Genomic variation and molecular mechanisms of the host response to gastrointestinal nematodes in small ruminants

Gastrointestinal nematode (GIN) infections are one of the major constrains for sheep and goat production worldwide. One of the promising control strategies is the genetic selection for resistant animals as there are no issues due to anthelmintic resistance and it aligns to demands for chemical-free food. Exploring possible phenotypic and genomic markers that could be used in breeding scheme besides understanding the mechanisms responsible for resistance were the main goals of this thesis. Thesis consists of General introduction, a brief description of GIN biology and methods to control GIN with focus on phenotypic and genomic markers, four papers and General discussion. In paper Ⅰ, a systematic review and meta-analysis were conducted to re-analyse and summarize the findings on immunoglobulins response to GIN in the literature and discuss the potential to use immunoglobulins as biomarkers of the host resistance. A conceptual model summarizing the role of immunoglobulins in resistance to GIN is proposed. In paper Ⅱ, transcriptome profiling of the abomasal mucosa and lymph node tissues were compared between non-infected, resistant and susceptible Creole goats experimentally infected with Haemonchus contortus. Results indicated that the maintenance of the integrity of the mucosa has probably the priority for the host at late infection stage. In paper Ⅲ, the dynamics of the response of the abomasal mucosa of resistant and susceptible Creole goats experimentally infected with H. contortus were compared. The immune response was activated through many relevant pathways including the Th1 immune response at different time post-infection. Interestingly, the results showed a simultaneous time series activation of Th2 related genes in resistant compared to susceptible kids. In paper Ⅳ, the genomic variants of Creole goats resistant and susceptible to H. contortus were discovered from RNAsequencing data at four different times post-infection. Single nucleotide polymorphisms, insertions and deletions that distinguish the resistant and the susceptible groups were identified and characterized through functional analysis. The T cell receptor signalling pathway was one of the top significant pathways that distinguish the resistant from the susceptible group with genomic variants in 78% of genes in this pathway

