QTL Detection For Milk Production Traits In French Dairy Goats Using The Caprine 50K Illumina Chip

A large scale research x development program has been carried out for mapping traits of interest in French Alpine and Saanen dairy goats. The program is part of both the national « Phénofinlait »  (www.phenofinlait.fr) and the EU «3SR»  (www.3srbreeding.eu) projects.

The project is based on a large daughter design of Alpine and Saanen families. The traits considered included milk production, fatty acids estimated by mid-infrared spectra, udder morphology, milking speed and resistance to mastitis (milk somatic cell counts).

A total of 2 254 goats and their 20 Artificial Insemination sires were genotyped with the caprine 50K SNP goat chip. Quality control of genotype included essentially SNP call rate (>99%), animal call rate (>98%), minimum allele frequency (>1%), Hardy Weinberg equilibrium and pedigree consistency. After editing, a total of 49 647 out of 53 347 synthetized SNPs were validated for further analyses. QTL detection was based on linkage and linkage disequilibrium analyses using the QTLmap software. Chromosome- and genome-wise significance thresholds were estimated by permutation tests and simulations.

Linkage analyses on production traits and somatic cell count evidenced over twenty QTLs per breed at the 5% chromosome-wise threshold. The two most significant QTLs (1% genome wise) were located on chromosomes 6 (protein content) and 14 (fat content), in the region of two genes whose major impact on protein and fat contents in milk is already known (αs1-casein and DGAT1, respectively). LA and LD analyses further supported for a QTL influencing somatic cell count on chromosome 19.