Enlarging a training set for genomic selction by imputation of un-genotyped animals in populations of varying genetic architecture

Background: The most common application of imputation is to infer genotypes of a high-density panel of markers on animals that are genotyped for a low-density panel. However, the increase in accuracy of genomic predictions resulting from an increase in the number of markers tends to reach a plateau beyond a certain density. Another application of imputation is to increase the size of the training set with un-genotyped animals. This strategy can be particularly successful when a set of closely related individuals are genotyped. ----- Methods: Imputation on completely un-genotyped dams was performed using known genotypes from the sire of each dam, one offspring and the offspring’s sire. Two methods were applied based on either allele or haplotype frequencies to infer genotypes at ambiguous loci. Results of these methods and of two available software packages were compared. Quality of imputation under different population structures was assessed. The impact of using imputed dams to enlarge training sets on the accuracy of genomic predictions was evaluated for different populations, heritabilities and sizes of training sets. ----- Results: Imputation accuracy ranged from 0.52 to 0.93 depending on the population structure and the method used. The method that used allele frequencies performed better than the method based on haplotype frequencies. Accuracy of imputation was higher for populations with higher levels of linkage disequilibrium and with larger proportions of markers with more extreme allele frequencies. Inclusion of imputed dams in the training set increased the accuracy of genomic predictions. Gains in accuracy ranged from close to zero to 37.14%, depending on the simulated scenario. Generally, the larger the accuracy already obtained with the genotyped training set, the lower the increase in accuracy achieved by adding imputed dams. ----- Conclusions: Whenever a reference population resembling the family configuration considered here is available, imputation can be used to achieve an extra increase in accuracy of genomic predictions by enlarging the training set with completely un-genotyped dams. This strategy was shown to be particularly useful for populations with lower levels of linkage disequilibrium, for genomic selection on traits with low heritability, and for species or breeds for which the size of the reference population is limited.

Carcinoma de tiroides una verdadera pandemia?

El diagnóstico de cáncer de tiroides se ha incrementado y las posibilidades de detección de una enfermedad subclínica son altas, toda vez que disponemos de herramientas de detección más sensibles y de fácil acceso. Por ende, el clínico requiere conocer la historia natural del nódulo tiroideo y del carcinoma papilar de tiroides de bajo riesgo para brindar a su paciente el mejor tratamiento basado en la evidencia clínica. El objetivo de esta revision es reconocer los elementos clínicos que han condicionado el aumento inusitado de casos de cáncer de tiroides. Conclusión: El sobrediagnóstico del cáncer de tiroides es una realidad, que se posibilita por el uso extendido de biopsia por aspiración con aguja fina ((BACAF)) después de la detección de un nódulo tiroideo, en gran parte de manera incidental, sin acarrear la mayoría de las veces un mejor pronóstico después de su tratamiento.

The survival, growth and carcase characteristics of crossbred beef cattle in Tanzania

Sires of seven Bos taurus beef breeds were mated with Bos indicus Boran cows at two sites, one near sea level and the other at about 1000 m altitude, and over three years. Purebred Boran calves provided controls for comparisons between sire breeds for growth to 4 years of age, mortality and carcase characteristics in a range environment where all the animals were kept under a similar management regime. Numerous sire breed x site, sire breed x year of birth and site x year of birth interactions were established. Mortality was high, but there was no significant sire breed effect, although purebred Borans had a higher survival than crossbred calves. There was no significant difference between genotypes in birth weight. Generally, Bos taurus cross steers achieved greater live weight gains and heavier carcase weights at 4 years of age than did purebred Borans. Limousin-cross steers had significantly (p<0.05) less fat in the tenth rib sample joint than any of the other genotypes. A productivity index that combined calf survival and carcase weight indicated that the Chianina crosses were more productive than any other genotype at either site. Purebred Borans were more productive than all the Bos taurus crossbreds with the exception of the Chianina crosses at site 1, but were only superior to the Limousin crosses at site 2, which was at the higher altitude. When lean meat yield was introduced into the productivity index, the Boran purebreds were the least productive at site 2.

