Selection Signatures in Worldwide Sheep Populations

The diversity of populations in domestic species offers great opportunities to study genome response to selection. The recently published Sheep HapMap dataset is a great example of characterization of the world wide genetic diversity in sheep. In this study, we re-analyzed the Sheep HapMap dataset to identify selection signatures in worldwide sheep populations. Compared to previous analyses, we made use of statistical methods that (i) take account of the hierarchical structure of sheep populations, (ii) make use of linkage disequilibrium information and (iii) focus specifically on either recent or older selection signatures. We show that this allows pinpointing several new selection signatures in the sheep genome and distinguishing those related to modern breeding objectives and to earlier post-domestication constraints. The newly identified regions, together with the ones previously identified, reveal the extensive genome response to selection on morphology, color and adaptation to new environments

Transcriptome profiling of sheep granulosa cells and oocytes during early follicular development obtained by Laser Capture Microdissection

<p>Abstract</p> <p>Background</p> <p>Successful achievement of early folliculogenesis is crucial for female reproductive function. The process is finely regulated by cell-cell interactions and by the coordinated expression of genes in both the oocyte and in granulosa cells. Despite many studies, little is known about the cell-specific gene expression driving early folliculogenesis. The very small size of these follicles and the mixture of types of follicles within the developing ovary make the experimental study of isolated follicular components very difficult.</p> <p>The recently developed laser capture microdissection (LCM) technique coupled with microarray experiments is a promising way to address the molecular profile of pure cell populations. However, one main challenge was to preserve the RNA quality during the isolation of single cells or groups of cells and also to obtain sufficient amounts of RNA.</p> <p>Using a new LCM method, we describe here the separate expression profiles of oocytes and follicular cells during the first stages of sheep folliculogenesis.</p> <p>Results</p> <p>We developed a new tissue fixation protocol ensuring efficient single cell capture and RNA integrity during the microdissection procedure. Enrichment in specific cell types was controlled by qRT-PCR analysis of known genes: six oocyte-specific genes (<it>SOHLH2</it>, <it>MAEL</it>, <it>MATER</it>, <it>VASA</it>, <it>GDF9</it>, <it>BMP15</it>) and three granulosa cell-specific genes (<it>KL</it>, <it>GATA4</it>, <it>AMH</it>).</p> <p>A global gene expression profile for each follicular compartment during early developmental stages was identified here for the first time, using a bovine Affymetrix chip. Most notably, the granulosa cell dataset is unique to date. The comparison of oocyte vs. follicular cell transcriptomes revealed 1050 transcripts specific to the granulosa cell and 759 specific to the oocyte.</p> <p>Functional analyses allowed the characterization of the three main cellular events involved in early folliculogenesis and confirmed the relevance and potential of LCM-derived RNA.</p> <p>Conclusions</p> <p>The ovary is a complex mixture of different cell types. Distinct cell populations need therefore to be analyzed for a better understanding of their potential interactions. LCM and microarray analysis allowed us to identify novel gene expression patterns in follicular cells at different stages and in oocyte populations.</p

Breeding for resistance to gastrointestinal nematodes - the potential in low-input/output small ruminant production systems

AbstractThe control of gastrointestinal nematodes (GIN) is mainly based on the use of drugs, grazing management, use of copper oxide wire particles and bioactive forages. Resistance to anthelmintic drugs in small ruminants is documented worldwide. Host genetic resistance to parasites, has been increasingly used as a complementary control strategy, along with the conventional intervention methods mentioned above. Genetic diversity in resistance to GIN has been well studied in experimental and commercial flocks in temperate climates and more developed economies. However, there are very few report outputs from the more extensive low-input/output smallholder systems in developing and emerging countries. Furthermore, results on quantitative trait loci (QTL) associated with nematode resistance from various studies have not always been consistent, mainly due to the different nematodes studied, different host breeds, ages, climates, natural infections versus artificial challenges, infection level at sampling periods, among others. The increasing use of genetic markers (Single Nucleotide Polymorphisms, SNPs) in GWAS or the use of whole genome sequence data and a plethora of analytic methods offer the potential to identify loci or regions associated nematode resistance. Genomic selection as a genome-wide level method overcomes the need to identify candidate genes. Benefits in genomic selection are now being realised in dairy cattle and sheep under commercial settings in the more advanced countries. However, despite the commercial benefits of using these tools, there are practical problems associated with incorporating the use of marker-assisted selection or genomic selection in low-input/output smallholder farming systems breeding schemes. Unlike anthelmintic resistance, there is no empirical evidence suggesting that nematodes will evolve rapidly in response to resistant hosts. The strategy of nematode control has evolved to a more practical manipulation of host-parasite equilibrium in grazing systems by implementation of various strategies, in which improvement of genetic resistance of small ruminant should be included. Therefore, selection for resistant hosts can be considered as one of the sustainable control strategy, although it will be most effective when used to complement other control strategies such as grazing management and improving efficiency of anthelmintics currently

