ABSTRACT The wild boar (Sus scrofa) has been a part of the Swedish fauna for thousands of years. Although it became extinct in the 17th century, populations reemerged in the 1970s and 1980s after escapes from enclosures. The country of origin of the wild boars kept in these enclosures is unknown. This study aims to investigate the origin and level of genetic diversity of Swedish wild boars, as well as to compare them with Swedish domestic pigs. Swedish wild boar samples were collected from four regions of Sweden: Skåne, Blekinge, Södermanland and Uppland. In total, 107 wild boars and 427 domestic pigs were genotyped using the 80 K SNP chip. Wild boars from Skåne and Blekinge were shown to belong to the same genetic group, whereas the Södermanland and Uppland formed separate clusters. Results from both principal component analysis (PCA) and fixation index (FST) analyses demonstrate that Swedish wild boars are genetically distinct from Swedish domestic pigs. Moreover, the ADMIXTURE analysis revealed no evidence of introgression from domestic pigs into Swedish wild boar populations. The genetic differentiation observed among Swedish wild boar populations further indicates that they originate from more than one external source population.

The supply of farmed animals with agriculturally produced biomass, which can also be consumed by humans, is currently criticised by society. Monogastric animals (pigs, chickens) are often at the centre of this discussion, as the feed used is essentially based on rations containing cereals and soy bean products. Studies are conducted to investigate which alternative feedstuffs, which are not used for human consumption, would be suitable for feeding pigs. The increased use of co-products or by-products would defuse this competitive situation. With these feedstuffs, however, there is a risk that the pigs will temporarily not be fed according to their needs due to fluctuating nutrient contents and possible anti- nutritive ingredients. Against this background, breeding strategies are currently being developed to improve the feed and nutrient utilisation efficiency of pigs. This would enable the pigs to better compensate for possible imbalances in feeding and also minimise environmentally harmful nutrient excretions. The nutrient utilisation efficiency can be indirectly measured using established traits in pig breeding, such as average daily gain or feed conversion rate. In addition, attempts are being made to record the excretion and absorption capacity of the most important nutrients nitrogen and phosphorus more specifically and precisely in order to achieve improved breeding success in nutrient efficiency. Possible genotype x environment interactions represent a major challenge here. The effects of altered feeding strategies with incompletely balanced feed rations can be partially compensated for by breeding if traits of nutrient efficiency and adaptability are integrated into balanced breeding objectives.

Livestock farming has a key role in many rural communities both economically and culturally. It plays an important role in overcoming the deficiencies of meat, milk, wool and various by-products. Pakistan has a large number of livestock, well-adapted to local conditions. and has some of the best tropical dairy breeds. Native sheep breeds stand a vital asset to the country’s livestock sector because of their adaptability and unique genetic traits. However, knowledge of the genetic diversity of these sheep breeds remains limited. This study aims to investigate the genetic diversity of 10 local sheep breeds from Khyber Pakhtunkhwa by analyzing the mitochondrial D-loop from 159 individual samples of females. The sequenced data from the mtDNA D-loop showed 106 different haplotypes, with a haplotype diversity of 0.9854 ± 0.0041. Analysis of the mitochondrial D-loop revealed three distinct haplogroups (HapA, HapB, and HapC). Out of the 159 sequences, 125 (77.99

Local livestock breeds play an important role in the food security of smallholders in developing countries in the Global South. They are also a reservoir of potentially valuable genes for adaptation of global animal genetic resources. The Creole cattle population from Pasorapa, Bolivia, is threatened by effects of climate change and unplanned crossbreeding. The aim of this study was to assess the current situation in this population and to evaluate factors to be considered before implementing conservation and genetic improvement programs in order to achieve the sustainable development goals 1, 2, 13 and 15, which refer to no poverty, zero hunger, climate change and life on land, respectively. We examined and analyzed the most important elements related to the production system and farmers’ perceptions that could affect the design of such programs. Open-ended and closed-ended questionnaires and interviews were performed with 81 smallholders from 11 communities in Pasorapa. A rearing system based on two stages and animals feeding mainly on native plants during both, involves a strong interaction between the environment and the production system. A survey of farmers’ perceptions about diseases, mortality causes, and selection criteria revealed that farmers in Pasorapa consider coat color an important trait when selecting breeding and replacement animals. Half of all interviewees perceived an association between coat color and traits such as temperament, milk yield, and beef production. In a SWOT analysis we discussed the vulnerability of the system to climate change impacts and the contribution of this traditional system to rural mitigation. Overall, this work revealed the importance of this local ecotype and identified key factors to consider when developing breeding and conservation programs.

