ORCID Profile
0000-0002-2030-7590
Current Organisations
Deakin University
,
Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Marine and Estuarine Ecology (incl. Marine Ichthyology) | Fisheries Sciences not elsewhere classified | Fisheries Sciences | Fisheries Management
ANZSRC Socio-Economic Objective (SEO)
Wild Caught Fin Fish (excl. Tuna) | Marine Flora, Fauna and Biodiversity |
Related Links
Publications
Genomic analysis of stayability in Nellore cattle
Publisher: Public Library of Science (PLoS)
Date: 07-06-2017
Analysis of genetic correlations of hip height with selection indices and mature weight in Nelore cattle
Publisher: Springer Science and Business Media LLC
Date: 09-11-2012
DOI: 10.1007/S13353-012-0121-1
Abstract: Body size is directly related to the productive and reproductive performance of beef cattle raised under free-range conditions. In an attempt to better plan selection criteria, avoiding extremes in body size, this study estimated the heritabilities and genetic correlations of yearling hip height (YH) and mature hip height (MH) with selection indices obtained at weaning (WI) and yearling (YI) and mature weight (MW). Data from 102,373 Nelore animals born between 1984 and 2010, which belong to 263 farms that participate in genetic evaluation programmes of beef cattle conducted in Brazil and Paraguay, were used. The (co)variance components and genetic parameters were estimated by Bayesian inference in multi-trait analysis using an animal model. The mean heritabilities for YH, MH and MW were 0.56 ± 0.06, 0.47 ± 0.02 and 0.42 ± 0.02, respectively. The genetic correlation of YH with WI (0.13 ± 0.01) and YI (0.11 ± 0.01) was practically zero, whereas a higher correlation was observed with MW (0.22 ± 0.03). Positive genetic correlations of medium magnitude were estimated between MH and WI and YI (0.23 ± 0.01 and 0.43 ± 0.02, respectively). On the other hand, a high genetic correlation (0.68 ± 0.03) was observed between the indicator traits of mature body size (MH and MW). Considering the top 20 % of sire (896 sires) in terms of breeding values for the yearling index, the rank sire correlations between breeding values for MH and MW was 0.62. In general, the results indicate that selection based on WI and YI should not lead to important changes in YH. However, an undesired correlated response in mature cow height is expected, particularly when selection is performed using YI. Therefore, changes in the body structure of Nelore females can be obtained when MH and MW is used as a selection criterion for cows.
Amh Polymorphisms and their association with traits indicative of sexual precocity in nelore heifers
Publisher: Universidade Estadual de Londrina
Date: 07-06-2019
DOI: 10.5433/1679-0359.2019V40N4P1489
Abstract: Anti-Müllerian Hormone (AMH) is a protein expressed in the gonads and related to ovarian follicular development. The aim of this study was to investigate the presence of polymorphisms in the AMH gene in a Nelore herd to analyze the genetic constitution of this population and to perform association studies with early pregnancy occurrence (EPO) and age at first calving (AFC). Phenotypic data consisted of verification of early pregnancy and age at first calving of 197 unrelated heifers exposed to the mating season and aged between 15 and 17 months (precocious group) and 24 months (non-precocious group). The "precocious" group consisted of 67 heifers with age at first calving of 26.5 ± 0.59 months, and the "non-precocious" group was composed of 130 heifers with age at first calving of 36.4 ± 0.99 months. All five exons of the AMH gene were lified by Polymerase Chain Reaction (PCR) and sequenced. A total of three SNPs were identified in this study, all of them located in exon 5 (rs527023314, rs722016629, and rs134387246), the latter one positioned in the stop codon. All three SNPs identified in exon 5 characterized synonymous mutations. Only SNP rs134387246 exhibited a significant value (P ? 0.10) for EPO and AFC. The association study of SNP rs134387246 revealed an over-dominance effect (P = 0.056), and no additive effect was observed (P = 0.67). A reduction of 2.5 months (75 days) in the age at first calving of heterozygous heifers for the SNP rs134387246 was observed. For the first time, polymorphisms of the AMH gene were described in Nelore heifers and associated with sexual precocity traits.
RAPID COMMUNICATION: Multi-breed validation study unraveled genomic regions associated with puberty traits segregating across tropically adapted breeds1
Publisher: Oxford University Press (OUP)
Date: 11-04-2019
DOI: 10.1093/JAS/SKZ121
Abstract: An efficient strategy to improve QTL detection power is performing across-breed validation studies. Variants segregating across breeds are expected to be in high linkage disequilibrium (LD) with causal mutations affecting economically important traits. The aim of this study was to validate, in a Tropical Composite cattle (TC) population, QTL associations identified for sexual precocity traits in a Nellore and Brahman meta-analysis genome-wide association study. In total, 2,816 TC, 8,001 Nellore, and 2,210 Brahman animals were available for the analysis. For that, genomic regions significantly associated with puberty traits in the meta-analysis study were validated for the following sexual precocity traits in TC: age at first corpus luteum (AGECL), first postpartum anestrus interval (PPAI), and scrotal circumference at 18 months of age (SC). We considered validated QTL those underpinned by significant markers from the Nellore and Brahman meta-analysis (P ≤ 10–4) that were also significant for a TC trait, i.e., presenting a P-value of ≤10–3 for AGECL, PPAI, or SC. We also considered as validated QTL those regions where significant markers in the reference population were at ±250 kb from significant markers in the validation population. Using this criteria, 49 SNP were validated for AGECL, 4 for PPAI, and 14 for SC, from which 5 were in common with AGECL, totaling 62 validated SNP for these traits and 30 candidate genes surrounding them. Considering just candidate genes closest to the top SNP of each chromosome, for AGECL 8 candidate genes were identified: COL8A1, PENK, ENSBTAG00000047425, BPNT1, ADAMTS17, CCHCR1, SUFU, and ENSBTAG00000046374. For PPAI, 3 genes emerged as candidates (PCBP3, KCNK10, and MRPS5), and for SC 8 candidate genes were identified (SNORA70, TRAC, ASS1, BPNT1, LRRK1, PKHD1, PTPRM, and ENSBTAG00000045690). Several candidate regions presented here were previously associated with puberty traits in cattle. The majority of emerging candidate genes are related to biological processes involved in reproductive events, such as maintenance of gestation, and some are known to be expressed in reproductive tissues. Our results suggested that some QTL controlling early puberty seem to be segregating across cattle breeds adapted to tropical conditions.
Genome-wide association study of reproductive traits in Nellore heifers using Bayesian inference
Publisher: Springer Science and Business Media LLC
Date: 19-08-2015
First polymorphisms in JY-1 gene in cattle (Bos taurus indicus) and their association with sexual precocity and growth traits
Publisher: Springer Science and Business Media LLC
Date: 06-09-2012
DOI: 10.1007/S11033-012-1884-5
Abstract: Protein JY-1 is a bovine oocyte-specific protein that regulates granulosa cell function and is involved in early embryonic development, influencing the chance of pregnancy. This study investigated molecular markers for the JY-1 gene. Seven SNPs were identified in exon 3 of the gene. The positions of the SNPs in the exon and the respective substitutions are: 163 (T/C), 281 (T/C), 321 (T/C), 532 (T/C), 652 (A/G), 679 (T/C), and 722 (G/C) (GenBank: JN592587 and JF262042.2). SNP 163 is located in a coding region and causes a proline-to-leucine substitution. The other SNPs are located in the 3'UTR region. SNPs 163, 281, 321, and 679 were genotyped in 297 Nellore heifers and the haplotypes were constructed. The haplotypes of JY-1 were not correlated with the traits studied at 5 %.
