60 000 SNP chip to fine map QTL affecting production traits, resistance to diseases and behaviour in sheep. – SheepSNPQTL

During the last 15 years in France, 10 different QTL studies have been carried out in sheep. Numerous economically important traits (milk and meat production and/or quality, reproduction, behaviour and disease resistance traits …) recorded on farm or in specialized experimental designs have been considered. Usually, whole genome scans were performed by genotyping 100 to 200 microsatellite markers on sire or grand-sire designs. This allowed the identification of more than 100 QTL locations to date. However, due to the relatively low number of markers used, some QTLs were likely missed, and most of the discovered QTLs were located within large confidence intervals (20-60 cM). Such results would be technically sufficient to carry out marker-assisted selection (MAS) programmes, like, for instance, in the French dairy cattle breeds. However, such “1st generation” MAS1 programmes are unrealistic in sheep breeding, mainly for economical reasons. On the other hand, the fine QTL mapping or better the identification of causal mutations having major impact on economically important traits would allow implementation of MAS2 or gene assisted selection (GAS). Examples of selection on PrnP or BMP15 (myostatin) genes show clearly the feasibility in sheep. The use of the newly developed 60,000 ovine SNP chip should allow the fine mapping of such genes. The aim of the present project is to use this new and powerful tool to refine the localization (in 2 to 5 cM intervals) of some (about 70) well chosen QTL in 5 of the 10 French designs. This work will allow postulating candidate genes affecting production, behaviour and disease resistance traits in sheep. This large genotyping project will also allow progressing in two other topics. On the one hand, the information produced by the genotyping of 100 irradiated hybrids will be aggregated to the former to build the first real SNP map in sheep (with the collaboration of the International Sheep Genomics Consortium). In fact, the SNP map currently available is only virtual because it was built by merging partial information coming from sheep and other sequenced species (human and bovine). On the other hand, this information will be used to test genomic selection approaches. Finally, the use of such a density of markers is a new challenge in an animal genetics context and will require some methodological developments.