Gastrointestinal nematodes (GIN) are an important constraint in small ruminant production. Genetic selection for resistant animals is a potential sustainable control strategy. Advances in molecular genetics have led to the identification of several molecular genetic markers associated with genes affecting economic relevant traits. In this study, the variants in the genome of Creole goats resistant or susceptible to GIN were discovered from RNA-sequencing. We identified SNPs, insertions and deletions that distinguish the two genotypes, resistant and susceptible and we characterized these variants through functional analysis. The T cell receptor signalling pathway was one of the top significant pathways that distinguish the resistant from the susceptible genotype with 78% of the genes involved in this pathway showing genomic variants. These genomic variants are expected to provide useful resources especially for molecular breeding for GIN resistance in goats.

Gastrointestinal nematode (GIN) infections are one of the major constraints for grazing sheep and goat production worldwide. Genetic selection for resistant animals is a promising control strategy. Whole-transcriptome analysis via RNA-sequencing (RNA-seq) provides knowledge of the mechanisms responsible for complex traits such as resistance to GIN infections. In this study, we used RNA-seq to monitor the dynamics of the response of the abomasal mucosa of Creole goat kids infected with Haemonchus contortus by comparing resistant and susceptible genotypes. A total of 8 cannulated kids, 4 susceptible and 4 resistant to GIN, were infected twice with 10 000 L3 H. contortus. During the second infection, abomasal mucosal biopsies were collected at 0, 8, 15 and 35 days post-infection (dpi) from all kids for RNA-seq analysis. The resistant animals showed early activation of biological processes related to the immune response. The top 20 canonical pathways of differentially expressed genes for different comparison showed activation of the immune response through many relevant pathways including the Th1 response. Interestingly, our results showed a simultaneous time series activation of Th2 related genes in resistant compared to susceptible kids.

Background Native Swedish sheep breeds are part of the North European short-tailed sheep group; characterized in part by their genetic uniqueness. Our objective was to study the population structure of native Swedish sheep. Five breeds were genotyped using the 600 K SNP array. Dalapäls and Klövsjö sheep are from the middle of Sweden; Gotland and Gute sheep from Gotland, an island in the Baltic Sea; and Fjällnäs sheep from northern Sweden. We studied population structure by: principal component analysis (PCA), cluster-based analysis of admixture, and an estimated population tree. Results The analyses of the five Swedish breeds revealed that these breeds are five distinct breeds, while Gute and Gotland are more closely related to each other as seen in all analyses. All breeds had long branch lengths in the population tree indicating they’ve been subjected to drift. We repeated our analyses using 39 K SNP and including 50 K SNP genotypes from other European and southwestern Asian breeds from the Sheep HapMap project and 600 K SNP genotypes from a dataset of French sheep. Results arranged breeds into five groups: south-west Asia, south-west Europe, central Europe, north Europe and north European short-tailed sheep. Within this last group, Norwegian and Icelandic breeds, Finn and Romanov sheep, Scottish breeds, and Gute and Gotland sheep were more closely related while the remaining Swedish breeds and Ouessant sheep were distinct from all breeds and had longer branches in the population tree. Conclusions We showed population structure of five Swedish breeds and their structure within European and southwestern Asian breeds. Swedish breeds are unique, distinct breeds that have been subjected to drift but group with other north European short-tailed sheep.

