The sheep genome reference sequence: a work in progress

Production performance analysis of sheep MSTN gene C2361T locus

The myostatin (MSTN) gene exhibits significant nucleotide sequence variations in sheep, impacting growth characteristics and muscular traits of the body. However, its influence on specific growth traits in some sheep remains to be further elucidated. This study utilized single nucleotide polymorphism sequence analysis to investigate the role of the MSTN gene in meat production performance across four sheep breeds: Charolais sheep, Australian White sheep, crossbreeds of Australian White and Small-tailed Han, and crossbreeds of Charolais and Small-tailed Han. At a SNP locus of the MSTN gene, the C2361T site was identified, with three genotypes detected: CC, CT, and TT, among which CC predominated. Gene substitution effect analysis revealed that replacing C with T could elevate the phenotypic value. Comparative analysis of data from different genotypes within the same breed highlighted the superiority of CC and TT genotypes in phenotypic values, underscoring the significance of specific genotypes in influencing key traits. Contrasting the performance of different genotypes across breeds, Charolais sheep and Charolais Han hybrids demonstrated superiority across multiple indicators, offering valuable insights for breeding new sheep varieties. Analysis of gender effects on growth characteristics indicated that ewes exhibited significantly wider chest, waist, and hip widths compared to rams, while rams displayed better skeletal growth and muscle development. Additionally, the MSTN gene also exerted certain effects on lamb growth characteristics, with the CC genotype closely associated with weight. These findings not only contribute crucial insights for sheep breeding but also pave the way for future research exploring the interaction of this gene with others.

Two mutations at KRT74 and EDAR synergistically drive the fine-wool production in Chinese sheep

INTRODUCTION

Fine-wool sheep are the most common breed used by the wool industry worldwide. Fine-wool sheep have over a three-fold higher follicle density and a 50% smaller fiber diameter than coarse-wool sheep.

OBJECTIVES

This study aims to clarify the underlying genetic basis for the denser and finer wool phenotype in fine-wool breeds.

METHOD

Whole-genome sequences of 140 samples, Ovine HD630K SNP array data of 385 samples, including fine, semi-fine, and coarse wool sheep, as well as skin transcriptomes of nine samples were integrated for genomic selection signature analysis.

RESULTS

Two loci at keratin 74 (KRT74) and ectodysplasin receptor (EDAR) were revealed. Fine-scale analysis in 250 fine/semi-fine and 198 coarse wool sheep narrowed this association to one C/A missense variant of KRT74 (OAR3:133,486,008, P = 1.02E-67) and one T/C SNP in the regulatory region upstream of EDAR (OAR3:61,927,840, P = 2.50E-43). Cellular over-expression and ovine skin section staining assays confirmed that C-KRT74 activated the KRT74 protein and specifically enlarged cell size at the Huxley's layer of the inner root sheath (P < 0.01). This structure enhancement shapes the growing hair shaft into the finer wool than the wild type. Luciferase assays validated that the C-to-T mutation upregulated EDAR mRNA expression via a newly created SOX2 binding site and potentially led to the formation of more hair placodes.

CONCLUSIONS

Two functional mutations driving finer and denser wool production were characterized and offered new targets for genetic breeding during wool sheep selection. This study not only provides a theoretical basis for future selection of fine wool sheep breeds but also contributes to improving the value of wool commodities.

Livestock species as emerging models for genomic imprinting

Genomic imprinting is an epigenetically-regulated process of central importance in mammalian development and evolution. It involves multiple levels of regulation, with spatio-temporal heterogeneity, leading to the context-dependent and parent-of-origin specific expression of a small fraction of the genome. Genomic imprinting studies have therefore been essential to increase basic knowledge in functional genomics, evolution biology and developmental biology, as well as with regard to potential clinical and agrigenomic perspectives. Here we offer an overview on the contribution of livestock research, which features attractive resources in several respects, for better understanding genomic imprinting and its functional impacts. Given the related broad implications and complexity, we promote the use of such resources for studying genomic imprinting in a holistic and integrative view. We hope this mini-review will draw attention to the relevance of livestock genomic imprinting studies and stimulate research in this area.

Sheep as a large animal model for hearing research: comparison to common laboratory animals and humans

Sensorineural hearing loss (SNHL), caused by pathology in the cochlea, is the most common type of hearing loss in humans. It is generally irreversible with very few effective pharmacological treatments available to prevent the degenerative changes or minimise the impact. Part of this has been attributed to difficulty of translating "proof-of-concept" for novel treatments established in small animal models to human therapies. There is an increasing interest in the use of sheep as a large animal model. In this article, we review the small and large animal models used in pre-clinical hearing research such as mice, rats, chinchilla, guinea pig, rabbit, cat, monkey, dog, pig, and sheep to humans, and compare the physiology, inner ear anatomy, and some of their use as model systems for SNHL, including cochlear implantation surgeries. Sheep have similar cochlear anatomy, auditory threshold, neonatal auditory system development, adult and infant body size, and number of birth as humans. Based on these comparisons, we suggest that sheep are well-suited as a potential translational animal model that bridges the gap between rodent model research to the clinical use in humans. This is especially in areas looking at changes across the life-course or in specific areas of experimental investigation such as cochlear implantation and other surgical procedures, biomedical device development and age-related sensorineural hearing loss research. Combined use of small animals for research that require higher throughput and genetic modification and large animals for medical translation could greatly accelerate the overall translation of basic research in the field of auditory neuroscience from bench to clinic.

Progress and future perspectives of livestock genomics in India: a mini review

The field of genetics has evolved a lot after the emergence of molecular and advanced genomic technologies. The advent of Next Generation Sequencing, SNP genotyping platforms and simultaneous reduction in the cost of sequencing had opened the door to genomic research in farm animals. There are various applications of genomics in livestock, such as the use of genomic data: (i) to investigate genetic diversity and breed composition/population structure (ii) to identify genetic variants and QTLs related to economically important and ecological traits, genome-wide association studies (GWAS) and genomic signatures of selection; (iii) to enhance breeding programs by genomic selection. Compared to traditional methods, genomic selection is expected to improve selection response by increasing selection accuracy and reducing the generation interval due to early selection. Genomic selection (GS) in developed countries has led to rapid genetic gains, especially in dairy cattle, due to a well-established genetic evaluation system. Indian livestock system is still lagging behind developed nations in adopting these technologies. This review discusses the current status, challenges, and future perspectives of livestock genomics in India.

Whole genome sequence and diversity in multigene families of Babesia ovis

Ovine babesiosis, caused by Babesia ovis, is an acute, lethal, and endemic disease worldwide and causes a huge economic loss to animal industry. Pathogen genome sequences can be utilized for selecting diagnostic markers, drug targets, and antigens for vaccine development; however, those for B. ovis have not been available so far. In this study, we obtained a draft genome sequence for B. ovis isolated from an infected sheep in Turkey. The genome size was 7.81 Mbp with 3,419 protein-coding genes. It consisted of 41 contigs, and the N50 was 526 Kbp. There were 259 orthologs identified among eight Babesia spp., Plasmodium falciparum, and Toxoplasma gondii. A phylogeny was estimated on the basis of the orthologs, which showed B. ovis to be closest to B. bovis. There were 43 ves genes identified using hmm model as well. They formed a discriminating cluster to other ves multigene family of Babesia spp. but showed certain similarities to those of B. bovis, B. caballi, and Babesia sp. Xinjiang, which is consistent with the phylogeny. Comparative genomics among B. ovis and B. bovis elucidated uniquely evolved genes in these species, which may account for the adaptation.

