance components were plotted for TNB, NBA, and LS2 to LS30 using univariate animal models to determine how variances changed over time. Additive genetic variance was minimized at d 7 in Large White and at d 14 in Landrace pigs. Total phenotypic variance for litter size traits decreased over the first 10 d and then stabilized. Heritability estimates increased between TNB and LS30. Genetic correlations between TNB, NBA, and LS2 to LS29 with LS30 plateaued within the first 10 d. A genetic correlation with LS30 of 0.95 was reached at d 4 for Large White and at d 8 for Landrace pigs. Heritability estimates ranged from 0.07 to 0.13 for litter size traits and MortD30. Birth weight had an h of 0.24 and 0.26 for Large White and Landrace pigs, respectively. Genetic correlations among LS30, LSW, and NW ranged from 0.97 to 1.00. In the Large White breed, genetic correlations between MortD30 with TNB and LS30 were 0.23 and -0.64, respectively. These correlations were 0.10 and -0.61 in the Landrace breed. A high genetic correlation of 0.98 and 0.97 was observed between LS10 and NW for Large White and Landrace breeds, respectively. This would indicate that NW could possibly be used as an effective maternal trait, given a low level of cross-fostering, to avoid back calculating litter size traits from piglet records. Litter size at d 10 would be a compromise between gain in litter size at weaning and minimizing the potentially negative effects of the nurse dam and direct additive genetics of the piglets, as they are expected to increase throughout lactation.

Genetic parameters for thermoregulation and production traits in lactating sows reared in tropical climate

The objective of this study was to estimate the genetic parameters for thermoregulation traits and the relationships with performance of Large White lactating sows reared in a tropical humid climate. The thermoregulation traits were rectal temperature (RT), cutaneous temperature (CT) and respiratory rate (RR) during lactation measured in the afternoon (1200 h) and in the morning (0700 h). The production traits were sow's average daily feed intake (ADFI), litter BW gain (LBWg) and sow's proportion of BW change between farrowing and weaning (BWc). Complete data included 931 lactating performance on 329 Large White sows from the INRA experimental unit in Guadeloupe (French West Indies). Random regression models using linear spline functions were used for longitudinal data (RT, CT, RR and daily feed intake). Results showed that when ignoring values at the beginning and the end of lactation, the traits studied can be treated as the same trait throughout days of lactation, with fairly constant heritability and variance. However, largest heritabilities and genetic variances were estimated in mid-lactation. Heritability estimates on average performance during lactation were low to moderate for thermoregulation traits (0.35±0.09 for RT, 0.34±0.12 for CT and 0.39±0.13 for RR). Heritability estimates for production traits were 0.26±0.08 for ADFI, 0.20±0.07 for BWc and 0.31±0.09 for LBWg. Significant genetic correlations between thermoregulation traits and production traits were only obtained for ADFI and RR (0.35±0.12). From this study it can be concluded that thermoregulation traits are heritable, indicating that there are genetic differences in heat stress tolerance in lactating Large White sows.

Genome-wide association study reveals novel loci for litter size and its variability in a Large White pig population

Background

In many traits, not only individual trait levels are under genetic control, but also the variation around that level. In other words, genotypes do not only differ in mean, but also in (residual) variation around the genotypic mean. New statistical methods facilitate gaining knowledge on the genetic architecture of complex traits such as phenotypic variability. Here we study litter size (total number born) and its variation in a Large White pig population using a Double Hierarchical Generalized Linear model, and perform a genome-wide association study using a Bayesian method.

Results

In total, 10 significant single nucleotide polymorphisms (SNPs) were detected for total number born (TNB) and 9 SNPs for variability of TNB (varTNB). Those SNPs explained 0.83 % of genetic variance in TNB and 1.44 % in varTNB. The most significant SNP for TNB was detected on Sus scrofa chromosome (SSC) 11. A possible candidate gene for TNB is ENOX1, which is involved in cell growth and survival. On SSC7, two possible candidate genes for varTNB are located. The first gene is coding a swine heat shock protein 90 (HSPCB = Hsp90), which is a well-studied gene stabilizing morphological traits in Drosophila and Arabidopsis. The second gene is VEGFA, which is activated in angiogenesis and vasculogenesis in the fetus. Furthermore, the genetic correlation between additive genetic effects on TNB and on its variation was 0.49. This indicates that the current selection to increase TNB will also increase the varTNB.

Conclusions

To the best of our knowledge, this is the first study reporting SNPs associated with variation of a trait in pigs. Detected genomic regions associated with varTNB can be used in genomic selection to decrease varTNB, which is highly desirable to avoid very small or very large litters in pigs. However, the percentage of variance explained by those regions was small. The SNPs detected in this study can be used as indication for regions in the Sus scrofa genome involved in maintaining low variability of litter size, but further studies are needed to identify the causative loci.

PBMC transcriptomic responses to primary and secondary vaccination differ due to divergent lean growth and antibody titers in a pig model

The genetic relationship between immune responsiveness and performance is not well understood, but a major topic of the evolution of resource allocation and of relevance in human medicine and livestock breeding, for instance. This study aims to show differences of transcript abundance changes during the time intervals before and after two tetanus toxoid (TT) vaccinations in domestic pigs differing in lean growth (LG) and anti-TT-antibody titers (AB) parameters of performance and immunocompetence. During response to the first vaccination all animals had a general decrease in transcript abundances related to various functional pathways as measured by comparative Affymetrix microarray hybridization and Ingenuity Pathway analyses. Low-AB phenotypes had predominantly decreased immune response transcripts. Combined phenotypes high-AB/high-LG had decreased transcripts related to growth factor signaling pathways. However, during the interval after the booster vaccination, high-LG and high-AB animals responded exclusively with increased immune transcripts, such as B-cell receptor signaling and cellular immune response pathways. In addition, high-LG and low-AB animals had predominantly increased transcripts of several cellular immune response pathways. Conversely, low-LG and high-AB animals had few elevated immune transcripts and decreased transcripts related to only two nonimmune-specific pathways. In response to booster vaccination high-LG phenotypes revealed enriched transcripts related to several different immune response pathways, regardless of AB phenotype. Different from the expected impact of AB titers, divergent AB phenotypes did not reflect considerable differences between immune transcripts. However, highly significant differences observed among divergent LG phenotypes suggest the compatibility of high performance and high vaccine responses.