Variance in male reproductive success and sexual size dimorphism in pinnipeds: testing an assumption of sexual selection theory

The theory of evolution by sexual selection for sexual size dimorphism (SSD) postulates that SSD primarily reflects the adaptation of males and females to their different reproductive roles. For example, competition among males for access to females increases male body size because larger males are better able to maintain dominant status than smaller males. Larger dominant males sire most offspring while smaller subordinate males are unsuccessful, leading to skew in reproductive success. Therefore, species with male-biased SSD are predicted to have greater variance in male reproductive success than those in which both sexes are similar in size. We tested this prediction among the Pinnipedia, a mammalian group with a great variation in SSD. From a literature review, we identified genetic estimates of male reproductive success for 10 pinniped taxa (eight unique species and two subspecies of a ninth species) that range from seals with similarly sized males and females to species in which males are more than four times as large as females. We found no support for a positive relationship between variance in reproductive success and SSD among pinnipeds after excluding the elephant seals Mirounga leonina and Mirounga angustirostris, which we discuss as distinctive cases. Several explanations for these results are presented, including the revival of one of Darwin's original ideas. Darwin proposed that natural selection may explain SSD based on differences in energetic requirements between sexes and the potential for sexual niche segregation. Males may develop larger bodies to exploit resources that remain unavailable to females due to the energetic constraints imposed on female mammals by gestation and lactation. The importance of this alternative explanation remains to be tested.

Estimation of genetic variance for macro- and micro-environmental sensitivity using double hierarchical generalized linear models

Background: Genetic variation for environmental sensitivity indicates that animals are genetically different in their response to environmental factors. Environmental factors are either identifiable (e.g. temperature) and called macro-environmental or unknown and called micro-environmental. The objectives of this study were to develop a statistical method to estimate genetic parameters for macro- and micro-environmental sensitivities simultaneously, to investigate bias and precision of resulting estimates of genetic parameters and to develop and evaluate use of Akaike’s information criterion using h-likelihood to select the best fitting model. Methods: We assumed that genetic variation in macro- and micro-environmental sensitivities is expressed as genetic variance in the slope of a linear reaction norm and environmental variance, respectively. A reaction norm model to estimate genetic variance for macro-environmental sensitivity was combined with a structural model for residual variance to estimate genetic variance for micro-environmental sensitivity using a double hierarchical generalized linear model in ASReml. Akaike’s information criterion was constructed as model selection criterion using approximated h-likelihood. Populations of sires with large half-sib offspring groups were simulated to investigate bias and precision of estimated genetic parameters. Results: Designs with 100 sires, each with at least 100 offspring, are required to have standard deviations of estimated variances lower than 50% of the true value. When the number of offspring increased, standard deviations of estimates across replicates decreased substantially, especially for genetic variances of macro- and micro-environmental sensitivities. Standard deviations of estimated genetic correlations across replicates were quite large (between 0.1 and 0.4), especially when sires had few offspring. Practically, no bias was observed for estimates of any of the parameters. Using Akaike’s information criterion the true genetic model was selected as the best statistical model in at least 90% of 100 replicates when the number of offspring per sire was 100. Application of the model to lactation milk yield in dairy cattle showed that genetic variance for micro- and macro-environmental sensitivities existed. Conclusion: The algorithm and model selection criterion presented here can contribute to better understand genetic control of macro- and micro-environmental sensitivities. Designs or datasets should have at least 100 sires each with 100 offspring.

