Genomic association study for age at first calving and calving interval in Romosinuano and Costeño con Cuernos cattle

Inheritance of fertility traits in cattle is complex since they are controlled by multiple loci. Genome-wide association studies are an efficient tool to detect genomic regions that explain the phenotypic variation for a trait of interest. The aim of this study was to identify genomic regions that affect the age at first calving (AFC) and the calving interval (CI) in the Romosinuano (ROMO) and Costeño con Cuernos (CCC) creole cattle breeds and nominate candidate genes that influence these reproductive traits. AFC and CI records were obtained from 4,063 ROMO and 3,922 CCC, and a total of 962 animals were genotyped using the BovineSNP50. Based on the single-step GBLUP methodology, the effects of 54K single nucleotide polymorphisms (SNPs) were grouped within windows of eight adjacent SNPs to explain the genetic variance. Sixty-six SNP windows were significantly associated with AFC (31 regions) and CI (35 regions). Of these regions, 17 were associated with AFC in ROMO, 14 with AFC in CCC, 17 with CI in ROMO and 18 with CI in CCC. From these, nine candidate genes (CACNA1A, CACNA1D, CACTIN, IARS2, PGRMC2, PTGDR, SYT10, UBE4A, RNF17) were identified as possible candidates involved in molecular mechanism that affect physiological mechanisms, such as hormonal regulation, ovarian cyclicity, growth rate, gametogenesis, acceleration of puberty, regulation of immune system, early embryonic development and the pathways to embryo-maternal recognition and maintenance of pregnancy. Furthermore, some genomic regions located in BTA1, BTA5 and BTA14 showed a pleiotropic effect on both AFC and CI. The polymorphisms identified in this study can help determine gene networks involved in the physiology of reproduction in cattle and to explain the inherent genetic variance of traits that measure reproductive performance in cattle. Some of these polymorphisms might be considered for breeding selection strategies to improve complex traits such as AFC and CI in beef and dairy cattle production systems.