Whole-Genome Genotyping for Detecting Mutations in the Genes that are Directly Responsible for the Trait Variation

Genomic model selection can only be applied to the population where genomic associations have been  detected, so restricting the benefits that the whole-genome genotyping can offer. We have here genotyped 160 milk recorded sheep with the 50K Illumina Bead Chip. Similarly to the selective genotyping method, we have performed the Fisher’s exact test of significance of differences of allele frequency between the two tails of the distribution (±1.5 standard deviations) i.e. the extreme divergent animals for milk yield, corrected by environmental factors and sheep random effect.  The highest chi-square value (P<.00000001) was detected between the two markers OAR1_81453876 and OAR1_81533009 of the OAR v2.0 Genome Assembly, this region not encoding, to date, any annotated ovine gene. This sequence, when blasted to the GenBank ESTs, showed a very high homology (98%) with Bos taurus PALMD mRNA (NM_001035079.1), and encoded exons 4 to 8 and the 3’UTR of the gene. Direct sequencing of the five exons, located between the markers, in  5 + 5 sheep, that showed opposite homozygous genotype at the two makers, revealed a non-synonymous (Thr/Ser) SNP in exon 5, and the sheep presented homozygous opposite genotype at this SNP. Thirty more sheep, of which 15 were heterozygous for the two markers, were genotyped for the non-synonymous SNP; allelic correlation between the marker genotypes and the Thr/Ser genotype was .98.  We showed that the whole-genome genotyping of phenotyped animals can allow to unravel the genes, which influence important traits, also in those livestock where many genes have not yet been annotated.