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1.
Genomics ; 113(3): 1386-1395, 2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-33716185

RESUMO

We conducted analysis to estimate genetic parameters and to identify genomic regions and candidate genes affecting direct and maternal effects of preweaning calf mortality (PWM) in Nellore cattle. Phenotypic records of 67,196 animals, and 8443 genotypes for 410,936 SNPs were used. Analysis were performed through the weighted single-step GBLUP approach and considering a threshold animal model via Bayesian Inference. Direct and maternal heritability estimates were of 0.2143 ± 0.0348 and 0.0137 ± 0.0066, respectively. The top 10 genomic regions accounted for 13.61 and 14.23% of the direct and maternal additive genetic variances and harbored a total of 63 and 91 positional candidate genes, respectively. Two overlapping regions on BTA2 were identified for both direct and maternal effects. Candidate genes are involved in biological mechanisms i.e. embryogenesis, immune response, feto-maternal communication, circadian rhythm, hormone alterations, myometrium adaptation, and milk secretion, which are critical for the successful calf growth and survival during preweaning period.


Assuntos
Genoma , Herança Materna , Animais , Teorema de Bayes , Bovinos , Feminino , Estudo de Associação Genômica Ampla/veterinária , Genômica , Fenótipo , Polimorfismo de Nucleotídeo Único
2.
Anim Genet ; 52(1): 32-46, 2021 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-33191532

RESUMO

This study aimed to assess the predictive ability of different machine learning (ML) methods for genomic prediction of reproductive traits in Nellore cattle. The studied traits were age at first calving (AFC), scrotal circumference (SC), early pregnancy (EP) and stayability (STAY). The numbers of genotyped animals and SNP markers available were 2342 and 321 419 (AFC), 4671 and 309 486 (SC), 2681 and 319 619 (STAY) and 3356 and 319 108 (EP). Predictive ability of support vector regression (SVR), Bayesian regularized artificial neural network (BRANN) and random forest (RF) were compared with results obtained using parametric models (genomic best linear unbiased predictor, GBLUP, and Bayesian least absolute shrinkage and selection operator, BLASSO). A 5-fold cross-validation strategy was performed and the average prediction accuracy (ACC) and mean squared errors (MSE) were computed. The ACC was defined as the linear correlation between predicted and observed breeding values for categorical traits (EP and STAY) and as the correlation between predicted and observed adjusted phenotypes divided by the square root of the estimated heritability for continuous traits (AFC and SC). The average ACC varied from low to moderate depending on the trait and model under consideration, ranging between 0.56 and 0.63 (AFC), 0.27 and 0.36 (SC), 0.57 and 0.67 (EP), and 0.52 and 0.62 (STAY). SVR provided slightly better accuracies than the parametric models for all traits, increasing the prediction accuracy for AFC to around 6.3 and 4.8% compared with GBLUP and BLASSO respectively. Likewise, there was an increase of 8.3% for SC, 4.5% for EP and 4.8% for STAY, comparing SVR with both GBLUP and BLASSO. In contrast, the RF and BRANN did not present competitive predictive ability compared with the parametric models. The results indicate that SVR is a suitable method for genome-enabled prediction of reproductive traits in Nellore cattle. Further, the optimal kernel bandwidth parameter in the SVR model was trait-dependent, thus, a fine-tuning for this hyper-parameter in the training phase is crucial.


Assuntos
Bovinos/genética , Aprendizado de Máquina , Modelos Genéticos , Reprodução/genética , Animais , Brasil , Feminino , Genômica , Fenótipo , Polimorfismo de Nucleotídeo Único , Gravidez
3.
Animal ; 11(12): 2113-2119, 2017 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-28534726