Genetic parameter estimates for buffalo milk yield, milk quality and mozzarella production and Bayesian inference analysis of their relationships
Publisher: Genetics and Molecular Research
Date: 2010
DOI: 10.4238/VOL9-3GMR846
Abstract: Buffalo milk has excellent physical and chemical qualities as a consequence of the high percentage of constituents. This milk property is desirable for the dairy industry because it facilitates manufacture of mozzarella cheese. We estimated genetic parameters for milk yield, milk fat and protein and their effects on mozzarella cheese production using Bayesian inference. Using information from 4907 lactation records of buffaloes, genetic and non-genetic parameters were estimated for accumulated 305-day milk yield (MY), milk fat (%F) and protein (%P) percentages and mozzarella production per lactation (MP). The (co)variance components were obtained by Bayesian inference using a multiple trait model, which included as fixed effects contemporary group, milking number and buffalo age at calving as covariables (linear and quadratic), along with the additive genetic, permanent environmental and residual random effects. Mean a posteriori heritability distributions for MY, %F, %P, and MP were 0.25, 0.30, 0.38, and 0.23, respectively. The genetic correlation estimates between MY with %P and %F were negative and moderate. Positive genetic correlation estimates varying from 0.19 (%P/MP) to 0.95 (MY/MP) were obtained among the traits. Milk yield, milk components, and mozzarella production in Murrah buffaloes have enough genetic variation for selection purposes. We conclude that selection to increase milk yield would be effective in improving mozzarella production.
Copy number variation regions in Nellore cattle: Evidences of environment adaptation
Publisher: Elsevier BV
Date: 2018
Genome-Wide Association Study for Indicator Traits of Sexual Precocity in Nellore Cattle
Publisher: Public Library of Science (PLoS)
Date: 05-08-2016
Differential expression of immune response genes associated with subclinical mastitis in dairy buffaloes
Publisher: Elsevier BV
Date: 2019
Genome-Wide Association Study of Meat Quality Traits in Nellore Cattle
Publisher: Public Library of Science (PLoS)
Date: 30-06-2016
Important effect of the X chromosome in genomic evaluations of reproductive traits in beef cattle
Publisher: Cold Spring Harbor Laboratory
Date: 02-07-2020
DOI: 10.1101/2020.06.30.178558
Abstract: The aim of this study was to evaluate the efficiency of inclusion and the prediction ability of the X chromosome for reproductive (occurrence of early pregnancy – P16 and age at first calving - AFC) and andrological traits (scrotal circumference -SC) in a herd of Nellore beef cattle herd. 3,263 genotypes of females and males were used. Genomic prediction for SC, AFC and P16 was carried out considering two scenarios: 1) only autosomal markers or 2) autosomal + X chromosome markers. To evaluate the effect of inclusion of the X chromosome on selection, the responses to the selection performed were compared including or not the X chromosome in the evaluation of the traits. Higher heritability estimates were obtained for SC (0.40 and 0.31), AFC (0.11 and 0.09) and P16 (0.43 and 0.38) for the analyses including the X chromosome compared to those without. The percent reduction on mean genomic breeding values when selection was based on the results of analysis that did not include the X chromosome to 1, 5 and 10% of the top males, was for SC slightly more than 7% of the mean genomic breeding value of the selected animals. For P16, the loss can reach more than 4%, while this loss does not seem to be as important for AFC. Average predictive correlation of 0.79, 0.98 and 0.84 for SC, AFC and P16 was obtained, respectively. These estimates demonstrate that inclusion of the X chromosome in the analysis can improve the prediction of genomic breeding values, especially for SC.
Evaluation of longevity modeling censored records in Nellore
Publisher: Elsevier BV
Date: 2017
Genomic selection for meat quality traits in Nelore cattle
Publisher: Elsevier BV
Date: 02-2019
DOI: 10.1016/J.MEATSCI.2018.09.010
Abstract: The objective of this study was to present heritability estimates and accuracy of genomic prediction using different methods for meat quality traits in Nelore cattle. Approximately 5000 animals with phenotypes and genotypes of 412,000 SNPs, were ided into two groups: (1) training population: animals born from 2008 to 2013 and (2) validation population: animals born in 2014. A single-trait animal model was used to estimate heritability and to adjust the phenotype. The methods of GBLUP, Improved Bayesian Lasso and Bayes Cπ were performed to estimate the SNP effects. Accuracy of genomic prediction was calculated using Pearson's correlations between direct genomic values and adjusted phenotypes, ided by the square root of heritability of each trait (0.03-0.19). The accuracies varied from 0.23 to 0.73, with the lowest accuracies estimated for traits associated with fat content and the greatest accuracies observed for traits of meat color and tenderness. There were small differences in genomic prediction accuracy between methods.
Milk fatty acid characterization and genetic parameter estimates for milk conjugated linoleic acid in buffaloes
Publisher: Cambridge University Press (CUP)
Date: 04-03-2011
DOI: 10.1017/S0022029911000045
Abstract: The objectives of this study were to analyse buffalo milk fat composition, to verify the activity of Delta(9)-desaturase enzyme in the mammary gland, as well as to estimate additive genetic variances for milk, fat and protein yield, and milk cis -9, trans -11 conjugated linoleic acid percentage ( cis -9, trans -11 CLA%). A total of 3929 lactation milk yields (MY) records from 2130 buffaloes and 1598 lactation fat (FY) and protein (PY) yield records from 914 buffaloes were analysed. For cis -9, trans -11 CLA%percentage, a total of 661 milk s les from 225 buffaloes, daughters of 8 sires, belonging to 4 herds and calving in 2003 and 2004, were used. The genetic parameters and variance components were estimated by Restricted Maximum Likelihood applying an animal model. The fixed effects considered in the model were: contemporary group (herd, year, calving season) and age at calving (linear and quadratic effects) and lactation length (linear and quadratic effects) as covariables. Additive genetic and permanent environment effects were considered as random. The MY, FY, PY and CLA% means were 1482±355 kg, 90·1±24·6 kg, 56·9±15·2 kg and 0·69±0·16%, respectively. Heritability estimates for MY, FY, PY and CLA% were 0·28±0·05, 0·26±0·11, 0·25±0·11 and 0·35±0·14, respectively. There is enough additive genetic variation for buffalo milk, protein and fat yield to improve these traits through selection. The cis -9, trans -11 CLA% can be enhanced by selection in buffaloes and will contribute to improving human health. The activity and efficiency of Delta(9)-desaturase in the mammary was measured and confirmed.
Accuracies of genomic prediction of feed efficiency traits using different prediction and validation methods in an experimental Nelore cattle population1
Publisher: Oxford University Press (OUP)
Date: 09-2016
Abstract: Animal feeding is the most important economic component of beef production systems. Selection for feed efficiency has not been effective mainly due to difficult and high costs to obtain the phenotypes. The application of genomic selection using SNP can decrease the cost of animal evaluation as well as the generation interval. The objective of this study was to compare methods for genomic evaluation of feed efficiency traits using different cross-validation layouts in an experimental beef cattle population genotyped for a high-density SNP panel (BovineHD BeadChip assay 700k, Illumina Inc., San Diego, CA). After quality control, a total of 437,197 SNP genotypes were available for 761 Nelore animals from the Institute of Animal Science, Sertãozinho, São Paulo, Brazil. The studied traits were residual feed intake, feed conversion ratio, ADG, and DMI. Methods of analysis were traditional BLUP, single-step genomic BLUP (ssGBLUP), genomic BLUP (GBLUP), and a Bayesian regression method (BayesCπ). Direct genomic values (DGV) from the last 2 methods were compared directly or in an index that combines DGV with parent average. Three cross-validation approaches were used to validate the models: 1) YOUNG, in which the partition into training and testing sets was based on year of birth and testing animals were born after 2010 2) UNREL, in which the data set was split into 3 less related subsets and the validation was done in each subset a time and 3) RANDOM, in which the data set was randomly ided into 4 subsets (considering the contemporary groups) and the validation was done in each subset at a time. On average, the RANDOM design provided the most accurate predictions. Average accuracies ranged from 0.10 to 0.58 using BLUP, from 0.09 to 0.48 using GBLUP, from 0.06 to 0.49 using BayesCπ, and from 0.22 to 0.49 using ssGBLUP. The most accurate and consistent predictions were obtained using ssGBLUP for all analyzed traits. The ssGBLUP seems to be more suitable to obtain genomic predictions for feed efficiency traits on an experimental population of genotyped animals.