Genetic polymorphism in European and African sheep breeds reared in Hungary based on 48 SNPs associated with resistance to gastrointestinal parasite infection using KASP-PCR technique

This pilot study used an alternative and economically efficient technique, the Kompetitive Allele-Specific Polymerase Chain Reaction (KASP-PCR) to examine 48 SNPs from 11 parasite-resistance genes found on 8 chromosomes in 110 animals from five sheep breeds reared in Hungary; Hungarian Tsigai, White Dorper, Dorper, Ile de France, and Hungarian Merino. Allele and genotype frequencies, fixation index, observed heterozygosity, expected heterozygosity, F statistic, and their relationship with the Hardy-Weinberg equilibrium (WHE) and the polymorphic information content (PIC) were determined, followed by principal component analysis (PCA). As much as 32 SNPs out of the 48 initially studied were successfully genotyped. A total of 9 SNPs, 4 SNPs in TLR5, 1 SNP in TLR8, and 4 SNPs in TLR2 genes, were polymorphic. The variable genotype and allele frequency of the TLRs gene indicated genetic variability among the studied sheep breeds, with the Hungarian Merino exhibiting the most polymorphisms, while Dorper was the population with the most SNPs departing from the HWE. According to the PIC value, the rs430457884-TLR2, rs55631273-TLR2, and rs416833129-TLR5 were found to be informative in detecting polymorphisms among individuals within the populations, whereas the rs429546187-TLR5 and rs424975389-TLR5 were found to have a significant influence in clustering the population studied. This study reported a moderate level of genetic variability and that a low to moderate within-breed diversity was maintained in the studied populations.

Molecular Cytogenetics in Domestic Bovids: A Review

The discovery of the Robertsonian translocation (rob) involving cattle chromosomes 1 and 29 and the demonstration of its deleterious effects on fertility focused the interest of many scientific groups on using chromosome banding techniques to reveal chromosome abnormalities and verify their effects on fertility in domestic animals. At the same time, comparative banding studies among various species of domestic or wild animals were found useful for delineating chromosome evolution among species. The advent of molecular cytogenetics, particularly the use of fluorescence in situ hybridization (FISH), has allowed a deeper investigation of the chromosomes of domestic animals through: (a) the physical mapping of specific DNA sequences on chromosome regions; (b) the use of specific chromosome markers for the identification of the chromosomes or chromosome regions involved in chromosome abnormalities, especially when poor banding patterns are produced; (c) better anchoring of radiation hybrid and genetic maps to specific chromosome regions; (d) better comparisons of related and unrelated species by comparative FISH mapping and/or Zoo-FISH techniques; (e) the study of meiotic segregation, especially by sperm-FISH, in some chromosome abnormalities; (f) better demonstration of conserved or lost DNA sequences in chromosome abnormalities; (g) the use of informatic and genomic reconstructions, in addition to CGH arrays, to predict conserved or lost chromosome regions in related species; and (h) the study of some chromosome abnormalities and genomic stability using PCR applications. This review summarizes the most important applications of molecular cytogenetics in domestic bovids, with an emphasis on FISH mapping applications.

Trajectory of livestock genomics in South Asia: A comprehensive review

Livestock plays a central role in sustaining human livelihood in South Asia. There are numerous and distinct livestock species in South Asian countries. Several of them have experienced genetic development in recent years due to the application of genomic technologies and effective breeding programs. This review discusses genomic studies on cattle, buffalo, sheep, goat, pig, horse, camel, yak, mithun, and poultry. The frontiers covered in this review are genetic diversity, admixture studies, selection signature research, QTL discovery, genome-wide association studies (GWAS), and genomic selection. The review concludes with recommendations for South Asian livestock systems to increasingly leverage genomic technologies, based on the lessons learned from the numerous case studies. This paper aims to present a comprehensive analysis of the dichotomy in the South Asian livestock sector and argues that a realistic approach to genomics in livestock can ensure long-term genetic advancements.

Activating ligands of Uncoupling protein 1 identified by rapid membrane protein thermostability shift analysis

OBJECTIVE

Uncoupling protein 1 (UCP1) catalyses mitochondrial proton leak in brown adipose tissue to facilitate nutrient oxidation for heat production, and may combat metabolic disease if activated in humans. During the adrenergic stimulation of brown adipocytes, free fatty acids generated from lipolysis activate UCP1 via an unclear interaction. Here, we set out to characterise activator binding to purified UCP1 to clarify the activation process, discern novel activators and the potential to target UCP1.

METHODS

We assessed ligand binding to purified UCP1 by protein thermostability shift analysis, which unlike many conventional approaches can inform on the binding of hydrophobic ligands to membrane proteins. A detailed activator interaction analysis and screening approach was carried out, supported by investigations of UCP1 activity in liposomes, isolated brown fat mitochondria and UCP1 expression-controlled cell lines.

RESULTS

We reveal that fatty acids and other activators influence UCP1 through a specific destabilising interaction, behaving as transport substrates that shift the protein to a less stable conformation of a transport cycle. Through the detection of specific stability shifts in screens, we identify novel activators, including the over-the-counter drug ibuprofen, where ligand analysis indicates that UCP1 has a relatively wide structural specificity for interacting molecules. Ibuprofen successfully induced UCP1 activity in liposomes, isolated brown fat mitochondria and UCP1-expressing HEK293 cells but not in cultured brown adipocytes, suggesting drug delivery differs in each cell type.

CONCLUSIONS

These findings clarify the nature of the activator-UCP1 interaction and demonstrate that the targeting of UCP1 in cells by approved drugs is in principle achievable as a therapeutic avenue, but requires variants with more effective delivery in brown adipocytes.

Ubiquitination pathway model for the barber's pole worm - Haemonchus contortus

The ubiquitin-mediated pathway has been comprehensively explored in the free-living nematode Caenorhabditis elegans, but very little is known about this pathway in parasitic nematodes. Here, we inferred the ubiquitination pathway for an economically significant and pathogenic nematode - Haemonchus contortus - using abundant resources available for C. elegans. We identified 215 genes encoding ubiquitin (Ub; n = 3 genes), ubiquitin-activating enzyme (E1; one), -conjugating enzymes (E2s; 21), ligases (E3s; 157) and deubiquitinating enzymes (DUBs; 33). With reference to C. elegans, Ub, E1 and E2 were relatively conserved in sequence and structure, and E3s and DUBs were divergent, likely reflecting functional and biological uniqueness in H. contortus. Most genes encoding ubiquitination pathway components exhibit high transcription in the egg compared with other stages, indicating marked protein homeostasis in this early developmental stage. The ubiquitination pathway model constructed for H. contortus provides a foundation to explore the ubiquitin-proteasome system, crosstalk between autophagy and the proteasome system, and the parasite-host interactions. Selected E3 and DUB proteins which are very divergent in sequence and structure from host homologues or entirely unique to H. contortus and related parasitic nematodes may represent possible anthelmintic targets.

The Complex and Diverse Genetic Architecture of the Absence of Horns (Polledness) in Domestic Ruminants, including Goats and Sheep

Horns are the most obvious common feature of Bovidae. The naturally occurring absence of horns in these species, also known as polledness, is of surprisingly heterogeneous nature, although they are Mendelian traits. This review compares in detail the molecular differences among the causes of inherited polledness in the domestic ruminant species of cattle, yak, sheep, and goat based on the causal gene variants that have been discovered in recent years. The genetic causes for the lack of horns in small ruminants seem not only to be more complex, e.g., in sheep, breed-specific characteristics are still unexplained, but in goats, there is also the associated disorder of intersexuality—polled intersex syndrome (PIS). In connection with animal welfare and the associated discussion about a legal ban on the dehorning of all farm animals, naturally hornless animals and the causal genetic variants are of increasing research interest in the age of genome editing. However, the low acceptance of genetic engineering in livestock, especially in European societies, limits its use in food-producing animals. Therefore, genotype-based targeted selection of naturally occurring variants is still a widely used method for spreading this desired trait within and across populations, at least in cattle and sheep.

