Uncovering structural variants in Creole cattle from Guadeloupe and their impact on environmental adaptation through whole genome sequencing.

Structural variants play an important role in evolutionary processes. Besides, they constitute a large source of inter individual genetic variation that might represent a major factor in the aetiology of complex, multifactorial traits. Their importance in adaptation is becoming increasingly evident in literature. Yet, the characterization of the genomic landscape of structural variants in local breeds remains scarce to date. Herein, we investigate patterns and gene annotation of structural variants in the Creole cattle from Guadeloupe breed using whole genome sequences from 23 bulls representative of the population. In total, we detected 32821 ascertained SV defining 15258 regions, representing ~ 17% of the Creole cattle genome. Among these, 6639 regions have not been previously reported in the Database of Genomic Variants archive. Average number of structural variants detected per individual in the studied population is in the same order of magnitude of that observed in indicine populations and higher than that reported in taurine breeds. We observe an important within-individual variability where approximately half of the detected structural variants have low frequency (MAF < 0.25). Most of the detected structural variants (55%) occurred in intergenic regions. Genic structural variants overlapped with 7793 genes and the predicted effect of most of them is ranked as "modifier". Among the structural variants that were predicted to have a high functional impact on the protein, a 5.5 Kb in length, highly frequent deletion on chromosome 2, affects ALPI, a gene associated with the interaction between gut microbiota and host immune system. The 6639 newly identified structural variants regions include three deletions and three duplications shared by more than 80% of individuals that are significantly enriched for genes related to tRNA threonylcarbamoyladenosine metabolic process, important for temperature adaptation in thermophilic organisms, therefore suggesting a potential role in the thermotolerance of Creole cattle from Guadeloupe cattle to tropical climate. Overall, highly frequent structural variants that are specific to the Creole cattle population encompass olfactory receptor and immunity genes as well as genes involved in muscle tone, muscle development and contraction. Beyond mapping and characterizing structural variants in the Creole cattle from Guadeloupe breed, this study provides valuable information for a better understanding of the potential role of chromosomal rearrangements in adaptive traits in cattle.

Whole genome sequencing reveals signals of adaptive admixture in Creole cattle.

The Creole cattle from Guadeloupe (GUA) are well adapted to the tropical environment. Its admixed genome likely played an important role in such adaptation. Here, we sought to detect genomic signatures of selection in the GUA genome. For this purpose, we sequenced 23 GUA individuals and combined our data with sequenced genomes of 99 animals representative of European, African and indicine groups. We detect 17,228,983 single nucleotide polymorphisms (SNPs) in the GUA genome, providing the most detailed exploration, to date, of patterns of genetic variation in this breed. We confirm the higher level of African and indicine ancestries, compared to the European ancestry and we highlight the African origin of indicine ancestry in the GUA genome. We identify five strong candidate regions showing an excess of indicine ancestry and consistently supported across the different detection methods. These regions encompass genes with adaptive roles in relation to immunity, thermotolerance and physical activity. We confirmed a previously identified horn-related gene, RXFP2, as a gene under strong selective pressure in the GUA population likely owing to human-driven (socio-cultural) pressure. Findings from this study provide insight into the genetic mechanisms associated with resilience traits in livestock.

Mixed Grazing and Dietary Supplementation Improve the Response to Gastrointestinal Nematode Parasitism and Production Performances of Goats.

Small ruminants are very affected by gastrointestinal nematode (GIN) parasitism worldwide. The improvement of the host protective response and the reduction of the probability of contact between hosts and parasites appear as very promising strategies. The objective of this study was to evaluate the effect of a combination of two components of these two strategies on natural GIN infection and production performances of Creole goat kids: dietary supplementation and a rotational mixed grazing system. One hundred and twenty weaned Creole kids and six Creole heifers were divided into four experimental batches: Splus (supplemented) vs. Szero (non-supplemented) × Mixed grazing (kids associated with heifers) vs. Control (kids alone), and grazing plots of forage grasses were balanced for live weight (LW) in both species. The feed intake, blood, and parasitological parameters and production performances between 3 and 11 months of age were monitored. The fecal egg count (FEC) was significantly lower and the packed cell volume (PCV) significantly higher in the Mixed grazing groups. No effect of supplementation was observed for FEC. In contrast, PCV, body condition score, and live weight were significantly higher in supplemented animals whatever the groups. Mixed grazing system and supplementation had significant effects on the slaughter parameters (P < 0.05), but there was no significant interaction. Our results suggested that the advantage driven either by mixed grazing or dietary supplementation on kids' performances would be equivalent, and the combination of both would improve the animal performances.

Genomic variants from RNA-seq for goats resistant or susceptible to gastrointestinal nematode infection.

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

Mixed grazing of adult goats and cattle: Lessons from long-term monitoring.