Evaluation of mature cow weight: Genetic correlations with traits used in selection indices, correlated responses, and genetic trends in Nelore cattle
Publisher: Oxford University Press (OUP)
Date: 2013
Abstract: Genetic correlations of selection indices and the traits considered in these indices with mature weight (MW) of Nelore females and correlated responses were estimated to determine whether current selection practices will result in an undesired correlated response in MW. Genetic trends for weaning and yearling indices and MW were also estimated. Data from 612,244 Nelore animals born between 1984 and 2010, belonging to different beef cattle evaluation programs from Brazil and Paraguay, were used. The following traits were studied: weaning conformation (WC), weaning precocity (WP), weaning muscling (WM), yearling conformation (YC), yearling precocity (YP), yearling muscling (YM), weaning and yearling indices, BW gain from birth to weaning (BWG), postweaning BW gain (PWG), scrotal circumference (SC), and MW. The variance and covariance components were estimated by Bayesian inference in a multitrait analysis, including all traits in the same analysis, using a nonlinear (threshold) animal model for visual scores and a linear animal model for the other traits. The mean direct heritabilities were 0.21±0.007 (WC), 0.22±0.007 (WP), 0.20±0.007 (WM), 0.43±0.005 (YC), 0.40±0.005 (YP), 0.40±0.005 (YM), 0.17±0.003 (BWG), 0.21±0.004 (PWG), 0.32±0.001 (SC), and 0.44±0.018 (MW). The genetic correlations between MW and weaning and yearling indices were positive and of medium magnitude (0.30±0.01 and 0.31±0.01, respectively). The genetic changes in weaning index, yearling index, and MW, expressed as units of genetic SD per year, were 0.26, 0.27, and 0.01, respectively. The genetic trend for MW was nonsignificant, suggesting no negative correlated response. The selection practice based on the use of sires with high final index giving preference for those better ranked for yearling precocity and muscling than for conformation generates only a minimal correlated response in MW.
Genome-wide scan reveals population stratification and footprints of recent selection in Nelore cattle
Publisher: Springer Science and Business Media LLC
Date: 02-05-2018
Analysis of culling probability in dairy buffalo using survival models
Publisher: Elsevier BV
Date: 2010
Genomic association for sexual precocity in beef heifers using pre-selection of genes and haplotype reconstruction
Publisher: Public Library of Science (PLoS)
Date: 02-01-2018
Intertrip consistency in hunting behavior improves foraging success and efficiency in a marine top predator
Publisher: Wiley
Date: 13-03-2021
DOI: 10.1002/ECE3.7337
Genome Association Study for Visual Scores in Nellore Cattle Measured at Weaning
Publisher: Springer Science and Business Media LLC
Date: 20-02-2019
Influence of environmental variation on spatial distribution and habitat-use in a benthic foraging marine predator
Publisher: The Royal Society
Date: 10-2021
DOI: 10.1098/RSOS.211052
Abstract: The highly dynamic nature of the marine environment can have a substantial influence on the foraging behaviour and spatial distribution of marine predators, particularly in pelagic marine systems. However, knowledge of the susceptibility of benthic marine predators to environmental variability is limited. This study investigated the influence of local-scale environmental conditions and large-scale climate indices on the spatial distribution and habitat use in the benthic foraging Australian fur seal ( Arctocephalus pusillus doriferus AUFS). Female AUFS provisioning pups were instrumented with GPS or ARGOS platform terminal transmitter tags during the austral winters of 2001–2019 at Kanowna Island, south-eastern Australia. In iduals were most susceptible to changes in the Southern Oscillation Index that measures the strength of the El Niño Southern Oscillation, with larger foraging ranges, greater distances travelled and more dispersed movement associated with 1-yr lagged La Niña-like conditions. Additionally, the total distance travelled was negatively correlated with the current year sea surface temperature and 1-yr lagged Indian Ocean Dipole, and positively correlated with 1-yr lagged chlorophyll- a concentration. These results suggest that environmental variation may influence the spatial distribution and availability of prey, even within benthic marine systems.
Association between single nucleotide polymorphisms and sexual precocity in Nellore heifers
Publisher: Elsevier BV
Date: 02-2017
DOI: 10.1016/J.ANIREPROSCI.2016.12.009
Abstract: The aim of this study was to determine the extent (r
Erratum to: Genome-wide association study of reproductive traits in Nellore heifers using Bayesian inference
Publisher: Springer Science and Business Media LLC
Date: 17-09-2015
Genomic prediction of breeding values for carcass traits in Nellore cattle
Publisher: Springer Science and Business Media LLC
Date: 29-01-2016
Genetic parameters for test-day yield of milk, fat and protein in buffaloes estimated by random regression models
Publisher: Cambridge University Press (CUP)
Date: 23-03-2012
DOI: 10.1017/S0022029912000143
Abstract: The test-day yields of milk, fat and protein were analysed from 1433 first lactations of buffaloes of the Murrah breed, daughters of 113 sires from 12 herds in the state of São Paulo, Brazil, born between 1985 and 2007. For the test-day yields, 10 monthly classes of lactation days were considered. The contemporary groups were defined as the herd-year-month of the test day. Random additive genetic, permanent environmental and residual effects were included in the model. The fixed effects considered were the contemporary group, number of milkings (1 or 2 milkings), linear and quadratic effects of the covariable cow age at calving and the mean lactation curve of the population (modelled by third-order Legendre orthogonal polynomials). The random additive genetic and permanent environmental effects were estimated by means of regression on third- to sixth-order Legendre orthogonal polynomials. The residual variances were modelled with a homogenous structure and various heterogeneous classes. According to the likelihood-ratio test, the best model for milk and fat production was that with four residual variance classes, while a third-order Legendre polynomial was best for the additive genetic effect for milk and fat yield, a fourth-order polynomial was best for the permanent environmental effect for milk production and a fifth-order polynomial was best for fat production. For protein yield, the best model was that with three residual variance classes and third- and fourth-order Legendre polynomials were best for the additive genetic and permanent environmental effects, respectively. The heritability estimates for the characteristics analysed were moderate, varying from 0·16±0·05 to 0·29±0·05 for milk yield, 0·20±0·05 to 0·30±0·08 for fat yield and 0·18±0·06 to 0·27±0·08 for protein yield. The estimates of the genetic correlations between the tests varied from 0·18±0·120 to 0·99±0·002 from 0·44±0·080 to 0·99±0·004 and from 0·41±0·080 to 0·99±0·004, for milk, fat and protein production, respectively, indicating that whatever the selection criterion used, indirect genetic gains can be expected throughout the lactation curve.
