Genome-Wide Association Studies for Anogenital Distance and Linear Type Traits in Gir Cattle.

Although linear type traits have been under selection in the Dairy Gir cattle for the past three decades, there are few studies exploring genetic architecture for these traits. The aim of this study was to identify candidate genes for anogenital distance and linear type traits in the Gir breed. For this study, the body measures of rump length (cm, RL), ilium width (cm, ILW), hip height (cm, HH), body length (cm, BL), thoracic perimeter (cm, TP) and rump area (cm2, RA) along with anogenital distance (cm, AGD) were collected from 604 Gir dairy cows, around 5.69 years old. The pedigree file included 2206 animals, of which 742 were genotyped with different SNP panels and imputed to Illumina BovineHD BeadChip (777 K). Genome-wide association studies were carried out using the blupf90+ program for all traits and for a phenotypic index created to assist selecting candidate genes. The top 5 windows for the traits and top 10 windows for the index explaining the highest percentage of additive genetic variance were selected for gene search. Biological processes and transcription factors were searched from the genes found. In total, 90 genes were identified for all seven traits, of which 17 were pleiotropic, that is, they were common results for pairs or trios of traits. From that, the candidate genes (chromosome) identified from the phenotypic index were CXCL13 (6), CNOT6L (6), MRPL1 (6), CCSER1 (6), CDH26 (13), DOCK8 (8), ZNG1 (8) and PGM5 (8). For those eight genes, 11 transcription factors and 59 biological processes were identified. In conclusion, BTA6 seems to have a deeper role in linear type traits in the Gir breed. Even though there are few studies confirming the action of those genes on body conformation, all eight candidate genes are recommended for future studies to validate their action on muscle and skeletal development or fat deposition due to their biological process functions, which could be pleiotropically affecting linear traits in cattle.