New Mendelian genetic conditions, which adversely affect livestock, arise all the time. To manage them effectively, some methods need to be devised that are quick and accurate. Until recently, finding the causal genomic site of a new autosomal recessive genetic disease has required a two-stage approach using single-nucleotide polymorphism (SNP) chip genotyping to locate the region containing the new variant. This region is then explored using fine-mapping methods to locate the actual site of the new variant. This study explores bioinformatic methods that can be used to identify the causative variants of recessive genetic disorders with full penetrance with just nine whole genome-sequenced animals to simplify and expedite the process to a one-step procedure. Using whole genome sequencing of only three cases and six carriers, the site of a novel variant causing perinatal mortality in Irish moiled calves was located. Four methods were used to interrogate the variant call format (VCF) data file of these nine animals, they are genotype criteria (GCR), autozygosity-by-difference (ABD), variant prediction scoring, and registered SNP information. From more than nine million variants in the VCF file, only one site was identified by all four methods (Chr4: g.77173487A>T (ARS-UCD1.2 (GCF_002263795.1)). This site was a splice acceptor variant located in the glucokinase gene (GCK). It was verified on an independent sample of animals from the breed using genotyping by polymerase chain reaction at the candidate site and autozygosity-by-difference using SNP-chips. Both methods confirmed the candidate site. Investigation of the GCR method found that sites meeting the GCR were not evenly spread across the genome but concentrated in regions of long runs of homozygosity. Locating GCR sites was best performed using two carriers to every case, and the carriers should be distantly related to the cases, within the breed concerned. Fewer than 20 animals need to be sequenced when using the GCR and ABD methods together. The genomic site of novel autosomal recessive Mendelian genetic diseases can be located using fewer than 20 animals combined with two bioinformatic methods, autozygosity-by-difference, and genotype criteria. In many instances it may also be confirmed with variant prediction scoring. This should speed-up and simplify the management of new genetic diseases to a single-step process.

Abstract In this chapter, the factors which affect responses to within-breed selection, and some of the tools and technologies used, especially for more effective within-breed selection are discussed. Highlights focused on the factors affecting rates of genetic gain, and controlling inbreeding.

Abstract This chapter discussed the effects of applying the different principles in animal breeding such genetic analysis, predicting breeding values, use of tools and breeding technology, selection response within breeds, and strategies for genetic improvements in dairy cattle.

Abstract The purpose of this final chapter is to explore some of the key challenges facing farm animal production in general, and animal breeding and genetics in particular, and to discuss how livestock breeders might respond to ensure wide societal and animal benefits.

Abstract This chapter discusses approaches to predicting breeding values and presents an outline of the steps that are required to obtain the most appropriate breeding values for any species. This process of predicting breeding values is often termed genetic evaluation.

In this chapter, topics focused on how to quantify the extent to which genes affect measured traits and how to use this information in breeding programmes. Highlights include: estimating heritability; estimating non-additive parameters, correlations, and genotype by environment interactions, molecular genetics and trait variations; and calculating inbreeding using SNP markers.

This 484-paged book is an extensively updated and expanded edition of the previous book by Simm, which focused on cattle and sheep. It has 14 chapters, the first chapter in the book sets the scene for modern livestock breeding, by looking at the origins and roles of today's livestock breeds. The next four chapters deal with the scientific principles of livestock improvement. Chapter 2 outlines some of the basic principles in genetics and attempts to illustrate the link between genes and the performance of individual farm animals, or populations of them. In Chapter 3 the main strategies for genetic improvement are discussed. The factors which affect responses to within-breed selection, and some of the tools and technologies used, especially for more effective within-breed selection, are discussed in Chapters 4 and 5. Chapter 6 explores in more depth how we analyse variation in farm animals. Chapter 7 discusses approaches to predicting breeding values. Chapters 8 to 13 deal with the application of these principles in practical breeding programmes in dairy cattle, beef cattle, sheep and goats, poultry, pigs and aquaculture. Finally, Chapter 14 discusses some of the key societal, technical and ethical challenges facing farm animal production in general, and animal breeding and genetics in particular. It discusses how livestock breeders, scientists and others might respond to ensure wide societal and animal benefits from future breeding schemes. There is a glossary of technical terms at the end of the book.

Abstract The huge variety of animal and other species that we see today, together with those now extinct, evolved by the process of natural selection. The key to natural selection, and to the artificial selection practised by breeders, is the inherited variation in many characteristics that exists between individual animals. Domestication of animals began 12,000 to 10,000 years ago. Whether or not it has been done knowingly, artificial selection, as well as natural selection, has been practised among domestic animals ever since then. Although distinct breeds or strains of cattle and sheep existed long before then, the practices of pedigree recording and selection of related animals with the aim of breed improvement date from the mid-1700s. The formation of herd books began early in the following century. Livestock continue to have a wide range of important rôles globally, with a range of positive and negative societal and environmental impacts, which need to be managed and balanced.

Abstract This chapter reviews the state of play in aquaculture breeding and presents an outlook, together with opportunities and challenges, for this sector.

Abstract This chapter discussed the factors which affect responses to within-breed selection, and some of the tools and technologies used, especially for more effective within-breed selection. Highlights focused on the current reproductive technologies in animal breeding, molecular genetic tools, and modern data capture tools.