Genetic heterogeneity of within-family variance of body weight in Atlantic salmon (Salmo salar)

BACKGROUND: Canalization is defined as the stability of a genotype against minor variations in both environment and genetics. Genetic variation in degree of canalization causes heterogeneity of within-family variance. The aims of this study are twofold: (1) quantify genetic heterogeneity of (within-family) residual variance in Atlantic salmon and (2) test whether the observed heterogeneity of (within-family) residual variance can be explained by simple scaling effects. RESULTS: Analysis of body weight in Atlantic salmon using a double hierarchical generalized linear model (DHGLM) revealed substantial heterogeneity of within-family variance. The 95% prediction interval for within-family variance ranged from ~0.4 to 1.2 kg2, implying that the within-family variance of the most extreme high families is expected to be approximately three times larger than the extreme low families. For cross-sectional data, DHGLM with an animal mean sub-model resulted in severe bias, while a corresponding sire-dam model was appropriate. Heterogeneity of variance was not sensitive to Box-Cox transformations of phenotypes, which implies that heterogeneity of variance exists beyond what would be expected from simple scaling effects. CONCLUSIONS: Substantial heterogeneity of within-family variance was found for body weight in Atlantic salmon. A tendency towards higher variance with higher means (scaling effects) was observed, but heterogeneity of within-family variance existed beyond what could be explained by simple scaling effects. For cross-sectional data, using the animal mean sub-model in the DHGLM resulted in biased estimates of variance components, which differed substantially both from a standard linear mean animal model and a sire-dam DHGLM model. Although genetic differences in canalization were observed, selection for increased canalization is difficult, because there is limited individual information for the variance sub-model, especially when based on cross-sectional data. Furthermore, potential macro-environmental changes (diet, climatic region, etc.) may make genetic heterogeneity of variance a less stable trait over time and space.

Musculosidade e composição da perna de ovinos de diferentes genótipos e idades ao abate

Foram avaliadas as características morfológicas da carcaça, musculosidade e composição tecidual da perna de cordeiros criados em regime de pasto, provenientes de ovelhas Romney, acasaladas com três raças paternas (Romney, East Friesian x (Finn x Texel) e Finn x Poll Dorset). Aos 150 e 300 dias de idade, os cordeiros foram abatidos em dois lotes, cada um com 15 animais de cada raça paterna, num total de 90 animais. O grupo oriundo de animais East Friesian x (Finn x Texel) apresentou maior quantidade de músculo na perna (1.975 g) e, em comparação ao grupo Romney, semelhante musculosidade da perna (0,45) e maior relação músculo:osso (7x6,69). A musculosidade da perna nos animais descendentes de Finn x Poll Dorset foi menor (0,44), quando comparada à dos demais grupos. Cordeiros abatidos mais tardiamente apresentaram carcaças mais longas e magras, provavelmente pelas condições adversas do verão e do outono, em que são típicas a menor taxa de crescimento e a qualidade inferior de forragem. O genótipo e a idade de abate influem nas características morfológicas da carcaça, no índice de musculosidade e de composição tecidual da perna dos cordeiros.

Características de qualidade da carne de ovinos de diferentes genótipos e idades ao abate

Cordeiros criados em regime de pasto, provenientes de ovelhas Romney acasaladas com três raças paternas (Romney, East Friesian x (Finn x Texel) e Finn x Poll Dorset), foram avaliados quanto às características de qualidade da carne. Os cordeiros foram abatidos aos 150 e 300 dias de idade, cada lote com 15 animais de cada raça paterna, totalizando 90 animais. A carne dos cordeiros Romney foi mais macia que a dos demais genótipos. O pH final do músculo Semimembranosus dos cordeiros abatidos mais precocemente foi superior (5,61) ao dos abatidos mais tardiamente (5,58), entretanto estes últimos apresentaram carne com menor maciez (11,16 kg) que os abatidos aos 150 dias de idade (7,45 kg). Com relação à cor, a luminosidade da carne de cordeiros abatidos aos 150 dias foi maior (38,20) que a dos abatidos mais tardiamente (36,80), mas não foi afetada pelo genótipo. Concluiu-se que o genótipo e a idade de abate influíram na produção e qualidade da carne ovina.