Mixed grazing of breeding goats and cattle (goats to cattle ratio: about 50 %, based on metabolic weight) was monitored for 2 years on a rotational pasture with the two species grazing together, then for 5 years with cattle grazing immediately after goats. For both modalities, the level of goat parasite infection was not significantly different from that of the control groups. Nevertheless, the association allowed a slight improvement in kid growth and goat productivity, probably in relation to a better food quality. The response of adult goats to mixed grazing is therefore very different from that previously obtained with kids post-weaning. The question of the relationship between heterogeneity of pastures, knowledge of their environment, grazing behaviour of adult goats and risk of infection with gastrointestinal nematodes requires further investigation.

Dynamic transcriptomic changes of goat abomasal mucosa in response to Haemonchus contortus infection.

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

Transcriptome variation in response to gastrointestinal nematode infection in goats.

Gastrointestinal nematodes (GIN) are a major constraint for small ruminant production. Due to the rise of anthelmintic resistance throughout the world, alternative control strategies are needed. The development of GIN resistance breeding programs is a promising strategy. However, a better understanding of the mechanisms underlying genetic resistance might lead to more effective breeding programmes. In this study, we compare transcriptome profiling of abomasal mucosa and lymph node tissues from non-infected, resistant and susceptible infected Creole goats using RNA-sequencing. A total of 24 kids, 12 susceptible and 12 GIN resistant based on the estimated breeding value, were infected twice with 10,000 L3 Haemonchus contortus. Physiological and parasitological parameters were monitored during infection. Seven weeks after the second infection, extreme kids (n = 6 resistant and 6 susceptible), chosen on the basis of the fecal egg counts (FEC), and 3 uninfected control animals were slaughtered. Susceptible kids had significantly higher FEC compared with resistant kids during the second infection with no differences in worm burden, male and female worm count or establishment rate. A higher number of differentially expressed genes (DEG) were identified in infected compared with non-infected animals in both abomasal mucosa (792 DEG) and lymph nodes (1726 DEG). There were fewer DEG in resistant versus susceptible groups (342 and 450 DEG, in abomasal mucosa and lymph nodes respectively). 'Cell cycle' and 'cell death and survival' were the main identified networks in mucosal tissue when comparing infected versus non-infected kids. Antigen processing and presentation of peptide antigen via major histocompatibility complex class I were in the top biological functions for the DEG identified in lymph nodes. The TGFß1 gene was one of the top 5 upstream DEG in mucosal tissue. Our results are one of the fist investigating differences in the expression profile induced by GIN infection in goats.

Goats worm burden variability also results from non-homogeneous larval intake.

For small ruminants, Gastrointestinal Nematodes (GINs) are responsible for severe economic losses and they are also an animal welfare problem. GIN use their host to reproduce and disperse eggs on the pasture, from where they can re-infect another animal. The high density of hosts on the pasture and the extreme tolerance of GIN to environmental constraints make GIN eradication almost impossible. In addition, significant resistance to anthelmintic treatment requires sustainable and integrated management to maintain the health and financial well-being of livestock farming. In this context, models of the complex interactions between host, GIN and environment can help us to design long term optimal management strategies. To build such models, quantitative information is needed but are generally very challenging to collect. In this article, we focus on the number of ingested larvae per animal, which we propose to characterise by using a simulation framework based on the estimation of the spatial distribution of the host over time. Our framework allows us to show that worm burden individual variation is not only explained by the host's genetics, as is often the case, but is also a result of the grazing spatial process.

Feasibility of a "leader-follower" grazing system instead of specialised paddocks with regard to integrated gastrointestinal control in small ruminant farming.

In the humid tropics, small ruminant farmers have to deal with gastrointestinal parasitic nematodes (GIN), among which anthelmintic resistant (AR) populations are rapidly spreading. Although targeted selective treatments (TSTs) are being increasingly used in breeding stock, suppressive drenchings remain the rule in younger animals, for safety and ease of implementation. Until now, the weaned animals are grazed on dedicated plots, making the selection and spread of AR parasites inevitable. Given that GINs disseminate through pastures, we compared the usual grazing system (control) to a "leader-follower" grazing system (LF) for managing the entire GIN population at the farm scale. There were no significant differences between treatments for the dam reproductive parameters and level of GIN infection nor for the pre-weaning death rate of the kids. The 70-day weight of the litter was significantly lower for LF than for control goats (9.71 vs. 11.64 kg, P < 0.05). Although they were more infested with GIN (1860 vs. 966 epg, P < 0.05), the LF weaned animals grew faster (53.4 vs. 40.8 g day(-1), P < 0.05) and their death rate was lower (4.0 vs. 7.7 %, P < 0.05). The overall animal output was estimated to 1010 [911; 1086] vs. 966 [885; 1046] kg LW ha(-1) year(-1), for LF and control grazing systems, respectively. Additionally, the LF grazing system would make the stocking rate easier to manage. Therefore, it is to be recommended as a complement of TSTs in sustainable small ruminant farming.

