Genotype imputation from various low-density SNP panels and its impact on accuracy of genomic breeding values in pigs.

The uptake of genomic selection (GS) by the swine industry is still limited by the costs of genotyping. A feasible alternative to overcome this challenge is to genotype animals using an affordable low-density (LD) single nucleotide polymorphism (SNP) chip panel followed by accurate imputation to a high-density panel. Therefore, the main objective of this study was to screen incremental densities of LD panels in order to systematically identify one that balances the tradeoffs among imputation accuracy, prediction accuracy of genomic estimated breeding values (GEBVs), and genotype density (directly associated with genotyping costs). Genotypes using the Illumina Porcine60K BeadChip were available for 1378 Duroc (DU), 2361 Landrace (LA) and 3192 Yorkshire (YO) pigs. In addition, pseudo-phenotypes (de-regressed estimated breeding values) for five economically important traits were provided for the analysis. The reference population for genotyping imputation consisted of 931 DU, 1631 LA and 2103 YO animals and the remainder individuals were included in the validation population of each breed. A LD panel of 3000 evenly spaced SNPs (LD3K) yielded high imputation accuracy rates: 93.78% (DU), 97.07% (LA) and 97.00% (YO) and high correlations (>0.97) between the predicted GEBVs using the actual 60 K SNP genotypes and the imputed 60 K SNP genotypes for all traits and breeds. The imputation accuracy was influenced by the reference population size as well as the amount of parental genotype information available in the reference population. However, parental genotype information became less important when the LD panel had at least 3000 SNPs. The correlation of the GEBVs directly increased with an increase in imputation accuracy. When genotype information for both parents was available, a panel of 300 SNPs (imputed to 60 K) yielded GEBV predictions highly correlated (⩾0.90) with genomic predictions obtained based on the true 60 K panel, for all traits and breeds. For a small reference population size with no parents on reference population, it is recommended the use of a panel at least as dense as the LD3K and, when there are two parents in the reference population, a panel as small as the LD300 might be a feasible option. These findings are of great importance for the development of LD panels for swine in order to reduce genotyping costs, increase the uptake of GS and, therefore, optimize the profitability of the swine industry.

Estimates of genetic parameters and genetic trends for reproductive traits and weaning weight in Tabapuã cattle.

The Tabapuã breed is a beef cattle Brazilian breed known for its sexual precocity and desirable characteristics for tropical conditions. However, this is a newly formed breed and few studies have been conducted regarding genetic parameters and genetic trends for its reproductive traits. The objective of the present study was to estimate the genetic parameters, genetic trends, and relative selection efficiency for weaning weight adjusted to 210 d of age (W210), age at first calving (AFC), average calving interval (ACI), first calving interval (CI1), and accumulated productivity (ACP) among Tabapuã beef cattle. Pedigree data on 15,241 Tabapuã animals born between 1958 and 2011 and phenotype records from 7,340 cows born between 1970 and 2011 were supplied by the National Association of Breeders and Researchers (Associação Nacional de Criadores e Pesquisadores). Analysis through the least squares method assisted in defining the fixed effects that were considered within the models. The estimates for the genetic parameters were obtained through the REML, using a multitrait animal model. The likelihood ratio test applied for W210 was significant ( < 0.05) for the inclusion of maternal additive genetic and permanent environmental effects in the model. Genetic trends were calculated through linear regression of the EBV of the animals, according to the year of birth. The heritability estimates obtained ranged from 0.04 ± 0.03 for CI1 to 0.25 ± 0.05 for W210. The genetic correlations ranged from 0.004 ± 0.19 for W210-AFC and 0.93 ± 0.12 for ACI-CI1. The genetic trend was significant ( < 0.05) and favorable for CI1 and the maternal genetic effect of W210 and was significant ( < 0.05) and unfavorable for AFC, ACI, and ACP. The ACP could be used in the selection index to assist the breeding goal of improved productive and reproductive performance. The genetic trends indicated small and unfavorable genetic changes for AFC, ACI, and ACP in light of the recent implementation of a genetic breeding program for this breed.

Genetic parameter estimates and principal component analysis of breeding values of reproduction and growth traits in female Canchim cattle.

