Genome-wide association study of reproduction traits in Nelore cattle, including additional phenotypic information from non-genotyped animals

Pós-graduação em Genética e Melhoramento Animal - FCAV

Genetic associations between scrotal circumference and female reproductive traits in Nelore cattle

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Genome-wide association study of reproductive traits in Nellore heifers using Bayesian inference

An important goal of Zebu breeding programs is to improve reproductive performance. A major problem faced with the genetic improvement of reproductive traits is that recording the time for an animal to reach sexual maturity is costly. Another issue is that accurate estimates of breeding values are obtained only a long time after the young bulls have gone through selection. An alternative to overcome these problems is to use traits that are indicators of the reproductive efficiency of the herd and are easier to measure, such as age at first calving. Another problem is that heifers that have conceived once may fail to conceive in the next breeding season, which increases production costs. Thus, increasing heifer's rebreeding rates should improve the economic efficiency of the herd. Response to selection for these traits tends to be slow, since they have a low heritability and phenotypic information is provided only later in the life of the animal. Genome-wide association studies (GWAS) are useful to investigate the genetic mechanisms that underlie these traits by identifying the genes and metabolic pathways involved. Data from 1853 females belonging to the Agricultural Jacarezinho LTDA were used. Genotyping was performed using the BovineHD BeadChip (777 962 single nucleotide polymorphisms (SNPs)) according to the protocol of Illumina - Infinium Assay II ® Multi-Sample HiScan with the unit SQ ™ System. After quality control, 305 348 SNPs were used for GWAS. Forty-two and 19 SNPs had a Bayes factor greater than 150 for heifer rebreeding and age at first calving, respectively. All significant SNPs for age at first calving were significant for heifer rebreeding. These 42 SNPs were next or within 35 genes that were distributed over 18 chromosomes and comprised 27 protein-encoding genes, six pseudogenes and two miscellaneous noncoding RNAs. The use of Bayes factor to determine the significance of SNPs allowed us to identify two sets of 42 and 19 significant SNPs for heifer rebreeding and age at first calving, respectively, which explain 11.35 % and 6.42 % of their phenotypic variance, respectively. These SNPs provide relevant information to help elucidate which genes affect these traits.

Genetic correlations between heifer subsequent rebreeding and age at first calving and growth traits in Nellore cattle by Bayesian inference

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Genetic associations between age at first calving and heifer body weight and scrotal circumference in Nelore cattle

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Genetic associations of visual scores with subsequent rebreeding and days to first calving in Nellore cattle

Records of Nellore animals born from 1990 to 2006 were used to estimate genetic correlations of visual scores at yearling (conformation, C; finishing precocity, P; and muscling, M) with primiparous subsequent rebreeding (SR) and days to first calving (DC), because the magnitude of these associations is still unknown. Genetic parameters were estimated by multiple-traits Bayesian analysis, using a nonlinear (threshold) animal models for visual scores and SR and a linear animal models for weaning weight (WW) and DC. WW was included in the analysis to account for the effects of sequential selection. The posterior means of heritabilities estimated for C, P, M, SR and DC were 0.24 +/- 0.01, 0.31 +/- 0.01, 0.30 +/- 0.01, 0.18 +/- 0.02 and 0.06 +/- 0.02, respectively. The posterior means of genetic correlations estimated between SR and visual scores were low and positive, with values of 0.09 +/- 0.02 (C), 0.19 +/- 0.03 (P) and 0.18 +/- 0.05 (M). on the other hand, negative genetic correlations were found between DC and C (-0.11 +/- 0.09), P (-0.19 +/- 0.09) and M (-0.16 +/- 0.09). The primiparous rebreeding trait has genetic variability in Nellore cattle. The genetic correlations between visual scores, and SR and DC were low and favourable. The genetic changes in C, P and M were 0.02, 0.03 and 0.03/year, respectively. For SR and DC, genetic trends were 0.01/year and -0.01 days/year, respectively, indicating that the increase in genetic merit for reproductive traits was small over time. Direct selection for visual scores together with female reproductive traits is recommended to increase the fertility of beef cows.