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

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Estimativa de parâmetros genéticos da habilidade de permanência aos 48, 60 e 72 meses de idade em vacas da raça Caracu

Objetivou-se estimar a herdabilidade da característica habilidade de permanência (HP) em um rebanho de bovinos da raça Caracu visando sua utilização como critério de seleção. A característica em estudo foi definida como a probabilidade de a vaca estar presente no rebanho aos 48 (HP48), aos 60 (HP60) e aos 72 (HP72) meses, desde que possuíssem registros de pelo menos duas lactações nas específicas idades. Observações binárias, com zero (0 = fracasso) e um (1 = sucesso) foram designadas aos animais. Para análise da HP, foram utilizados dados de 5.487, 4.947 e 4.308 animais aos 48, 60 e 72 meses, respectivamente. Os componentes de variância e as herdabilidades foram estimados mediante inferência Bayesiana, via amostragem de Gibbs, pelo programa MTGSAM - threshold, utilizando-se um modelo touro. Foram utilizadas como variáveis explanatórias grupo de contemporâneos, classe de produção de leite na primeira lactação, classe de idade ao primeiro parto e sua interação. As análises forneceram estimativas médias de herdabilidade iguais a 0,28 ± 0,07 para HP48, 0,27 ± 0,07 para HP60 e 0,23 ± 0,07 para HP72. Os resultados evidenciaram que a característica HP apresentou variação aditiva em todas as idades estudadas e, portanto, pode ser empregada como critério de seleção para longevidade produtiva.

Desempenho reprodutivo, características do pelame e taxa de sudação em vacas da raça Braford

Foram investigados os efeitos das características do pelame e da taxa de sudação (TS) sobre o intervalo de partos (IEP, n = 423) e os dias para o parto (DPP, n = 1.202) de vacas da raça Braford criadas em sistema extensivo em região tropical úmida no Mato Grosso do Sul, Brasil. As análises foram realizadas pelo método dos quadrados mínimos considerando para intervalo de partos os seguintes efeitos das classes de idade da vaca ao parto: grupo genético; pai; e regressão sobre a refletância da superfície da capa (R), a espessura da capa (E), o comprimento dos pêlos (C), o número de pêlos por unidade de área (N), o diâmetro dos pêlos (D) e a taxa de sudação. Para dias para o parto, foram considerados os efeitos: R, E, C, N, D, TS, divididos em classes; grupo genético; idade no início da estação de monta; e pai. Os componentes de variância e co-variância foram estimados pelo método de Máxima Verossimilhança Restrita sob o modelo touro. As características adaptativas não foram importantes para a variação do intervalo de parto e dos dias para o parto, mas a taxa de sudação apresentou efeito importante sobre dias ao parto. As estimativas de herdabilidade foram quase nulas para IEP e DPP e maiores para as características adaptativas (E = 0,16 ± 0,09; C = 0,18 ± 0,09; N = 0,08 ± 0,06; D = 0,12 ± 0,07; R = 0,30 ± 0,12; TS = 0,10 ± 0,06). Os resultados obtidos para as correlações genéticas de IEP e DPP com TS e entre as características do pelame indicaram que a seleção simultânea para menores valores de C pode ser favorável à redução do intervalo de partos. em geral, as correlações genéticas entre TS, IEP e DPP apresentaram elevado erro-padrão. Considerando os resultados deste estudo e a importância das características do pelame e da sudação, confirma-se a necessidade de se estudarem as correlações genéticas entre as características adaptativas e o desempenho reprodutivo para o progresso da adaptação de bovinos da raça Braford no Brasil.

Effect of sequence of insemination after simultaneous thawing of multiple semen straws on conception rate to timed AI in suckled multiparous Nelore cows

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Efeito da idade sobre as principais características andrológicas de touros Brangus- Efeito da idade sobre as principais características andrológicas de touros BrangusIbagé criados extensivamente no estado do Mato Grosso do Sul - Brasil Ibagé criados extensivamente no estado do Mato Grosso do Sul - Brasil