Genetic response of heat stress on performance of Spanish local dairy goat breed

[EN] In the present thesis the effect of heat stress on milk, fat, and protein yields and fat and protein contents has been studied in the Spanish Florida breed of dairy goats. It comprises three chapters: The first one is a bibliographic review of the state of the art. The second one is a phenotypic analysis carried out to determine the climatic variables most correlated to the production traits and to estimate the tolerance thresholds and slopes of the responses of the dairy traits studied to heat stress. The third chapter is a genetic analysis of formerly cited responses, undertaken with the objective to estimate the environmental and genetic (co)variance components of heat stress tolerance. A total of 185,675 test-day records belonging to 13,481 lactating goats distributed in 20 flocks, collected between 2006 and 2012, combined with maximum and average temperatures and the values of an index of temperature and relative humidity (THI), registered the day of milk recording and one and two days before in meteorological stations located less than 22 Km from the farms, were used for the phenotypic and genetic analysis. For the first study, a Ridge regression analysis and a GLM select analysis were carried out in order to select the climatic variables and dates that were recorded, having the highest correlations with the dairy traits under study. Then, tolerance thresholds and slopes of the regressions of these traits with the selected climatic variables were estimated with spline and polynomial models by means of Bayesian methods. Results shows that the maximum and average temperatures (mean of maximum and minimum temperatures) explain the change in dairy traits caused by climatic effects better than the THI. Temperatures registered the day of milk recording or one day before have more effect on the traits studied than those registered two days before. Generally, yields and contents of milk components decrease when temperature increases. However, milk yield seem to be less affected by high temperatures, being more affected by cold temperatures. Climatic variables have a higher effect on milk composition in high productive animals in respect to the rest. For the genetic analysis, a reaction norm animal model (RNM) was used to estimate the genetic and permanent environmental (co)variance components of the relation of dairy traits with THI, maximum and average temperature, modeling this relation by means of Legendre polynomials. Results show that the heritability of dairy traits tends to decrease for increasing values of the climatic variables. Genetic correlations between the intercept and the slope of each model, and between the first and the subsequent points in the scales of the climatic variables, provide evidences that selection for better milk performance will Ab s t r a c t IX reduce heat stress tolerance. The genetic variation of the response to heat stress found in this analyses could be used to select animals according to their response to heat stress (robust, tolerant and non-tolerant). Key words: Florida goats, heat stress, climatic variables, genetic parameters[ES] La presente tesis trata del efecto del estrés térmico sobre las producciones de leche, grasa y proteína y sobre los contenidos de estas dos últimas componentes de la leche de las cabras de la raza autóctona española Florida. La tesis está organizada en tres capítulos: En el primero de ellos se realizó una revisión bibliográfica del tema. En el segundo se describe un análisis realizado para determinar, a nivel fenotípico, las variables climáticas más correlacionadas con los caracteres productivos y estimar el umbral y la pendiente de la tolerancia de la respuesta al estrés térmico de dichos caracteres. El tercer capítulo trata de un análisis genético realizado con el objetivo de estimar los componentes de (co)varianza genéticos y ambientales de la tolerancia al estrés térmico. Para llevar a cabo los análisis fenotípico y genético 185675 registros del día de control de la producción y composición de la leche de, tomados de 13481 cabras distribuidas en 20 rebaños, se combinaron con los datos de temperatura máxima y media y un índice de temperatura y humedad relativa (THI), registrados el mismo día del control lechero, dos y un día antes, en estaciones meteorológicas ubicadas a menos de 22 Km de cada explotación. En este primer estudio, se utilizaron los métodos de regresión “Ridge” y “GLM select” para seleccionar las variables climáticas, y las fechas de registro de las mismas, mas correlacionadas con los registros de los caracteres lecheros en estudio. A continuación, se estimaron el umbral y la pendiente de la respuesta de los caracteres lecheros a cada una de las variables climáticas seleccionadas anteriormente, mediante modelos lineales y polinómicos, utilizando para ello métodos Bayesianos. Los resultados muestran que las temperaturas máxima y media (promedio de las temperaturas máxima y mínima) explican el cambio en las características lecheras causados por los efectos climáticos mejor que el THI. Las temperaturas registradas el día de control o un día antes tienen más efecto sobre los caracteres estudiados que la registrada dos días antes. En general, las producciones y los contenidos de los componentes de la leche estudiados disminuyen cuando aumenta la temperatura. Sin embargo, la producción de leche parece ser menos sensible a las altas temperaturas y más sensible al frio. Las variables climáticas tienen un efecto mayor sobre la composición de la leche de los animales de alto nivel productivo que sobre el resto. En el genético estudio, se utilizó un modelo de norma de reacción (RNM) para estimar los componentes de (co)varianza genéticos y ambientales permanente de las relaciones entre los caracteres lecheros y cada una de las variables climáticas (THI y temperaturas máxima Re sume n XI y media), incorporadas en los modelos de análisis mediante polinomios de Legendre. Los resultados obtenidos reflejan que las heredabilidades de las características lecheras muestran una tendencia negativa cuando los valores de las variables climáticas aumentan. Las correlaciones genéticas entre la intersección y la pendiente de cada uno de los modelos, y entre el primero y los puntos posteriores en las escalas de valores de las variables climáticas, proporcionan una evidencia de que selección para lograr un mejor rendimiento lechero disminuye la tolerancia al estrés térmico. La variación genética de la respuesta al estrés térmico observada en estos análisis podría ser utilizada para seleccionar los animales en función de dichas repuestas (robustas, tolerantes y no tolerantes). Palabras clave: Cabras de la raza Florida, estrés térmico, variables climáticas, parámetrosAboshady, HMMA. (2013). Genética de la respuesta al estrés térmico en una raza autóctona de ganado caprino lechero. http://hdl.handle.net/10251/44463Archivo delegad

Variation génomique et mécanismes moléculaires de la réponse de l'hôte aux nématodes gastro-intestinaux chez les petits ruminants

