
Sebastián MunillaFacultad de Agronomía, Universidad de Buenos Aires, Argentina · Producción Animal
Sebastián Munilla
PhD
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59
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Introduction
Skills and Expertise
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November 2013 - March 2015
Publications
Publications (59)
Background
Cross-validation techniques in genetic evaluations encounter limitations due to the unobservable nature of breeding values and the challenge of validating estimated breeding values (EBVs) against pre-corrected phenotypes, challenges which the Linear Regression (LR) method addresses as an alternative. Furthermore, beef cattle genetic eval...
The Junín sheep contribute to livestock production in the Peruvian Andes, but face problems related to gastrointestinal parasitism. In this study, we estimated the heritability and repeatability of traits associated with resistance to gastrointestinal parasitism in the genetic nucleus of Junín sheep raised at altitudes above 3600 m. For this purpos...
Traditionally, in forest genetic evaluations, the pedigree-based individual-tree mixed model (ABLUP) has been utilized to identify individuals with the highest breeding value (BV). The ABLUP is considered a Markov causal model as the BV of an individual is independent of all its non-descendants, conditional to including the BV of its parents. Under...
Multiple trait animal models (MTM) allow to estimate the breeding values (BV) of several traits simultaneously while accounting for genetic and environmental correlations among them. However, relationships among traits may not be reciprocal but rather causal in nature. In these cases, and given a causal network, structural equations models (SEM) ar...
Genomic selection methods are particularly useful for traits that are difficult or expensive to measure. We investigated the impact of using predictor growth traits and/or genomic information to increase the breeding value (BV) predictive accuracies for target scarcely recorded wood quality traits in an open-pollinated Eucalyptus grandis population...
Background
The covariance matrix of breeding values is at the heart of prediction methods. Prediction of breeding values can be formulated using either an “observed” or a theoretical covariance matrix, and a major argument for choosing one or the other is the reduction of the computational burden for inverting such a matrix. In this regard, covaria...
Brangus is a composite cattle breed developed with the objective of combining the advantages of Angus and Zebuine breeds (Brahman, mainly) in tropical climates. The aim of this work was to estimate breed composition both genome‐wide and locally, at the chromosome level, and to uncover genomic regions evidencing positive selection in the Argentinean...
In the two decades of continuous development of genomic selection, a great variety of models have been proposed to make predictions from the information available in dense marker panels. Besides deciding which particular model to use, practitioners also need to make many minor choices for those parameters in the model which are not typically estima...
Genomic selection based on the single-step genomic best linear unbiased prediction (ssGBLUP) approach is becoming an important tool in forest tree breeding. The quality of the variance components and the predictive ability of the estimated breeding values (GEBV) depends on how well marker-based genomic relationships describe the actual genetic rela...
Cultivated bread wheat (Triticum aestivum L.) is an allohexaploid species resulting from the natural hybridization and chromosome doubling of allotetraploid durum wheat (T. turgidum) and a diploid goat grass Aegilops tauschii Coss (Ae. tauschii). Synthetic hexaploid wheat (SHW) was developed through the interspecific hybridization of Ae. tauschii a...
Genomic selection uses whole-genome marker models to predict phenotypes or genetic values for complex traits. Some of these models fit interaction terms between markers, and are therefore called epistatic. The biological interpretation of the corresponding fitted effects is not straightforward and there is the threat of overinterpreting their funct...
The molecule Dimethyl sulfoxide is widely used as drug solvent. However, its antioxidant property was poorly explored. In this study, we evaluated the effect of DMSO supplementation during oocyte in vitro maturation (IVM) on embryo development and quality. Bovine oocytes were matured with different DMSO concentrations (0, 0.1, 0.25, 0.5, 0.75, 1 an...
In organisms with sexual reproduction, genetic diversity, and genome evolution are governed by meiotic recombination caused by crossing-over, which is known to vary within the genome. In this study, we propose a simple method to estimate the recombination rate that makes use of the persistency of linkage disequilibrium (LD) phase among closely rela...
In cow-calf operations the moment the heifer achieves her first pregnancy set up her future productivity. Although puberty itself is a yes-or-no condition, time to the event has a quantitative genetic basis and thus is suitable for genetic selection. However, the trait is difficult to measure directly and proxies such as age at first calving (AFC),...
Background:
The single-step covariance matrix H combines the pedigree-based relationship matrix [Formula: see text] with the more accurate information on realized relatedness of genotyped individuals represented by the genomic relationship matrix [Formula: see text]. In particular, to improve convergence behavior of iterative approaches and to red...
Individually transferred hemi-embryos generated 60-day fetuses with almost no differences in growth and development compared with the control embryos. The compensation phenomenon should have occurred before Day 60 of gestation
This study investigated the potential application of genomic selection under a multi-breed scheme in the Spanish autochthonous beef cattle populations using a simulation study that replicates the structure of linkage disequilibrium obtained from a sample of 25 triplets of sire/dam/offspring per population and using the BovineHD Beadchip . Purebred...
