Resende R.M.S.,Embrapa Beef Cattle |
Casler M.D.,U.S. Department of Agriculture |
de Resende M.D.V.,Federal University of Viçosa
Crop Science | Year: 2014
The main benefits expected from genomic selection in forage grasses and legumes are to increase selection accuracy, reduce cycle time, and potentially reduce evaluation costs per genotype. Aiming at designing a training population and first generation of selection, deterministic equations were used to compare the gain and accuracy of six genomic selection methods implemented within the context of traditional experimental plot designs used in forage breeding. Combined use of both phenotypic and genotypic information was superior to other methods using low density markers (approximately three per cM) and for heritability lower than 0.6 but resulted in lower selection gain per year in relation to individual genomic selection using higher marker density. Initial accuracies were increased by a selection index method proposed as a procedure to improve long-term rates of gain for advanced generations using genomic selection. Application of genomic selection methods to forage breeding is expected to be of greatest value under the following circumstances: (i) when phenotypic evaluation of individual plants is incapable of predicting performance under sward conditions, (ii) when it is difficult or impossible to apply meaningful selection pressure within families, or (iii) when time-intensive phenotypic evaluations necessitate long cycle times, for example, 4 to 5 yr. © Crop Science Society of America.
Resende R.M.S.,Embrapa Beef Cattle |
Casler M.D.,U.S. Department of Agriculture |
de Resende M.D.V.,Federal University of Viçosa
Crop Science | Year: 2013
Forage breeding can be extraordinarily complex because of the number of species, perenniality, mode of reproduction, mating system, and a variable genetic correlation between spaced plants and sward plots. Aiming to compare eight forage breeding methods for direct selection gain and correlated response, different scenarios of trait heritability and genetic correlation have been evaluated based on deterministic equations of expected (theoretical) breeding accuracy applied to half-sib progenies evaluated in spaced-plant trails, sward-plot trials, or both. Relative efficiency for each method is given in relation to individual selection. Methods differ most when heritability is lower than 0.3, which coincides with the majority of the situations met by forage breeders. Genetic gain of best linear unbiased prediction (BLUP)-based methods is superior to all other methods for trait heritability lower than 0.3, independent of field-trail plot methods, except for parental selection. Methods based on BLUP have also shown higher efficiency when the genetic correlation between spaced-plant and sward-plot trials evaluations of a trait is lower than 0.7 and indirect-trait heritability is lower than 0.3. The choice of forage breeding method should include consideration of the mode of reproduction and the target-trait heritability. The benefits of BLUP-based selection methods should receive more serious consideration by forage breeders. © Crop Science Society of America All rights reserved.
PubMed | Embrapa Agricultural Informatics, Embrapa Southeast Livestock, State University of Mato Grosso do Sul, Embrapa Beef Cattle and 4 more.
Type: | Journal: BMC genomics | Year: 2016
Nelore is the major beef cattle breed in Brazil with more than 130 million heads. Genome-wide association studies (GWAS) are often used to associate markers and genomic regions to growth and meat quality traits that can be used to assist selection programs. An alternative methodology to traditional GWAS that involves the construction of gene network interactions, derived from results of several GWAS is the AWM (Association Weight Matrices)/PCIT (Partial Correlation and Information Theory). With the aim of evaluating the genetic architecture of Brazilian Nelore cattle, we used high-density SNP genotyping data (~770,000 SNP) from 780 Nelore animals comprising 34 half-sibling families derived from highly disseminated and unrelated sires from across Brazil. The AWM/PCIT methodology was employed to evaluate the genes that participate in a series of eight phenotypes related to growth and meat quality obtained from this Nelore sample.Our results indicate a lack of structuring between the individuals studied since principal component analyses were not able to differentiate families by its sires or by its ancestral lineages. The application of the AWM/PCIT methodology revealed a trio of transcription factors (comprising VDR, LHX9 and ZEB1) which in combination connected 66 genes through 359 edges and whose biological functions were inspected, some revealing to participate in biological growth processes in literature searches.The diversity of the Nelore sample studied is not high enough to differentiate among families neither by sires nor by using the available ancestral lineage information. The gene networks constructed from the AWM/PCIT methodology were a useful alternative in characterizing genes and gene networks that were allegedly influential in growth and meat quality traits in Nelore cattle.
