The African Goat Improvement Network: a scientific group empowering smallholder farmers.

The African Goat Improvement Network (AGIN) is a collaborative group of scientists focused on genetic improvement of goats in small holder communities across the African continent. The group emerged from a series of workshops focused on enhancing goat productivity and sustainability. Discussions began in 2011 at the inaugural workshop held in Nairobi, Kenya. The goals of this diverse group were to: improve indigenous goat production in Africa; characterize existing goat populations and to facilitate germplasm preservation where appropriate; and to genomic approaches to better understand adaptation. The long-term goal was to develop cost-effective strategies to apply genomics to improve productivity of small holder farmers without sacrificing adaptation. Genome-wide information on genetic variation enabled genetic diversity studies, facilitated improved germplasm preservation decisions, and provided information necessary to initiate large scale genetic improvement programs. These improvements were partially implemented through a series of community-based breeding programs that engaged and empowered local small farmers, especially women, to promote sustainability of the production system. As with many international collaborative efforts, the AGIN work serves as a platform for human capacity development. This paper chronicles the evolution of the collaborative approach leading to the current AGIN organization and describes how it builds capacity for sustained research and development long after the initial program funds are gone. It is unique in its effectiveness for simultaneous, multi-level capacity building for researchers, students, farmers and communities, and local and regional government officials. The positive impact of AGIN capacity building has been felt by participants from developing, as well as developed country partners.

Whole Genome Sequencing Provides Information on the Genomic Architecture and Diversity of Cultivated Gilthead Seabream (Sparus aurata) Broodstock Nuclei.

The gilthead seabream (Sparus aurata) is a species of relevance for the Mediterranean aquaculture industry. Despite the advancement of genetic tools for the species, breeding programs still do not often include genomics. In this study, we designed a genomic strategy to identify signatures of selection and genomic regions of high differentiation among populations of farmed fish stocks. A comparative DNA pooling sequencing approach was applied to identify signatures of selection in gilthead seabream from the same hatchery and from different nuclei that had not been subjected to genetic selection. Identified genomic regions were further investigated to detect SNPs with predicted high impact. The analyses underlined major genomic differences in the proportion of fixed alleles among the investigated nuclei. Some of these differences highlighted genomic regions, including genes involved in general metabolism and development already detected in QTL for growth, size, skeletal deformity, and adaptation to variation of oxygen levels in other teleosts. The obtained results pointed out the need to control the genetic effect of breeding programs in this species to avoid the reduction of genetic variability within populations and the increase in inbreeding level that, in turn, might lead to an increased frequency of alleles with deleterious effects.

Signatures of Selection and Genomic Diversity of Muskellunge (Esox masquinongy) from Two Populations in North America.

Muskellunge (Esox masquinongy) is the largest and most prized game fish in North America. However, little is known about Muskellunge genetic diversity in Iowa's propagation program. We used Whole-Genome Sequencing of 12 brooding individuals from Iowa and publicly available RAD-seq of 625 individuals from the St. Lawrence River in Canada to study the genetic differences between populations, analyze signatures of selection, and evaluate the levels of genetic diversity in both populations. Given that there is no reference genome available, reads were aligned to the genome of Pike (Esox lucius). Variant calling produced 7,886,471 biallelic variants for the Iowa population and 16,867 high-quality SNPs that overlap with the Canadian samples. Principal component analysis (PCA) and Admixture analyses showed a large genetic difference between Canadian and Iowan populations. Window-based pooled heterozygosity found 6 highly heterozygous windows in the Iowa population and Fst between populations found 14 windows with fixation statistic (Fst) values larger than 0.9. Canadian inbreeding rate (Froh = 0.32) appears to be higher due to the inbreeding of Iowa population (Froh = 0.03), presumably due to isolation of subpopulations. Although inbreeding does not seem to be an immediate concern for Muskellunge in Iowa, the Canadian population seems to have a high rate of inbreeding. Finally, this approach can be used to assess the long-term viability of the current management practices of Muskellunge populations across North America.

A genome-wide analysis of cardiac lesions of pigs that die during transport: Is heart failure of in-transit-loss pigs associated with a heritable cardiomyopathy?

