Luiz Otávio Campos da Silva
Other affiliations: National Council for Scientific and Technological Development
Bio: Luiz Otávio Campos da Silva is an academic researcher from Empresa Brasileira de Pesquisa Agropecuária. The author has contributed to research in topics: Heritability & Beef cattle. The author has an hindex of 17, co-authored 59 publications receiving 1553 citations. Previous affiliations of Luiz Otávio Campos da Silva include National Council for Scientific and Technological Development.
Papers published on a yearly basis
Baylor College of Medicine1, University of Missouri2, United States Department of Agriculture3, Commonwealth Scientific and Industrial Research Organisation4, University of New England (United States)5, Texas A&M University6, Norwegian University of Life Sciences7, George Mason University8, AgResearch9, Catholic University of the Sacred Heart10, International Atomic Energy Agency11, Empresa Brasileira de Pesquisa Agropecuária12, Sao Paulo State University13, International Livestock Research Institute14, Parco Tecnologico Padano15, University of Edinburgh16, Ethiopian Institute of Agricultural Research17, Livestock Improvement Corporation18, Cornell University19, University of Alberta20, Tuscia University21, Wellcome Trust Sanger Institute22, University of Melbourne23, Government of Victoria24, Trinity College, Dublin25, Simon Fraser University26
TL;DR: Data show that cattle have undergone a rapid recent decrease in effective population size from a very large ancestral population, possibly due to bottlenecks associated with domestication, selection, and breed formation.
Abstract: The imprints of domestication and breed development on the genomes of livestock likely differ from those of companion animals. A deep draft sequence assembly of shotgun reads from a single Hereford female and comparative sequences sampled from six additional breeds were used to develop probes to interrogate 37,470 single-nucleotide polymorphisms (SNPs) in 497 cattle from 19 geographically and biologically diverse breeds. These data show that cattle have undergone a rapid recent decrease in effective population size from a very large ancestral population, possibly due to bottlenecks associated with domestication, selection, and breed formation. Domestication and artificial selection appear to have left detectable signatures of selection within the cattle genome, yet the current levels of diversity within breeds are at least as great as exists within humans.
TL;DR: Meat quality traits in Nelore are controlled by numerous QTL of small effect, except for a small number of large-effect QTL identified for a*fat, CL, and pH, which appear to differ from those identified in taurine cattle for meat quality traits.
Abstract: Meat quality traits are economically important because they affect consumers' acceptance, which, in turn, influences the demand for beef. However, selection to improve meat quality is limited by the small numbers of animals on which meat tenderness can be evaluated due to the cost of performing shear force analysis and the resultant damage to the carcass. Genome wide-association studies for Warner-Bratzler shear force measured at different times of meat aging, backfat thickness, ribeye muscle area, scanning parameters [lightness, redness (a*), and yellowness] to ascertain color characteristics of meat and fat, water-holding capacity, cooking loss (CL), and muscle pH were conducted using genotype data from the Illumina BovineHD BeadChip array to identify quantitative trait loci (QTL) in all phenotyped Nelore cattle. Phenotype count for these animals ranged from 430 to 536 across traits. Meat quality traits in Nelore are controlled by numerous QTL of small effect, except for a small number of large-effect QTL identified for a*fat, CL, and pH. Genomic regions harboring these QTL and the pathways in which the genes from these regions act appear to differ from those identified in taurine cattle for meat quality traits. These results will guide future QTL mapping studies and the development of models for the prediction of genetic merit to implement genomic selection for meat quality in Nelore cattle.
TL;DR: These traits should respond to direct selection, except for RF and AFP, according to estimates of heritability, permanent environment, as well as on genetic and phenotypic correlations, estimated using MTDFREML.
Abstract: The objective of the present work was to investigate the effects of some genetic and environmental factors on production (weaning weight WW; eighteen month weight W18) and reproduction (scrotal perimeter at 18 months SP18; calving interval CI; age at first calving AFC; True fertility TF, calving date CD) traits in a Nellore cattle herd in the Mato Grosso do Sul State, Brazil. The observations were analysed using the least squares methodology, and the statistical models included the fixed effects: year (YB) and month (MB) of calving, interaction YB*MB, sex (S) of animal (except for W18, SP18 and AFC) and calving number. Significant effects were found for all factors studied on WW, and animals born in August (179 kg) and December (156 kg) had highest and lowest WW respectively. The male calves (174 kg) were heavier at weaning than females (162 kg), a difference of 7.4% in favour of males. No tendency was observed in terms of mean values over the years for this trait. W18 was influenced only by birth year, with a mean value of 281.0 kg. Only calving number did not influence Scrotal perimeter (SP18), which had a mean value of 26.8 cm. The mean CI was 465 days, and all effects were significant, except for calf sex. TF was significantly influenced by all effects studied, and had a mean value of 144 kg. Age at first calving was high (1.279 days or 41.93 months) and influenced by month and year of calving. In terms of calving date, month and year were significant effects, as was the interaction between these effects but sex and calving number did not affect this trait. Based on estimates of heritability, permanent environment, as well as on genetic and phenotypic correlations, estimated using MTDFREML, it was concluded that these traits should respond to direct selection, except for RF and AFP. Genetic correlations between production traits were favourable, indicating the possibility of genetic progress through indirect selection.
TL;DR: Data related to weights of animals of the Tabapua breed, born from 1959 to 1996, in several areas of Brazil, were analyzed with the objective of evaluating the direct and maternal genetic trends, for body weights adjusted for 205, 365 and 550 days of age.
