Genomic selection and assisted reproduction technologies to foster cattle breeding

Genomics has been propagated as a paradigm shifting innovation in livestock during the last decade. The possibility of predicting breeding values using genomic information has revolutionized the dairy cattle industry and is now being implemented in beef cattle. In this paper we discuss how genomics is changing cattle breeding through genomic selection, and how this change is creating new ways to articulate assisted reproduction technologies with animal breeding. We also debate that the scientific community is still starting the long journey to reveal the functional aspects of the cattle genome, and that knowledge in this field is the frontier to a whole new venue for the development of novel applications in the livestock sector.

The development of genomics applied to dairy breeding

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Study of using marker assisted selection on a beef cattle breeding program by model comparison

A data set of a commercial Nellore beef cattle selection program was used to compare breeding models that assumed or not markers effects to estimate the breeding values, when a reduced number of animals have phenotypic, genotypic and pedigree information available. This herd complete data set was composed of 83,404 animals measured for weaning weight (WW), post-weaning gain (PWG), scrotal circumference (SC) and muscle score (MS), corresponding to 116,652 animals in the relationship matrix. Single trait analyses were performed by MTDFREML software to estimate fixed and random effects solutions using this complete data. The additive effects estimated were assumed as the reference breeding values for those animals. The individual observed phenotype of each trait was adjusted for fixed and random effects solutions, except for direct additive effects. The adjusted phenotype composed of the additive and residual parts of observed phenotype was used as dependent variable for models' comparison. Among all measured animals of this herd, only 3160 animals were genotyped for 106 SNP markers. Three models were compared in terms of changes on animals' rank, global fit and predictive ability. Model 1 included only polygenic effects, model 2 included only markers effects and model 3 included both polygenic and markers effects. Bayesian inference via Markov chain Monte Carlo methods performed by TM software was used to analyze the data for model comparison. Two different priors were adopted for markers effects in models 2 and 3, the first prior assumed was a uniform distribution (U) and, as a second prior, was assumed that markers effects were distributed as normal (N). Higher rank correlation coefficients were observed for models 3_U and 3_N, indicating a greater similarity of these models animals' rank and the rank based on the reference breeding values. Model 3_N presented a better global fit, as demonstrated by its low DIC. The best models in terms of predictive ability were models 1 and 3_N. Differences due prior assumed to markers effects in models 2 and 3 could be attributed to the better ability of normal prior in handle with collinear effects. The models 2_U and 2_N presented the worst performance, indicating that this small set of markers should not be used to genetically evaluate animals with no data, since its predictive ability is restricted. In conclusion, model 3_N presented a slight superiority when a reduce number of animals have phenotypic, genotypic and pedigree information. It could be attributed to the variation retained by markers and polygenic effects assumed together and the normal prior assumed to markers effects, that deals better with the collinearity between markers. (C) 2012 Elsevier B.V. All rights reserved.

Comparison of genetic gains per year for carcass traits among breeding programs in the Japanese Brown and the Japanese Black cattle

The breeding program for beef cattle in Japan has changed dramatically over 4 decades. Visual judging was done initially, but progeny testing in test stations began in 1968. In the 1980s, the genetic evaluation program using field records, so-called on-farm progeny testing, was first adopted in Oita, Hyogo, and Kumamoto prefectures. In this study, genetic trends for carcass traits in these 3 Wagyu populations were estimated, and genetic gains per year were compared among the 3 different beef cattle breeding programs. The field carcass records used were collected between 1988 and 2003. The traits analyzed were carcass weight, LM area, rib thickness, s.c. fat thickness, and beef marbling standard number. The average breeding values of reproducing dams born the same year were used to estimate the genetic trends for the carcass traits. For comparison of the 3 breeding programs, birth years of the dams were divided into 3 periods reflecting each program. Positive genetic trends for beef marbling standard number were clearly shown in all populations. The genetic gains per year for all carcass traits were significantly enhanced by adopting the on-farm progeny testing program. These results indicate that the on-farm progeny testing program with BLUP is a very powerful approach for genetic improvement of carcass traits in Japanese Wagyu beef cattle.

Predictive ability of Genomic Estimated Family Values (GEFV).