While heart failure is a primary cause of death for many in-transit-loss (ITL) pigs, the underlying cause of these deaths is not known. Cardiomyopathies are considered a common cause of heart failure in humans and often have a genetic component. The objective of this study was to determine if genes associated with cardiomyopathies could be identified in ITL pigs. Samples from the hearts of pigs that died during transport to an abattoir in Ontario, Canada were collected and genotyped along with samples from pigs that did not die during transport (ILT hearts: n = 149; non-ITL/control hearts: n = 387). Genome-wide analyses were carried out on each of the determined phenotypes (gross cardiac lesions) using a medium density single nucleotide polymorphism (SNP) chip and 500 kb windows/regions for analysis, with 250 kb regions of overlap. The distribution derived by a multidimensional scaling (MDS) analysis of all phenotypes demonstrated a lack of complete separation between phenotypes of affected and unaffected animals, which made diagnosis difficult. Although genetic differences were small, a few genes associated with dilated cardiomyopathy (DCM) and arrhythmogenic right ventricular cardiomyopathy (ARVM) were identified. In addition, multiple genes associated with cardiac arrhythmias and ventricular hypertrophy were identified that can possibly result in heart failure. The results of this preliminary study did not provide convincing evidence that a single, heritable cardiomyopathy is the cause of heart failure in ITL pigs.

Bien que l'insuffisance cardiaque soit la principale cause de décès chez de nombreux porcs perdus en transit (ITL), la cause sous-jacente de ces décès n'est pas connue. Les cardiomyopathies sont considérées comme une cause fréquente d'insuffisance cardiaque chez l'homme et ont souvent une composante génétique. L'objectif de cette étude était de déterminer si des gènes associés aux cardiomyopathies pouvaient être identifiés chez les porcs ITL. Des échantillons de coeurs de porcs morts pendant le transport vers un abattoir en Ontario, au Canada, ont été prélevés et génotypés avec des échantillons de porcs qui ne sont pas morts pendant le transport (coeurs ILT: n = 149; coeurs non ITL/témoins: n = 387). Des analyses à l'échelle du génome ont été effectuées sur chacun des phénotypes déterminés (lésions cardiaques macroscopiques) en utilisant une puce de polymorphisme nucléotidique unique (SNP) de densité moyenne et des fenêtres/régions de 500 kb pour l'analyse, avec des régions de chevauchement de 250 kb. La distribution dérivée par une analyse de mise à l'échelle multidimensionnelle (MDS) de tous les phénotypes a démontré un manque de séparation complète entre les phénotypes des animaux affectés et non affectés, ce qui a rendu le diagnostic difficile. Bien que les différences génétiques soient minimes, quelques gènes associés à la cardiomyopathie dilatée (DCM) et à la cardiomyopathie arythmogène ventriculaire droite (ARVM) ont été identifiés. De plus, plusieurs gènes associés aux arythmies cardiaques et à l'hypertrophie ventriculaire ont été identifiés, pouvant éventuellement entraîner une insuffisance cardiaque. Les résultats de cette étude préliminaire n'ont pas fourni de preuves convaincantes qu'une seule cardiomyopathie héréditaire est la cause de l'insuffisance cardiaque chez les porcs ITL.(Traduit par Docteur Serge Messier).

Transcriptome Response of Liver and Muscle in Heat-Stressed Laying Hens.

Exposure to high ambient temperature has detrimental effects on poultry welfare and production. Although changes in gene expression due to heat exposure have been well described for broiler chickens, knowledge of the effects of heat on laying hens is still relatively limited. In this study, we profiled the transcriptome for pectoralis major muscle (n = 24) and liver (n = 24), during a 4-week cyclic heating experiment performed on layers in the early phase of egg production. Both heat-control and time-based contrasts were analyzed to determine differentially expressed genes (DEGs). Heat exposure induced different changes in gene expression for the two tissues, and we also observed changes in gene expression over time in the control animals suggesting that metabolic changes occurred during the transition from onset of lay to peak egg production. A total of 73 DEGs in liver were shared between the 3 h heat-control contrast, and the 4-week versus 3 h time contrast in the control group, suggesting a core set of genes that is responsible for maintenance of metabolic homeostasis regardless of the physiologic stressor (heat or commencing egg production). The identified DEGs improve our understanding of the layer's response to stressors and may serve as targets for genetic selection in the future to improve resilience.