A user-friendly and scalable process to prepare a ready-to-use inactivated vaccine: the example of heartwater in ruminants under tropical conditions.

The use of cheap and thermoresistant vaccines in poor tropical countries for the control of animal diseases is a key issue. Our work aimed at designing and validating a process for the large-scale production of a ready-to-use inactivated vaccine for ruminants. Our model was heartwater caused by the obligate intracellular bacterium Ehrlichia ruminantium (ER). The conventional inactivated vaccine against heartwater (based on whole bacteria inactivated with sodium azide) is prepared immediately before injection, using a syringe-extrusion method with Montanide ISA50. This is a fastidious time-consuming process and it limits the number of vaccine doses available. To overcome these issues, we tested three different techniques (syringe, vortex and homogenizer) and three Montanide ISA adjuvants (50, 70 and 70M). High-speed homogenizer was the optimal method to emulsify ER antigens with both ISA70 and 70M adjuvants. The emulsions displayed a good homogeneity (particle size below 1 µm and low phase separation), conductivity below 10 µS/cm and low antigen degradation at 4 °C for up to 1 year. The efficacy of the different formulations was then evaluated during vaccination trials on goats. The inactivated ER antigens emulsified with ISA70 and ISA70M in a homogenizer resulted in 80% and 100% survival rates, respectively. A cold-chain rupture assay using ISA70M+ER was performed to mimic possible field conditions exposing the vaccine at 37 °C for 4 days before delivery. Surprisingly, the animal survival rate was still high (80%). We also observed that the MAP-1B antibody response was very similar between animals vaccinated with ISA70+ER and ISA70M+ER emulsions, suggesting a more homogenous antigen distribution and presentation in these emulsions. Our work demonstrated that the combination of ISA70 or ISA70M and homogenizer is optimal for the production of an effective ready-to-use inactivated vaccine against heartwater, which could easily be produced on an industrial scale.

Fifteen years later, anthelmintic resistances have dramatically spread over goat farms in Guadeloupe.

Faecal egg count reduction tests (FECRTs) were performed on 21 goat farms in Guadeloupe (FWI). Anthelmintic resistance (AR) to netobimin (benzimidazole) was found in all 15 herds in which it was tested. AR to ivermectin (avermectin) and levamisole (imidazothiazole) were also very largely spread (14 out of 17 farms and 7 out of 9 farms, respectively). AR to the final moxidectin (milbemycin) released was already present in 2 out of 9 farms in which it was tested. Haemonchus was the dominant genus of gastrointestinal nematodes and was more frequently found to be resistant to netobimin, ivermectin and moxidectin than Trichostrongylus, the latter appeared to be more often resistant to levamisole. A first survey 15 years ago revealed only AR to benzimidazoles and one suspected case of AR to ivermectin.

Genetic analysis of the potential role of IgA and IgE responses against Haemonchus contortus in parasite resistance of Creole goats.

Small ruminants are affected by gastrointestinal nematode (GIN) infection. A promising alternative strategy for control of GIN infection is to increase the level of resistance in the population by taking advantage of the host's immune response. Immunoglobulin A (IgA) and E (IgE) are known to be involved in immune response to GIN. The aim of this study was thus to investigate genetic parameters of IgA and IgE responses against Haemonchus contortus in Creole kids naturally challenged at pasture and to determine the relationship with other resistance criteria such as faecal egg counts, packed-cell volume, eosinophil counts and bodyweight. Variance and covariance components for genetic and residuals effects for each trait were estimated on 3862 males at 11 months of age. Heritability estimates for IgA and IgE ranged between 0.15 and 0.57. Strong positive genetic correlations were observed between either IgE or IgA responses against L3 and adult excretory/secretory products (ESP) antigens of H. contortus, suggesting that the humoral immune response is not specific to the life cycle stage of the parasite suggesting that there is substantial cross recognition between the different parasite antigens. Heritability estimates for faecal egg count (FEC), packed-cell volume (PCV) and bodyweight (BW) were in accordance with previous results in Creole kids. Blood eosinophil counts were found moderately heritable and negatively correlated with FEC, suggesting that this cell population plays a role in resistance to nematode parasite infection in Creole goats. IgA response was positively correlated to FEC, in contrast with the negative correlation between IgE against L3 of H. contortus and FEC. In Creole goats, IgA response against L3 or ESP of H. contortus would rather be associated with the worm burden than an immune protective response. The immune response involving activity of IgE against L3 of H. contortus may be one important pathway for development of resistance to gastrointestinal nematode infections in Creole goats.