Phenotypic data from female Canchim beef cattle were used to obtain estimates of genetic parameters for reproduction and growth traits using a linear animal mixed model. In addition, relationships among animal estimated breeding values (EBVs) for these traits were explored using principal component analysis. The traits studied in female Canchim cattle were age at first calving (AFC), age at second calving (ASC), calving interval (CI), and bodyweight at 420 days of age (BW420). The heritability estimates for AFC, ASC, CI and BW420 were 0.03±0.01, 0.07±0.01, 0.06±0.02, and 0.24±0.02, respectively. The genetic correlations for AFC with ASC, AFC with CI, AFC with BW420, ASC with CI, ASC with BW420, and CI with BW420 were 0.87±0.07, 0.23±0.02, -0.15±0.01, 0.67±0.13, -0.07±0.13, and 0.02±0.14, respectively. Standardised EBVs for AFC, ASC and CI exhibited a high association with the first principal component, whereas the standardised EBV for BW420 was closely associated with the second principal component. The heritability estimates for AFC, ASC and CI suggest that these traits would respond slowly to selection. However, selection response could be enhanced by constructing selection indices based on the principal components.

Estimation of genetic parameters for partial egg production periods by means of random regression models.

We estimated genetic parameters for egg production in different periods by means of random regression models, aiming at selection based on partial egg production from a generation of layers. The production was evaluated for each individual by recording the number of eggs produced from 20 to 70 weeks of age, with partial records taken every three weeks for a total of 17 periods. The covariance functions were estimated with a random regression model by the restricted maximum likelihood method. A model composed of third-order polynomials for the additive effect, ninth-order polynomials for the permanent environment, and a residual variance structure with five distinct classes, was found to be most suitable for adjusting the egg production data for laying hens. The heritability estimates varied from 0.04 to 0.14. The genetic correlations were all positive, varying from 0.10 to 0.99. Selection applied in partial egg production periods will result in greater genetic profit for the adjacent periods. However, as the distance in time between periods increases, selection becomes less efficient. Selection based on the second period (23 to 25 weeks of age), where greater heritability was estimated, would note benefit the final egg-laying cycle periods.

Whole-genome analysis for backfat thickness in a tropically adapted, composite cattle breed from Brazil.

Backfat thickness affects the preservation of the beef carcass after slaughter and confers organoleptic characteristics assessed by the consumer. One of the breeding goals for Canchim, a tropically adapted breed, is to comprehensively increase fat thickness. Our goals were to identify genomic regions associated with backfat in Canchim populations and validate the association of single nucleotide polymorphisms (SNPs) overlapping previously identified QTL regions known to affect fat deposition. Fifteen animals with lower and 15 animals with higher residues for backfat, according to a linear model using the SAS GLM procedure, were selected from a population of 1171 animals and genotyped using the BovineSNP50 BeadChip. Initial analysis revealed more than 100 SNPs that discriminated the tails of phenotypic distribution. One extended region of association included the centromeric region of chromosome (Chr) 14. Because this region overlapped with QTL from previous reports, we developed SNP assays to interrogate two linkage disequilibrium blocks, one in the centromeric region and another in the middle region of Chr 14 to confirm the association. The analysis validated the presence of specific haplotypes affecting fat thickness.

Genetic analysis on growth and carcass traits in Nelore cattle.

In this study, the objective was to estimate genetic parameters of body weight at 210 (BW210) and 365 (BW365) days of age in relation to rib eye area (REA), subcutaneous back fat thickness (BF) and rump fat (RF), and their respective genetic trends, in Nelore beef cattle. Estimates of genetic parameters and breeding values for the studied traits were obtained using the REML method. The direct and maternal heritability estimates were respectively: 0.25±0.02 and 0.21±0.01, for BW210, and 0.29±0.02 and 0.09±0.01, for BW365. The heritability estimates for transformed REA, BF and RF were 0.29±0.03, 0.21±0.02 and 0.23±0.03, respectively. There were genetic associations between BW210 and REA, BW365 and REA, and BF and RF, while the other correlations were low. The selection process that was conducted at the farms participating in the breeding program, taking the proposed selection index into consideration, caused genetic changes to these traits.

Prospecting candidate SNPs for backfat in Canchim beef cattle.

Canchim is a composite cattle breed developed in Brazil for beef production. One of the breeding objectives is to increase fat deposition. QTLs for fat thickness and/or marbling have been reported on BTA4 and BTA14. The IGFBP3 and DDEF1 genes, mapped to BTA4 and BTA14, respectively, affect adipogenesis. We looked for SNPs in the IGFBP3 and DDEF1 genes that could be associated with backfat thickness in Canchim beef cattle. For SNP identification, sires with the highest accuracy were ranked according to expected breeding value for fat thickness; the 12 extremes (six sires with the highest and six with the lowest expected breeding value for the trait) were chosen. Six regions of the IGFBP3 and 14 regions of the DDEF1 were sequenced using the Sanger method. Nine SNPs were identified in IGFBP3 and 76 in the DDEF1. After an initial analysis, two SNPs were selected to be genotyped for the whole population; these were DDEF1g.279401A>G and IGFBP3c.4394T>C(Trp>Arg). We found a significant effect (P ≤ 0.05) of allele substitution on backfat thickness; however, the IGFBP3 SNP did not significantly affect this trait.

