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

Abstract

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 ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 18 (2): gmr18258 J.C. Fernández et al. 2 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.

Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions

“…Some of the genes located in at least two different metrics were considered as relevant genes for further investigation. For instance, some of these genes are related to heat shock proteins (e.g., DNAJB13 ), oxygen transport (e.g., HBB and HBG ; Neupane et al, 2017 ), mitochondrial DNA maintenance (e.g., PIF1 ; Foury and Kolodynski, 1983 ), metabolic activity (e.g., HSPE1 ; Kumar et al, 2015 ), feed intake (e.g., SNORA70 ; Pitt et al, 2018 ), carcass conformation (e.g., SNORA70 ; Pitt et al, 2018 ; PLCL1 ; Shin et al, 2015 ), fertility and reproduction traits (e.g., RBPMS2 , OAZ2 ; Fernández et al, 2019 ; IL6ST ; Song et al, 2009 ; IGSF8 ; Glazar and Evans, 2009 ), and olfactory receptors (e.g., OR51A7 ; Olivieri et al, 2016 ).…”

“…Despite the limitation of the ascertainment bias and reduced genomic coverage of the SNP dataset used, an interesting list of potential genes under selection in multiple cattle breeds, YAK, and BLI, which will be the foundation for future investigations could be still provided. For instance, the RBPMS2 gene, found in YAK is related to age at first calving in Romosinuano and Costeño-con-Cuernos cattle breeds ( Fernández et al, 2019 ) and the gene ATG16L2 found in MG cattle is related to mastitis recovery in Danish HOL cows ( Welderufael et al, 2017 ). Angrecka and Herbut (2016) observed that cows in excessive cold temperatures may show fertility impairments and the potential candidate gene RBPMS2 found in YAK might be an indication of adaptation for the cold environments.…”

“…Letters in the figure represent the decomposition of the: (A) first and second; (B) first and third; and (C) second and third principal components, respectively (*see SupplementaryTable 1 for abbreviations). (e.g., SNORA70;Pitt et al, 2018), carcass conformation (e.g., SNORA70;Pitt et al, 2018; PLCL1;Shin et al, 2015), fertility and reproduction traits (e.g., RBPMS2, OAZ2;Fernández et al, 2019; IL6ST;Song et al, 2009; IGSF8;Glazar and Evans, 2009), and olfactory receptors (e.g., OR51A7;Olivieri et al, 2016).Several novel candidate genes were found when combining different methods.…”

Meta-Analysis of Heifer Traits Identified Reproductive Pathways in Bos indicus Cattle

“…The protein coded by IDH3A was up regulated in the ovaries of post-pubertal heifers as compared to pre-pubertal heifers [ 96 ]. The gene PTGDR was within a peak SNP region in this study and had been reported as a candidate in a previous GWAS as associated with age at first calving in cattle [ 97 ]. In short, these candidate genes suggested by peak SNPs have supporting evidence from previous studies.…”

A multi-breed GWAS for morphometric traits in four Beninese indigenous cattle breeds reveals loci associated with conformation, carcass and adaptive traits

“…Two other SNP suggestively associated with BL, rs109186122 and rs43616983, are located in the genes GYPC and SLC16A4, respectively. According to its annotation in DAVID, GYPC is involved in oligosaccharide binding and is reported to be associated with intramuscular fat deposition and reproduction performances in cattle [117][118][119]. The SLC16A4 gene had effects on postweaning weight gain, feed efficiency and resistance to the bovine viral diarrhea virus in cattle [120][121][122].…”