Genomic selection (GS) has been used to compute genomic estimated breeding values (GEBV) of individuals; however, it has only been applied to animal and major plant crops due to high costs. Besides, breeding and selection is performed at the family level in some crops. We aimed to study the implementation of genome-wide family selection (GWFS) in two loblolly pine (Pinus taeda L.) populations: i) the breeding population CCLONES composed of 63 families (5-20 individuals per family), phenotyped for four traits (stem diameter, stem rust susceptibility, tree stiffness and lignin content) and genotyped using an Illumina Infinium assay with 4740 polymorphic SNPs, and ii) a simulated population that reproduced the same pedigree as CCLONES, 5000 polymorphic loci and two traits (oligogenic and polygenic). In both populations, phenotypic and genotypic data was pooled at the family level in silico. Phenotypes were averaged across replicates for all the individuals and allele frequency was computed for each SNP. Marker effects were estimated at the individual (GEBV) and family (GEFV) levels with Bayes-B using the package BGLR in R and models were validated using 10-fold cross validations. Predicted ability, computed by correlating phenotypes with GEBV and GEFV, was always higher for GEFV in both populations, even after standardizing GEFV predictions to be comparable to GEBV. Results revealed great potential for using GWFS in breeding programs that select families, such as most outbreeding forage species. A significant drop in genotyping costs as one sample per family is needed would allow the application of GWFS in minor crops.

Evaluation of breeding strategies for polledness in dairy cattle using a newly developed simulation framework for quantitative and Mendelian traits

Background: Intensified selection of polled individuals has recently gained importance in predominantly horned dairy cattle breeds as an alternative to routine dehorning. The status quo of the current polled breeding pool of genetically-closely related artificial insemination sires with lower breeding values for performance traits raises questions regarding the effects of intensified selection based on this founder pool. Methods: We developed a stochastic simulation framework that combines the stochastic simulation software QMSim and a self-designed R program named QUALsim that acts as an external extension. Two traits were simulated in a dairy cattle population for 25 generations: one quantitative (QMSim) and one qualitative trait with Mendelian inheritance (i.e. polledness, QUALsim). The assignment scheme for qualitative trait genotypes initiated realistic initial breeding situations regarding allele frequencies, true breeding values for the quantitative trait and genetic relatedness. Intensified selection for polled cattle was achieved using an approach that weights estimated breeding values in the animal best linear unbiased prediction model for the quantitative trait depending on genotypes or phenotypes for the polled trait with a user-defined weighting factor. Results: Selection response for the polled trait was highest in the selection scheme based on genotypes. Selection based on phenotypes led to significantly lower allele frequencies for polled. The male selection path played a significantly greater role for a fast dissemination of polled alleles compared to female selection strategies. Fixation of the polled allele implies selection based on polled genotypes among males. In comparison to a base breeding scenario that does not take polledness into account, intensive selection for polled substantially reduced genetic gain for this quantitative trait after 25 generations. Reducing selection intensity for polled males while maintaining strong selection intensity among females, simultaneously decreased losses in genetic gain and achieved a final allele frequency of 0.93 for polled. Conclusions: A fast transition to a completely polled population through intensified selection for polled was in contradiction to the preservation of high genetic gain for the quantitative trait. Selection on male polled genotypes with moderate weighting, and selection on female polled phenotypes with high weighting, could be a suitable compromise regarding all important breeding aspects.

Avaliação genética multirracial para ganho de peso pré-desmama em bovinos de uma população composta

Objetivou-se neste trabalho estudar modelos com efeitos não-aditivos diretos e maternos em uma população composta em clima tropical, tentando minimizar esses efeitos para obtenção dos valores genéticos dos animais avaliados. Foram utilizados dados de animais de uma população composta, por meio da comparação de três modelos que incluíram os efeitos fixos de grupo contemporâneo, ordem de parto e heterose direta e materna e os efeitos aleatórios de efeito genético aditivo direto e materno. As análises foram realizadas em duas etapas; na primeira foram estudadas as estimativas dos efeitos raciais e de heterose individual e materna e na segunda etapa, calculadas as variâncias, herdabilidades e os valores genéticos dos animais. O efeito materno, quando não foi considerado no modelo, pareceu superestimar o efeito aditivo racial. Os efeitos aditivos raciais, racial materno e de heterose individual e materna influenciaram significativamente o ganho médio diário no pré-desmame, obtendo-se diferentes estimativas entre os tipos biológicos. Considerando o arquivo de dados corrigidos para os efeitos não-aditivos diretos e maternos, as herdabilidades direta e materna foram de 0,22 e 0,20, respectivamente. Os efeitos racial materno e de heterose individual e materna foram importantes fontes de variação para o ganho médio diário no pré-desmame e devem ser considerados durante a avaliação genética de uma população multirracial.