State of the art on the physical mapping of the Y-chromosome in the <i>Bovidae</i> and comparison with other species

The next generation sequencing has significantly contributed to clarify the genome structure of many species of zootechnical interest. However, to date, some portions of the genome, especially those linked to a heterogametic nature such as the Y chromosome, are difficult to assemble and many gaps are still present. It is well known that the fluorescence in situ hybridization (FISH) is an excellent tool for identifying genes unequivocably mapped on chromosomes. Therefore, FISH can contribute to the localization of unplaced genome sequences, as well as to correct assembly errors generated by comparative bioinformatics. To this end, it is necessary to have starting points; therefore, in this study, we reviewed the physically mapped genes on the Y chromosome of cattle, buffalo, sheep, goats, pigs, horses and alpacas. A total of 208 loci were currently mapped by FISH. 89 were located in the male-specific region of the Y chromosome (MSY) and 119 were identified in the pseudoautosomal region (PAR). The loci reported in MSY and PAR were respectively: 18 and 25 in Bos taurus, 5 and 7 in Bubalus bubalis, 5 and 24 in Ovis aries, 5 and 19 in Capra hircus, 10 and 16 in Sus scrofa, 46 and 18 in Equus caballus. While in Vicugna pacos only 10 loci are reported in the PAR region. The correct knowledge and assembly of all genome sequences, including those of genes mapped on the Y chromosome, will help to elucidate their biological processes, as well as to discover and exploit potentially epistasis effects useful for selection breeding programs.

A comprehensive genome-wide scan detects genomic regions related to local adaptation and climate resilience in Mediterranean domestic sheep

Background

The management of farm animal genetic resources and the adaptation of animals to climate change will probably have major effects on the long-term sustainability of the livestock sector. Genomic data harbour useful relevant information that needs to be harnessed for effectively managing genetic resources. In this paper, we report the genome characterization of the highly productive Mediterranean Chios dairy sheep and focus on genetic diversity measures related with local adaptation and selection and the genetic architecture of animal resilience to weather fluctuations as a novel adaptative trait linked to climate change.

Results

We detected runs of homozygosity (ROH) and heterozygosity (ROHet) that revealed multiple highly homozygous and heterozygous hotspots across the Chios sheep genome. A particularly highly homozygous region was identified on chromosome 13 as a candidate of directional genetic selection associated with milk traits, which includes annotated genes that were previously shown to be linked to local adaptation to harsh environmental conditions. Favourable heterozygosity related with a potentially protective role against livestock diseases and enhanced overall fitness was revealed in heterozygous-rich regions on sheep chromosomes 3, 10, 13 and 19. Furthermore, genomic analyses were conducted on sheep resilience phenotypes that display changes in milk production in response to weather variation. Sheep resilience to heat stress was a significantly heritable trait (h² = 0.26) and genetically antagonistic to milk production. Genome-wide association and regional heritability mapping analyses revealed novel genomic markers and regions on chromosome 5 that were significantly associated with sheep resilience to climate change. Subsequently, an annotation analysis detected a set of genes on chromosome 5 that were associated with olfactory receptor complexes that could participate in heat stress mitigation through changes in respiration rate and respiratory evaporation. Other genes were grouped in previously reported biological processes relevant to livestock heat dissipation, including stress and immune response.

Conclusions

Our results may contribute to the optimal management of sheep genetic resources and inform modern selective breeding programmes that aim at mitigating future environmental challenges towards sustainable farming, while better balancing animal adaptation and productivity. Our results are directly relevant to the studied breed and the respective environmental conditions; however, the methodology may be extended to other livestock species of interest.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-021-00682-7.

A Trifecta of New Insights into Ovine Footrot for Infection Drivers, Immune Response, and Host-Pathogen Interactions

Footrot is a polymicrobial infectious disease in sheep causing severe lameness, leading to one of the industry's largest welfare problems. The complex etiology of footrot makes in situ or in vitro investigations difficult. Computational methods offer a solution to understanding the bacteria involved and how they may interact with the host, ultimately providing a way to identify targets for future hypothesis-driven investigative work. Here, we present the first combined global analysis of bacterial community transcripts together with the host immune response in healthy and diseased ovine feet during a natural polymicrobial infection state using metatranscriptomics. The intratissue and surface bacterial populations and the most abundant bacterial transcriptomes were analyzed, demonstrating that footrot-affected skin has reduced diversity and increased abundances of not only the causative bacterium Dichelobacter nodosus but also other species such as Mycoplasma fermentans and Porphyromonas asaccharolytica. Host transcriptomics reveals the suppression of biological processes related to skin barrier function, vascular functions, and immunosurveillance in unhealthy interdigital skin, supported by histological findings that type I collagen (associated with scar tissue formation) is significantly increased in footrot-affected interdigital skin compared to outwardly healthy skin. Finally, we provide some interesting indications of host and pathogen interactions associated with virulence genes and the host spliceosome, which could lead to the identification of future therapeutic targets.

Evolution of the sheep industry and genetic research in the United States: opportunities for convergence in the twenty-first century

The continuous development and application of technology for genetic improvement is a key element for advancing sheep production in the United States. The US sheep industry has contracted over time but appears to be at a juncture where a greater utilization of technology can facilitate industry expansion to new markets and address inefficiencies in traditional production practices. Significant transformations include the increased value of lamb in relation to wool, and a downtrend in large-scale operations but a simultaneous rise in small flocks. Additionally, popularity of hair breeds not requiring shearing has surged, particularly in semi-arid and subtropical US environments. A variety of domestically developed composite breeds and newly established technological approaches are now widely available for the sheep industry to use as it navigates these ongoing transformations. These genetic resources can also address long-targeted areas of improvement such as growth, reproduction and parasite resistance. Moderate progress in production efficiency has been achieved by producers who have employed estimated breeding values, but widespread adoption of this technology has been limited. Genomic marker panels have recently shown promise for reducing disease susceptibility, identifying parentage and providing a foundation for marker-assisted selection. As the ovine genome is further explored and genomic assemblies are improved, the sheep research community in the USA can capitalize on new-found information to develop and apply genetic technologies to improve the production efficiency and profitability of the sheep industry.

British Sheep Breeds as a Part of World Sheep Gene Pool Landscape: Looking into Genomic Applications

Sheep farming has been an important sector of the UK's economy and rural life for many centuries. It is the favored source of wool, meat and milk products. In the era of exponential progress in genomic technologies, we can now address the questions of what is special about UK sheep breed genotypes and how they differ genetically form one another and from other countries. We can reflect how their natural history has been determined at the level of their genetic code and what traces have been left in their genomes because of selection for phenotypic traits. These include adaptability to certain environmental conditions and management, as well as resistance to disease. Application of these advancements in genetics and genomics to study sheep breeds of British domestic selection has begun and will continue in order to facilitate conservation solutions and production improvement.

Association of TLR2 haplotypes encoding Q650 with reduced susceptibility to ovine Johne's disease in Turkish sheep

Ovine Johne’s disease (OJD) is caused by Mycobacterium avium subsp. paratuberculosis (MAP) and carries a potential zoonotic risk for humans. Selective breeding strategies for reduced OJD susceptibility would be welcome tools in disease eradication efforts, if available. The Toll-like receptor 2 gene (TLR2) plays an important signaling role in immune response to MAP, and missense variants are associated with mycobacterial infections in mammals. Our aim was to identify and evaluate ovine TLR2 missense variants for association with OJD in Turkish sheep. Eleven TLR2 missense variants and 17 haplotype configurations were identified in genomic sequences of 221 sheep from 61 globally-distributed breeds. The five most frequent haplotypes were tested for OJD association in 102 matched pairs of infected and uninfected ewes identified in 2257 Turkish sheep. Ewes with one or two copies of TLR2 haplotypes encoding glutamine (Q) at position 650 (Q650) in the Tir domain were 6.6-fold more likely to be uninfected compared to ewes with arginine (R650) at that position (CI₉₅ = 2.6 to 16.9, p-value = 3.7 × 10^–6). The protective TLR2 Q650 allele was present in at least 25% of breeds tested and thus may facilitate selective breeding for sheep with reduced susceptibility to OJD.