Genome inheritance is by segments of DNA rather than by independent loci. We introduce the ancestral regression (AR) as a recursive system of simultaneous equations, with grandparental path coefficients as novel parameters. The information given by the pedigree in the AR is complementary with that provided by a dense set of genomic markers, such th...
The Brangus breed was developed to combine the superior characteristics of both of its founder breeds, Angus and Brahman. It combines the high adaptability to tropical and subtropical environments, disease resistance, and overall hardiness of Zebu cattle with the reproductive potential and carcass quality of Angus. It is known that the major histoc...
The Spanish local beef cattle breeds have most likely common origin followed by a process of differentiation. This particular historical evolution has most probably left detectable signatures in the genome. The objective of this study was to identify genomic regions associated with differentiation processes in seven Spanish autochthonous population...
This study evaluated different strategies for implementing a single-step genomic selection programme in two autochthonous Spanish beef cattle populations (Pirenaica—Pi and Rubia Gallega—RG). The strategies were compared in terms of accuracy attained under different scenarios by simulating genomic data over the known genealogy. Several genotyping ap...
The objective of this study was to evaluate the pattern of linkage disequilibrium along the genome in seven autochthonous Spanish cattle beef populations (Asturiana de los Valles, Avileña Negra-Ibérica, Bruna dels Pirineus, Morucha, Pirenaica, Retinta and Rubia Gallega). The BovineHD BeadChip was used to genotype 171 trios of individual/sire/dam. 5...
Oocyte in vitro maturation (IVM) is crucial for subsequent in vitro embryo production. It involves acquisition of competence for fertilization and embryo development. Therefore, its optimization could have a direct impact on in vitro embryo development. Dimethyl sulfoxide (DMSO) is commonly used as solvent or vehicle, but also increases the membran...
Background:
Procedures for the detection of signatures of selection can be classified according to the source of information they use to reject the null hypothesis of absence of selection. Three main groups of tests can be identified that are based on: (1) the analysis of the site frequency spectrum, (2) the study of the extension of the linkage d...
Genomic relationships based on markers capture the actual instead of the expected (based on pedigree) proportion of genome shared identical by descent (IBD). Several methods exist to estimate genomic relationships. In this research, we compare four such methods that were tested looking at the empirical distribution of the estimated relationships ac...
The κ-casein (CSN-3) and β-lactoglobulin (BLG) genes are extensively polymorphic in ruminants. Several association studies have estimated the effects of polymorphisms in these genes on milk yield, milk composition, and cheese-manufacturing properties. Usually, these results are based on production integrated over the lactation curve or on cross-sec...
Los procedimientos de detección de señales de adaptación están basados en la teoría de evolución neutral (Kimura, 1983) en equilibrio mutación-deriva. Esta teoría postula que: 1. muchas de las mutaciones que surgen en una población son deletéreas y, en consecuencia, son rápidamente eliminadas; 2. una ínfima proporción de las mutaciones que surgen s...
The availability of SNP chips for massive genotyping has proven to be useful to genetically characterize populations of domestic cattle and to assess their degree of divergence. In this study, the Illumina BovineHD Beadchip genotyping array was used to describe the genetic variability and divergence among seven important autochthonous Spanish beef...
The BovineHD 770K BeadChip was used on 171 sire/dam/offspring triplets from seven Spanish local beef cattle breeds (Asturiana de los Valles, Avileña-Negra Ibérica, Bruna dels Pirineus, Morucha, Pirenaica, Retinta and Rubia Gallega). The parents were chosen to be as unrelated as possible. We performed a Bayesian analysis by the software SELESTIM to...
The advances in the area of molecular genetics have allowed the development of dense SNP genotyping devices that provide information throughout the genome of several livestock species. Along with these molecular advances, new statistical methods have been developed with the purpose of predicting the genomic breeding values of candidates to selectio...
Background
Mixed models are commonly used for the estimation of variance components and genetic evaluation of livestock populations. Some evaluation models include two types of additive genetic effects, direct and maternal. Estimates of variance components obtained with models that account for maternal effects have been the subject of a long-standi...
A long standing controversy in animal breeding is related to the strong negative estimates of the direct-maternal genetic correlation obtained when fitting data on maternally influenced traits. In this article, we focused on a model that introduces a new correlation parameter among dam-offspring records. The extant theory allows estimation of the p...
A long standing controversy in animal breeding is related to the strong negative estimates of the direct-maternal genetic correlation obtained when fitting data on maternally influenced traits. In this article, we focused on a model that introduces a new correlation parameter among dam–offspring records. The extant theory allows estimation of the p...
INTRODUCCIÓN Los procesos de selección y adaptación pueden dejar huellas en la estructura del genoma de las poblaciones. En la literatura, se han descrito un gran número de procedimientos para la detección de esta huella (Qanbari y Simianer, 2014), tanto basados en el espectro de frecuencias como en la longitud de los haplotipos. Otros procedimient...