RESUMO

The aim of the present study was to evaluate the prediction ability of models that cope with longevity phenotypic expression as uncensored and censored in Nellore cattle. Longevity was defined as the difference between the dates of last weaned calf and cow birth. There were information of 77 353 females, being 61 097 cows with uncensored phenotypic information and 16 256 cows with censored records. These data were analyzed considering three different models: (1) Gaussian linear model (LM), in which only uncensored records were considered; and two models that consider both uncensored and censored records: (2) Censored Gaussian linear model (CLM); and (3) Weibull frailty hazard model (WM). For the model prediction ability comparisons, the data set was randomly divided into training and validation sets, containing 80% and 20% of the records, respectively. There were considered 10 repetitions applying the following restrictions: (a) at least three animals per contemporary group in the training set; and (b) sires with more than 10 progenies with uncensored records (352 sires) should have daughters in the training and validation sets. The variance components estimated using the whole data set in each model were used as true values in the prediction of breeding values of the animals in the training set. The WM model showed the best prediction ability, providing the lowest χ 2 average and the highest number of sets in which a model had the smallest value of χ 2 statistics. The CLM and LM models showed prediction abilities 2.6% and 3.7% less efficient than WM, respectively. In addition, the accuracies of sire breeding values for LM and CLM were lower than those obtained for WM. The percentages of bulls in common, considering only 10% of sires with the highest breeding values, were around 75% and 54%, respectively, between LM-CLM and LM-WM models, considering all sires, and 75% between LM-CLM and LM-WM, when only sires with more than 10 progenies with uncensored records were taken into account. These results are indicative of reranking of animals in terms of genetic merit between LM, CLM and WM. The model in which censored records of longevity were excluded from the analysis showed the lowest prediction ability. The WM provides the best predictive performance, therefore this model would be recommended to perform genetic evaluation of longevity in this population.


Assuntos
Bovinos/fisiologia , Longevidade/genética , Longevidade/fisiologia , Animais , Cruzamento , Feminino , Modelos Lineares , Modelos Biológicos , Parto , Gravidez , Modelos de Riscos Proporcionais , Reprodução , Desmame
4.
Genet Mol Res ; 14(3): 11133-44, 2015 Sep 22.
Artigo em Inglês | MEDLINE | ID: mdl-26400344

RESUMO

The objective of this study was to evaluate associations between single nucleotide polymorphism (SNP) markers and carcass traits measured postmortem in Nellore cattle. Records of loin eye area (LEA) and backfat thickness (BF) from 740 males and records of hot carcass weight (HCW) from 726 males were analyzed. All of the animals were genotyped using the BovineHD BeadChip. Association analyses were performed by the restricted maximum likelihood method that considered one SNP at a time. Significant SNPs were identified on chromosomes 2 and 6 for LEA and on chromosomes 7, 1, and 2 for BF. For HCW, associations with SNPs were found on chromosomes 13, 14, and 28, in addition to genome regions that were directly related to this trait, such as the EFCAB8 and VSTM2L genes, and to bone development (RHOU). Some SNPs were located in very close proximity to genes involved in basal metabolism (BLCAP, NNAT, CTNNBL1, TGM2, and LOC100296770) and the immune system (BPI).


Assuntos
Carne/normas , Animais , Peso Corporal/genética , Bovinos/genética , Bovinos/crescimento & desenvolvimento , Qualidade dos Alimentos , Frequência do Gene , Marcadores Genéticos , Estudo de Associação Genômica Ampla , Genótipo , Masculino , Músculo Esquelético/fisiologia , Polimorfismo de Nucleotídeo Único , Gordura Subcutânea/anatomia & histologia
5.
Arq. bras. med. vet. zootec ; 67(3): 732-740, May-Jun/2015. tab, graf
Artigo em Inglês | LILACS | ID: lil-753937

RESUMO

The aim of this study was to compare the following four genetic groups of hair sheep: Santa Inês (SI), Morada Nova (MN), Brazilian Somali (BS), and the F1 1/2Dorper x 1/2Morada Nova crossbreed on traits related to growth and parasitic infection. Thirty-three male lambs of the same age and of simple birth, under the same pre-weaning management conditions were used in the experiment. After weaning the animals were housed in a completely randomized design in paddocks made of Panicum maximum cv. Tanzania. Along the course of the research, the performance of the four groups of sheep was observed to be negatively affected by gastrointestinal parasites, but there was a genotype effect to the average daily weight gain (ADWG), where the SI and F1 genotypes presented higher values. The effects of genotype, time and genotype x time interaction were significant in weight and corporal score (CS) measurements. The BS lambs had the highest CS values throughout the experiment despite not presenting greater weight gain when compared to the SI and F1 breeds. There were also significant effects of time and genotype x time interaction for packed cell volume (PCV) and FAMACHA© score (FAM) and only the time effect was significant in the total number of eggs per gram (EPG) and total plasma protein (TPP). The MN lambs showed higher PCV values and unlike the other groups, presented a FAMACHA© score below 3 and PCV above 23% even having a higher EPG tendency, especially in the initial phase, indicating a possible higher resilience to infection caused by gastrointestinal parasites.