Associations between single nucleotide polymorphisms and carcass traits in Nellore cattle using high-density panels
Publisher: Genetics and Molecular Research
Date: 2015
Genetic parameter estimates for temperament, heifer rebreeding, and stayability in Nellore cattle
Publisher: Elsevier BV
Date: 12-2017
Genome-Wide Association Study for Carcass Traits in an Experimental Nelore Cattle Population
Publisher: Public Library of Science (PLoS)
Date: 24-01-2017
Short communication: Variable number of tandem repeat polymorphisms in DGAT1 gene of buffaloes (Bubalus bubalis) is associated with milk constituents
Publisher: American Dairy Science Association
Date: 05-2015
Abstract: The diacylglycerol-O-transferase 1 gene is a positional and functional candidate for milk composition traits. The objective of this study was to evaluate the segregation of the variable number of tandem repeat polymorphisms in the regulatory region of diacylglycerol-O-transferase 1 gene in a water buffalo herd, and to assess the association of this mutation with milk production traits. For this purpose, 196 Murrah buffalo cows were genotyped by PCR. The association of the marker with total milk, fat, and protein yields at 305 d of lactation, milk fat and protein percentage, and somatic cell scores were evaluated by single-trait analyses using a generalized mixed model. Two segregating alleles were identified in the population. The allele with 2 repeats affected fat percentage favorably. The present results suggest that this polymorphism is an interesting marker to include in the genetic evaluation of buffaloes.
Influence of X-chromosome markers on reproductive traits of beef cattle
Publisher: Elsevier BV
Date: 02-2019
Association between JY-1 gene polymorphisms and reproductive traits in beef cattle
Publisher: Elsevier BV
Date: 2014
DOI: 10.1016/J.GENE.2013.09.126
Abstract: Reproductive traits have a high economic value and it is interesting to include them in the selection objectives of an animal breeding program. These traits generally show low heritability and molecular markers may therefore be used in genetic evaluations to improve the accuracy of predictions. The JY-1 gene is expressed in the oocyte and it is associated with folliculogenesis and early embryo development. It has been suggested to affect reproductive traits. In this study, exons 1 and 2 of the JY-1 gene were studied in 385 Nellore females by PCR-sequencing. Seventeen polymorphisms were identified. After analysis of linkage disequilibrium, association tests were performed between eight SNPs and the occurrence of early pregnancy, age at first calving, days to calving, and reconception of primiparous heifers. Seven SNPs were significant for three traits. The most significant was chr29:12,999 T/A (p=0.003) which was associated with the occurrence of early pregnancy. This SNP might be involved in protein translation inhibition since it affects the initial methionine codon. The JY-1, an oocyte specific gene, influences reproductive traits further studies investigating other regions of the gene or other genes expressed in tissues of the female reproductive system would be interesting to be performed.
Genome scan for postmortem carcass traits in Nellore cattle1
Publisher: Oxford University Press (OUP)
Date: 10-2016
Abstract: Carcass traits measured after slaughter are economically relevant traits in beef cattle. In general, the slaughter house payment system is based on HCW. Ribeye area (REA) is associated with the amount of the meat in the carcass, and a minimum of backfat thickness (BFT) is necessary to protect the carcass during cooling. The aim of this study was to identify potential genomic regions harboring candidate genes affecting those traits in Nellore cattle. The data set used in the present study consisted of 1,756 Nellore males with phenotype records. A subset of 1,604 animals had both genotypic and phenotypic information. Genotypes were generated based on a panel with 777,962 SNPs from the Illumina Bovine HD chip. The SNP effects were calculated based on the genomic breeding values obtained by using the single-step GBLUP approach and a genomic matrix re-weighting procedure. The proportion of the variance explained by moving windows of 100 consecutive SNPs was used to assess potential genomic regions harboring genes with major effects on each trait. The top 10 non-overlapping SNP-windows explained 8.72%, 11.38%, and 9.31% of the genetic variance for REA, BFT, and HCW, respectively. These windows are located on chromosomes 5, 7, 8, 10, 12, 20, and 29 for REA chromosomes 6, 8, 10, 13, 16, 17, 18, and 24 for BFT and chromosomes 4, 6, 7, 8, 14, 16, 17, and 21 for HCW. For REA, there were identified genes ( and ) involved in the cell cycle biological process which affects many aspects of animal growth and development. The and genes, both from AA transporter family, was also associated with REA. The AA transporters are essential for cell growth and proliferation, acting as carriers of tissue nutrient supplies. Various genes identified for BFT (, , , , , and ) have been associated with lipid metabolism in different mammal species. One of the most promising genes identified for HCW was the . There is evidence, in the literature, that this gene is located in putative QTL affecting carcass weight in beef cattle. Our results showed several genomic regions containing plausible candidate genes that may be associated with carcass traits in Nellore cattle. Besides contributing to a better understanding of the genetic control of carcass traits, the identified genes can also be helpful for further functional genomic studies.
Unraveling genetic sensitivity of beef cattle to environmental variation under tropical conditions
Publisher: Springer Science and Business Media LLC
Date: 20-06-2019
Across‐breed validation study confirms and identifies new loci associated with sexual precocity in Brahman and Nellore cattle
Publisher: Wiley
Date: 14-08-2019
DOI: 10.1111/JBG.12429
Abstract: The aim of this study was to identify candidate regions associated with sexual precocity in Bos indicus. Nellore and Brahman were set as validation and discovery populations, respectively. SNP selected in Brahman to validate in Nellore were from gene regions affecting reproductive traits (G1) and significant SNP (p ≤ 10
Genetic correlation of traits measured by ultrasound at yearling and 18 months of age in Nellore beef cattle
Publisher: Elsevier BV
Date: 10-2015
Assessing the value of phenotypic information from non-genotyped animals for QTL mapping of complex traits in real and simulated populations
Publisher: Springer Science and Business Media LLC
Date: 21-06-2016
Effect of genomic X-chromosome regions on Nelore bull fertility
Publisher: Springer Science and Business Media LLC
Date: 18-06-2021
Water buffalo genome characterization by the Illumina BovineHD BeadChip
Publisher: Genetics and Molecular Research
Date: 2014
Polymorphisms in TOX and NCOA2 genes and their associations with reproductive traits in cattle
Publisher: CSIRO Publishing
Date: 2015
DOI: 10.1071/RD13360
Abstract: Reproductive traits are an important component of the economic selection index for beef cattle in the tropics. Phenotypic expression of these traits occurs late because they are measured when the animals reach reproductive age. Association studies using high-density markers have been conducted to identify genes that influence certain traits. The identification of causal mutations in these genes permits the inclusion of these single nucleotide polymorphisms (SNPs) in customised DNA chips to increase efficiency and validity. Therefore, the aim of the present study was to detect causal mutations in the TOX and NCOA2 genes, previously identified by genome-wide association studies of zebu cattle. DNA was extracted from 385 Nellore females and polymorphisms were investigated by polymerase chain reaction sequencing. Five polymorphisms were detected in the NCOA2 gene and four in the TOX gene that were associated with reproductive traits. Analysis of variance showed that SNP 1718 in the NCOA2 gene was significant for early pregnancy probability (P = 0.02) and age at first calving (P = 0.03), and SNP 2038 in the same gene was significant for days to calving (P = 0.03). Studies investigating polymorphisms in other regions of the gene and in other genes should be conducted to identify causal mutations.