INTRODUCCIÓN La disponibilidad de marcadores moleculares ha revolucionado la mejora genética animal (véase, por ejemplo, la revisión de Dekkers y Hospital, 2002). Entre sus aplicaciones más recientes, el empleo de SNPs con el fin de detectar huellas de selección se ha posicionado como una alternativa valiosa en la búsqueda de genes asociados a cara...
Epigenetics has become one of the major areas of biological research. However, the degree of phenotypic variability that is explained by epigenetic processes still remains unclear. From a quantitative genetics perspective, the estimation of variance components is achieved by means of the information provided by the resemblance between relatives. In...
This study analyzed the persistency of the linkage disequilibrium between 7 Spanish beef cattle populations. The persistency was calculated as the correlation between the LD values of the SNPs of regions of 1 Mb each, between two populations. The results yielded positive values in all cases of comparison and regions. The persistency values of 42 re...
The BovineHD 770K BeadChip was used on 171 triplets (sire/dam/offspring) from seven Spanish local beef cattle breeds (Asturiana de los Valles, Avileña-Negra Ibérica, Morucha, Bruna dels Pirineus, Pirenaica, Retinta and Rubia Gallega). The parents were chosen to be as unrelated as possible. We use the software SELESTIM to identify loci targeted by a...
Orthogonal Legendre polynomials (LP) are used to model the shape of additive genetic and permanent environmental effects in random regression models (RRM). Frequently, the Akaike (AIC) and the Bayesian (BIC) information criteria are employed to select LP order. However, it has been theoretically shown that neither AIC nor BIC is simultaneously opti...
Epigenetics has become one of the major areas of biological research. However, the degree of phenotypic variability that is explained by epigenetic processes still remains unclear. From a quantitative genetics perspective, the estimation of variance components is achieved by means of the information provided by the resemblance between relatives. In...
The availability of SNP chips for massive genotyping has proven to be useful to genetically characterize populations of domestic cattle and to assess their degree of divergence. In this study, the Illumina BovineHD Beadchip genotyping array was used to describe the genetic variability and divergence among seven important autochthonous Spanish beef...
Animals born by embryo transfer (ET) are usually not included in the genetic evaluation of beef cattle for preweaning growth if the recipient dam is unknown. This is primarily to avoid potential bias in the estimation of the unknown age of dam. We present a method that allows including records of calves with unknown age of dam. Assumptions are as f...
A total of 116 triplets from 5 Spanish beef cattle populations were genotyped using the BovineHD BeadChip. After the quality control, the phases of the parental chromosomes were established. From them, a base population for each breed was defined and 3 generations of 500, 1000 and 1000 individuals were simulated. Phenotypes and true genomic breedin...
High-density SNP genotyping was used to describe the genetic variability and relationships among five Spanish beef cattle breeds (Asturiana de los Valles, Avileña – Negra Ibérica, Bruna dels Pirineus, Pirenaica and Retinta). A total of 239 samples were genotyped with the BovineHD (778 K) Beadchip, which proved its suitability for the study of these...
Abstract Text: The aim of this study is to present a general procedure to calculate, from SNP markers, the covariances between individuals due to additive, dominant and epistatic effects, e.g. “additive x dominant genomic relationships”. The proposed method expands the orthogonal approach called NOIA and does not assume Hardy-Weinberg equilibrium....
Autochthonous cattle breeds are a valuable
reservoir of genetic diversity in Spain. Along their history,
these breeds had been subjected to strong forces of
differentiation and common selection. Based on genomewide
SNP data from five different autochthonous breeds, in
this study we computed two classical selection signatures
statistics in a sliding...
Five Spanish autochthonous beef cattle breeds: Asturiana de los Valles, Avileña-Negra Ibérica, Bruna de los Pirineos, Pirenaica and Retinta, were sampled. The 246 animals obtained were genotyped with the Illumina HD 777K chip and the genotypic information was subjected to a factorial discriminant analysis (fda), yielding the following conclusions:...
Consider the estimation of genetic (co)variance components from a maternal animal model (MAM) using a conjugated Bayesian approach. Usually, more uncertainty is expected a priori on the value of the maternal additive variance than on the value of the direct additive variance. However, it is not possible to model such differential uncertainty when a...
It has been argued that multibreed animal models should include a heterogeneous covariance structure. However, the estimation of the (co)variance components is not an easy task, because these parameters can not be factored out from the inverse of the additive genetic covariance matrix. An alternative model, based on the decomposition of the genetic...
Pedigree records of 72,808 animals (45,668 females and 27,140 males) from the genetic evaluation program of the Argentine Brangus Association were used to estimate effective number of founders (Nf), effective number of ancestors (Na), and effective population size under random mating (Ne) or selection (NeS), in order to assess genetic variability....
Evidence is presented for 'generalized autoregressive conditional heteroskedasticity' processes (GARCH(1,1)), in the residuals of beef cattle growth traits. This process can account for differences in variance at different time points, with the advantage of using a parsimonious parametrization. Data used were 10271 birth weights (BW), 19992 weaning...