Study of recombination rate in Lacaune sheep informs its evolution in Soay sheep

Study of recombination rate in Lacaune sheep informs its evolution in Soay sheep. XVI Gordon Research Conference : Quantitative Genetics & Genomic

Inbreeding and its effects on small and isolated sheep population: the case of Rambouillet's Merino breed

Threatened populations that have undergone a strong reduction of their size are subsequently more likely to reproduce under inbred conditions. The adverse effects of such matings on the fitness of the progeny have long been known. Unlike natural populations for which detailed records of genealogy are scarce, domestic and captive populations can benefit from available pedigree data. In this regard, the Merino population from Rambouillet, which has been maintained at small size since its arrival at the Bergerie Nationale de Rambouillet, is a valuable model to study the effects of a small population size associated with a closed registry system on genome structure and genetic diversity. This study showed that, despite a low genetic diversity and a strong structure of the genome, the population management, aiming to minimize matings between the most closely related animals was an adequate breeding policy: the population is not structured into family groups. Furthermore inbreeding depression is low. This project should help to assess the evolutionary potential of the flock. In the long term, it should contribute to the development of recommendations on the management of endangered populations where inbreeding and genetic drift are inevitable, due to their small size

Development of a SNP panel dedicated to parentage assignment in French sheep populations

The efficiency of breeding programs partly relies on the accuracy of the estimated breeding values which decreases when pedigrees are incomplete. Two reproduction techniques are mainly used by sheep breeders to identify the sires of lambs: animal insemination and natural matings with a single ram per group of ewes. Both methods have major drawbacks, notably time-consuming tasks for breeders, and are thus used at varying levels in breeding programs. As a consequence, the percentage of known sires can be very low in some breeds and results in less accurate estimated breeding values.In order to address this issue and offer an alternative strategy for obtaining parentage information, we designed a set of 249 SNPs for parentage assignment in French sheep breeds and tested its efficiency in one breed. The set was derived from the 54 K SNP chip that was used to genotype the thirty main French sheep populations. Only SNPs in Hardy-Weinberg equilibrium, displaying the highest Minor Allele Frequency across all the thirty populations and not associated with Mendelian errors in verified family trios were selected. The panel of 249 SNPs was successfully used in an on-farm test in the BMC breed and resulted in more than 95% of lambs being assigned to a unique sire.In this study we developed a SNP panel for assignment that achieved good results in the on-farm testing. We also raised some conditions for optimal use of this panel: at least 180 SNPs should be used and a minute preparation of the list of candidate sires. Our panel also displays high levels of MAF in the SheepHapMap breeds, particularly in the South West European breeds

Comparison between rumen bacterial composition of growing and adult Romane sheep

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Supplemental Data to: Variation in recombination rate and its genetic determinism in sheep (Ovis Aries) populations from combining multiple genome-wide datasets.

<p>Supplemental Data to reproduce the analysis of</p> <p><strong>Variation in recombination rate and its genetic determinism  in sheep (Ovis Aries) populations from combining multiple genome-wide datasets.</strong></p> <p>Morgane Petit*, Jean-Michel Astruc✝, Julien Sarry*, Laurence Drouilhet*,  Stéphane Fabre*,  Carole Moreno*, Bertrand Servin*</p> <p>*INRA, Génétique, Physiologie et Systèmes d’Elevage, F-31326 Castanet-Tolosan, France</p> <p>✝Institut de l’Elevage, F-31326 Castanet-Tolosan, France</p> <p><strong>Abstract</strong></p> <p>Recombination is a complex biological process that results from a cascade of multiple events during meiosis. Understanding the genetic determinism of recombination can help to understand if and how these events are interacting. To tackle this question, we studied the patterns of recombination in sheep, using multiple approaches and datasets. We constructed male recombination maps in a dairy breed from the south of France (the Lacaune breed) at a fine scale by combining meiotic recombination rates from a large pedigree genotyped with a 50K SNP array and historical recombination rates from a sample of unrelated individuals genotyped with a 600K SNP array. This analysis revealed recombination patterns in sheep similar to other mammals but also genome regions that have likely been affected by directional and diversifying selection. We estimated the average recombination rate of Lacaune sheep at 1.5 cM/Mb, identified about 50,000 crossover hotspots on the genome and found a high correlation between historical and meiotic recombination rate estimates. A genome-wide association study revealed two major loci affecting inter-individual variation in recombination rate in Lacaune, including the <em>RNF212</em> and<em> HEI10</em> genes and possibly 2 other loci of smaller effects including  the <em>KCNJ15</em>  and <em>FSHR</em> genes. Finally, we compared our results to those obtained previously in a distantly related population of domestic sheep, the Soay. This comparison revealed that Soay and Lacaune males have a very similar distribution of recombination along the genome and that the two datasets can be combined to create more precise male meiotic recombination maps in sheep. Despite their similar recombination maps, we show that Soay and Lacaune males exhibit different heritabilities and QTL effects for inter-individual variation in genome-wide recombination rates.</p> <p> </p

Comparison between rumen bacterial composition of growing and adult Romane sheep

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Data and model code of "<i>Inferring the energy cost of resistance to parasitic infection and its link to a genetic trade-off in a vertebrate host</i>"

Data, Model code, Parameter files and supporting analytical output values used to generate figures/tablesDouhard_et_al_Fig2 Supporting data to build Fig2 (xlsx file)Douhard_et_al_Fig3 Supporting data to build Fig3 (xlsx file)model Code of the model to predict individual responses to infection and default parameters (R file) multiplot Code of a function to combine multiple ggplots (R file) predictions Main script to generate model predictions of each individual (R file)Douhard_et_al_Parameters Individuals parameters obtained atfer parameter optimization (xlsx file)Douhard_et_al_Data Observed data of the 42 individuals during infection (xlsx file)</p

Comparison of imputation accuracy using different SNPs densities and SNP selection strategies based on a physical map or on a genetic map

International audienceThe imputation is a robust approach to infer genotypes at un-genotyped loci based on known genotypes of loci in the vicinity. It allowed to predict genotypes of thousands of SNPs with a low-density array, which is less expensive and thus can improve the genomic selection, while maintaining good genotyping information. In Sheep, 4 SNPs arrays exists and the markers were chosen according to regular physical distances between them and the highest SNP Minor Allele Frequency (MAF). In this paper, we test this hypothesis by exploiting a recently published sheep recombination map. To do so, we virtually created low-density SNP panels where SNPs were either selected from physical or genetic distance information, and of varying density: 16,000 SNPs (16K), 10,000 SNPs (10K), 3,000 SNPs (3K) and 300 SNPs (300). The 10K or 3K SNPs set based on the genetic distances instead of physical distances improves the imputation accuracy, especially at the extremities of the chromosomes, where recombination events are more concentrated. For the 300 SNPs and 16K SNPs set, whatever the selection with genetic or physical distances, the imputation accuracy is very similar