Felismino M.F.,State University of Maringá |
Pagliarini M.S.,State University of Maringá |
Do Valle C.B.,Embrapa Beef Cattle |
Resende R.M.S.,Embrapa Beef Cattle
Plant Breeding | Year: 2012
In an attempt to increase genetic variability in the genus Brachiaria, crosses were made between sexual tetraploidized accessions of B. ruziziensis and apomictic tetraploid accessions of B. brizantha (2n=4x=36). Among the F 1 progenies, two hybrids (Hb331, apomictic; and Hb336, sexual) displayed several agronomically desirable traits. These hybrids were evaluated for several years, and the apomictic one is now being tested under grazing to be released as a new cultivar, whereas the sexual one is in a reciprocal recurrent selection programme. The possibility of gene exchange through recombination of genitors and their meiotic behaviour was investigated. Both hybrids were evaluated for meiotic stability during three consecutive years. Analyses of meiocytes at diakinesis revealed multivalent chromosome associations among the parental genomes, indicating that their gene pools are interchangeable. Irregular chromosome segregation, chromosome stickiness and a putative meiotic mutation were recorded. The frequency of abnormalities varied among years and also between the hybrids. The sexual hybrid Hb336 had a more stable meiotic behaviour, but pollen fertility was higher in apomictic Hb331, ensuring more viable seed formation. © 2012 Blackwell Verlag GmbH.
Mattar M.,Centro Universitaio Da Fundacao Educacional Of Barretos Unifeb |
Silva L.O.C.,Embrapa Beef Cattle |
Alencar M.M.,Embrapa Southeast Cattle |
Cardoso F.F.,Embrapa South Cattle and Sheep
Journal of Animal Science | Year: 2011
The objective of this study was to investigate the presence of genotype × environment interactions (G×E) for long-yearling weight in Canchim cattle (5/8 Charolais + 3/8 zebu) in Brazil using reaction norms (RN). The hierarchical RN model included the fixed effect of age of the animal (linear coefficient) and random effects of contemporary groups and additive animal genetic intercept and slope of the RN and contemporary group effects as random effects. Contemporary groups as the most elemental representation of management conditions in beef cattle were chosen to represent the environmental covariate of the RN. The deviance information criteria demonstrated that a homoskedastic residual RN model provided a better data fit compared with a heteroskedastic counterpart and with a traditional animal model, which had the worst fit. The environmental gradient for long-yearling weight based on contemporary group effects ranged from -105 to 150 kg. The additive direct variance and heritability estimates increased with increasing environmental gradient from 74.33 ± 22.32 to 1,922.59 ± 258.99 kg2 and from 0.08 ± 0.02 to 0.68 ± 0.03, respectively. The high genetic correlation (0.90 ± 0.03) between the intercept and the slope of the RN shows that animals with the greatest breeding values best responded to environmental improvement, characterizing scale effect as the source of G×E for long-yearling weight. The phenotypic plasticity demonstrated by the slope of the RN of the animal indicates the possibility to change genotype expression along the environmental gradient through selection. The results demonstrate the importance of accounting for G×E in the genetic evaluation of this population. © 2011 American Society of Animal Science. All rights reserved.
Cabral G.B.,Embrapa Genetic Resources and Biotechnology |
Cabral G.B.,University of Sao Paulo |
Carneiro V.T.C.,Embrapa Genetic Resources and Biotechnology |
Lacerda A.L.,Embrapa Genetic Resources and Biotechnology |
And 3 more authors.
Plant Cell, Tissue and Organ Culture | Year: 2011
Brachiaria brizantha (syn. Urochloa brizantha) is an important tropical forage grass widely cultivated in Brazil. In order to optimize tissue culture conditions for B. brizantha, in vitro culture of mature seeds, basal segments and leaf segments from in vitro plants of an apomictic and a sexual genotype of B. brizantha was performed. When cultured on different media, leaf segments yielded non-embryogenic calluses which formed several roots. Friable calluses from mature seeds and basal segments explants incubated on Murashige and Skoog medium supplemented with 2,4-dichlorophenoxyacetic acid and 6-benzyladenine yielded 80% compact and nodular embryogenic structures. Calluses with such compact embryogenic structures were highly regenerable upon transfer to medium supplemented with kinetin and naphthalene acetic acid. They produced isolated somatic embryos, multiple fused scutelli or isolated scutellum with polyembryos that germinated into isolated or multiple shoots. Green and morphologically normal plants were obtained for the two genotypes. Changing the media from pH 5. 8 to pH 4. 0 increased the number of explants that formed calluses as well as the number of shoots per explant. When embryogenic calluses from mature seeds were successively sub-cultured for 4 months, aiming at repetitive somatic embryogenesis, all the regenerated plants were albinos. The embryogenic nature of the compact structure was confirmed by scanning electron microscopy. © 2011 Springer Science+Business Media B.V.