Serum antibody responses in Creole kids experimentally infected with Haemonchus contortus.

The objective of this study was to evaluate the relationship of parasite-specific serum antibodies with the resistance status of Creole kids. The average breeding values on egg output predicted in a context of natural infection at 11 months of age were distant of 1.07 genetic standard deviation between resistant and susceptible animals. After drenching the animals were maintained worm-free during 1 month until experimental infection with 10,000 Haemonchus contortus infective larvae (L3). Enzyme-linked immunosorbent assay was carried out in serum samples to determine the level of IgG, IgA and IgE anti-H. contortus L3 crude extracts and adult excretion/secretion products (ESP). Parasitological and blood immunological parameters were measured on the 2 extreme groups. Despite the absence of any typical signs of haemonchosis, susceptible kids had more than 11 times higher faecal egg counts (FEC) at 35 days post-infection (d.p.i.) than resistant kids had. Levels of immunoglobulin against H. contortus L3 and ESP increased significantly after infection in both groups. However, no difference in the host immune response mediated by immunoglobulin against H. contortus was evidenced between groups. This finding suggests that, in goats previously infected by H. contortus, a degree of protection occurred and the phenotypic and genetic segregation in resistant and susceptible animals were not related to the humoral immune response. The correlation coefficients between FEC and IgE anti-ESP (r=0.593; P<0.05 was significant in both resistant and susceptible animals. Such correlation suggesting a hypersensitivity reaction dependent on worm prolificacy has never been described. This result needs further studies to understand the mechanisms underlying this observation.

Evaluation of targeted drenching using Famacha method in Creole goat: reduction of anthelmintic use, and effects on kid production and pasture contamination.

Haemonchus infection was monitored for 2 years (six kidding periods) in a Creole goat flock grazing under oceanic-tropical climate. Two hundred and thirty individual does were involved from late pregnancy to weaning. Anaemia diagnoses using Famacha method and packed cell volume (PCV) were compared. The best agreement (Kappa=0.33) was found if anaemia was declared when PCV values fell to 16 or below and Famacha score was 4 or 5. Drenching policy according to Famacha method was compared to systematic drenching policy. Using the Famacha method allowed a dramatic decrease in anthelmintic use during the periparturient period (0.57 individual dose instead of three doses for the control). The proportion of the nematode population on the pasture not derived from previously-treated goats (in refugia) was estimated to about 79% (65-90%) of the pasture contamination derived from the Famacha group. On the average, goats which needed to be drenched produced less than the control or undrenched goats (kid average daily gain was decreased by about 15%). The repeatability of the need for drenching individual does was estimated to 0.41. The older goats or the goats in poorer body condition at kidding needed more drenching than the younger animals and the animals in good body condition. Consequently the Famacha method may be used as an additional tool for the culling management.

A short-term divergent selection for resistance to Teladorsagia circumcincta in Romanov sheep using natural or artificial challenge.

This experiment was conducted to assess the efficiency of selection on the basis of response to artificial challenges in order to breed sheep resistant to natural infection. A short-term divergent selection process was designed to estimate the genetic parameters of these two traits. Two flocks, including 100 Romanov ram lambs each, were challenged in 1990 when they were 6 months old. One flock received three artificial infections with 20 000 third-stage Teladorsagia circumcincta larvae, at intervals of 7 weeks. Faecal egg counts (FEC) were performed on Days 22, 25 and 28 post infection (p.i.) and the animals were drenched on Day 28 p.i. The other flock was grazed for 5 months on a pasture contaminated with the same species. Faecal samples were taken from the lambs at similar ages. About 5 rams with the lowest FEC and 5 with the highest FEC were selected in each flock and mated with unselected ewes. Their offspring (200 animals) were challenged in 1992, half in the same way as their sires, and the other half by the other method. Because of a drought in the summer of 1990, it was necessary to repeat part of the experiment, and in 1992 the 5 and 8 rams with the lowest and highest FEC, respectively, were selected from the offspring challenged on the pasture in 1992 and were mated with unselected ewes. Their progeny (about 80 animals) were challenged in 1994, half by natural infection, half by artificial infection. The mean FEC of the flock increased from the first to the third artificial infection. The natural infection was highly variable in different years, reflecting the difficulty of assessing resistance using this mode of challenge. Genetic parameters were estimated using animal models and REML solutions. The repeatabilities of the FEC following artificial and natural infection were 0.49 and 0.70 respectively within a period of one week, and 0.22 and 0.41 respectively for periods separated by intervals of 7 weeks; the heritabilities of the single egg count were 0.22 and 0.38 respectively. The genetic correlation was 0.87: the FEC recorded under natural or artificial infection appear to depend on the same genetic potential.