Abstract: Data related to weights of animals of the Tabapua breed, born from 1959 to 1996, in several areas of Brazil, were analyzed with the objective of evaluating the direct and maternal genetic trends, for body weights adjusted for 205 (W205), 365 (W365) and 550 (W550) days of age. The (co)variance component estimates used in the calculation of the breeding values were obtained by the restricted maximum likelihood method (REML), with a model containing the random additive direct, maternal and permanent environmental effects, and the fixed effects of contemporary group (unit of the federation, farm, sex, season and year of birth of the animal) and the covariable age of the cow at calving (linear and quadratic effects). The genetic trends of the direct and maternal genetic effects were estimated by the regression of the breeding value annual means on year of birth of the animals. The genetic trends of the direct effects were 0.134, 0.199 and 0.276 kg/year, for W205, W365 and W550, respectively. The estimates of the maternal genetic trends were, in the same order, 0.019, -0.010 and -0.022 kg/year, respectively. Due to the existing genetic variability on the traits, the genetic changes attained are bellow the possible ones.
TL;DR: Evidence of genotype x environment interaction is shown, and that regional genetic evaluations, when available, can be more useful than a state evaluation, is shown.
Abstract: The effect of genotype x environment interaction on body weight at birth (BW), weaning (W205), 12 (W365) and 18 (W550) months of age of Nellore cattle raised in the regions of Alto Taquari, Campo Grande and Pantanal, MS, Brazil, was studied. The data were analyzed for each region separately and for all regions together. Variance and covariance components and genetic parameters were estimated by the restricted maximum likelihood method, using an animal model that included the random additive direct effect, and the fixed effects of sex and contemporary group (herd, year, season and region of birth), and sires were ranked based on their breeding values (BV). The results showed that the additive direct and residual variances were different among regions. The heritability estimates ranged from 0.16 to 0.66 (BW), 0.36 to 0.59 (W205), 0.35 to 0.49 (W365) and 0.30 to 0.45 (W550), depending on the region. Pearson's correlation coefficients between BVs of sires, obtained for each pair of regions, showed means equal to 0.11 (BW), 0.38 (W205), 0.38 (W365) and 0.39 (W550). When the correlations were for the BVs obtained for each region with the BVs obtained for all regions together, the estimates were higher showing means equal to 0.80 (BW), 0.88 (W205), 0.88 (W365) and 0.87 (W550). Despite the high values of these last ones, the results show evidence of genotype x environment interaction, and that regional genetic evaluations, when available, can be more useful than a state evaluation.
28 Jul 2005
TL;DR: For the next few weeks the course is going to be exploring a field that’s actually older than classical population genetics, although the approach it’ll be taking to it involves the use of population genetic machinery.
Abstract: So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to
TL;DR: A high level of linkage disequilibrium in the soybean genome is identified, suggesting that marker-assisted breeding of soybean will be less challenging than map-based cloning and to facilitate future breeding and quantitative trait analysis.
Abstract: We report a large-scale analysis of the patterns of genome-wide genetic variation in soybeans. We re-sequenced a total of 17 wild and 14 cultivated soybean genomes to an average of approximately ×5 depth and >90% coverage using the Illumina Genome Analyzer II platform. We compared the patterns of genetic variation between wild and cultivated soybeans and identified higher allelic diversity in wild soybeans. We identified a high level of linkage disequilibrium in the soybean genome, suggesting that marker-assisted breeding of soybean will be less challenging than map-based cloning. We report linkage disequilibrium block location and distribution, and we identified a set of 205,614 tag SNPs that may be useful for QTL mapping and association studies. The data here provide a valuable resource for the analysis of wild soybeans and to facilitate future breeding and quantitative trait analysis.
TL;DR: This work uses genome-wide SNP panels as markers and statistical methods that capture the effects of large numbers of SNPs simultaneously to double the rate of genetic improvement per year in many livestock systems.
Abstract: Genome-wide panels of SNPs have recently been used in domestic animal species to map and identify genes for many traits and to select genetically desirable livestock. This has led to the discovery of the causal genes and mutations for several single-gene traits but not for complex traits. However, the genetic merit of animals can still be estimated by genomic selection, which uses genome-wide SNP panels as markers and statistical methods that capture the effects of large numbers of SNPs simultaneously. This approach is expected to double the rate of genetic improvement per year in many livestock systems.
TL;DR: The scope of genomic predictions is expanded, with predictions available for more than 200 organisms, and the SIFT 4G algorithm, which is a faster version of SIFT that enables practical computations on reference genomes, is described.
Abstract: The SIFT (sorting intolerant from tolerant) algorithm helps bridge the gap between mutations and phenotypic variations by predicting whether an amino acid substitution is deleterious. SIFT has been used in disease, mutation and genetic studies, and a protocol for its use has been previously published with Nature Protocols. This updated protocol describes SIFT 4G (SIFT for genomes), which is a faster version of SIFT that enables practical computations on reference genomes. Users can get predictions for single-nucleotide variants from their organism of interest using the SIFT 4G annotator with SIFT 4G's precomputed databases. The scope of genomic predictions is expanded, with predictions available for more than 200 organisms. Users can also run the SIFT 4G algorithm themselves. SIFT predictions can be retrieved for 6.7 million variants in 4 min once the database has been downloaded. If precomputed predictions are not available, the SIFT 4G algorithm can compute predictions at a rate of 2.6 s per protein sequence. SIFT 4G is available from http://sift-dna.org/sift4g.