The rise of anthelmintic resistance worldwide has led to the development of alternative control strategies for gastrointestinal nematodes (GIN) infections, which are one of the main constraints on the health of grazing small ruminants. Presently, breeding schemes rely mainly on fecal egg count (FEC) measurements on infected animals which are time-consuming and requires expertise in parasitology. Identifying and understanding the role of immunoglobulins in the mechanisms of resistance could provide a more efficient and sustainable method of identifying nematode-resistant animals for selection. In this study we review the findings on immunoglobulin response to GIN in the literature published to date (june 2019) and discuss the potential to use immunoglobulins as biomarkers. The literature review revealed 41 studies which measured at least one immunoglobulin: 35 focused on lamb immune response (18 used non-naïve lambs) and 7 on yearlings. In this review we propose a conceptual model summarizing the role of immunoglobulins in resistance to GIN. We highlight the need for more carefully designed and documented studies to allow comparisons across different populations on the immunoglobulin response to GIN infection.

By studying genes associated with coat colour, we can understand the role of these genes in pigmentation but also gain insight into selection history. North European short-tailed sheep, including Swedish breeds, have variation in their coat colour, making them good models to expand current knowledge of mutations associated with coat colour in sheep. We studied ASIP and MC1R, two genes with known roles in pigmentation, and their association with black coat colour. We did this by sequencing the coding regions of ASIP in 149 animals and MC1R in 129 animals from seven native Swedish sheep breeds in individuals with black, white or grey fleece. Previously known mutations in ASIP [recessive black allele: g.100_105del (D5 ) and/or g.5172T>A] were associated with black coat colour in Klövsjö and Roslag sheep breeds and mutations in both ASIP and MC1R (dominant black allele: c.218T>A and/or c.361G>A) were associated with black coat colour in Swedish Finewool. In Gotland, Gute, Värmland and Helsinge sheep breeds, coat colour inheritance was more complex: only 11 of 16 individuals with black fleece had genotypes that could explain their black colour. These breeds have grey individuals in their populations, and grey is believed to be a result of mutations and allelic copy number variation within the ASIP duplication, which could be a possible explanation for the lack of a clear inheritance pattern in these breeds. Finally, we found a novel missense mutation in MC1R (c.452G>A) in Gotland, Gute and Värmland sheep and evidence of a duplication of MC1R in Gotland sheep.

Gastrointestinal nematodes (GIN) are a major constraint for small ruminant production. Due to the rise of anthelmintic resistance throughout the world, alternative control strategies are needed. The development of GIN resistance breeding programs is a promising strategy. However, a better understanding of the mechanisms underlying genetic resistance might lead to more effective breeding programmes. In this study, we compare transcriptome profiling of abomasal mucosa and lymph node tissues from non-infected, resistant and susceptible infected Creole goats using RNA-sequencing. A total of 24 kids, 12 susceptible and 12 GIN resistant based on the estimated breeding value, were infected twice with 10,000 L3 Haemonchus contortus. Physiological and parasitological parameters were monitored during infection. Seven weeks after the second infection, extreme kids (n = 6 resistant and 6 susceptible), chosen on the basis of the fecal egg counts (FEC), and 3 uninfected control animals were slaughtered. Susceptible kids had significantly higher FEC compared with resistant kids during the second infection with no differences in worm burden, male and female worm count or establishment rate. A higher number of differentially expressed genes (DEG) were identified in infected compared with non-infected animals in both abomasal mucosa (792 DEG) and lymph nodes (1726 DEG). There were fewer DEG in resistant versus susceptible groups (342 and 450 DEG, in abomasal mucosa and lymph nodes respectively). 'Cell cycle' and 'cell death and survival' were the main identified networks in mucosal tissue when comparing infected versus non-infected kids. Antigen processing and presentation of peptide antigen via major histocompatibility complex class I were in the top biological functions for the DEG identified in lymph nodes. The TGFβ1 gene was one of the top 5 upstream DEG in mucosal tissue. Our results are one of the fist investigating differences in the expression profile induced by GIN infection in goats.

