Mining the genome of livestock species to identify markers associated with economically relevant morphological traits and breed-specific features

Morphological traits in livestock breeding especially the ones that are associated with production or reproduction efficiency are of great importance since they could affect in some aspects the profitability of farm animals. With regard to the economic values of the Reggiana cattle, we have conducted different genome-wide association studies (GWAS) for different morphological traits. GWASs for stature showed a significant peak on Bos taurus chromosome (BTA) 6, with the single nucleotide polymorphisms (SNPs) located on LCORL-NCAPG genes and another suggestively significant SNP on BTA14 and PLAG1 gene which is in a cluster with CHCHD7. For muzzle colour including all possible comparisons between pink, grey and black muzzle, GWASs highlighted significant SNPs on BTA18, in a genome region harbouring the MC1R gene. Considering genome scan for presence or absence of supernumerary nipples, results showed two peaks on BTA17 including TBX3 and TBX5 genes as the known genes associated with this phenotype and BTA10 with MCC gene. GWAS for horn shape identified only a suggestive significant marker on BTA19. Considering the importance of the number of teats in pigs, we carried out GWASs for the total number of teats and other 12 related parameters. For four investigated parameters (total number of teats, number of teats of the left and right lines, and maximum number of teats comparing the two sides), significant markers were identified on SSC7, in the region of the vertnin (VRTN) gene. Significant markers for the number of posterior teats and absolute difference between anterior and posterior teat numbers were consistently identified on SSC6 with the most significant SNP that was an intron variant in TOX high mobility group box family member 3 (TOX3) gene. The GWASs highlighted genomic regions potentially affecting biological mechanisms controlling the developmental programme of morphological features in Reggiana cattle and Italian Large White pig populations.