A Systematic Review of Genomic Regions and Candidate Genes Underlying Behavioral Traits in Farmed Mammals and Their Link with Human Disorders

Simple Summary

This study is a comprehensive review of genomic regions associated with animal behavior in farmed mammals (beef and dairy cattle, pigs, and sheep) which contributes to a better understanding of the biological mechanisms influencing the target indicator trait and to gene expression studies by suggesting genes likely controlling the trait, and it will be useful in optimizing genomic predictions of breeding values incorporating biological information. Behavioral mechanisms are complex traits, genetically controlled by multiple genes spread across the whole genome. The majority of the genes identified in cattle, pigs, and sheep in association with a plethora of behavioral measurements (e.g., temperament, terrain use, milking speed, tail biting, and sucking reflex) are likely controlling stimuli reception (e.g., olfactory), internal recognition of stimuli (e.g., neuroactive ligand–receptor interaction), and body response to a stimulus (e.g., blood pressure, fatty acidy metabolism, hormone signaling, and inflammatory pathways). Six genes were commonly identified between cattle and pigs. About half of the genes for behavior identified in farmed mammals were also identified in humans for behavioral, mental, and neuronal disorders. Our findings indicate that the majority of the genes identified are likely controlling animal behavioral outcomes because their biological functions as well as potentially differing allele frequencies between two breed groups (subjectively) clustered based on their temperament characteristics.

Abstract

The main objectives of this study were to perform a systematic review of genomic regions associated with various behavioral traits in the main farmed mammals and identify key candidate genes and potential causal mutations by contrasting the frequency of polymorphisms in cattle breeds with divergent behavioral traits (based on a subjective clustering approach). A total of 687 (cattle), 1391 (pigs), and 148 (sheep) genomic regions associated with 37 (cattle), 55 (pigs), and 22 (sheep) behavioral traits were identified in the literature. In total, 383, 317, and 15 genes overlap with genomic regions identified for cattle, pigs, and sheep, respectively. Six common genes (e.g., NR3C2, PITPNM3, RERG, SPNS3, U6, and ZFAT) were found for cattle and pigs. A combined gene-set of 634 human genes was produced through identified homologous genes. A total of 313 out of 634 genes have previously been associated with behavioral, mental, and neurologic disorders (e.g., anxiety and schizophrenia) in humans. Additionally, a total of 491 candidate genes had at least one statistically significant polymorphism (p-value < 0.05). Out of those, 110 genes were defined as having polymorphic regions differing in greater than 50% of exon regions. Therefore, conserved genomic regions controlling behavior were found across farmed mammal species and humans.

The Future of Livestock Management: A Review of Real-Time Portable Sequencing Applied to Livestock

Oxford Nanopore Technologies' MinION has proven to be a valuable tool within human and microbial genetics. Its capacity to produce long reads in real time has opened up unique applications for portable sequencing. Examples include tracking the recent African swine fever outbreak in China and providing a diagnostic tool for disease in the cassava plant in Eastern Africa. Here we review the current applications of Oxford Nanopore sequencing in livestock, then focus on proposed applications in livestock agriculture for rapid diagnostics, base modification detection, reference genome assembly and genomic prediction. In particular, we propose a future application: 'crush-side genotyping' for real-time on-farm genotyping for extensive industries such as northern Australian beef production. An initial in silico experiment to assess the feasibility of crush-side genotyping demonstrated promising results. SNPs were called from simulated Nanopore data, that included the relatively high base call error rate that is characteristic of the data, and calling parameters were varied to understand the feasibility of SNP calling at low coverages in a heterozygous population. With optimised genotype calling parameters, over 85% of the 10,000 simulated SNPs were able to be correctly called with coverages as low as 6×. These results provide preliminary evidence that Oxford Nanopore sequencing has potential to be used for real-time SNP genotyping in extensive livestock operations.

Whole transcriptome approach to evaluate the effect of aluminium hydroxide in ovine encephalon

Aluminium hydroxide adjuvants are crucial for livestock and human vaccines. Few studies have analysed their effect on the central nervous system in vivo. In this work, lambs received three different treatments of parallel subcutaneous inoculations during 16 months with aluminium-containing commercial vaccines, an equivalent dose of aluminium hydroxide or mock injections. Brain samples were sequenced by RNA-seq and miRNA-seq for the expression analysis of mRNAs, long non-coding RNAs and microRNAs and three expression comparisons were made. Although few differentially expressed genes were identified, some dysregulated genes by aluminium hydroxide alone were linked to neurological functions, the lncRNA TUNA among them, or were enriched in mitochondrial energy metabolism related functions. In the same way, the miRNA expression was mainly disrupted by the adjuvant alone treatment. Some differentially expressed miRNAs had been previously linked to neurological diseases, oxidative stress and apoptosis. In brief, in this study aluminium hydroxide alone altered the transcriptome of the encephalon to a higher degree than commercial vaccines that present a milder effect. The expression changes in the animals inoculated with aluminium hydroxide suggest mitochondrial disfunction. Further research is needed to elucidate to which extent these changes could have pathological consequences.

Molecular basis of a new ovine model for human 3M syndrome-2

Background

Brachygnathia, cardiomegaly and renal hypoplasia syndrome (BCRHS, OMIA 001595–9940) is a previously reported recessively inherited disorder in Australian Poll Merino/Merino sheep. Affected lambs are stillborn with various congenital defects as reflected in the name of the disease, as well as short stature, a short and broad cranium, a small thoracic cavity, thin ribs and brachysternum. The BCRHS phenotype shows similarity to certain human short stature syndromes, in particular the human 3M syndrome-2. Here we report the identification of a likely disease-causing variant and propose an ovine model for human 3M syndrome-2.

Results

Eight positional candidate genes were identified among the 39 genes in the approximately 1 Mb interval to which the disease was mapped previously. Obscurin like cytoskeletal adaptor 1 (OBSL1) was selected as a strong positional candidate gene based on gene function and the resulting phenotypes observed in humans with mutations in this gene. Whole genome sequencing of an affected lamb (BCRHS3) identified a likely causal variant ENSOARG00000020239:g.220472248delC within OBSL1. Sanger sequencing of seven affected, six obligate carrier, two phenotypically unaffected animals from the original flock and one unrelated control animal validated the variant. A genotyping assay was developed to genotype 583 animals from the original flock, giving an estimated allele frequency of 5%.

Conclusions

The identification of a likely disease-causing variant resulting in a frameshift (p.(Val573Trpfs*119)) in the OBSL1 protein has enabled improved breeding management of the implicated flock. The opportunity for an ovine model for human 3M syndrome and ensuing therapeutic research is promising given the availability of carrier ram semen for BCRHS.

Ovine congenital progressive muscular dystrophy (OCPMD) is a model of TNNT1 congenital myopathy

Ovine congenital progressive muscular dystrophy (OCPMD) was first described in Merino sheep flocks in Queensland and Western Australia in the 1960s and 1970s. The most prominent feature of the disease is a distinctive gait with stiffness of the hind limbs that can be seen as early as 3 weeks after birth. The disease is progressive. Histopathological examination had revealed dystrophic changes specifically in type I (slow) myofibres, while electron microscopy had demonstrated abundant nemaline bodies. Therefore, it was never certain whether the disease was a dystrophy or a congenital myopathy with dystrophic features. In this study, we performed whole genome sequencing of OCPMD sheep and identified a single base deletion at the splice donor site (+ 1) of intron 13 in the type I myofibre-specific TNNT1 gene (KT218690 c.614 + 1delG). All affected sheep were homozygous for this variant. Examination of TNNT1 splicing by RT-PCR showed intron retention and premature termination, which disrupts the highly conserved 14 amino acid C-terminus. The variant did not reduce TNNT1 protein levels or affect its localization but impaired its ability to modulate muscle contraction in response to Ca²⁺ levels. Identification of the causative variant in TNNT1 finally clarifies that the OCPMD sheep is in fact a large animal model of TNNT1 congenital myopathy. This model could now be used for testing molecular or gene therapies.