An initial genome-wide investigation of protein-losing enteropathy in Gordon setters: Exploratory observations.

The objective of this preliminary study was to identify genomic regions that may predispose Gordon setters from the United Kingdom to familial protein-losing enteropathy (PLE) at a young age. A total of 106 related Gordon setters was used, including 6 affected dogs from an affected litter, 6 case controls from the same litter, 10 related/affected dogs, and 84 related/unaffected dogs. Genomic DNA was collected from each Gordon setter and extracted from buccal mucosal swabs. Genotyping of affected and unaffected dogs was carried out using the Canine Illumina HD SNP array and data generated were analyzed with PLINK software, using fixation index (Fst) and runs of homozygosity (ROH) methods. Pairwise Fst analyses between the affected and unaffected Gordon setter dogs identified various regions of differentiation on chromosomes 10, 18, 21, and 23 that contained several important genes. These regions revealed 5 candidate genes, including RARB, TTC7A, SOCS5, PIGF, and RHOD, that are associated with human inflammatory bowel disease (IBD) and could potentially be associated with PLE in Gordon setters. Run of homozygosity (ROH) analyses revealed additional unique regions on chromosomes 15 and 17. These regions contained genes SYT1, UCN, and FNDC that could also be potential candidates for PLE in Gordon setters. The biological functions of the identified genes provided initial insights into the pathophysiology of PLE. Further large-scale studies are warranted to investigate the possible causality of these genomic regions and any possible genetic markers that could be used in predicting susceptibility to PLE syndrome.

L'objectif de cette étude préliminaire était d'identifier les régions génomiques susceptibles de prédisposer les chiens Gordon setter du Royaume-Uni à l'entéropathie familiale de perte de protéines (PLE) à un jeune âge. Un total de 106 Gordon setter apparentés a été utilisé, dont six chiens affectés d'une portée affectée, six cas témoins de la même portée, 10 chiens apparentés/affectés et 84 chiens apparentés/non affectés. L'ADN génomique a été obtenu à partir de chaque Gordon setter et extrait des écouvillons de la muqueuse buccale. Le génotypage des chiens affectés et non affectés a été effectué à l'aide de la matrice SNP Canine Illumina HD et les données générées ont été analysées avec le logiciel PLINK, en utilisant des méthodes d'indice de fixation (Fst) et d'homozygotie (ROH). Des analyses Fst par paires entre les chiens Gordon setter affectés et non affectés ont identifié diverses régions de différenciation sur les chromosomes 10, 18, 21 et 23 qui contenaient plusieurs gènes importants. Ces régions ont révélé cinq gènes candidats, dont RARB, TTC7A, SOCS5, PIGF et RHOD, qui sont associés à la maladie inflammatoire de l'intestin (IBD) humaine et pourraient potentiellement être associés à la PLE chez les Gordon setter. Les analyses d'homozygotie (ROH) ont révélé des régions uniques supplémentaires sur les chromosomes 15 et 17. Ces régions contenaient les gènes SYT1, UCN et FNDC qui pourraient également être des candidats potentiels pour la PLE chez les Gordon setter. Les fonctions biologiques des gènes identifiés ont fourni un aperçu initial de la physiopathologie de la PLE. D'autres études à grande échelle sont nécessaires pour étudier la causalité possible de ces régions génomiques et tous les marqueurs génétiques possibles qui pourraient être utilisés pour prédire la sensibilité au syndrome PLE.(Traduit par Docteur Serge Messier).

Genetic Basis of Blood-Based Traits and Their Relationship With Performance and Environment in Beef Cattle at Weaning.