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

Summary Age at first calving (AFC) measures the entry of heifers into the beef cattle production system. This trait can be used as a selection criterion for earlier reproductive performance. Using data from Nelore cattle participating in the 'Program for Genetic Improvement of the Nelore Breed' (PMGRN-Nelore Brazil), bi-trait analyses were performed using the restricted maximum likelihood method, based on an AFC animal model and the following traits: female body weight adjusted to 365 (BW365) and 450 (BW450) days of age, and male scrotal circumference adjusted to 365 (SC365), 450 (SC450), 550 (SC550) and 730 (SC730) days of age. The heritability estimates for AFC ranged from 0.02 +/- 0.02 to 0.04 +/- 0.02. The estimates of additive direct heritabilities (with standard error) for BW365, BW450, SC365, SC450, SC550 and SC730 were 0.36 +/- 0.07, 0.38 +/- 0.07, 0.48 +/- 0.07, 0.65 +/- 0.07, 0.64 +/- 0.07 and 0.42 +/- 0.07, respectively, and the genetic correlations with AFC were -0.38, -0.33, 0.10, -0.13, -0.13 and 0.06, respectively. In the herds studied, selection for SC365, SC450, SC550 or SC730 should not cause genetic changes in AFC. Selection based on BW365 or BW450 would favor smaller AFC breeding values. However, the low magnitude of direct heritability estimates for AFC in these farms indicates that changes in phenotypical expression depend mostly on non-genetic factors.

Heritability estimates and genetic correlations for body weight and scrotal circumference adjusted to 12 and 18 months of age for male Nellore cattle.

Heritability estimates and genetic correlations were obtained for body weight and scrotal circumference, adjusted, respectively, to 12 (BW12 and SC12) and 18 (BW18 and SC18) months of age, for 10 742 male Nellore cattle. The adjustments to SC12 and SC18 were made using a nonlinear logistic function, while BW12 and BW18 were obtained by linear adjustment. The contemporary groups (CGs) were defined from animals born on the same farm, in the same year and birth season. The mean heritability estimates obtained using the restricted maximum likelihood method in bi-trait analysis were 0.25, 0.25, 0.29 and 0.42 for BW12, BW18, SC12 and SC18, respectively. The genetic correlations were 0.30 ± 0.11, 0.21 ± 0.13, 0.21 ± 0.11, -0.08 ± 0.15, 0.16 ± 0.12 and 0.89 ± 0.04 between the traits BW12 and BW18; BW12 and SC12; BW12 and SC18; BW18 and SC12; BW18 and SC18; and SC12 and SC18. The heritability for SC18 was considerably greater than for SC12, suggesting that this should be included as a selection criterion. The genetic correlation between BW18 and SC12 was close to zero, indicating that these traits did not influence each other. The contrary occurred between SC12 and SC18, indicating that selection using one of these could alter the other. Because of the mean magnitudes of heritabilities in the various measurements of weight and scrotal perimeter, it is suggested that the practice of individual selection for these traits is possible.

Association of an insulin-like growth factor 1 gene microsatellite with phenotypic variation and estimated breeding values of growth traits in Canchim cattle.

A population of 1398 Canchim (CA) cattle was genotyped to assess the association of an insulin-like growth factor 1 (IGF1) gene microsatellite with phenotypic variation and estimated breeding values of pre-weaning, weaning and post-weaning growth traits. After an initial analysis, the IGF1 genotype only had a significant effect (P < 0.05) on birth weight (BW) and weaning weight adjusted to 240 days (WW240). For these two traits, direct and maternal breeding values were estimated using the restricted maximum likelihood (reml). Two analyses were carried out. In the first (Model I), all fixed effects were fitted. In the second (Model II), the fixed effect of the IGF1 genotype was omitted. The estimated genetic and phenotypic components of variance were similar for every trait in both models. For Model I, estimated direct and maternal heritabilities were 0.26 and 0.16 for BW and 0.23 and 0.14 for WW240 respectively. The genetic and phenotypic correlations between BW and WW240 were 0.38 and 0.38 (Model I) and 0.19 and 0.38 (Model II) respectively. Fifty animals were classified according to their direct and maternal breeding values for both traits. Spearman rank-order correlation between animal rankings in the two models was used to assess the effect of including the IGF1 genotype in the model. Non-significant values from this correlation were indicative of a difference in breeding value rankings between the two approaches. The IGF1 gene was found to be associated with phenotypic variation and breeding values in the early phase of growth.