The First Draft Genome Assembly of Snow Sheep (Ovis nivicola)

The snow sheep, Ovis nivicola, which is endemic to the mountain ranges of northeastern Siberia, are well adapted to the harsh cold climatic conditions of their habitat. In this study, using long reads of Nanopore sequencing technology, whole-genome sequencing, assembly, and gene annotation of a snow sheep were carried out. Additionally, RNA-seq reads from several tissues were also generated to supplement the gene prediction in snow sheep genome. The assembled genome was ∼2.62 Gb in length and was represented by 7,157 scaffolds with N50 of about 2 Mb. The repetitive sequences comprised of 41% of the total genome. BUSCO analysis revealed that the snow sheep assembly contained full-length or partial fragments of 97% of mammalian universal single-copy orthologs (n = 4,104), illustrating the completeness of the assembly. In addition, a total of 20,045 protein-coding sequences were identified using comprehensive gene prediction pipeline. Of which 19,240 (∼96%) sequences were annotated using protein databases. Moreover, homology-based searches and de novo identification detected 1,484 tRNAs; 243 rRNAs; 1,931 snRNAs; and 782 miRNAs in the snow sheep genome. To conclude, we generated the first de novo genome of the snow sheep using long reads; these data are expected to contribute significantly to our understanding related to evolution and adaptation within the Ovis genus.

Bovine Genome Database: new annotation tools for a new reference genome

The Bovine Genome Database (BGD) (http://bovinegenome.org) has been the key community bovine genomics database for more than a decade. To accommodate the increasing amount and complexity of bovine genomics data, BGD continues to advance its practices in data acquisition, curation, integration and efficient data retrieval. BGD provides tools for genome browsing (JBrowse), genome annotation (Apollo), data mining (BovineMine) and sequence database searching (BLAST). To augment the BGD genome annotation capabilities, we have developed a new Apollo plug-in, called the Locus-Specific Alternate Assembly (LSAA) tool, which enables users to identify and report potential genome assembly errors and structural variants. BGD now hosts both the newest bovine reference genome assembly, ARS-UCD1.2, as well as the previous reference genome, UMD3.1.1, with cross-genome navigation and queries supported in JBrowse and BovineMine, respectively. Other notable enhancements to BovineMine include the incorporation of genomes and gene annotation datasets for non-bovine ruminant species (goat and sheep), support for multiple assemblies per organism in the Regions Search tool, integration of additional ontologies and development of many new template queries. To better serve the research community, we continue to focus on improving existing tools, developing new tools, adding new datasets and encouraging researchers to use these resources.

Ovine C-type lectin receptor hFc-fusion protein library - A novel platform to screen for host-pathogen interactions

C-type lectin receptors (CTLRs) are pattern recognition receptors which are important constituents of the innate immunity. However, their role has mostly been studied in humans and in mouse models. To bridge the knowledge gap concerning CTLRs of veterinary relevant species, a novel ovine CTLR hFc-fusion protein library which allows in vitro ligand identification and pathogen binding studies has been established. Its utility was tested with known ligands of corresponding murine CTLRs in ELISA- and flow cytometry based binding studies. The ovine CTLR-hFc library was subsequently used in a proof-of-principle pathogen binding study with the ruminant pathogen Mycoplasma mycoides subsp. capri. Some ovine CTLRs, such as Dendritic Cell Immunoreceptor (DCIR, Clec4a), Macrophage C-Type Lectin (MCL, Clec4d) and Myeloid Inhibitory C-Type Lectin-Like Receptor (MICL, Clec12a) were identified as possible candidate receptors whose role in Mycoplasma recognition can now be unraveled in further studies. This study thus shows the utility of this novel ovine CTLR-hFc fusion protein library to screen for CTLR/pathogen interactions.

Comparing the diversity of the casein genes in the Asian mouflon and domestic sheep

We aimed to determine whether casein variants that are currently segregating in ovine populations existed before the domestication of sheep or, to the contrary, if their emergence is much more recent. To this end, we have retrieved whole-genome sequences from Iranian and domestic sheep from Africa, Europe, South and East Asia and West Asia. Population structure analysis based on 55,352,935 SNPs revealed a clear separation between Iranian mouflons and domestic sheep. Moreover, we also observed a strong genetic differentiation between Iranian mouflons sampled in geographic areas close to Tehran and Tabriz. Based on sequence data, hundreds of SNPs mapping to the casein α_S1 (CSN1S1, 248 SNPs), casein α_S2 (CSN1S2, 268 SNPs), casein ß (CSN2, 146 SNPs) and casein κ (CSN3, 112 SNPs) genes were identified. Approximately 25-63.02% of the casein variation was shared between Iranian mouflons and domestic sheep, and the four domestic sheep populations also shared 44.2-57.4% of the casein polymorphic sites. These findings suggest that an important fraction of the casein variation present in domestic sheep was already segregating in the mouflon prior to its domestication. Genomic studies performed in horses and dogs are consistent with this view, suggesting that much of the diversity that we currently detect in domestic animals comes from standing variation already segregating in their wild ancestors.

Identification of Some Errors in the Genome Assembly of Bovidae by FISH

From an economic point of view, Bovidae represent the most important family of the Ruminantia suborder. Thus, the mitochondrial and nuclear genomes of Bos taurus were among the first genomes to be sequenced after the sequencing of the human genomes. Over the millennia, the evolution of the genomes of the 3 main species belonging to the Bovidae family - B. taurus (BTA), Ovis aries (OAR), and Capra hircus (CHI) - has led to few chromosome rearrangements. Certainly, the availability and free access to the animal genomes significantly contributed to the improvement of animal genetics; however, some errors may exist due to the high automation in the genomic assembly construction process. In this work, some differences between the genomes of cattle, goat, and sheep highlighted by bioinformatics analysis have been verified by FISH, confirming that some errors persist even in the most recent genome assemblies. This type of approach has allowed us to detect a misassembly of a region belonging to BTA16 and to the homologues OAR12 and CHI16, a misassembly of a short tract in BTA22, OAR19, and CHI22, an incorrect mapping of a region of BTA21 and of CHI27 and OAR26, a discrepancy in the BTA26, OAR22, and CHI26 assemblies, a missed inversion in CHI1 compared to BTA1 and OAR1, and the exact assembly of a region of about 7 Mb in OAR10 and CHI12. Incorrect positioning of genomic tracts can cause unintended consequences in genetic analyses, especially when the data represent a starting point for the construction of genetic tools. In the new genomic assemblies published after the conclusion of our experiments, however, the accuracy in the construction of animal assemblies has been much improved, even if the new assemblies present more extended unmapped portions than the previous versions. The gap could be filled by comparative analyses between similar species or FISH.

Molecular Characterization and Expression Profiles of the Ovine LHβ Gene and Its Association with Litter Size in Chinese Indigenous Small-Tailed Han Sheep

Simple Summary

Litter size is one of the most important reproductive traits in sheep, and the luteinizing hormone beta polypeptide (LHβ) plays an important role in mammalian follicular development. In this study, we cloned and analyzed the cDNA sequence of the ovine LHβ gene, and the expression patterns of LHβ were determined. Furthermore, the synonymous mutation g.727C > T detected in the LHβ gene was confirmed to be significantly associated with litter size (p < 0.01). These findings support LHβ g.727C > T as a genetic marker for litter size in sheep.

Abstract

The luteinizing hormone beta polypeptide (LHβ) is a glycoprotein hormone secreted by basophilic granular cells of the adenohypophysis, and plays an important role in mammalian follicular development. In this study, we cloned and analyzed the cDNA sequence of the ovine LHβ gene. RT-qPCR analysis showed that ovine LHβ was widely expressed in tissues, with significantly higher expression in the hypophysis than that in other tissues (heart, liver, spleen, lung, kidney, rumen, duodenum, muscle, fat, hypothalamus, and sex glands) (p < 0.01). Hypophyseal expression of LHβ mRNA in lamb increased with age and reached a peak at 70 days, although a slight decrease was observed at 84 days of age. In addition, the synonymous mutation g.727C > T detected in the LHβ gene was confirmed to be significantly associated with the litter size (p < 0.01). Ewes carrying the TT genotype produced more lambs than those carrying the TC and CC genotypes (0.42 and 0.39 per delivery, respectively; p < 0.05). Our results confirm the association of ovine LHβ with litter size in Small-Tailed Han Sheep and implicate LHβ as a candidate for improving reproductive traits in agricultural sheep breeding programs.