Estimates of genetic trend for carcass traits in a commercial broiler line

Data from the slaughter of 24,001 chickens that were part of a selection program for the production of commercial broilers were used to estimate genetic trend for absolute carcass (CW), breast meat (BRW), and leg (LW) weights, and relative carcass (CY), breast meat (BRY), and leg (LY) weights. The components of (co) variance and breeding values of individuals were obtained by the restricted maximum likelihood method applied to animal models. The relationship matrix was composed of 132,442 birds. The models included as random effects, maternal additive genetic and permanent environmental for CW, BRW, LW, CY, and BRY, and only maternal permanent environmental for LY, besides the direct additive genetic and residual effects, and as fixed effects, hatch week, parents' mating group and sex. The estimates of genetic trend were obtained by average regression of breeding value on generation, and the average genetic trend was estimated by regression coefficients. The genetic trends for CW (+ 6.0336 g/generation), BRW (+ 3.6723 g/generation), LW (+ 1.5846 g/generation), CY (+ 0.1195%/generation), and BRY (+ 0.1388%/generation) were positive, and they were in accordance with the objectives of the selection program for these traits. The genetic trend for LY(-0.0019%/generation) was negative, possibly due to the strong emphasis on selection for BRY and the negative correlations between these two traits.

Genetic associations between accumulated productivity, and reproductive and growth traits in Nelore cattle

The total meat yield in a beef cattle production cycle is economically very important and depends on the number of calves born per year or birth season, being directly related to reproductive potential. Accumulated Productivity (ACP) is an index that expresses a cow`s capacity to give birth regularly at a young age and to wean animals of greater body weight. Using data from cattle participating in the ""Program for Genetic Improvement of the Nelore Breed"" (PMGRN - Nelore Brasil), bi-trait analyses were performed using the Restricted Maximum Likelihood method based on an ACP animal model and the following traits: age at first calving (AFC), female body weight adjusted for 365 (BW365) and 450 (BW450) days of age, and male scrotal circumference adjusted for 365 (SC365), 450 (SC450), 550 (SC550) and 730 (SC730) days of age. Median estimated ACP heritability was 0.19 and the genetic correlations with AFC, BW365, BW450, SC365, SC450, SC550 and SC730 were 0.33, 0.70, 0.65, 0.08, 0.07, 0.12 and 0.16, respectively. ACP increased and AFC decreased over time, revealing that the selection criteria genetically improved these traits. Selection based on ACP appears to favor the heaviest females at 365 and 450 days of age who showed better reproductive performance as regards AFC. Scrotal circumference was not genetically associated with ACP. (C) 2007 Elsevier B.V. All rights reserved.

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

P>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.

Biometrical analysis and selection of tetraploid progenies of Panicum maximum using mixed model methods

The objectives of this work were to estimate the genetic and phenotypic parameters and to predict the genetic and genotypic values of the selection candidates obtained from intraspecific crosses in Panicum maximum as well as the performance of the hybrid progeny of the existing and projected crosses. Seventy-nine intraspecific hybrids obtained from artificial crosses among five apomictic and three sexual autotetraploid individuals were evaluated in a clonal test with two replications and ten plants per plot. Green matter yield, total and leaf dry matter yields and leaf percentage were evaluated in five cuts per year during three years. Genetic parameters were estimated and breeding and genotypic values were predicted using the restricted maximum likelihood/best linear unbiased prediction procedure (REML/BLUP). The dominant genetic variance was estimated by adjusting the effect of full-sib families. Low magnitude individual narrow sense heritabilities (0.02-0.05), individual broad sense heritabilities (0.14-0.20) and repeatability measured on an individual basis (0.15-0.21) were obtained. Dominance effects for all evaluated characteristics indicated that breeding strategies that explore heterosis must be adopted. Less than 5% increase in the parameter repeatability was obtained for a three-year evaluation period and may be the criterion to determine the maximum number of years of evaluation to be adopted, without compromising gain per cycle of selection. The identification of hybrid candidates for future cultivars and of those that can be incorporated into the breeding program was based on the genotypic and breeding values, respectively. The prediction of the performance of the hybrid progeny, based on the breeding values of the progenitors, permitted the identification of the best crosses and indicated the best parents to use in crosses.