The objectives of this study were to explore the usefulness of blood-based traits as indicators of health and performance in beef cattle at weaning and identify the genetic basis underlying the different blood parameters obtained from complete blood counts (CBCs). Disease costs represent one of the main factors determining profitability in animal production. Previous research has observed associations between blood cell counts and an animal's health status in some species. CBC were recorded from approximately 570 Angus based, crossbred beef calves at weaning born between 2015 and 2016 and raised on toxic or novel tall fescue. The calves (N = ∼600) were genotyped at a density of 50k SNPs and the genotypes (N = 1160) were imputed to a density of 270k SNPs. Genetic parameters were estimated for 15 blood and 4 production. Finally, with the objective of identifying the genetic basis underlying the different blood-based traits, genome-wide association studies (GWAS) were performed for all traits. Heritability estimates ranged from 0.11 to 0.60, and generally weak phenotypic correlations and strong genetic correlations were observed among blood-based traits only. Genome-wide association study identified ninety-one 1-Mb windows that accounted for 0.5% or more of the estimated genetic variance for at least 1 trait with 21 windows overlapping across two or more traits (explaining more than 0.5% of estimated genetic variance for two or more traits). Five candidate genes have been identified in the most interesting overlapping regions related to blood-based traits. Overall, this study represents one of the first efforts represented in scientific literature to identify the genetic basis of blood cell traits in beef cattle. The results presented in this study allow us to conclude that: (1) blood-based traits have weak phenotypic correlations but strong genetic correlations among themselves. (2) Blood-based traits have moderate to high heritability. (3) There is evidence of an important overlap of genetic control among similar blood-based traits which will allow for their use in improvement programs in beef cattle.

Genome-wide scans identify known and novel regions associated with prolificacy and reproduction traits in a sub-Saharan African indigenous sheep (Ovis aries).

Maximizing the number of offspring born per female is a key functionality trait in commercial- and/or subsistence-oriented livestock enterprises. Although the number of offspring born is closely associated with female fertility and reproductive success, the genetic control of these traits remains poorly understood in sub-Saharan Africa livestock. Using selection signature analysis performed on Ovine HD BeadChip data from the prolific Bonga sheep in Ethiopia, 41 candidate regions under selection were identified. The analysis revealed one strong selection signature on a candidate region on chromosome X spanning BMP15, suggesting this to be the primary candidate prolificacy gene in the breed. The analysis also identified several candidate regions spanning genes not reported before in prolific sheep but underlying fertility and reproduction in other species. The genes associated with female reproduction traits included SPOCK1 (age at first oestrus), GPR173 (mediator of ovarian cyclicity), HB-EGF (signalling early pregnancy success) and SMARCAL1 and HMGN3a (regulate gene expression during embryogenesis). The genes involved in male reproduction were FOXJ1 (sperm function and successful fertilization) and NME5 (spermatogenesis). We also observed genes such as PKD2L2, MAGED1 and KDM3B, which have been associated with diverse fertility traits in both sexes of other species. The results confirm the complexity of the genetic mechanisms underlying reproduction while suggesting that prolificacy in the Bonga sheep, and possibly African indigenous sheep is partly under the control of BMP15 while other genes that enhance male and female fertility are essential for reproductive fitness.

Effects of acute and chronic heat stress on the performance, egg quality, body temperature, and blood gas parameters of laying hens.

The goal of this experiment was to measure the physiological response of individual laying hens exposed to heat stress (HS). Performance, egg quality, body temperature (BT), and blood chemistry of laying hens were individually recorded before and after various intervals of daily cyclic HS. In total, 407 18-week-old W-36 parent-line laying hens (Hy-Line International, Dallas Center, IA) were housed individually in battery cages. After an acclimation period, baseline data were collected from 22 to 24-wk before the hens were subjected to a daily cyclic HS consisting of 7 h at 35°C returning to 30°C for the remaining 17 h/D from 24 to 28-wk of age. Eggs were collected and individually weighed daily. Feed intake (FI), egg production (EP), egg weights, egg mass, BW, and feed efficiency (FE) (g egg/kg FI) were calculated over 2-wk time periods. Eggs were collected for quality assessment the day before HS began, the 2nd day of HS, and on a weekly basis throughout the 4-wk HS. Blood was collected and BT measured the day before heat HS was initiated, on the first day of HS, and again at 2 and 4-wk of HS. Blood PCO2 and iCa decreased, and blood pH increased within 4 to 6 h of HS (P ≤ 0.01). Shell weights decreased with acute HS, possibly due to the reduction in blood iCa (P ≤ 0.01). After 4-wk of HS the blood pH returned to pre-HS levels but iCa remained decreased (P ≤ 0.01). Shell weights remained low and Haugh units decreased after 2 and 4-wk of HS (P ≤ 0.01). Feed efficiency was increased and FI, EP, and BW decreased by 2-wk of HS and remained low through 4-wk (P ≤ 0.01). The cyclic HS had a significant effect on the performance, egg quality, and blood chemistry over the 4-wk HS.