Fetal androgen exposure is a determinant of adult male metabolic health

Androgen signalling is a critical driver of male development. Fetal steroid signalling can be dysregulated by a range of environmental insults and clinical conditions. We hypothesised that poor adult male health was partially attributable to aberrant androgen exposure during development. Testosterone was directly administered to developing male ovine fetuses to model excess prenatal androgenic overexposure associated with conditions such as polycystic ovary syndrome (PCOS). Such in utero androgen excess recreated the dyslipidaemia and hormonal profile observed in sons of PCOS patients. 1,084 of 15,134 and 408 of 2,766 quantifiable genes and proteins respectively, were altered in the liver during adolescence, attributable to fetal androgen excess. Furthermore, prenatal androgen excess predisposed to adolescent development of an intrahepatic cholestasis-like condition with attendant hypercholesterolaemia and an emergent pro-fibrotic, pro-oxidative stress gene and protein expression profile evident in both liver and circulation. We conclude that prenatal androgen excess is a previously unrecognised determinant of lifelong male metabolic health.

New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes

BACKGROUND

Mammalian X chromosomes are mainly euchromatic with a similar size and structure among species whereas Y chromosomes are smaller, have undergone substantial evolutionary changes and accumulated male specific genes and genes involved in sex determination. The pseudoautosomal region (PAR) is conserved on the X and Y and pair during meiosis. The structure, evolution and function of mammalian sex chromosomes, particularly the Y chromsome, is still poorly understood because few species have high quality sex chromosome assemblies.

RESULTS

Here we report the first bovine sex chromosome assemblies that include the complete PAR spanning 6.84 Mb and three Y chromosome X-degenerate (X-d) regions. The PAR comprises 31 genes, including genes that are missing from the X chromosome in current cattle, sheep and goat reference genomes. Twenty-nine PAR genes are single-copy genes and two are multi-copy gene families, OBP, which has 3 copies and BDA20, which has 4 copies. The Y chromosome X-d1, 2a and 2b regions contain 11, 2 and 2 gametologs, respectively.

CONCLUSIONS

The ruminant PAR comprises 31 genes and is similar to the PAR of pig and dog but extends further than those of human and horse. Differences in the pseudoautosomal boundaries are consistent with evolutionary divergence times. A bovidae-specific expansion of members of the lipocalin gene family in the PAR reported here, may affect immune-modulation and anti-inflammatory responses in ruminants. Comparison of the X-d regions of Y chromosomes across species revealed that five of the X-Y gametologs, which are known to be global regulators of gene activity and candidate sexual dimorphism genes, are conserved.

Blood transcriptome analysis in a buck-ewe hybrid and its parents

Examples of living sheep-goat hybrids are rare, mainly due to incorrect chromosome pairing, which is thought to be the main cause for species incompatibility. This case represents the first report of a buck-ewe hybrid and the first mammalian hybrid to be analyzed with next generation sequencing. The buck-ewe hybrid had an intermediate karyotype to the parental species, with 57 chromosomes. Analysis of the blood transcriptomes of the hybrid and both parents revealed that gene expression levels differed between the hybrid and its parents. This could be explained in part by age-dependent differences in gene expression. Contribution to the geep transcriptome was larger from the paternal, compared to the maternal, genome. Furthermore, imprinting patterns deviated considerably from what is known from other mammals. Potentially deleterious variants appeared to be compensated for by monoallelic expression of transcripts. Hence, the data imply that the buck-ewe hybrid compensated for the phylogenetic distance between the parental species by several mechanisms: adjustment of gene expression levels, adaptation to imprinting incompatibilities, and selective monoallelic expression of advantageous transcripts. This study offers a unique opportunity to gain insights into the transcriptome biology and regulation of a hybrid mammal.

Molecular Dating of the Emergence of Anaerobic Rumen Fungi and the Impact of Laterally Acquired Genes

The anaerobic gut fungi (AGF), or Neocallimastigomycota, inhabit the rumen and alimentary tract of herbivorous mammals, where they play important roles in the degradation of plant fiber. Comparative genomic and phylogenomic analyses of the AGF have long been hampered by their fastidious growth condition, as well as their large (up to 200 Mb) and AT-biased (78 to 84%) genomes. We sequenced 21 AGF transcriptomes and combined them with 5 available AGF genome sequences to explore their evolutionary relationships, time their divergence, and characterize gene gain/loss patterns associated with their evolution. We estimate that the most recent common ancestor of the AGF diverged 66 (±10) million years ago, a time frame that coincides with the evolution of grasses (Poaceae), as well as the mammalian transition from insectivory to herbivory. The concordance of independent estimations suggests that AGF have been important in shaping the success of mammalian herbivory transition by improving the efficiency of energy acquisition from recalcitrant plant materials. Comparative genomics identified multiple lineage-specific genes in the AGF, two of which were acquired from rumen gut bacteria and animal hosts via horizontal gene transfer (HGT). A third AGF domain, plant-like polysaccharide lyase, represents a novel gene in fungi that potentially aids AGF to degrade pectin. Analysis of genomic and transcriptomic sequences confirmed both the presence and expression of these lineage-specific genes in nearly all AGF clades. These genetic elements may contribute to the exceptional abilities of AGF to degrade plant biomass and enable metabolism of the rumen microbes and animal hosts.IMPORTANCE Anaerobic fungi living in the rumen of herbivorous mammals possess an extraordinary ability to degrade plant biomass. We examined the origin and genomic composition of these poorly characterized anaerobic gut fungi using both transcriptome and genomic data. Phylogenomics and molecular dating analyses found remarkable concurrence of the divergence times of the rumen fungi, the forage grasses, and the dietary shift of ancestral mammals from primarily insectivory to herbivory. Comparative genomics identified unique machinery in these fungi to utilize plant polysaccharides. The rumen fungi were also identified with the ability to code for three protein domains with putative functions in plant pectin degradation and microbial defense, which were absent from all other fungal organisms (examined over 1,000 fungal genomes). Two of these domains were likely acquired from rumen gut bacteria and animal hosts separately via horizontal gene transfer. The third one is a plant-like polysaccharide lyase, representing a unique fungal enzyme with potential pectin breakdown abilities.

Low genome-wide homozygosity in 11 Spanish ovine breeds

The population of Spanish sheep has decreased from 24 to 15 million heads in the last 75 years due to multiple social and economic factors. Such a demographic reduction might have caused an increase in homozygosity and inbreeding, thus limiting the viability of local breeds with excellent adaptations to harsh ecosystems. The main goal of our study was to investigate the homozygosity patterns of 11 Spanish ovine breeds and to elucidate the relationship of these Spanish breeds with reference populations from Europe, Africa and the Near East. By using Ovine SNP50 BeadChip data retrieved from previous publications, we have found that the majority of studied Spanish ovine breeds have close genetic relatedness with other European populations; the one exception is the Canaria de Pelo breed, which is similar to North African breeds. Our analysis has also demonstrated that, with few exceptions, the genomes of Spanish sheep harbor fewer than 50 runs of homozygosity (ROH) with a total length of less than 350 Mb. Moreover, the frequencies of very long ROH (>30 Mb) are very low, and the inbreeding coefficients (F_ROH ) are generally small (F_ROH  < 0.10), ranging from 0.008 (Rasa Aragonesa) to 0.086 (Canaria de Pelo). The low levels of homozygosity observed in the 11 Spanish sheep under analysis might be due to their extensive management and the high number of small to medium farms.

