Genome-wide association studies in the Reggiana cattle breed identify several candidate genes affecting pigmentation-related traits,stature and udder defects

Reggiana is an Italian autochthonous cattle breed reared mainly in the Emilia Romagna region (North of Italy) and utilized for the production of a mono-breed Parmigiano-Reggiano cheese. Local production systems and breeding strategies have shaped the genome of Reggiana animals and resulted in the selection of exterior traits characterizing the breed (e.g., the typical solid red coat color). However, Reggiana animals still present a degree of phenotypic variability, opening the possibility to better characterize the genetic architecture of this breed. As such, we investigated at the genome-wise level the within-breed variability affecting different exterior traits and defects, including 3 pigmentation-related traits (intensity of red coat color, piebaldism and muzzle color), stature, presence/absence and the number of supernumerary teats and teat length. A total of 1,776 animals was genotyped with the GeneSeek GGP Bovine 150k SNP array and single-marker and haplotype-based genome scans were carried out. The genome scans for coat color included animals characterized by 3 intensity of red (light-red 10.7% of the animals; normal-red, 83.7%; darkred, 5.6%) and highlighted associations with DNA markers located on the bovine chromosome (BTA) 5, BTA7, BTA13 and BTA14. Piebaldism was observed in 4.3% cattle and associated with KIT gene markers (BTA6). The genome scans for muzzle color pointed out the involvement of the MC1R gene markers (BTA18) and other DNA markers on BTA3 and BTA20. Stature was associated with DNA markers located upstream to the NCAPG-LCORL genes (BTA6). Another suggestive peak of association was closed to the PLAG1 gene (BTA14). Teats related traits associated with DNA markers on BTA8, BTA10, BTA17. Overall, this study returned a series of genetic elements determining the main phenotypic differences characterizing Reggiana and that contribute to clarify the genetic mechanisms regulating relevant exterior traits in cattle and that can be applied in the conservation and selection of this breed.