Transcriptomic profile of longissimus thoracis associated with fatty acid content in Nellore beef cattle
Publisher: Wiley
Date: 06-04-2022
DOI: 10.1111/AGE.13199
Abstract: The beef fatty acid (FA) profile has the potential to impact human health, and displays polygenic and complex features. This study aimed to identify the transcriptomic FA profile in the longissimus thoracis muscle in Nellore beef cattle finished in feedlot. Forty‐four young bulls were s led to assess the beef FA profile by considering 14 phenotypes and including differentially expressed genes (DEG), co‐expressed (COE), and differentially co‐expressed genes (DCO) analyses. All s les ( n = 44) were used for COE analysis, whereas 30 s les with extreme phenotypes for the beef FA profile were used for DEG and DCO. A total of 912 DEG were identified, and the polyunsaturated ( n = 563) and unsaturated ω‐3 ( n = 346) FA sums groups were the most frequently observed. The COE analyses identified three modules, of which the blue module ( n = 1776) was correlated with eight of 14 FA phenotypes. Also, 759 DCO genes were listed, and the oleic acid ( n = 358) and monounsaturated fatty acids sum ( n = 120) were the most frequent. Furthermore, 243 and 13, 319 and seven, and 173 and 12 gene ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways were enriched respectively for the DEG, COE, and DCO analyses. Combining the results, we highlight the unexplored GIPC2 , ASB5 , and PPP5C genes in cattle. Besides LIPE and INSIG2 genes in COE modules, the ACSL3 , ECI1 , DECR2 , FITM1 , and SDHB genes were signaled in at least two analyses. These findings contribute to understand the genetic mechanisms underlying the beef FA profile in Nellore beef cattle finished in feedlot.
Correlações genéticas entre escores visuais e características de carcaça medidas por ultrassom em bovinos de corte
Publisher: FapUNIFESP (SciELO)
Date: 02-2009
DOI: 10.1590/S0100-204X2009000200012
Abstract: O objetivo deste trabalho foi estimar correlações genéticas e fenotípicas entre escores visuais e características de carcaça medidas por ultrassom, para verificar a eficácia desses escores na determinação da musculosidade e na avaliação da carcaça. As características de carcaça medidas por ultrassom foram área de olho de lombo (AOL) e espessura de gordura subcutânea (EG), mensuradas entre a região da 12ª e 13ª costelas, bem como a espessura de gordura subcutânea na garupa (EGP8). As características de estrutura (E), precocidade (P) e musculosidade (M) foram avaliadas por meio de escores visuais. Os componentes de covariância usados para estimar as correlações genéticas e fenotípicas foram obtidos pelo método da máxima verossimilhança restrita, em uma análise multicaracterística. As estimativas de correlações genéticas entre AOL e E, P e M foram 0,54, 0,58 e 0,61, respectivamente, e indicaram que, a longo prazo, a utilização da AOL como critério de seleção poderá produzir animais com maiores escores visuais para essas características. As correlações genéticas estimadas entre as espessuras de gordura (EG e EGP8) e os escores P e M apresentaram comportamento semelhante. Entretanto, as correlações genéticas entre as espessuras de gordura (EG e EGP8) e E foram próximas de zero. As correlações fenotípicas seguiram as mesmas tendências das respectivas correlações genéticas. Essas estimativas indicam que os escores visuais são determinados, em parte, pelos mesmos conjuntos de genes que influenciam a AOL.
Quantifying killer whale depredation in the blue-eye trevalla commercial fisheries of south-east Australia
Publisher: Elsevier BV
Date: 04-2022
Associations of FASN gene polymorphisms with economical traits in Nellore cattle (Bos primigenius indicus)
Publisher: Springer Science and Business Media LLC
Date: 09-2012
DOI: 10.1007/S11033-012-1883-6
Abstract: The aim of this study was to identify molecular markers to be applied to marker-assisted selection. Three SNPs of the FASN gene were studied. PCR-RFLP was used for genotyping. The SNPs g.17924A>G, g.17860C>T and g.15603A>G all in the FASN gene were genotyped using the enzymes MscI, DdeI and Hae III, respectively. The animals were raised in extensive systems and belong to three lines selected for growth as part of the Selection Program of Zebu and Caracu Breeds, São Paulo, Brazil. Allele and genotype frequencies were compared between selection lines using the Genepop 3.4. Associations between polymorphisms and the traits studied were evaluated using the PROC MIXED procedure of the SAS/STAT 9.1.3. The G and C alleles were the most frequent alleles of the g.15603A>G and g.17860C>T loci, respectively. The g.17924A>G locus showed no polymorphism in the population studied. Allele and genotype frequencies differed significantly between the NeT line and the NeC and NeS lines. The g.15603A>G polymorphism tended to exert an additive effect on rump fat thickness and male yearling height. For g.17860C>T, an additive effect on male yearling height was observed. Genotype combination analysis revealed a significant effect on loin eye area. Although this study provided evidence of an association between the FASN gene and some traits, more detailed analyses are needed to obtain more efficient molecular markers.
The effect of mitochondrial DNA polymorphisms on cattle reproduction
Publisher: Springer Science and Business Media LLC
Date: 2021
Genotype × environment interaction for age at first calving, scrotal circumference, and yearling weight in Nellore cattle using reaction norms in multitrait random regression models
Publisher: Oxford University Press (OUP)
Date: 04-2015
Abstract: The aim of this study was to evaluate the effect of genotype × environment interaction (G×E) on age at first calving (AFC), scrotal circumference (SC), and yearling weight (YW) and to estimate genetic correlations between these traits in Nellore cattle using reaction norms in multitrait random regression models. In this study, 28,871, 41,386, and 89,152 records of Nellore cattle for AFC, SC, and YW, respectively, were used. The data were obtained from farms located in the north, northeast, midwest, and southeast regions of Brazil that participate in the DeltaGen Breeding Program. Environmental levels were defined as a function of contemporary groups, that is, animals born in the same herd and year, from the same management group (from birth to yearling), and of the same sex. Postweaning weight gain was used as a criterion to evaluate the environmental conditions for all traits. For reaction norm analyses, residual variances were modeled with homogeneous and heterogeneous classes. The model for SC and YW included the fixed effects of contemporary group and age of the animal as a covariate as well as random direct additive genetic and residual effects. The same model, excluding the covariate age of the animal, was used for AFC. The heritability estimates were low to high for AFC (0.09 to 0.50), high for SC (0.51 to 0.67), and moderate to high for YW (0.33 to 0.71). The genetic correlations (within each trait) along the environmental levels varied from -0.27 to 1.0 for AFC, from 0.73 to 1.0 for SC, and from 0.26 to 1.0 for YW. The genetic correlations between different traits in different environments varied from -0.14 to -0.60 between AFC and SC, from -0.05 to -0.32 between AFC and YW, and from -0.05 to 0.72 between YW and SC. The genetic correlations have had different magnitudes for AFC, SC, and YW, which could indicate the presence of G×E. The present results should support researchers and farmers in defining selection criteria to improve growth traits and sexual precocity. Our results suggest that animals for breeding have to be selected in the same environment and management conditions as their progeny will be reared.