Molecular cloning and cellular expression of the cholesterol synthesizing enzymes during the prenatal development of the optic nerve in the dromedary camel (Camelus Dromedarius)

The Cholesterol-synthesizing proteins (HMGCS1 and HMGCS2) are mitochondrial enzymes that believed to catalyze the first reaction of ketogenesis, the process by which energy is provided from fats in the absence of carbohydrates. Typically, astrocytes developed from its progenitor cells in the embryonic optic nerve and enriched with HMGCS1 and 2. However, the detailed histomorphology of camel HMGCS1 and 2 remains to be clearly defined. Here, we investigated the changes that associate with astrocytes differentiation within the developing camel optic nerve. Firstly, we isolated cDNAs encoding HMGCS1 and 2 from the optic nerve. Then, we found that HMGCS1 shared high similarity to human, while HMGCS2 showed a lower similarity and was more diverse. Immunohistochemical studies revealed that distinct correlation of astrocytes differentiation with HMGCS1 and 2 expressions in the developing camel optic nerve. Both encoded proteins were localized throughout the cytoplasm, as well as the nuclei of the astrocytes. In addition, semi-quantitative PCR analysis and western analysis confirmed that both HMGCS1 and 2 were highly expressed in camel optic nerve as well as other tissue, but they were lower in both skeletal and heart muscles. Moreover, various stains such as Sudan black and florescence filipin stains were used to visualize the free cholesterol in the astrocytes, indicating the enzymatic activity of HMGCS1 and 2. Together, our study reported the first comprehensive investigation of the molecular cloning and cellular expression of HMGCS1 and 2 in the optic nerve of dromedary camel.

Screening and evaluating of long non-coding RNAs in prenatal and postnatal pituitary gland of sheep

Long non-coding RNAs are transcribed into RNA molecules that are >200 nucleotides in length. However, the expression and function analysis of lncRNAs in the sheep pituitary gland are still lacking. In this study, we identified 1755 lncRNAs (545 annotated lncRNAs and 1210 novel lncRNAs) from RNA-seq data in the pituitary gland of embryonic and adult sheep. A total of 235 lncRNAs were differentially expressed between embryonic and adult group. We verified the presence of some lncRNAs using RT-PCR and DNA sequencing, and identified some differentially expressed lncRNAs using qPCR. We also investigated the role of cis-acting lncRNAs on target genes. GO and KEGG enrichment analysis revealed that the target genes of lncRNAs were involved in the regulation of hormones secretion and some signaling pathways in the sheep pituitary gland. Our study provides comprehensive expression profiles of lncRNAs and valuable resource for understanding their function in the pituitary gland.

Novel report on mutation in exon 3 of myostatin (MSTN) gene in Nilagiri sheep: an endangered breed of South India

The variability in breeding program leads to rapid loss of genetic potential for which National Bureau of Animal Genetic Resources is emphasized to conserve the indigenous breeds. The variation in myostatin (MSTN) gene and its association with growth traits will throw light on its potential use as marker in selection. Hence, the study was conducted to detect polymorphism in exon 3 of MSTN, one of the most important growth regulatory gene and its association with growth in Nilagiri sheep breed. Blood samples were collected from Nilagiri sheep (n = 103) of South India and growth data up to 1 year of age was recorded. Genomic DNA was isolated and amplified for part of MSTN gene; PCR products were genotyped by restriction digestion (MspI) and confirmed by sequencing. Restriction digestion has revealed a single nucleotide polymorphism at locus G5622C in exon 3 which was confirmed by sequencing. The wild-type DNA molecule (MM) cleaved by MspI produced 301-bp and 314-bp fragments and those with mutation (mm) would remain undigested. The genotypic frequencies were MM (0.689) and Mm (0.311) with complete absence of mm genotype; and allelic frequencies were M (0.8445) and m (0.1555). The locus was in Hardy-Weinberg equilibrium. The association analysis revealed that there was no significant difference in mean birth, weaning, 6-, 9-, and 12-month weight between MM and Mm genotypes at g.5622G>C locus of exon 3 of MSTN gene. This is the first report of mutation in exon 3 of MSTN gene. The non-significant effect and absence of mm genotype at this locus needs further studies based on large population size and haplotype analysis.

Accuracy of imputation to whole-genome sequence in sheep

Background

The use of whole-genome sequence (WGS) data for genomic prediction and association studies is highly desirable because the causal mutations should be present in the data. The sequencing of 935 sheep from a range of breeds provides the opportunity to impute sheep genotyped with single nucleotide polymorphism (SNP) arrays to WGS. This study evaluated the accuracy of imputation from SNP genotypes to WGS using this reference population of 935 sequenced sheep.

Results

The accuracy of imputation from the Ovine Infinium^® HD BeadChip SNP (~ 500 k) to WGS was assessed for three target breeds: Merino, Poll Dorset and F1 Border Leicester × Merino. Imputation accuracy was highest for the Poll Dorset breed, although there were more Merino individuals in the sequenced reference population than Poll Dorset individuals. In addition, empirical imputation accuracies were higher (by up to 1.7%) when using larger multi-breed reference populations compared to using a smaller single-breed reference population. The mean accuracy of imputation across target breeds using the Minimac3 or the FImpute software was 0.94. The empirical imputation accuracy varied considerably across the genome; six chromosomes carried regions of one or more Mb with a mean imputation accuracy of < 0.7. Imputation accuracy in five variant annotation classes ranged from 0.87 (missense) up to 0.94 (intronic variants), where lower accuracy corresponded to higher proportions of rare alleles. The imputation quality statistic reported from Minimac3 (R²) had a clear positive relationship with the empirical imputation accuracy. Therefore, by first discarding imputed variants with an R² below 0.4, the mean empirical accuracy across target breeds increased to 0.97. Although accuracy of genomic prediction was less affected by filtering on R² in a multi-breed population of sheep with imputed WGS, the genomic heritability clearly tended to be lower when using variants with an R² ≤ 0.4.

Conclusions

The mean imputation accuracy was high for all target breeds and was increased by combining smaller breed sets into a multi-breed reference. We found that the Minimac3 software imputation quality statistic (R²) was a useful indicator of empirical imputation accuracy, enabling removal of very poorly imputed variants before downstream analyses.

Electronic supplementary material

The online version of this article (10.1186/s12711-018-0443-5) contains supplementary material, which is available to authorized users.

The Structure, Evolution, and Gene Expression Within the Caprine Leukocyte Receptor Complex

The leukocyte receptor complex (LRC) encodes a large number of immunoglobulin (Ig)-like receptors involved in the immune response, particularly in modulating natural killer (NK) cell function. The killer cell Ig-like receptors (KIR), the leukocyte Ig-like receptors (LILR), and a recently described novel Ig-like receptor family are highly variable between species, which is consistent with rapid evolution driven by selection pressure from pathogens. Among the species studied to date, only simians (such as humans) and bovids (such as cattle and goats) have an expanded complement of KIR genes and represent an interesting model to study KIR evolution. Using recently improved genome assemblies and an assembly of bacterial artificial chromosomes, we describe the structure of the LRC, and the KIR region in particular, in goats and compare this to sheep as the assemblies allow. These species diverged from a common ancestor ~10 million years ago and from cattle ~25 million years ago. We identified conserved KIR genes common to both goats and sheep and confirm a partial sheep haplotype shared between the Rambouillet and Texel breeds. Goats and sheep have independently expanded two novel KIR subgroups, and unlike cattle or any other mammal, they do not appear to possess a functional 3DL-lineage KIR gene. Investigation of LRC gene expression using available transcriptomic data for various sheep and goat tissues largely confirmed putative gene annotation and revealed that a relatively conserved caprinae-specific KIR subgroup is expressed in macrophages. The LILR and novel Ig-like receptors were also highly expressed across a diverse range of tissues. This further step toward our understanding of the LRC receptor repertoire will help inform future studies investigating immune response variation in these species.