Genetic lines respond uniquely within the chicken thymic transcriptome to acute heat stress and low dose lipopolysaccharide.

Exposure to high temperatures is known to impair immune functions and disease resistance of poultry. Characterizing changes in the transcriptome can help identify mechanisms by which immune tissues, such as the thymus, respond to heat stress. In this study, 22-day-old chickens from two genetic lines (a relatively resistant Fayoumi line and a more susceptible broiler line) were exposed to acute heat stress (35 °C) and/or immune simulation with lipopolysaccharide (LPS; 100 µg/kg). Transcriptome responses in the thymus were identified by RNA-sequencing (RNA-seq). Expression of most genes was unaffected by heat and/or LPS in the Fayoumi line, whereas these treatments had more impact in the broiler line. Comparisons between the broiler and Fayoumi transcriptomes identified a large number of significant genes both at homeostasis and in response to treatment. Functional analyses predicted that gene expression changes impact immune responses, apoptosis, cell activation, migration, and adhesion. In broilers, acute heat stress changed thymic expression responses to LPS and could impact thymocyte survival and trafficking, and thereby contribute to the negative effects of high temperatures on immune responses. Identification of these genes and pathways provides a foundation for testing targets to improve disease resistance in heat-stressed chickens.

Genetic analysis of production, physiological, and egg quality traits in heat-challenged commercial white egg-laying hens using 600k SNP array data.

BACKGROUND: Heat stress negatively affects the welfare and production of chickens. High ambient temperature is considered one of the most ubiquitous abiotic environmental challenges to laying hens around the world. In this study, we recorded several production traits, feed intake, body weight, digestibility, and egg quality of 400 commercial white egg-laying hens before and during a 4-week heat treatment. For the phenotypes that had estimated heritabilities (using 600k SNP chip data) higher than 0, SNP associations were tested using the same 600k genotype data. RESULTS: Seventeen phenotypes had heritability estimates higher than 0, including measurements at various time points for feed intake, feed efficiency, body weight, albumen weight, egg quality expressed in Haugh units, egg mass, and also for change in egg mass from prior to heat exposure to various time points during the 4-week heat treatment. Quantitative trait loci (QTL) were identified for 10 of these 17 phenotypes. Some of the phenotypes shared QTL including Haugh units before heat exposure and after 4 weeks of heat treatment. CONCLUSIONS: Estimated heritabilities differed from 0 for 17 traits, which indicates that they are under genetic control and that there is potential for improving these traits through selective breeding. The association of different QTL with the same phenotypes before heat exposure and during heat treatment indicates that genomic control of traits under heat stress is distinct from that under thermoneutral conditions. This study contributes to the knowledge on the genomic control of response to heat stress in laying hens.

Natural Selection Footprints Among African Chicken Breeds and Village Ecotypes.