Genetic parameters for drought-tolerance in cassava

The objective of this work was to evaluate the effect of drought on genetic parameters and breeding values of cassava. The experiments were carried out in a completely randomized block design with three replicates, under field conditions with (WD) or without (FI) water deficit. Yield of storage roots (RoY), shoot (ShY), and starch (StY), as well as the number of roots (NR), and root dry matter content (DMC) were evaluated in 47 cassava accessions. Significant differences were observed among accessions; according to heritability, these differences had mostly a genetic nature. Heritability estimates for genotypic effects () ranged from 0.25±0.12 (NR) to 0.60±0.18 (DMC), and from 0.51±0.17 (NR) to 0.80±0.21 (RoY and StY) for WD and FI, respectively, as a consequence of greater environmental influence on WD. Selective accuracy was lower in WD, and ranged from 0.71 (NR) to 0.89 (RoY, DMC, and StY). However, genetic gains were quite high and ranged from 24.43% (DMC) to 113.41% (StY), in WD, and from 8.5% (DMC) to 75.70% (StY) in FI. These genetic parameters may be useful for defining which selection strategies, breeding methods, and experimental designs are more suitable to obtain cassava genetic gains for tolerance to drought.

An expression of mixed animal model equations to account for different means and variances in the base population

This paper presents a general expression to predict breeding values using animal models when the base population is selected, i.e. the means and variances of breeding values in the base generation differ among individuals. Rules for forming the mixed model equations are also presented. A numerical example illustrates the procedure.

Estimación de los efectos del manejo reproductivo y su influencia en la selección del tamaño de la camada en porcino

Con datos procedentes de poblaciones de campo (37.920 partos porducidos en granjas de selección y 95.240 partos producidos en granjas de producción) se ha analizado la influencia de la edad al primer parto, de la duración de la lactación, de la duración del intervalo destete-cubrición fértil y del tipo de cubrición fértil sobre el número de lechones nacidos vivos por parto (NV). Además, utilizando datos simulados se ha evaluado el interés de considerar estos factores de manejo en el modelo de evaluación genética para NV. Los factores de manejo analizados influyen de forma significativa (P < 0,05) sobre NV, en magnitud y sentido similar en las poblaciones de selección y de producción. Mediante simulación se comprueba que omitir la influencia de los factores de manejo anteriores en el modelo de evaluación genética no interfiere en la respuesta a la selección, aunque puede conducir a la obtención de predictores sesgados del valor genético.

JUVENILE-MATURE GENETIC CORRELATIONS IN Pinus taeda CLONES PROPAGATED VIA SOMATIC EMBRYOGENESIS

ABSTRACT This study aimed to estimate the genetic correlation among selection ages (juvenile - adult) and efficiency of early selection for the height, diameter, and volume traits of individuals from Pinus taeda families propagated via somatic embryogenesis. This study was carried out by genetic-statistical analysis, estimation procedure of variance (Reml), and prediction components of breeding values (Blup), using the Selegen-Reml/Blup software. Genetic correlations among juvenile ages and rotation age were performed by applying the linear model developed by Lambeth (1980). In accordance with results of the established model, the early selection can be performed in clones of Pinus taeda with high selection efficiency. Ages from 4 to 6 years old are enough to select Pinus taeda clones propagated via somatic embryogenesis for harvesting at 8 and 12 years old; and 6 to 10 years old are enough to select them for harvesting at 20 years old. On the basis of the genetic correlations estimates from the environments, the clones' selection of Pinus taeda propagated via somatic embryogenesis should be developed specifically for each environment. The clones' selection can be performed considering the diameter due to the high correlation between volume and diameter.