Development of a SNP Parentage Assignment Panel for French Sheep Breeds

Parentage assignment is a priority for the French sheep breeding programs. Around 750 individuals from 30 French breeds were genotyped with the Illumina OvineSNP50 and OvineHD BeadChips (54,000 or 600,000). Genotypes were filtered on several criteria (call-freq, Minor Allele Frequency (MAF), Hardy-Weinberg equilibrium, Mendelian compatibilities, genomic distribution) to produce a single SNP panel for parentage assignment useful in a large variety of French breeds. Each SNP had the following MAF characteristics: higher than 0.10 in each of the 30 populations, higher than 0.30 in at least 20 populations out of the 30 analyzed, between 0.20 and 0.30 in a maximum of 10 populations, between 0.10 and 0.20 in a maximum of one population. A final set of 249 SNPs was retained.

These SNPs were first confirmed on a simulated population. An on-farm experiment is ongoing to validate these SNPs and optimize their number. The genotyping is being performed with the Sequenom technology. 192 SNPs and 19 causal mutations segregating in French breeds could be integrated into 4 plexes.

 The MAF of the 249 SNPs were checked on different international populations. For example, in the Spanish breeds, around 80% of the SNPs have a MAF higher than 0.30 whereas this percentage falls down to 55% in the Scottish breeds.

The final French panel will be integrated into the international LD chip, in construction within the International Sheep Genomics Consortium. The challenge is now to propose to the French breeding programs a low-cost genomic tool enabling parentage assignment and major genes genotyping.