Natural selection is likely a major factor in shaping genomic variation of the African indigenous rural chicken, driving the development of genetic footprints. Selection footprints are expected to be associated with adaptation to locally prevailing environmental stressors, which may include diverse factors as high altitude, disease resistance, poor nutrition, oxidative and heat stresses. To determine the existence of a selection footprint, 268 birds were randomly sampled from three indigenous ecotypes from East Africa (Rwanda and Uganda) and North Africa (Baladi), and two registered Egyptian breeds (Dandarawi and Fayoumi). Samples were genotyped using the chicken Affymetrix 600K Axiom® Array. A total of 494,332 SNPs were utilized in the downstream analysis after implementing quality control measures. The intra-population runs of homozygosity (ROH) that occurred in >50% of individuals of an ecotype or in >75% of a breed were studied. To identify inter-population differentiation due to genetic structure, FST was calculated for North- vs. East-African populations and Baladi and Fayoumi vs. Dandarawi for overlapping windows (500 kb with a step-size of 250 kb). The ROH and FST mapping detected several selective sweeps on different autosomes. Results reflected selection footprints of the environmental stresses, breed behavior, and management. Intra-population ROH of the Egyptian chickens showed selection footprints bearing genes for adaptation to heat, solar radiation, ion transport and immunity. The high-altitude-adapted East-African populations' ROH showed a selection signature with genes for angiogenesis, oxygen-heme binding and transport. The neuroglobin gene (GO:0019825 and GO:0015671) was detected on a Chromosome 5 ROH of Rwanda-Uganda ecotypes. The sodium-dependent noradrenaline transporter, SLC6A2 on a Chromosome 11 ROH in Fayoumi breed may reflect its active behavior. Inter-population FST among Egyptian populations reflected genetic mechanisms for the Fayoumi resistance to Newcastle Disease Virus (NDV), while FST between Egyptian and Rwanda-Uganda populations indicated the Secreted frizzled related protein 2, SFRP2, (GO:0009314) on Chromosome 4, that contributes to melanogenic activity and most likely enhances the Dandarawi chicken adaptation to high-intensity of solar radiation in Southern Egypt. These results enhance our understanding of the natural selection forces role in shaping genomic structure for adaptation to the stressful African conditions.

Venous blood gas and chemistry components are moderately heritable in commercial white egg-laying hens under acute or chronic heat exposure.

Heat stress has a large negative impact on poultry around the world in both intensive and small-scale production systems. Better understanding of genetic factors contributing to response to high ambient temperatures would provide a basis to develop strategies for alleviating negative impacts of heat on poultry production. The objective of this work was to characterize the genetic control (heritability estimate and quantitative trait loci (QTL)) of blood chemistry components before and after exposure to acute and chronic high ambient temperature in a commercial egg laying line Hy-Line W-36 female parent line mature hens were exposed to 4 wk of daily cyclic heat exposure. Blood was collected pre-heat, on the first day of heat, and 2 and 4 wk post heat initiation and analyzed immediately using an i-STAT® hand-held blood analyzer. Thirteen blood components were quantified at the 4 time points: pH, pCO2, pO2, HCO3, TCO2, sO2, iCa, Na, K, base excess, glucose, "hematocrit" (estimated from blood electrical conductivity, BEC), and "hemoglobin" (calculated from BEC). Heritabilities were estimated using genomic relationship information obtained from 600k SNP chip data. All 13 parameters exhibited a significant change after 5 h of heat exposure and most did not return to pre-heat levels throughout the duration of the study. Eight parameters (base excess, glucose, hemoglobin, HCO3, hematocrit, K, pCO2, TCO2) had heritability estimates differing from zero at one or more time points (0.21 to 0.45). The traits with significant heritability would be good candidates for use as biomarkers in a selection program if they are correlated with traits of economic importance that are more difficult to measure. QTL were identified for nine of the traits at one or more time point. These nine traits, however, did not have significant heritability estimates suggesting that while some QTL have been identified their effects are generally small.

Rapid Communication: A comparison of cardiac lesions and heart weights from market pigs that did and did not die during transport to one Ontario abattoir.