A genome scan for milk production traits in dairy goats reveals two new mutations in <i>Dgat1</i> 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

Indicateurs de régulation naturelle : revue des méthodes

National audienceL’évaluation du contrôle biologique et de la régulation des bio-agresseurs est essentielle pour comprendre les facteurs affectant les processus de régulation naturelle et pour essayer d’intégrer ce service dans la gestion des cultures. Diverses approches méthodologiques existent et, dans le cadre du RMT Biodiversité et Agriculture, celles-ci ont été rassemblées sous forme d’une boite à outils servant d’appui à cet exposé. Les caractéristiques principales des méthodes sont présentées selon trois niveaux d’objectifs qui marquent une progression dans la connaissance et les questions posées sur la régulation avec i) mettre en évidence et caractériser les ennemis naturels, ii) montrer qu’il existe un lien trophique et que la prédation ou le parasitisme s’exercent, iii) quantifier la prédation et évaluer la régulation. La plupart des approches utilisées aujourd’hui restent délicates à mettre en oeuvre et leur pertinence et opérationnalité est discutée. Il semble difficile de trouver un indicateur ou méthode de mesure universelle et intégrative du fait à la diversité des bio-agresseurs, de leurs ennemis naturels, des différentes productions végétales, et compte tenu de la complexité des mécanismes et échelle d’approche affectant la régulation. Si la dynamique des ravageurs en témoin non traité permet un diagnostic à postériori des situations favorables, ou pas, à la régulation, producteurs et techniciens ont besoin d’un indicateur d’évaluation de la régulation et surtout de son potentiel qui soit facile à mettre en oeuvre pour l’intégrer dans la panoplie des outils de pilotage. C’est un verrou à lever pour parvenir à une réduction plus poussée des intrants

Auximore : optimiser le controle biologique des bio-agresseurs en systèmes de grandes cultures

Concilier la compétitivité de l’agriculture avec la réduction des produits insecticides et molluscicides en grandes cultures demande de valoriser la faune auxiliaire naturellement présente dans les parcelles et dans leur environnement. Le projet Auximore vise à développer des connaissances de cette faune auxiliaire et les outils permettant de les diffuser auprès des conseillers agricoles et des agriculteurs. Auximore contribue ainsi à optimiser le contrôle biologique des bio-agresseurs en systèmes de grandes cultures. Il est né de la demande d’agriculteurs fortement engagés dans les techniques culturales favorables à l’environnement et aux auxiliaires des cultures. Un partenariat national a été mis en place pendant 3 ans de manière concrète et pragmatique entre ces agriculteurs volontaires, les partenaires de la recherche, du développement agricole et de l’enseignement. De nombreux outils de reconnaissance, de suivi, et d’identification des auxiliaires et ravageurs ainsi que de l’impact des pratiques et du paysage sur ces populations ont pu être produits grâce à un travail conséquent d’observation, de recherche, de partage et de co-construction. En contribuant à l’expression et au développement de l’agro-écologie, ce projet illustre l’importance du travail en réseau et du transfert des connaissances vers les agriculteurs et les conseillers. Le site http://unebetedansmonchamp.fr/ rassemble les outils produits

Les indicateurs de biodiversité pour accompagner les agriculteurs : embarras du choix ou pénurie ?

To reduce the negative impacts of agricultural systems, the agro-ecological transition first calls for theuse of greater cultivated biodiversity. Such diversification can be implemented at the field scale, mixingdifferent species, or different varieties of the same species. We discuss the advantages of this intra-fielddiversification by developing 5 examples: (1) varietal mixtures of wheat in France, (2) rice populations inYuanYang, (3) oilseed rape associated with service plants, (4) mixtures of forage species and (5) cerealand legume intercrops for grain production. We discuss the benefits conferred by this diversification on:(i) optimization and stabilization of production, (ii) interactions with cultural practices, (iii) breedingactivity, and (iv) the impact of these stands and practices on associated wild biodiversity