The objectives of this study were to 1) compare four models for breeding value prediction using genomic or pedigree information and 2) evaluate the impact of fixed effects that account for family structure. Comparisons were made in a Nellore-Angus population comprising F2, F3 and half-siblings to embryo transfer F2 calves with records for overall temperament at weaning (TEMP; n = 769) and Warner-Bratzler shear force (WBSF; n = 387). After quality control, there were 34,913 whole genome SNP markers remaining. Bayesian methods employed were BayesB ( π = 0.995 or 0.997 for WBSF or TEMP, respectively) and BayesC (π = 0 and π), where π is the ideal proportion of markers not included. Direct genomic values (DGV) from single trait Bayesian analyses were compared to conventional pedigree-based animal model breeding values. Numerically, BayesC procedures (using π) had the highest accuracy of all models for WBSF and TEMP ( ρgg = 0.843 and 0.923, respectively), but BayesB had the least bias (regression of performance on prediction closest to 1, βy,x = 2.886 and 1.755, respectively). Accounting for family structure decreased accuracy and increased bias in prediction of DGV indicating a detrimental impact when used in these prediction methods that simultaneously fit many markers.
Gestation length, birth weight, and weaning weight of F2 Nelore-Angus calves (n = 737) with designed extensive full-sibling and half-sibling relatedness were evaluated for association with 34,957 SNP markers. In analyses of birth weight, random relatedness was modeled three ways: 1) none, 2) random animal, pedigree-based relationship matrix, or 3) random animal, genomic relationship matrix. Detected birth weight-SNP associations were 1,200, 735, and 31 for those parameterizations respectively; each additional model refinement removed associations that apparently were a result of the built-in stratification by relatedness. Subsequent analyses of gestation length and weaning weight modeled genomic relatedness; there were 40 and 26 trait-marker associations detected for those traits, respectively. Birth weight associations were on BTA14 except for a single marker on BTA5. Gestation length associations included 37 SNP on BTA21, 2 on BTA27 and one on BTA3. Weaning weight associations were on BTA14 except for a single marker on BTA10. Twenty-one SNP markers on BTA14 were detected in both birth and weaning weight analyses.
The objective was to identify single nucleotide polymorphisms (SNP) associated to fertility in cows raised under a subtropical environment. Re-sequencing of nine genes associated to GH-IGF endocrine pathway, which are located in bovine chromosomes 5, 16 and 20, identified 73 SNP useful for associative genetic studies; however, only seven resulted as polymorphic and unique to the Romosinuano breed. Then, DNA samples were extracted from 129 beef heifers and used to determine genotypes corresponding to each SNP. Mixed model analysis identified one SNP from the PAPP-A2 gene (C/T, rs110490898) as predictor (P<0.05) of reproductive performance. The allele T was the most favorable allele (P<0.05), because it was associated with lower age at first calving (-37.1 ± 14.4 d) and age at second calving (-65.43 ± 30.8 d). In the contrast analysis, the linear term resulted as significant and quadratic term as non significant, which suggested an additive effect of the alleles. These results provide evidence to support the PAPP-A2 gene as a candidate gene associated to reproductive performance in heifers and first-calf cows from the Romosinuano breed, raised under a subtropical environment.
El objetivo fue identificar polimorfismos de un solo nucleótido (SNP) asociados a la fertilidad en hembras bovinas criadas en subtropico. La re-secuenciación de nueve genes relacionados al eje endocrino GH-IGF, localizados en los cromosomas 5, 16 y 20 del bovino, identificó 73 SNP útiles para estudios genéticos asociativos; sin embargo, sólo siete resultaron polimórficos y exclusivos de la raza Romosinuano. Muestras de ADN se extrajeron de 129 vaquillas Romosinuano y usadas para determinar los genotipos correspondientes a cada SNP. Un análisis de modelos mixtos identificó únicamente a un polimorfismo del gen PAPP-A2 (C/T, rs110490898) como predictor (P<0.05) del comportamiento reproductivo. El alelo T fue el más favorable (P<0.05) ya que éste se asoció a una reducción tanto en la edad al primer parto (-37.1 ± 14.4 días), como en la edad al segundo parto (-65.43 ± 30.8 días). En el análisis de contrastes el término lineal resultó significativo (P<0.05), pero no el quadrático, lo cual sugiere un efecto aditivo de los alelos. Los resultados proporcionan evidencia para proponer al gen PAPP-A2, como candidato asociado al comportamiento reproductivo en vaquillas y vacas primerizas de la raza Romosinuano.