In-transit losses of market hogs represent a small proportion of all market-weight pigs shipped in a year. This suggests that individual pig factors may be a significant cause of in-transit losses along with more traditionally considered environmental and transport factors. An investigation was performed to determine whether cardiac pathology and heart weights were associated with pigs that did or did not die during transport to an abattoir. The hearts from 70 pigs that died in-transit to one Ontario abattoir and 388 pigs that arrived alive were collected and examined. Hearts from pigs that died during transport demonstrated greater frequencies of cardiac lesions (P < 0.05). These included hypertrophy of ventricle walls (Left: 97% vs. 64%; Right: 86% vs. 57%), dilation of ventricle chambers (Left: 79% vs. 0.5%; Right: 100% vs. 5%), and dilation of the pulmonary artery and aorta (59% vs. 1.5%). Total heart weight to body weight ratios were increased (3.6 vs. 3.3 g/kg) and left ventricle plus septum weight over right ventricle weight ratio was decreased in pigs that died during transport over non-in-transit loss pigs (2.5 vs. 2.8; P < 0.05). This may indicate reduced cardiac function in hogs that died during transport. Pigs with reduced cardiac function would have exercise intolerance and be more susceptible to death during transport due to the increased cardiac workload required during sorting, loading, and transport of the pigs to the abattoir. Further research to quantify cardiac function in pigs with cardiac lesions or abnormal heart weight ratios is warranted.

Signatures of selection and environmental adaptation across the goat genome post-domestication.

BACKGROUND: Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems and/or purposes and (ii) adaptation to different environments. As a result, approximately 600 goat breeds have developed worldwide; they differ considerably from one another in terms of phenotypic characteristics and are adapted to a wide range of climatic conditions. In this work, we analyzed the AdaptMap goat dataset, which is composed of data from more than 3000 animals collected worldwide and genotyped with the CaprineSNP50 BeadChip. These animals were partitioned into groups based on geographical area, production uses, available records on solid coat color and environmental variables including the sampling geographical coordinates, to investigate the role of natural and/or artificial selection in shaping the genome of goat breeds. RESULTS: Several signatures of selection on different chromosomal regions were detected across the different breeds, sub-geographical clusters, phenotypic and climatic groups. These regions contain genes that are involved in important biological processes, such as milk-, meat- or fiber-related production, coat color, glucose pathway, oxidative stress response, size, and circadian clock differences. Our results confirm previous findings in other species on adaptation to extreme environments and human purposes and provide new genes that could explain some of the differences between goat breeds according to their geographical distribution and adaptation to different environments. CONCLUSIONS: These analyses of signatures of selection provide a comprehensive first picture of the global domestication process and adaptation of goat breeds and highlight possible genes that may have contributed to the differentiation of this species worldwide.

Genome-wide patterns of homozygosity provide clues about the population history and adaptation of goats.

BACKGROUND: Patterns of homozygosity can be influenced by several factors, such as demography, recombination, and selection. Using the goat SNP50 BeadChip, we genotyped 3171 goats belonging to 117 populations with a worldwide distribution. Our objectives were to characterize the number and length of runs of homozygosity (ROH) and to detect ROH hotspots in order to gain new insights into the consequences of neutral and selection processes on the genome-wide homozygosity patterns of goats. RESULTS: The proportion of the goat genome covered by ROH is, in general, less than 15% with an inverse relationship between ROH length and frequency i.e. short ROH (< 3 Mb) are the most frequent ones. Our data also indicate that ~ 60% of the breeds display low FROH coefficients (< 0.10), while ~ 30 and ~ 10% of the goat populations show moderate (0.10 < FROH < 0.20) or high (> 0.20) FROH values. For populations from Asia, the average number of ROH is smaller and their coverage is lower in goats from the Near East than in goats from Central Asia, which is consistent with the role of the Fertile Crescent as the primary centre of goat domestication. We also observed that local breeds with small population sizes tend to have a larger fraction of the genome covered by ROH compared to breeds with tens or hundreds of thousands of individuals. Five regions on three goat chromosomes i.e. 11, 12 and 18, contain ROH hotspots that overlap with signatures of selection. CONCLUSIONS: Patterns of homozygosity (average number of ROH of 77 and genome coverage of 248 Mb; FROH < 0.15) are similar in goats from different geographic areas. The increased homozygosity in local breeds is the consequence of their small population size and geographic isolation as well as of founder effects and recent inbreeding. The existence of three ROH hotspots that co-localize with signatures of selection demonstrates that selection has also played an important role in increasing the homozygosity of specific regions in the goat genome. Finally, most of the goat breeds analysed in this work display low levels of homozygosity, which is favourable for their genetic management and viability.