The hot topic of genetic modification and genome editing is sometimes presented as a rapid solution to various problems in the field of animal breeding and genetics. These technologies hold potential for future use in agriculture but we need to be aware of difficulties in large-scale application and integration in breeding schemes. In this review, we discuss applications of both classical genetic modifications (GM) using vectors and genome editing in dairy cattle breeding. We use an interdisciplinary approach considering both ethical and animal breeding perspectives. Decisions on how to make use of these techniques need to be made based not only on what is possible, but on what is reasonable to do. Principles of animal integrity, naturalness, risk perception, and animal welfare issues are examples of ethically relevant factors to consider. These factors also influence public perception and decisions about regulations by authorities. We need to acknowledge that we lack complete understanding of the genetic background of complex traits. It may be difficult, therefore, to predict the full effect of certain modifications in large-scale breeding programs. We present 2 potential applications: genome editing to dispense with dehorning, and insertion of human genes in bovine genomes to improve udder health as an example of classical GM. Both of these cases could be seen as beneficial for animal welfare but they differ in other aspects. In the former case, a genetic variant already present within the species is introduced, whereas in the latter case, transgenic animals are generated-this difference may influence how society regards the applications. We underline that the use of GM, as well as genome editing, of farm animals such as cattle is not independent of the context, and should be considered as part of an entire process, including, for example, the assisted reproduction technology that needs to be used. We propose that breeding organizations and breeding companies should take an active role in ethical discussions about the use of these techniques and thereby signal to society that these questions are being responsibly addressed.

Our study aimed to test if genes related to maternal ability can be used as genetic markers to improve piglet production. We considered polymorphisms in the oxytocin gene and other loci related to metabolic oxytocin levels and maternal behavior. We hypothesized that genetic variants in these genes can be used to select sows with good mothering ability, expressed as the ability to raise many fast-growing piglets. We identified polymorphisms in candidate genes and used additional closely located known polymorphisms to genotype sows and to test the association of the polymorphisms. Nine genes, oxytocin (OXT), oxytocin receptor (OXTR), mesoderm specific transcript (MEST), paternally expressed gene 3 (Peg3), growth factor receptor-bound substrate 10 (Grb10), FBJ murine osteosarcoma viral oncogene homolog B (FOSB), cluster of differentiation 38 (CD38), neurohypophyseal hormone arginine vasopressin (AVP) and protein kinase C, gamma (PRKCG) were selected for analysis. We identified four novel single nucleotide polymorphisms (SNP), while 23 SNP identified using sequencing were already reported in a public database. Sows were genotyped using SNP identified using sequencing and from a public database, and a total of 30 out of 65 SNP segregated in the population. We tested the association of 20 markers with traits from up to 164 sows, including number and weight of piglets born and weaned and growth rate of piglets until week 5. Polymorphisms in or close to genes FOSB, PRKCG, Grb10, OXTR, and AVP showed significant associations (after Bonferroni correction, P < 0.00256) with mean birth weight, piglets stillborn of total born and relative weight change of the sow during lactation. We identified some effects (P < 0.05) of SNP close to or within OXT; MEST, FOSB, AVP and PRKCG on number of piglets dead or stillborn from total or live born. Birth weight and piglet growth were slightly (P < 0.05) influenced by polymorphisms in or close to genes Grb10, Peg3 and PRKCG. Two markers in the regions of genes MEST and Grb10 showed an effect (P < 0.05) on the relative fat and weight change of the sow during lactation, respectively. Most of the associations were either identified in the first or second parity, indicating strong differences between the traits across these early parities. Future studies should investigate the correlation between maternal behavior traits and the traits investigated here and test the effect of the investigated loci on behavior in sows. If these genes are associated with favorable maternal behaviors in pigs and if they are useful indicators of the maternal ability, they could be used to identify sows with high genetic ability to raise many fast growing piglets.

Prediction of phenotypes is not only used for selection and breeding in animal and plant populations but also for the assessment of specific phenotypes, especially predisposition to diseases and disorders in human populations. The use of genetic markers has been shown to be useful for prediction and selection for phenotypic traits. The concept of using genetic markers for prediction of breeding values or phenotypes was suggested many decades ago, but applications of marker-assisted selection were limited due to the low number of markers that could be genotyped and the low number of confirmed quantitative trait loci (QTL) that could be selected upon. Genomic selection, in contrast, utilizes dense genetic markers across the whole genome for the prediction of phenotypes as all QTL can be assumed to be in linkage disequilibrium with at least one marker. Genomic selection allows thereby choosing the genetically best individuals without the need to confirm QTL. The concept of genomic selection, proposed in 2001, has since been further developed and applied. Nowadays, genomic selection is widely applied in breeding populations of plants and animals for the selection of future breeding individuals. The chapter introduces the general concept of genomic selection. It further discusses relevant prerequisites for the application of genomic selection, including genotyping platforms and reference populations. Some of the methods applied today as well as suggested advancements of methods are introduced. The final part of the chapter describes briefly applications in animal, plant, and human populations (status when writing this chapter), before concluding with some general notes on genomic selection.