Genetic parameters for milk, fat and protein yields in Murrah buffaloes (Bubalus bubalis Artiodactyla, Bovidae)
Publisher: FapUNIFESP (SciELO)
Date: 22-01-2010
Genetic and environmental factors affecting ultrasound measures of longissimus muscle area and backfat thickness in Nelore cattle
Publisher: Elsevier BV
Date: 09-2008
Prospecting polymorphisms in the PPP3CA and FABP4 genes and their association with early pregnancy probability in Nellore heifers
Publisher: Elsevier BV
Date: 09-2017
Comparison of models for the genetic evaluation of reproductive traits with censored data in Nellore cattle1
Publisher: Oxford University Press (OUP)
Date: 06-2016
Abstract: In typical genetic evaluation, often some females have missing records due to reproductive failure and due to voluntary and involuntary culling before the breeding season. These partially or unobserved phenotypes are known as censored records and their inclusion into genetic evaluations might lead to better inferences and breeding value predictions. Then, the objective was to compare prediction ability of models in which the phenotypic expression of age at the first calving (AFC) and days to calving (DC) were considered to be censored and uncensored in a Nellore cattle population. Age at first calving and days to calving were analyzed as following: uncensored animals (LM) penalization of 21 d (PLM) censored records simulated from truncated normal distributions (CLM) threshold-linear model in which censored records were handled as missing (TLM) or coded as the upper AFC/DC value within contemporary group (PTLM) and Weibull frailty hazard model (WM). Pearson correlations (PC), the percentage of the 10% best bulls in common (pTOP10%), accuracy of estimated breeding values (), and a cross-validation scheme were performed. Heritability estimates for AFC were 0.18, 0.12, 0.12, 0.17, 0.14, and 0.07 for LM, PLM, CLM, TLM, PTLM, and WM, respectively. PC and pTOP10% were higher among linear models and smaller between these models and WM. The models provided similar r of sire breeding values. Heritability estimates for DC were 0.03, 0.08, 0.06, 0.02, 0.07, and 0.10 for LM, PLM, CLM, TLM, PTLM, and WM, respectively. Strongly associated predictions were observed in CLM, PLM, PTLM, and WM. The highest coincidence levels of sires in the TOP10% were between CLM, PLM, and PTLM. The r of sire breeding values obtained applying CLM, PLM, PTLM, and WM were similar and higher than those obtained with LM and TLM. In terms of prediction ability, WM, PLM, TLM, and PTLM showed similar prediction performance for AFC. On the other hand, CLM, PLM, PTLM, and WM showed the similar prediction ability for DC Therefore, these models would be recommended to perform genetic evaluation of age at first calving and days to calving in this Nellore population.
Genetic parameter estimates for carcass traits and visual scores including or not genomic information1
Publisher: Oxford University Press (OUP)
Date: 05-2016
Abstract: The objective of this study was to determine whether visual scores used as selection criteria in Nellore breeding programs are effective indicators of carcass traits measured after slaughter. Additionally, this study evaluated the effect of different structures of the relationship matrix ( and ) on the estimation of genetic parameters and on the prediction accuracy of breeding values. There were 13,524 animals for visual scores of conformation (CS), finishing precocity (FP), and muscling (MS) and 1,753, 1,747, and 1,564 for LM area (LMA), backfat thickness (BF), and HCW, respectively. Of these, 1,566 animals were genotyped using a high-density panel containing 777,962 SNP. Six analyses were performed using multitrait animal models, each including the 3 visual scores and 1 carcass trait. For the visual scores, the model included direct additive genetic and residual random effects and the fixed effects of contemporary group (defined by year of birth, management group at yearling, and farm) and the linear effect of age of animal at yearling. The same model was used for the carcass traits, replacing the effect of age of animal at yearling with the linear effect of age of animal at slaughter. The variance and covariance components were estimated by the REML method in analyses using the numerator relationship matrix () or combining the genomic and the numerator relationship matrices (). The heritability estimates for the visual scores obtained with the 2 methods were similar and of moderate magnitude (0.23-0.34), indicating that these traits should response to direct selection. The heritabilities for LMA, BF, and HCW were 0.13, 0.07, and 0.17, respectively, using matrix and 0.29, 0.16, and 0.23, respectively, using matrix . The genetic correlations between the visual scores and carcass traits were positive, and higher correlations were generally obtained when matrix was used. Considering the difficulties and cost of measuring carcass traits postmortem, visual scores of CS, FP, and MS could be used as selection criteria to improve HCW, BF, and LMA. The use of genomic information permitted the detection of greater additive genetic variability for LMA and BF. For HCW, the high magnitude of the genetic correlations with visual scores was probably sufficient to recover genetic variability. The methods provided similar breeding value accuracies, especially for the visual scores.
Genetic and genomic analyses of testicular hypoplasia in Nellore cattle
Publisher: Public Library of Science (PLoS)
Date: 24-01-2019
Reaction norm for yearling weight in beef cattle using single-step genomic evaluation1
Publisher: Oxford University Press (OUP)
Date: 2018
DOI: 10.1093/JAS/SKX006
Association of ADIPOQ , OLR1 and PPARGC1A gene polymorphisms with growth and carcass traits in Nelore cattle
Publisher: Elsevier BV
Date: 06-2015
Polymorphism analysis in genes of the somatotropic axis in Nellore cattle selected for growth
Publisher: Elsevier BV
Date: 07-2014
DOI: 10.1016/J.GENE.2014.05.033
Abstract: The somatotropic axis consists of genes that are involved in muscular development. These genes are potential regions of study to identify possible QTL for economically important traits in beef cattle. The aim of this study was to verify the existence of GH1, POU1F1, and GHR polymorphisms in Nellore cattle to verify the influence of selection in these mutations and to analyse the association between molecular markers and body weight at different ages, yearling hip height, carcass fat thickness and loin eye area. Six hundred forty-five animals from the Centro APTA Bovinos de Corte, were genotyped by PCR-RFLP techniques. The association analyses were performed with general mixed models taking into consideration the effect of one marker, and other model taking into consideration interactions between two molecular markers. Only the molecular markers rs81109601 on GH1 and rs109136815 on GHR were polymorphic however, they were not found to be under selection. The association of the GHR rs109136815 marker and loin eye area was observed (p<0.05), as well as the effect of interaction between the markers and the female body weight at 550 days of age (p<0.04). The interaction effect should be considered in situations where the interactivity between two genes is known.
Linkage Disequilibrium-Based Inference of Genome Homology and Chromosomal Rearrangements Between Species
Publisher: Oxford University Press (OUP)
Date: 07-2020
Abstract: The aim of this study was to analyze the genomic homology between cattle (Bos taurus) and buffaloes (Bubalus bubalis) and to propose a rearrangement of the buffalo genome through linkage disequilibrium analyses of buffalo SNP markers referenced in the cattle genome assembly and also compare it to the buffalo genome assembly. A panel of bovine SNPs (single nucleotide polymorphisms) was used for hierarchical, non-hierarchical and admixture cluster analyses. Thus, the linkage disequilibrium information between markers of a specific panel of buffalo was used to infer chromosomal rearrangement. Haplotype ersity and imputation accuracy of the submetacentric chromosomes were also analyzed. The genomic homology between the species enabled us to use the bovine genome assembly to recreate a buffalo genomic reference by rearranging the submetacentric chromosomes. The centromere of the submetacentric chromosomes exhibited high linkage disequilibrium and low haplotype ersity. It allowed hypothesizing about chromosome evolution. It indicated that buffalo submetacentric chromosomes are a centric fusion of ancestral acrocentric chromosomes. The chronology of fusions was also suggested. Moreover, a linear regression between buffalo and cattle rearranged assembly and the imputation accuracy indicated that the rearrangement of the chromosomes was adequate. When using the bovine reference genome assembly, the rearrangement of the buffalo submetacentric chromosomes could be done by SNP BTA (chromosome of Bos taurus) calculations: shorter BTA (shorter arm of buffalo chromosome) was given as [(shorter BTA length – SNP position in shorter BTA)] and larger BTA length as [shorter BTA length + (larger BTA length – SNP position in larger BTA)]. Finally, the proposed linkage disequilibrium-based method can be applied to elucidate other chromosomal rearrangement events in other species with the possibility of better understanding the evolutionary relationship between their genomes.