Genome-wide SNP profiling of worldwide goat populations reveals strong partitioning of diversity and highlights post-domestication migration routes.

BACKGROUND: Goat populations that are characterized within the AdaptMap project cover a large part of the worldwide distribution of this species and provide the opportunity to assess their diversity at a global scale. We analysed genome-wide 50 K single nucleotide polymorphism (SNP) data from 144 populations to describe the global patterns of molecular variation, compare them to those observed in other livestock species, and identify the drivers that led to the current distribution of goats. RESULTS: A high degree of genetic variability exists among the goat populations studied. Our results highlight a strong partitioning of molecular diversity between and within continents. Three major gene pools correspond to goats from Europe, Africa and West Asia. Dissection of sub-structures disclosed regional gene pools, which reflect the main post-domestication migration routes. We also identified several exchanges, mainly in African populations, and which often involve admixed and cosmopolitan breeds. Extensive gene flow has taken place within specific areas (e.g., south Europe, Morocco and Mali-Burkina Faso-Nigeria), whereas elsewhere isolation due to geographical barriers (e.g., seas or mountains) or human management has decreased local gene flows. CONCLUSIONS: After domestication in the Fertile Crescent in the early Neolithic era (ca. 12,000 YBP), domestic goats that already carried differentiated gene pools spread to Europe, Africa and Asia. The spread of these populations determined the major genomic background of the continental populations, which currently have a more marked subdivision than that observed in other ruminant livestock species. Subsequently, further diversification occurred at the regional level due to geographical and reproductive isolation, which was accompanied by additional migrations and/or importations, the traces of which are still detectable today. The effects of breed formation were clearly detected, particularly in Central and North Europe. Overall, our results highlight a remarkable diversity that occurs at the global scale and is locally partitioned and often affected by introgression from cosmopolitan breeds. These findings support the importance of long-term preservation of goat diversity, and provide a useful framework for investigating adaptive introgression, directing genetic improvement and choosing breeding targets.

Immunomodulatory effects of heat stress and lipopolysaccharide on the bursal transcriptome in two distinct chicken lines.

BACKGROUND: Exposure to heat stress suppresses poultry immune responses, which can increase susceptibility to infectious diseases and, thereby, intensify the negative effects of heat on poultry welfare and performance. Identifying genes and pathways that are affected by high temperatures, especially heat-induced changes in immune responses, could provide targets to improve disease resistance in chickens. This study utilized RNA-sequencing (RNA-seq) to investigate transcriptome responses in the bursa of Fabricius, a primary immune tissue, after exposure to acute heat stress and/or subcutaneous immune stimulation with lipopolysaccharide (LPS) in a 2 × 2 factorial design: Thermoneutral + Saline, Heat + Saline, Thermoneutral + LPS and Heat + LPS. All treatments were investigated in two chicken lines: a relatively heat- and disease-resistant Fayoumi line and a more susceptible broiler line. RESULTS: Differential expression analysis determined that Heat + Saline had limited impact on gene expression (N = 1 or 63 genes) in broiler or Fayoumi bursa. However, Thermoneutral + LPS and Heat + LPS generated many expression changes in Fayoumi bursa (N = 368 and 804 genes). Thermoneutral + LPS was predicted to increase immune-related cell signaling and cell migration, while Heat + LPS would activate mortality-related functions and decrease expression in WNT signaling pathways. Further inter-treatment comparisons in the Fayoumi line revealed that heat stress prevented many of the expression changes caused by LPS. Although fewer significant expression changes were observed in the broiler bursa after exposure to Thermoneutral + LPS (N = 59 genes) or to Heat + LPS (N = 146 genes), both treatments were predicted to increase cell migration. Direct comparison between lines (broiler to Fayoumi) confirmed that each line had distinct responses to treatment. CONCLUSIONS: Transcriptome analysis identified genes and pathways involved in bursal responses to heat stress and LPS and elucidated that these effects were greatest in the combined treatment. The interaction between heat and LPS was line dependent, with suppressive expression changes primarily in the Fayoumi line. Potential target genes, especially those involved in cell migration and immune signaling, can inform future research on heat stress in poultry and could prove useful for improving disease resistance.