Gastrointestinal nematode (GIN) infections are one of the major constrains for sheep and goat production worldwide. One of the promising control strategies is the genetic selection for resistant animals as there are no issues due to anthelmintic resistance and it aligns to demands for chemical-free food. Exploring possible phenotypic and genomic markers that could be used in breeding scheme besides understanding the mechanisms responsible for resistance were the main goals of this thesis. Thesis consists of General introduction, a brief description of GIN biology and methods to control GIN with focus on phenotypic and genomic markers, four papersand General discussion. In paper , a systematic review and meta-analysis were conducted to re-analyse and summarize the findings on immunoglobulins response to GIN in the literature and discuss the potential to use immunoglobulins as biomarkers of the host resistance. A conceptual model summarizing the role of immunoglobulins in resistance to GIN is proposed. In paper , transcriptome profiling of the abomasal mucosa and lymph node tissues were compared between non-infected, resistant and susceptible Creole goats experimentally infected with Haemonchus contortus. Results indicated that the maintenance of the integrity of the mucosa has probably the priority for the host at late infection stage. In , the dynamics of the response of the abomasal mucosa of resistant and susceptible Creole goats experimentally infected with H. contortus were compared. The immune response was activated through many relevant pathways including the Th1 immune response at different time post-infection. Interestingly, the results showed a simultaneous time series activation of Th2 related genes in resistant compared to susceptible kids. In paper , the genomic variants of Creole goats resistant and susceptible to H. contortus were discovered from RNAsequencing data at four different times post-infection. Single nucleotide polymorphisms, insertions and deletions that distinguish the resistant and the susceptible groups were identified and characterized through functional analysis. The Tcell receptor signalling pathway was one of the top significant pathways that distinguish the resistant from the susceptible group with genomic variants in 78% of genes in this pathway.Les infections par les nématodes gastro-intestinaux (NGI) constituent l’une des contraintes principales de production chez les ovins et les caprins dans le monde. Une des solutions prometteuse est la sélection génétique d’animaux résistants aux NGI. Cette sélection permettrait de réduire l’utilisation des anthelminthiques et donc l’apparition de souches de NGI résistants à ces molécules, et de répondre à la demande sociétale de produits animaux sans résidus. Les principaux objectifs de cette thèse étaient de caractériser des marqueurs phénotypiques et génomiques qui pourraient être utilisés dans des schémas de sélection et de comprendre les mécanismes physiologiques sous-jacents.Ce manuscrit de thèse est structuré de la manière suivante : une introduction générale suivie d’une brève description de la biologie des NGI et des méthodes de contrôle en mettant l’accent sur les marqueurs phénotypiques et génomiques, puis les quatre articles scientifiques et la discussion générale. Dans l’article I, une revue systématique et une méta-analyse ont été réalisées pour ré-analyser et résumer les résultats de la littérature sur la réponse humorale contre les NGI et discuter de la possibilité d’utiliser les immunoglobulines comme biomarqueurs de la résistance de l’hôte. Un modèle conceptuel résumant le rôle des immunoglobulines dansla résistance au GIN est proposée. Dans l’article II, les transcriptomes de la muqueuse abomasale et des ganglions drainants d’animaux résistants et sensibles infestés par Haemonchus contortus et non-infestés ont été comparés. Les résultats ont montré qu’à un stade tardif de l'infestation le maintien de l'intégrité de la muqueuse est probablement la priorité pour l'hôte. Dans l’article III, les dynamiques de la réponse de l’hôte au niveau de la muqueuse abomasale ont été comparées entre animaux résistants et sensibles infestés par H. contortus. Nous avons montré l’activation de nombreuses voies de signalisation, notamment la voies Th1 et Th2 de manière concomitante. Dans l’article IV, des variants génomiques (SNP : insertions et délétions) de la résistance aux NGI ont été mis en évidence à partir des données de séquençage des ARN et caractérisés par une analyse fonctionnelle. L’une des voies de signalisation qui distinguent le mieux les deux génotypes est celle des récepteurs de lymphocytes T, près de 78% des gènes de cette voie de signalisation présentent des variants génomiques

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

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 over time in response to gastrointestinal nematode infection in goats

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

AbstractGastrointestinal 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 TGF beta 1 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