Genetic association between body composition measured by ultrasound and visual scores in Brazilian Nelore cattle1
Publisher: Oxford University Press (OUP)
Date: 12-2012
Abstract: The objective of this study was to evaluate the genetic variability of body composition traits measured by ultrasound, growth traits, and visual scores as well as their genetic associations in Nelore cattle. A total of 9,765, 13,285, 13,061, 12,811, 3,484, 3,484, 3,483, and 3,303 records of weight at time of ultrasound measure (W550), 12th-13th rib LM area (LMA), backfat thickness (BF), rump fat thickness (RF), visual scores for body structure (BS), finishing precocity (FP), muscling (MS), and sheath and navel characteristics (SN), respectively, were used. The model included contemporary group (defined as year and season of birth, sex, and management group) as a fixed effect and age of dam at calving and age of the animal (linear and quadratic effects) as covariates. The direct additive genetic effect was included as a random effect. The analyses also included 46,157 observations of BW adjusted to 120 d. The (co)variance components were estimated by the restricted maximum likelihood method using a multitrait animal model. Heritability estimates for W550, LMA, BF, RF, BS, FP, MS, and SN were 0.37 ± 0.030, 0.33 ± 0.03, 0.24 ± 0.02, 0.28 ± 0.03, 0.24 ± 0.04, 0.38 ± 0.05, 0.29 ± 0.05, and 0.38 ± 0.06, respectively. The estimated genetic correlations between visual scores and LMA were moderate and positive, ranging from 0.37 to 0.44. Similar results were obtained for the estimated genetic correlations between FP and MS with fat thickness measures (BF and RF). Low genetic correlations were estimated between SN and BS and between SN and the body composition traits, indicating that selection for body composition traits and BS will not affect sheath and navel size. The estimated genetic correlations between weight adjusted to 120 d of age (W120) and W550 and BS were high (0.87 and 0.91) and moderate with LMA (0.49 and 0.55), FP (0.37 and 0.41), and MS (0.47 and 0.55). The visual scores and ultrasound-measured body composition traits have enough genetic variation for selection purposes in Nelore cattle. Selection based on visual scores for body structure, finishing precocity and muscling should lead to desired changes in body composition albeit much more slowly than direct selection on those traits measured by ultrasound. Selection for heavier BW at early ages should lead to favorable changes in yearling LM area and visual scores.
Sliding window haplotype approaches overcome single SNP analysis limitations in identifying genes for meat tenderness in Nelore cattle
Publisher: Springer Science and Business Media LLC
Date: 14-01-2019
Multitrait meta-analysis identified genomic regions associated with sexual precocity in tropical beef cattle1
Publisher: Oxford University Press (OUP)
Date: 21-07-2018
DOI: 10.1093/JAS/SKY289
Animal lifestyle affects acceptable mass limits for attached tags
Publisher: The Royal Society
Date: 27-10-2021
Abstract: Animal-attached devices have transformed our understanding of vertebrate ecology. To minimize any associated harm, researchers have long advocated that tag masses should not exceed 3% of carrier body mass. However, this ignores tag forces resulting from animal movement. Using data from collar-attached accelerometers on 10 erse free-ranging terrestrial species from koalas to cheetahs, we detail a tag-based acceleration method to clarify acceptable tag mass limits. We quantify animal athleticism in terms of fractions of animal movement time devoted to different collar-recorded accelerations and convert those accelerations to forces (acceleration × tag mass) to allow derivation of any defined force limits for specified fractions of any animal's active time. Specifying that tags should exert forces that are less than 3% of the gravitational force exerted on the animal's body for 95% of the time led to corrected tag masses that should constitute between 1.6% and 2.98% of carrier mass, depending on athleticism. Strikingly, in four carnivore species encompassing two orders of magnitude in mass ( ca 2–200 kg), forces exerted by ‘3%' tags were equivalent to 4–19% of carrier body mass during moving, with a maximum of 54% in a hunting cheetah. This fundamentally changes how acceptable tag mass limits should be determined by ethics bodies, irrespective of the force and time limits specified.
Factors influencing prey capture success and profitability in Australasian gannets (Morus serrator)
Publisher: The Company of Biologists
Date: 2020
DOI: 10.1242/BIO.047514
Abstract: Knowledge of the factors influencing foraging efficiency in top predators can provide insights into the effects of environmental variability on their populations. Seabirds are important marine predators foraging in a highly temporally and spatially variable environment. While numerous studies have focussed on search time and its effects on foraging energetics in seabirds, relatively little is known of the factors influencing capture success and prey profitability in these predators. In the present study, animal-borne cameras were used to investigate the chase durations, capture success, handling durations and profitability of prey consumed by Australasian gannets (Morus serrator) (n=95) from two breeding colonies in south-eastern Australia exposed to different oceanographic conditions. Capture success was generally lower when in iduals foraged alone. However, foraging in multi-species groups and in high prey densities increased chase time, while larger prey elicited longer handling times. While prey type influenced profitability, high prey density and foraging in multispecies groups was found to lower prey profitability due to increased time expenditure. While previous studies have found group foraging reduces search time, the increased profitability explains why some animals may favour solitary foraging. Therefore future studies should combine search time and the currently found factors.
Prediction of meat quality traits in Nelore cattle by near-infrared reflectance spectroscopy1
Publisher: Oxford University Press (OUP)
Date: 14-07-2018
DOI: 10.1093/JAS/SKY284
Study of whole genome linkage disequilibrium in Nellore cattle
Publisher: Springer Science and Business Media LLC
Date: 05-05-2013
Abstract: Knowledge of the linkage disequilibrium (LD) between markers is important to establish the number of markers necessary for association studies and genomic selection. The objective of this study was to evaluate the extent of LD in Nellore cattle using a high density SNP panel and 795 genotyped steers. After data editing, 446,986 SNPs were used for the estimation of LD, comprising 2508.4 Mb of the genome. The mean distance between adjacent markers was 4.90 ± 2.89 kb. The minor allele frequency (MAF) was less than 0.20 in a considerable proportion of SNPs. The overall mean LD between marker pairs measured by r 2 and |D'| was 0.17 and 0.52, respectively. The LD (r 2 ) decreased with increasing physical distance between markers from 0.34 (1 kb) to 0.11 (100 kb). In contrast to this clear decrease of LD measured by r 2 , the changes in |D'| indicated a less pronounced decline of LD. Chromosomes BTA1, BTA27, BTA28 and BTA29 showed lower levels of LD at any distance between markers. Except for these four chromosomes, the level of LD (r 2 ) was higher than 0.20 for markers separated by less than 20 kb. At distances 3 kb, the level of LD was higher than 0.30. The LD (r 2 ) between markers was higher when the MAF threshold was high (0.15), especially when the distance between markers was short. The level of LD estimated for markers separated by less than 30 kb indicates that the High Density Bovine SNP BeadChip will likely be a suitable tool for prediction of genomic breeding values in Nellore cattle.