Background: Bull fertility is extremely important for beef cattle production systems and has a multiplier impact on the economical and zootechnical indexes of the herd. Bulls raised in tropical conditions may present varied seminal characteristics due to, among other causes, different management practices and quality of pastures. Another factor that influences the semen characteristics is the age of the sire. The reproductive potential of bull evaluated through the andrological exam aims to ensure the semen quality and to improve the herd reproductive efficiency. The aim of this study was to evaluate the main semen parameters of Brangus-Ibage bulls extensively reared in eastern Mato Grosso do Sul state and to verify the effect of age on the andrological characteristics analyzed. It was also evaluated the correlation between age, scrotal circumference, and physical and morphological sperm characteristics produced by the Brangus bulls.Materials, Methods & Results: The study took place in the month of July 2010, during the routine andrological examination of 168 synthetic Brangus-Ibage bulls (5/8 Angus x 3/8 Nelore), belonging to the same property. For data analysis the animals were divided by age groups: animals younger than 4 years (Age I), animals between 4 and 8 years of age (Age II), and animals between 8 and 15 years of age (Age III). In another analysis, the animals were grouped according to the sperm motility pattern obtained from the semen collection: sperm motility lower than 40% (Motility I), sperm motility between 40 and 70% (Motility II) and sperm motility between 70 and 90% (Motility III). The results of the present study demonstrated an effect of age (P < 0.05) on the following androgical characteristics: scrotal circumference, ejaculate volume, sperm vigor, major defects, minor defects and total defects. It was also observed that the animals with higher sperm motility presented higher (P < 0.05) scrotal circumference, and lower (P < 0.05) percentages of major and total defects. Among the andrological characteristics evaluated in the present work, it was observed positive correlations between age and scrotal circumference (R =0.299; P =0.000), age and volume of ejaculate (R =0.161; P =0.037), age and major defects (R =0.188; P =0.015), sperm motility and scrotal circumference (R =0.245; P =0.001), sperm motility and sperm vigor (R =0.483; P =0.000), and between major defects and total defects (R =0.946; P =0.000). Also, negative correlations were observed between sperm motility and total defects (R =-0.372; P =0.000), sperm vigor and major defects (R =-0.498; P =0.000), and sperm vigor and total defects (R =-0.432; P =0.000).Discussion: Based on the results of this study it was concluded that the Brangus-Ibage bulls utilized for natural breeding in eastern Mato Grosso do Sul, Brazil, presented satisfactory semen quality taking into account the quality of the pastures where the animals were located. In addition, the scrotal circumference, the ejaculate volume, the sperm vigor, and the percentage of morphological characteristics were influenced by the age of the bulls. Therefore, considering the production system and the environmental conditions, the animals with age between 4 and 8 years were superior regarding the sperm parameters evaluated.

Assessment of field fertility and several in vitro sperm characteristics following the use of different Angus sires in a timed-AI program with suckled Nelore cows

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Estimates of genetic correlations between days to calving and reproductive and weight traits in Nelore cattle

Data comprising 53,181 calving records were analyzed to estimate the genetic correlation between days to calving (DC), and days to first calving (DFC), and the following traits: scrotal circumference (SC), age at first calving (AFC), and weight adjusted for 550 d of age (W550) in a Nelore herd. (Co)variance components were estimated using the REML method fitting bivariate animal models. The fixed effects considered for DC were contemporary group, month of last calving, and age at breeding season (linear and quadratic effects). Contemporary groups were composed by herd, year, season, and management group at birth; herd and management group at weaning; herd, season, and management group at mating; and sex of calf and mating type (multiple sires, single sire, or AI). In DFC analysis, the same fixed effects were considered excluding the month of last calving. For DC, a repeatability animal model was applied. Noncalvers were not considered in analyses because an attempt to include them, attributing a penalty, did not improve the identification of genetic differences between animals. Heritability estimates ranged from 0.04 to 0.06 for DC, from 0.06 to 0.13 for DFC, from 0.42 to 0.44 for SC, from 0.06 to 0.08 for AFC, and was 0.30 for W550. The genetic correlation estimated between DC and SC was low and negative (-0.10), between DC and AFC was high and positive (0.76), and between DC and W550 was almost null (0.07). Similar results were found for genetic correlation estimates between DFC and SC (-0.14), AFC (0.94), and W550 (-0.02). The genetic correlation estimates indicate that the use of DC in the selection of beef cattle may promote favorable correlated responses to age at first mating and, consequently, higher gains in sexual precocity can be expected.