Abstract In this chapter, the major breeding goals for each of the poultry products (eggs and meat) are discussed. An outline on how the breeding and selection methods have been developed appropriately on chicken meat (broiler) and chicken egg sectors was also presented.

This chapter highlights the application of genetic principles such as strategies for genetic improvements, selection response within breeds, tools and technologies in animal breeding, genetic analysis, and predicting values in beef cattle.

Abstract This chapter highlights the application of genetic principles in sheep and goat breeding such as chromosome analysis, prediction of breeding values, and the use of the latest tools and technology in animal breeding.

Abstract In this chapter, the main strategies for genetic improvement are discussed. Highlights focused on the structure of livestock breeding industries, selection, crossbreeding, and conservation of genetic resosurces.

This chapter outlines some of the basic principles in genetics and attempts to illustrate the link between genes and the performance of individual farm animals, or populations of them.

Abstract This chapter presents a brief background on the global pig sector and pig-meat value chains. Topics focused on the breeding objectives, pig breeds and lines, genetic improvement strategies for pigs (for both large-scale and smallholder systems) and use of pig reproductive technologies. The final section of this chapter gives some practical guidelines for selection.

Multipotent mesenchymal stromal cells (MSCs) derived from synovial fluid (SF) are considered to be a promising cell type for therapeutic applications in joint disease. However, despite their potential relevance for clinical and experimental studies, there is insufficient knowledge about SF-derived MSCs isolated from horses and sheep. In this study, cells were recovered from healthy SF and bone marrow (BM) of sheep, and from healthy and osteoarthritic SF of horses. Ovine SF-MSCs were used to assess the efficiency of intracellular labelling with quantum dots (QDs). Colony forming units, generation times, trilineage differentiation potential and expression of CD73, CD90 and CD105 at mRNA level were assessed. QD labelling was efficient, with >98% positive cells directly after labelling at 10 nmol/L and >95% positive cells directly after labelling at 2 nmol/L. The label decreased over 7 days of culture, with more persistence at the higher labelling concentration. No significant differences in proliferation were observed. All MSCs had trilineage differentiation potential, but adipogenesis was more distinct in equine samples and chondrogenesis was most pronounced in ovine SF-MSCs. CD73, CD90 and CD105 were expressed in equine and ovine MSCs.

Mastitis reduces milk production and causes culling. The NF-κB transcription factor RelA plays a central regulatory role in innate immunity. This study used a candidate gene approach to investigate associations between the synonymous C/G SNP rs48035703 in RELA with somatic cell count (SCC) and survival time. Blood samples were collected from 337 Holstein-Friesian heifers on 19 farms and genotyped by PCR-restriction fragment length polymorphism. Animals were monitored from 6 months until 2340 d of age. Pedigree, milk production and disease records were obtained. Genotype frequencies were CC 0.63, CG 0.30 and GG 0.06. The C allele had a favourable additive effect on survival: average longevities from birth were CC, 1872 d; CG, 1745 d and GG 1596 d (P -0.04 ± 0.803, P RELA rs48035703 CC genotype cows were therefore less likely to experience a high SCC and survived longer. These results support a role for RelA in combating mammary gland infection and warrant further studies in additional populations.

Interestingly, considering the widespread use of recording in livestock work, there seems to be very little literature which can be used to address these questions. Key publications dealing with livestock recording are listed in the Bibliography. This paper, therefore, draws on a combination of the limited literature and other experiences of designing, running and evaluating livestock recording schemes in both developed and developing countries and involving livestock systems ranging from intensive to lowinput.

Equine degenerative myeloencephalopathy (EDM), a neurological disease of young horses, causes progressive development of symmetric ataxia predominantly in the pelvic limbs. Equine degenerative myeloencephalopathy is likely inherited and with no known treatment affected horses frequently need euthanasia. Alpha-tocopherol deficiency during early life appears to contribute to the phenotype. This study sought to identify any genetic variants correlated with EDM in Caspian foals. Two half-sibling EDM-diagnosed cases were genotyped at 52,063 loci and evaluated by the Autozygosity by Difference statistic. Additional horses not affected by EDM were used for genetic comparison to identify regions unique to the case phenotype. The associated region on chromosome 3 contains only one gene encoding adhesion G protein-coupled receptor L3 (ADGRL3). Adhesion G protein-coupled receptor L3 is a member of the latrophilin subfamily of G protein-coupled receptors and may contribute to attention deficit/ hyperactivity disorder in humans and hyperactive motor function in mice and zebrafish. Analysis of the predicted coding regions for Equine ADGRL3 in affected horses revealed a nonsynonymous single nucleotide polymorphism at Chr3:71,917,591 bp. Caspian and Caspian cross-relatives (n = 81) of the two initial cases and unrelated horses from similar breeds (n = 130, including Arabians, American Miniatures, and Shetlands) possessed this allele at 5% frequency, with no homozygotes observed within the non-Caspian breeds. This study suggests that a polymorphism in ADGRL3 could contribute to a genetic predisposition to Caspian horse EDM. (C) 2018 Elsevier Inc. All rights reserved.