Genetic associations between carcass traits measured by real-time ultrasound and scrotal circumference and growth traits in Nelore cattle1
Publisher: Oxford University Press (OUP)
Date: 2010
Abstract: The aim of the present study was to evaluate the genetic correlations among real-time ultrasound carcass, BW, and scrotal circumference (SC) traits in Nelore cattle. Carcass traits, measured by real-time ultrasound of the live animal, were recorded from 2002 to 2004 on 10 farms across 6 Brazilian states on 2,590 males and females ranging in age from 450 to 599 d. Ultrasound records of LM area (LMA) and backfat thickness (BF) were obtained from cross-sectional images between the 12th and 13th ribs, and rump fat thickness (RF) was measured between the hook and pin bones over the junction between gluteus medius and biceps femoris muscles. Also, BW (n = 22,778) and SC (n = 5,695) were recorded on animals born between 1998 and 2003. The BW traits were 120, 210, 365, 450, and 550-d standardized BW (W120, W210, W365, W450, and W550), plus BW (WS) and hip height (HH) on the ultrasound scanning date. The SC traits were 365-, 450-, and 550-d standardized SC (SC365, SC450, and SC550). For the BW and SC traits, the database used was from the Nelore Breeding Program-Nelore Brazil. The genetic parameters were estimated with multivariate animal models and REML. Estimated genetic correlations between LMA and other traits were 0.06 (BF), -0.04 (RF), 0.05 (HH), 0.58 (WS), 0.53 (W120), 0.62 (W210), 0.67 (W365), 0.64 (W450 and W550), 0.28 (SC365), 0.24 (SC450), and 0.00 (SC550). Estimated genetic correlations between BF and with other traits were 0.74 (RF), -0.32 (HH), 0.19 (WS), -0.03 (W120), -0.10 (W210), 0.04 (W365), 0.01 (W450), 0.06 (W550), 0.17 (SC365 and SC450), and -0.19 (SC550). Estimated genetic correlations between RF and other traits were -0.41 (HH), -0.09 (WS), -0.13 (W120), -0.09 (W210), -0.01 (W365), 0.02 (W450), 0.03 (W550), 0.05 (SC365), 0.11 (SC450), and -0.18 (SC550). These estimates indicate that selection for carcass traits measured by real-time ultrasound should not cause antagonism in the genetic improvement of SC and BW traits. Also, selection to increase HH might decrease subcutaneous fat as correlated response. Therefore, to obtain animals suited to specific tropical production systems, carcass, BW, and SC traits should be considered in selection programs.
Selection strategies for dairy buffaloes: economic and genetic consequences
Publisher: Wiley
Date: 13-03-2012
DOI: 10.1111/J.1439-0388.2012.00992.X
Abstract: Buffaloes are generally raised in Brazil without milk-recording programs, and thus without genetic evaluations of any of their traits. This study evaluated the economic impacts of three different selection strategies on buffalo populations and the evolution of genetic trends, genetic variances and inbreeding coefficients resulting from each of them. The selection strategies used were as follows: (i) random selection (ii) phenotypic selection and (iii) progeny testing (PT). As the numbers of herds enrolled in milk-recording programs increased, phenotypic selection and PT strategies increased both monetary benefits and genetic trends. The extra costs of implementing milk recording (MR) and PT procedures were exceeded by the income resulting from better buffalo performance. Progeny testing is known to result in beneficial genetic trends and the use of artificial insemination promoted better distributions of genetic material into herds that were not enrolled in milk-recording programs. Phenotypic selection and PT increased mean milk production--a key factor in profitability. Inbreeding levels remained stable with phenotypic selection, even as the numbers of MR herds increased. Increases in the numbers of sires that were evaluated reduced the mean inbreeding coefficient in PT. Increasing the number of herds enrolled in milk-recording programs resulted in increased numbers of sires needed for PT, but this did not increase the inbreeding coefficient. In summary, phenotypic selection and PT strategies appear to be economically viable for buffalo husbandry in south-eastern Brazil under current (2007-2008) economic conditions and should be encouraged.
Genome-wide association study for growth traits in Nelore cattle
Publisher: Elsevier BV
Date: 2018
Genome-wide association between single nucleotide polymorphisms with beef fatty acid profile in Nellore cattle using the single step procedure
Publisher: Springer Science and Business Media LLC
Date: 09-03-2016
Association between single-nucleotide polymorphisms and milk production traits in buffalo
Publisher: Genetics and Molecular Research
Date: 2014
Principal component analysis of breeding values for growth and reproductive traits and genetic association with adult size in beef cattle1
Publisher: Oxford University Press (OUP)
Date: 12-2016
Abstract: Principal component analysis was applied to evaluate the variability and relationships among univariate breeding values predicted for 9 weaning and yearling traits, as well as suggest functions of the traits that would promote a particular breeding objective. Phenotypic and pedigree information from 600,132 Nelore animals was used. Genetic parameters and breeding values were obtained from univariate analyses of birth to weaning weight gain weaning to yearling weight gain conformation, finishing precocity, and muscling scores at weaning and at yearling and yearling scrotal circumference. The principal component mainly associated with maturity (precocious vs. late animals) was used as a pseudophenotype in bivariate analyses with either adult weight or adult height of cows. Direct heritability estimates ranging from 0.19 ± 0.01 to 0.41 ± 0.01 indicate that these 9 traits are all heritable to varying degrees. Correlations between the breeding values for the various traits ranged from 0.14 to 0.88. Principal component analysis was performed on the standardized breeding values. The first 3 principal components attained the Kaiser criterion, retaining 48.06%, 18.03%, and 12.97% of the total breeding value variance, respectively. The first component was characterized by positive coefficients for all traits. The second component contrasted weaning traits with yearling traits. The third component represented a contrast between late maturity animals (better for weight gain and conformation) and early maturity animals (better for finishing precocity, muscling, and scrotal circumference). Thus, the first 3 components represent 3 different potential selection criteria. Selecting for the first principal component would identify animals with positive breeding values for all studied traits. The second principal component may be used to identify animals with higher or lower maturation rates (precocity). Animals with negative values in the third principal component are regarded as early maturing. Genetic correlations between maturity (third principal component) with adult weight and adult height were 0.19 ± 0.02 and 0.32 ± 0.02, respectively. These results showed that the weaning and yearling bovine maturity is genetically associated with the adult size of the cows used in reproduction.
Genome-wide association study provides strong evidence of genes affecting the reproductive performance of Nellore beef cows
Publisher: Public Library of Science (PLoS)
Date: 31-05-2017
Prediction of genomic breeding values for reproductive traits in Nellore heifers
Publisher: Elsevier BV
Date: 02-2019
DOI: 10.1016/J.THERIOGENOLOGY.2018.10.014
Abstract: The objective of this study was to assess the accuracy of genomic predictions for female reproductive traits in Nellore cattle. A total of 1853 genotyped cows and 305,348 SNPs were used for genomic selection analyses. GBLUP, BAYESCπ, and IBLASSO were applied to estimate SNP effects. The pseudo-phenotypes used as dependent variables were: observed phenotype (PHEN), adjusted phenotype (CPHEN), estimated breeding value (EBV), and deregressed estimated breeding value (DEBV). Predictive abilities were assessed by the average correlation between CPHEN and genomic estimated breeding value (GEBV) and by the average correlation between DEBV and GEBV in the validation population. Regression coefficients of pseudo-phenotypes on GEBV in the validation population were indicators of prediction bias in GEBV. BAYESCπ showed higher predictive ability to estimate SNP effects and GEBV for all traits.
Related Organisations
University Of Aberdeen
Location: United Kingdom of Great Britain and Northern Ireland
Universidade Estadual Paulista (UNESP), Faculdade De Ciências Agrárias E Veterinárias, Jaboticabal
Location: Brazil
Related Funding Activities
Linkage Projects - Grant ID: LP160100329
Start Date: 10-2016
End Date: 07-2021
Amount: $388,704.00
Funder: Australian Research Council
View Funded Activity