PubMed | Embrapa Beef Cattle, Embrapa Southeast Livestock and University of Sao Paulo
Type: | Journal: Meat science | Year: 2016
Five hundred and seventy-five Nellore steers were evaluated for residual feed intake and residual feed intake and gain and their relationships between carcass, non-carcass and meat quality traits. RFI was measured by the difference between observed and predicted dry matter intake and RIG was obtained by the sum of -1*RFI and residual gain. Efficient and inefficient animals were classified adopting 0.5 standard deviations from RFI and RIG mean. A mixed model was used including RFI or RIG and contemporary group as fixed effects, initial age as covariate and sire and experimental period as random effects, testing the significance of the regression slope for each evaluated trait. RIG was positively related to longissimus muscle area. Efficient-RFI animals had lower liver and internal fat proportions compared to inefficient-RFI animals. Efficient-RFI and efficient-RIG animals had 11.8% and 11.2% lower extracted intramuscular fat, compared to inefficient-RFI and inefficient-RIG animals, respectively. Efficient-RFI animals had tougher meat compared to inefficient-RFI animals.
Pereira M.A.,Embrapa Beef Cattle |
Fairweather J.R.,Lincoln University at Christchurch |
Woodford K.B.,Lincoln University at Christchurch |
Nuthall P.L.,Lincoln University at Christchurch
Agricultural Systems | Year: 2016
This paper analyses the diversity of goals and values amongst 26 Brazilian commercial-scale beef farmers previously identified as exhibiting progressive technology adoption behaviours, and considers the implications for the agricultural innovation system (AIS). Following the Q-methodology guidelines, four main sets of goals and values were identified and labelled: the Professional Farmer (PF), the Committed Environmentalist (CE), the Profit Maximiser (PM) and the Aspirant Top Farmer (ATF). All farmer types believed in operating the farm as a business and agreed with the notion that cattle production and nature conservation are compatible. The PF aimed to run the farm professionally, based on sound technical and managerial practices. The CE put a particularly strong emphasis on the long-term sustainability of the farming system. The PM focused on technical issues to pursue economic returns and efficiency, thereby also creating space for lifestyle objectives. The ATF sought physical farm and livestock excellence, was growth oriented, and sought recognition by peers. These four typologies have implications for the farmers' technology adoption and its promotion, e.g. they are likely to influence the uptake of particular types of innovations, and reinforce the importance of considering AIS within a social systems framework. This is the first Q-methodology study to demonstrate considerable diversity of values and goals within a subset of technology-adopting progressive farmers, with implications within agricultural innovation systems for the integration of goal diversity and adoption theory. © 2016 Elsevier Ltd.
PubMed | Embrapa Beef Cattle, Embrapa Cerrado, Embrapa Genetic Resources and Biotechnology and University of Brasilia
Type: Journal Article | Journal: Archives of virology | Year: 2016
The complete genome sequence (9,865 nucleotides) of a highly divergent johnsongrass mosaic virus isolate (JGMV-CNPGL) was determined using Illumina sequencing. This isolate infected 10 genotypes of gramineous plants including maize. A comparative analysis of the complete genome showed 80% nucleotide (nt) sequence identity (86% amino acid (aa) sequence identity) to a johnsongrass mosaic virus isolate from Australia. The coat protein (CP) identity values, however, were lower than those for the whole genome (78% and 80% for nt and aa, respectively) and were close to the species demarcation values (77% nt and 80% aa). Unexpectedly, the amino-terminal portion of CP of JGMV-CNPGL showed only 38% sequence identity to other JGMV isolates. The biological implications of this sequence divergence remain to be elucidated.
Toledo-Silva G.,University of Campinas |
Cardoso-Silva C.B.,University of Campinas |
Jank L.,Embrapa Beef Cattle |
Souza A.P.,University of Campinas
PLoS ONE | Year: 2013
Guinea grass (Panicum maximum Jacq.) is a tropical African grass often used to feed beef cattle, which is an important economic activity in Brazil. Brazil is the leader in global meat exportation because of its exclusively pasture-raised bovine herds. Guinea grass also has potential uses in bioenergy production due to its elevated biomass generation through the C4 photosynthesis pathway. We generated approximately 13 Gb of data from Illumina sequencing of P. maximum leaves. Four different genotypes were sequenced, and the combined reads were assembled de novo into 38,192 unigenes and annotated; approximately 63% of the unigenes had homology to other proteins in the NCBI non-redundant protein database. Functional classification through COG (Clusters of Orthologous Groups), GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses showed that the unigenes from Guinea grass leaves are involved in a wide range of biological processes and metabolic pathways, including C4 photosynthesis and lignocellulose generation, which are important for cattle grazing and bioenergy production. The most abundant transcripts were involved in carbon fixation, photosynthesis, RNA translation and heavy metal cellular homeostasis. Finally, we identified a number of potential molecular markers, including 5,035 microsatellites (SSRs) and 346,456 single nucleotide polymorphisms (SNPs). To the best of our knowledge, this is the first study to characterize the complete leaf transcriptome of P. maximum using high-throughput sequencing. The biological information provided here will aid in gene expression studies and marker-assisted selection-based breeding research in tropical grasses. © 2013 Toledo-Silva et al.