Genetic parameters and relationships between heifers rebreeding and hip height in Nellore cattle

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Genetic parameters and relationships of heifer pregnancy and age at first calving with weight gain, yearling and mature weight in Nelore cattle

The objectives of the current study were to investigate the additive genetic associations between heifer pregnancy at 16 months of age (HP16) and age at first calving (AFC) with weight gain from birth to weaning (WG), yearling weight (YW) and mature weight (MW), in order to verify the possibility of using the traits measured directly in females as selection criteria for the genetic improvement of sexual precocity in Nelore cattle. (Co)variance components were estimated by Bayesian inference using a linear animal model for AFC, WG, YW and MW and a nonlinear (threshold) animal model for HP16. The posterior means of direct heritability estimates were: 0.45 +/- 0.02; 0.10 +/- 0.01; 023 +/- 0.02; 0.36 +/- 0.01 and 0.39 +/- 0.04, for HP16, AFC, WG, YW and MW, respectively. Maternal heritability estimate for WG was 0.07 +/- 0.01. Genetic correlations estimated between HP16 and WG, YW and MW were 0.19 +/- 0.04; 0.25 +/- 0.06 and 0.14 +/- 0.05, respectively. The genetic correlations of AFC with WG, YW and MW were low to moderate and negative, with values of -0.18 +/- 0.06; -0.22 +/- 0.05 and -0.12 +/- 0.05, respectively. The high heritability estimated for HP16 suggests that this trait seem to be a better selection criterion for females sexual precocity than AFC. Long-term selection for animals that are heavier at young ages tends to improve the heifers sexual precocity evaluated by HP16 or AFC. Predicted breeding values for HP16 can be used to select bulls and it can lead to an improvement in sexual precocity. The inclusion of HP16 in a selection index will result in small or no response for females mature weight. (C) 2011 Elsevier B.V. All rights reserved.

Additive genetic relationships between scrotal circumference, heifer pregnancy, and stayability in Nellore cattle

Scrotal circumference data from 47,605 Nellore young bulls, measured at around 18 mo of age (SC18), were analyzed simultaneously with 27,924 heifer pregnancy (HP) and 80,831 stayability (STAY) records to estimate their additive genetic relationships. Additionally, the possibility that economically relevant traits measured directly in females could replace SC18 as a selection criterion was verified. Heifer pregnancy was defined as the observation that a heifer conceived and remained pregnant, which was assessed by rectal palpation at 60 d. Females were exposed to sires for the first time at about 14 mo of age (between 11 and 16 mo). Stayability was defined as whether or not a cow calved every year up to 5 yr of age, when the opportunity to breed was provided. A Bayesian linear-threshold-threshold analysis via Gibbs sampler was used to estimate the variance and covariance components of the multitrait model. Heritability estimates were 0.42 +/- 0.01, 0.53 +/- 0.03, and 0.10 +/- 0.01, for SC18, HP, and STAY, respectively. The genetic correlation estimates were 0.29 +/- 0.05, 0.19 +/- 0.05, and 0.64 +/- 0.07 between SC18 and HP, SC18 and STAY, and HP and STAY, respectively. The residual correlation estimate between HP and STAY was -0.08 +/- 0.03. The heritability values indicate the existence of considerable genetic variance for SC18 and HP traits. However, genetic correlations between SC18 and the female reproductive traits analyzed in the present study can only be considered moderate. The small residual correlation between HP and STAY suggests that environmental effects common to both traits are not major. The large heritability estimate for HP and the high genetic correlation between HP and STAY obtained in the present study confirm that EPD for HP can be used to select bulls for the production of precocious, fertile, and long-lived daughters. Moreover, SC18 could be incorporated in multitrait analysis to improve the prediction accuracy for HP genetic merit of young bulls.

Avaliação genética da reconcepção de fêmeas primíparas da raça Nelore

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Quantitative genetic study of age at subsequent rebreeding in Nellore cattle by using survival analysis

The continuous trait age at subsequent rebreeding (ASR) was evaluated using survival analysis in Nellore breed cows that conceived for the first time at approximately 14 months of age. This methodology was chosen because the restricted breeding season produces censored data. The dataset contained 2885 records of ASR (in days). Records of females that did not produce calves in the following year after being exposed to a sire were considered censored (48.3% of the total). The statistical model used was a Weibull mixed survival model, which included fixed effects of contemporary groups (CG) and period and a random effect of individual animal. The effect of contemporary groups on ASR was significant (P < 0.01). Heritabilities obtained for ASR were 0.03 and 0.04 in logarithmic and original scales, respectively. These results indicate that the genetic selection response for subsequent reproduction of 2-year-old Nellore breed females is not expected to be effective based on survival analysis. Furthermore, these results suggest that environmental improvement is fundamental to this important trait. It should be highlighted that an increase in the average date of birth can produce an adverse effect in the future, since this cannot be compensated by genetic improvement.

Fatores genéticos e ambientais sobre a probabilidade de prenhez precoce em bovinos Caracu

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)