Evaluating the genetic contribution of individuals to population structure is essential to select informative individuals for genome sequencing, genotype imputation and to ascertain complex population structures. Existing methods for the selection of informative individuals for genomic imputation solely focus on the identification of key ancestors, which can lead to a loss of phasing accuracy of the reference population. Currently many methods are independently applied to investigate complex population structures. Based on the Eigenvalue Decomposition (EVD) of a genomic relationship matrix we describe a novel approach to evaluate the genetic contribution of individuals to population structure. We combined the identification of key contributors with model-based clustering and population network visualization into an integrated three-step approach, which allows identification of high-resolution population structures and substructures around such key contributors. The approach was applied and validated in four disparate datasets including a simulated population (5,100 individuals and 10,000 SNPs), a highly structured experimental sheep population (1,421 individuals and 44,693 SNPs) and two large complex pedigree populations namely horse (1,077 individuals and 38,124 SNPs) and cattle (2,457 individuals and 45,765 SNPs). In the simulated and experimental sheep dataset, our method, which is unsupervised, successfully identified all known key contributors. Applying our three-step approach to the horse and cattle populations, we observed high-resolution population substructures including the absence of obvious important key contributors. Furthermore, we show that compared to commonly applied strategies to select informative individuals for genotype imputation including the computation of marginal gene contributions (Pedig) and the optimization of genetic relatedness (Rel), the selection of key contributors provided the highest phasing accuracies within the selected reference populations. The presented approach opens new perspectives in the characterization and informed management of populations in general, and in areas such as conservation genetics and selective animal breeding in particular, where assessing the genetic contribution of influential and admixed individuals is crucial for research and management applications. As such, this method provides a valuable complement to common applied tools to visualize complex population structures and to select individuals for re-sequencing.

The number of functional teats is an important selection criterion in pig breeding. Inherited defects of the udder, such as the inverted teat, do have a considerable negative impact on the nursing ability of the sow. To investigate the genetic background of this defect and the number of functional teats in Swedish maternal lines, samples from 230 Yorkshire pigs were selected for genotyping using the PorcineSNP60K BeadChip (Illumina Inc.), each pig with at least one inverted teat was matched with one non-affected pig (fullsib or pairs with matching herd and gender). A genome-wide association study on these 230 pigs was performed using the two-step approach implemented in GenABEL using 46,652 single nucleotide polymorphisms across all autosomes and the X chromosome. A number of significant regions were identified for the inverted teat defect on chromosomes 2, 10, and 18. Many of the regions associated with the number of functional teats were located in the same or close regions, except two associated markers on the X chromosome and one on chromosome 3. We identified some of the regions on chromosomes previously reported in one linkage and one gene expression study. We conclude, despite being able to suggest new candidate genes, that further studies are needed to better understand the biologic background of the teat development. Despite the in-depth comparison of identified regions for the inverted teat defect done here, more studies are required to allow a clear identification of genetic regions relevant for this defect across many pig populations.

