Identification of missense mutations in the PCP4 and CD109 genes to validate the effect of neutral genetic markers

The marker-assisted selection exploits anonymous genetic markers that have been associated with measurable differences on complex traits. Because it is based on the linkage disequilibrium (LD) between the polymorphic markers and the polymorphisms which code for the trait, its success is limited to the population in which the association has been assessed. The identification of the gene with effect on the target trait and the detection of the functional mutations will allow selection in independent populations, while encouraging studies on gene expression. In a flock of sheep infected with M. paratuberculosis, a genome-wide scan, performed with the Illumina OvineSNP50 BeadChip, had identified two candidate genes, the PCP4 and the CD109, located in proximity of the markers with significant allele substitution effect on the positivity level at paratuberculosis serological assessment. The coding region of the two genes was directly sequenced. Three missense mutations were detected: two in the PCP4 gene and one in the second exon of the CD109 gene, the latter showing a strong LD with the anonymous marker. Direct sequencing of the DNA of sheep of different populations showed that disequilibrium was maintained. Allele frequency at the hypothesized marker associated to immune response, calculated for other breeds of sheep, showed that the marker allele potentially associated to disease resistance is more frequent in the local breeds and in breeds that have not been submitted to selection programs.