Molecular Signature of Aluminum Hydroxide Adjuvant in Ovine PBMCs by Integrated mRNA and microRNA Transcriptome Sequencing

There have been few in vivo studies on the effect of aluminum hydroxide adjuvant and its influence on the immune response to vaccination. In this study, lambs received a parallel subcutaneous treatment with either commercial vaccines containing aluminum hydroxide or an equivalent dose of this compound only with the aim of identifying the activated molecular signature. Blood samples were taken from each animal at the beginning and at the end of the experiment and PBMCs isolated. Total RNA and miRNA libraries were prepared and sequenced. After alignment to the Oar3.1 reference genome and differential expression with 3 programs, gene enrichment modeling was performed. For miRNAs, miRBase and RNAcentral databases were used for detection and characterization. Three expression comparisons were made: vaccinated animals at the beginning and at the end of the treatment, adjuvanted animals at the same times, and animals of both treatments at the end of the experiment. After exposure to both treatments, a total of 2,473; 2,980 and 429 differentially expressed genes were identified in vaccinated animals, adjuvanted animals and animals at the end of both treatments, respectively. In both adjuvant and vaccine treated animals the NF-κB signaling pathway was enriched. On the other hand, it can be observed a downregulation of cytokines and cytokine receptors in the adjuvanted group compared to the vaccinated group at the final time, suggesting a milder induction of the immune response when the adjuvant is alone. As for the miRNA analysis, 95 miRNAs were detected: 64 previously annotated in Ovis aries, 11 annotated in Bos taurus and 20 newly described. Interestingly, 6 miRNAs were differentially expressed in adjuvant treated animals, and 3 and 1 in the other two comparisons. Lastly, an integrated miRNA-mRNA expression profile was developed, in which a miRNA-mediated regulation of genes related to DNA damage stimulus was observed. In brief, it seems that aluminum-containing adjuvants are not simple delivery vehicles for antigens, but also induce endogenous danger signals that can stimulate the immune system. Whether this contributes to long-lasting immune activation or to the overstimulation of the immune system remains to be elucidated.

Phylogenetic analysis of the cytochrome P450 (CYP450) nucleotide sequences of the horse and predicted CYP450s of the white rhinoceros (Ceratotherium simum) and other mammalian species

Background

The plight of the white rhinoceros (Ceratotherium simum) and the increasing need of treatment options for injured poaching victims led to the necessity to expand the knowledge on applicable drugs in this endangered species. With very little information available on drug pharmacokinetics in rhino, veterinarians have to rely on information generated from other species. The horse being a closely related species, has served as the model for dose extrapolations. However, from recent research on enrofloxacin and carprofen, the white rhino showed considerable differences in the pharmacokinetic properties of these drugs in comparison to the horse. While the reason for the differences is unknown, a likely cause may be a difference in present cytochrome P450 (CYP450), which may result in the rhino being genetically deficient in certain enzyme families.

Methods

For this paper we assess the degree of similarity of the CYP genome sequences across the different species, using BLAT (BLAST-like alignment tool) for the alignment of the nucleotide sequences of the equine CYP450 with potential homologous nucleotide sequences of the published database from white rhinos and other mammalian species (cow, pig, dog, sheep, elephant, mouse and human).

Results

The white rhino nucleotide sequences were 90.74% identical to the equine sequences. This was higher than the degree of similarity between any of the other evaluated species sequences. While no specific CYP family were found to be deficient in the published rhino genome, the horse genome contained additional genetic sequence for a larger number of iso-enzymes that were not present in the rhino.

Discussion

In pharmacokinetic study, it is well known that absence of a metabolic enzyme will result in constraints in drug metabolism and drug elimination. While this was our speculation, comparison to the horse and other mammalian species indicate that all the described CYP genes required for metabolism are present within the rhino genome. These results leave functional differences in enzyme activity and a lack of isoenzymes as the likely reason for the constraint in drug metabolism. Despite a more than 90% similarity of the equine and rhino gene sequences, seemingly small differences can have major effects on drug metabolism. Thus, in spite of the close anatomical relationship, the rhino should not simply be treated like a big horse.

Sheep as a model for evaluating mesenchymal stem/stromal cell (MSC)-based chondral defect repair

Osteoarthritis results from the degradation of articular cartilage and is one of the leading global causes of pain and immobility. Cartilage has a limited capacity for self-repair. While repair can be enhanced through surgical intervention, current methods often generate inferior fibrocartilage and repair is transient. The development of tissue engineering strategies to improve repair outcomes is an active area of research. While small animal models such as rodents and rabbits are often used in early pre-clinical work, larger animals that better recapitulate the anatomy and loading of the human joint are required for late-stage preclinical evaluation. Because of their physiological similarities to humans, and low cost relative to other large animals, sheep are routinely used in orthopedic research, including cartilage repair studies. In recent years, there has been considerable research investment into the development of cartilage repair strategies that utilize mesenchymal stem/stromal cells (MSC). In contrast to autologous chondrocytes derived from biopsies of articular cartilage, MSC offer some benefits including greater expansion capacity and elimination of the risk of morbidity at the cartilage biopsy site. The disadvantages of MSC are related to the challenges of inducing and maintaining a stable chondrocyte-like cell population capable of generating hyaline cartilage. Ovine MSC (oMSC) biology and their utility in sheep cartilage repair models have not been reviewed. Herein, we review the biological properties of MSC derived from sheep tissues, and the use of these cells to study articular cartilage repair in this large animal model.

Characterisation of the circulating acellular proteome of healthy sheep using LC-MS/MS-based proteomics analysis of serum

BACKGROUND

Unlike humans, there is currently no publicly available reference mass spectrometry-based circulating acellular proteome data for sheep, limiting the analysis and interpretation of a range of physiological changes and disease states. The objective of this study was to develop a robust and comprehensive method to characterise the circulating acellular proteome in ovine serum.

METHODS

Serum samples from healthy sheep were subjected to shotgun proteomic analysis using nano liquid chromatography nano electrospray ionisation tandem mass spectrometry (nanoLC-nanoESI-MS/MS) on a quadrupole time-of-flight instrument (TripleTOF® 5600+, SCIEX). Proteins were identified using ProteinPilot™ (SCIEX) and Mascot (Matrix Science) software based on a minimum of two unmodified highly scoring unique peptides per protein at a false discovery rate (FDR) of 1% software by searching a subset of the Universal Protein Resource Knowledgebase (UniProtKB) database (http://www.uniprot.org). PeptideShaker (CompOmics, VIB-UGent) searches were used to validate protein identifications from ProteinPilot™ and Mascot.

RESULTS

ProteinPilot™ and Mascot identified 245 and 379 protein groups (IDs), respectively, and PeptideShaker validated 133 protein IDs from the entire dataset. Since Mascot software is considered the industry standard and identified the most proteins, these were analysed using the Protein ANalysis THrough Evolutionary Relationships (PANTHER) classification tool revealing the association of 349 genes with 127 protein pathway hits. These data are available via ProteomeXchange with identifier PXD004989.

CONCLUSIONS

These results demonstrated for the first time the feasibility of characterising the ovine circulating acellular proteome using nanoLC-nanoESI-MS/MS. This peptide spectral data contributes to a protein library that can be used to identify a wide range of proteins in ovine serum.

Identification of key contributors in complex population structures

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.

A genome scan for milk production traits in dairy goats reveals two new mutations in Dgat1 reducing milk fat content

The quantity of milk and milk fat and proteins are particularly important traits in dairy livestock. However, little is known about the regions of the genome that influence these traits in goats. We conducted a genome wide association study in French goats and identified 109 regions associated with dairy traits. For a major region on chromosome 14 closely associated with fat content, the Diacylglycerol O-Acyltransferase 1 (DGAT1) gene turned out to be a functional and positional candidate gene. The caprine reference sequence of this gene was completed and 29 polymorphisms were found in the gene sequence, including two novel exonic mutations: R251L and R396W, leading to substitutions in the protein sequence. The R251L mutation was found in the Saanen breed at a frequency of 3.5% and the R396W mutation both in the Saanen and Alpine breeds at a frequencies of 13% and 7% respectively. The R396W mutation explained 46% of the genetic variance of the trait, and the R251L mutation 6%. Both mutations were associated with a notable decrease in milk fat content. Their causality was then demonstrated by a functional test. These results provide new knowledge on the genetic basis of milk synthesis and will help improve the management of the French dairy goat breeding program.