The relationships among nucleotide sequence polymorphisms in the genes for leptin (LEP) and leptin receptor (LEPR) and circulating concentrations of leptin and variables related to energy turnover were investigated in a Awassi-Merino crossbred sheep population. Blood sampled at several times during gestation and lactation was used for the assay of circulating leptin and for DNA extraction. Parts of the ovine LEP and LEPR genes were sequenced and, of a total of seven polymorphisms identified, two for each gene were used for genotyping. Feed intake and body weight were recorded for 199 ewes (age 2.9-9.4 years) daily and milk yield and composition were measured. The data were used for association studies between single nucleotide polymorphisms (SNPs), circulating leptin concentration and production traits. Both polymorphisms identified in the ovine LEP gene were associated with circulating leptin concentration (P<0.05) and one SNP was associated with feed intake per unit milk production (P<0.05). For the SNPs in the LEPR gene, there were significant effects for residual feed intake during lactation (P<0.05) and for feed intake and residual feed intake at defined times during gestation (P<0.05). We conclude that polymorphisms in the LEP and LEPR genes are associated with production and efficiency traits. The interaction between body condition, milk production, energy efficiency and leptin concentrations should be investigated in detail in future studies. Further studies are also needed to identify the specific roles played by LEP and LEPR in the regulation of circulating leptin concentrations and energy metabolism. (C) 2016 Elsevier B.V. All rights reserved.

Genomic Selection is an important topic in quantitative genetics and breeding. Not only does it allow the full use of current molecular genetic technologies, it stimulates also the development of new methods and models. Genomic selection, if fully implemented in commercial farming, should have a major impact on the productivity of various agricultural systems. But suggested approaches need to be applicable in commercial breeding populations. Many of the published research studies focus on methodologies. We conclude from the reviewed publications, that a stronger focus on strategies for the implementation of genomic selection in advanced breeding lines, introduction of new varieties, hybrids or multi-line crosses is needed. Efforts to find solutions for a better prediction and integration of environmental influences need to continue within applied breeding schemes. Goals of the implementation of genomic selection into crop breeding should be carefully defined and crop breeders in the private sector will play a substantial part in the decision-making process. However, the lack of published results from studies within, or in collaboration with, private companies diminishes the knowledge on the status of genomic selection within applied breeding programmes. Studies on the implementation of genomic selection in plant breeding need to evaluate models and methods with an enhanced emphasis on population-specific requirements and production environments. Adaptation of methods to breeding schemes or changes to breeding programmes for a better integration of genomic selection strategies are needed across species. More openness with a continuous exchange will contribute to successes.

Genomic selection is a promising development in agriculture, aiming improved production by exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. It opens opportunities for research, as novel algorithms and lab methodologies are developed. Genomic selection can be applied in many breeds and species. Further research on the implementation of genomic selection (GS) in breeding programs is highly desirable not only for the common good, but also the private sector (breeding companies). It has been projected that this approach will improve selection routines, especially in species with long reproduction cycles, late or sex-limited or expensive trait recording and for complex traits. The task of integrating GS into existing breeding programs is, however, not straightforward. Despite successful integration into breeding programs for dairy cattle, it has yet to be shown how much emphasis can be given to the genomic information and how much additional phenotypic information is needed from new selection candidates. Genomic selection is already part of future planning in many breeding companies of pigs and beef cattle among others, but further research is needed to fully estimate how effective the use of genomic information will be for the prediction of the performance of future breeding stock. Genomic prediction of production in crossbreeding and across-breed schemes, costs and choice of individuals for genotyping are reasons for a reluctance to fully rely on genomic information for selection decisions. Breeding objectives are highly dependent on the industry and the additional gain when using genomic information has to be considered carefully. This review synthesizes some of the suggested approaches in selected livestock species including cattle, pig, chicken, and fish. It outlines tasks to help understanding possible consequences when applying genomic information in breeding scenarios.

Researchers have put forward agricultural biotechnology as one possible tool for increasing food production and making agriculture more sustainable. In this paper, it is investigated how key actors in the Swedish food supply chain perceive the concept of agricultural sustainability and the role of biotechnology in creating more sustainable agricultural production systems. Based on policy documents and semi-structured interviews with representatives of five organizations active in producing, processing and retailing food in Sweden, an attempt is made to answer the following three questions: How do key actors in the Swedish food supply chain define and operationalize the concept of agricultural sustainability? Who/what influences these organizations' sustainability policies and their respective positions on agricultural biotechnology? What are the organizations' views and perceptions of biotechnology and its possible role in creating agricultural sustainability? Based on collected data, it is concluded that, although there is a shared view of the core constituents of agricultural sustainability among the organizations, there is less explicit consensus on how the concept should be put into practice or what role biotechnology can play in furthering agricultural sustainability.