O objetivo deste estudo foi comparar quatro grupos genéticos de ovinos: Santa Inês (SI), Somalis Brasileira (SB), Morada Nova (MN) e 1/2 Dorper - 1/2 Morada Nova (F1) quanto às características de crescimento e de infecção parasitária. Trinta e três cordeiros machos, de mesma idade, nascidos de parto simples e submetidos às mesmas condições de manejo pré-desmame foram utilizados no experimento. Após o desmame, os animais foram alojados em piquetes de capim Panicum maximum cv. Tanzânia, em um sistema rotativo de pastejo sob um delineamento inteiramente ao acaso. Os resultados mostraram que, ao longo do experimento, o desempenho ponderal dos quatro grupos genéticos foi negativamente afetado pela infecção por endoparasitas, mas o efeito de genótipo foi significativo para ganho de peso médio diário, e os grupos SI e F1 apresentaram melhores médias. O efeito do genótipo, tempo e interação genótipo x tempo foi significativo para o peso e o escore corporal. Os cordeiros da raça SB apresentaram maiores escores corporais ao longo do experimento, apesar do menor ganho de peso quando comparados aos dos grupos SI e F1. Houve efeito significativo do tempo e da interação genótipo x tempo para o hematócrito e para o grau FAMACHA©. Somente efeito do tempo foi verificado para as características OPG e proteína plasmática total. Os cordeiros da raça Morada Nova, ao contrário dos demais grupos, mantiveram o grau FAMACHA© inferior a 3 e hematócrito inferior a 23%, mesmo com tendência de maior OPG, principalmente na fase inicial, indicando uma possível maior capacidade de adaptação à infecção por endoparasitas.


Assuntos
Animais , Haemonchus/parasitologia , Ovinos/crescimento & desenvolvimento , Ovinos/parasitologia , Strongyloides/parasitologia , Trichostrongylus/parasitologia , Contagem de Ovos de Parasitas/veterinária , Pastagens/análise , Pesos e Medidas Corporais/veterinária
6.
Arq. bras. med. vet. zootec ; 65(4): 1208-1216, Aug. 2013. tab
Artigo em Inglês | LILACS | ID: lil-684481

RESUMO

The aim of this study was to compare four genetic groups of sheep on the carcass and meat quality traits. Thirty-three contemporary and unrelated male lambs, all of single birth were used in the experiment, being thirteen from the Santa Inês (SI) breed, seven from the Brazilian Somali breed (BS), six from the Morada Nova (MN) breed and seven from the ½ Dorper - ½ Morada Nova (F1) crossbreed. The genotypes SI, BS and F1 presented similar performances in relation to hot and cold carcass weights, which values were 10.76±0.53kg and 10.46±0.52kg for SI, 9.20±0.73kg and 8.99±0.71kg for BS, and 9.35±0.73kg and 9.13±0.71kg for F1, respectively. The BS had a better hot carcass yield (47.10±0.88%) and cold carcass yield (46.00±0.87%). Better carcass conformation was observed in SI and F1 (2.73±0.12 and 2.50±0.17, respectively) while the BS presented a better finishing (3.29±0.20). The average for the rib eye area (REA) was 9.94±0.49cm², 8.66±0.67cm², 7.18±0.72cm² and 9.8±0.67cm², and for the carcass compactness index (CCI) it was 0.17±0.01kg/cm, 0.17±0.01kg/cm, 0.11±0.01kg/cm and 0.16±0,01kg/cm, for SI, SB, MN and F1, respectively. There were no significant differences between SI, BS and F1 regarding REA and CCI. Although, in general, the MN presented a relatively lower performance than the other genotypes, this breed had similar carcass yields and fat thickness when compared to SI and F1 and similar conformation and REA in comparison to the BS. Regarding meat quality, no differences were observed between genotypes, except for redness and cooking losses. It is concluded that no one group had a higher or lower performance in all traits analyzed. Moreover, for the management conditions employed in this study, there was evidence of greater specialization in meat production for genotypes SI, BS and F1 when compared to MN, although there are no substantial differences between the four groups regarding meat quality.


O objetivo deste estudo foi comparar quatro grupos genéticos de ovinos quanto às características de carcaça e de qualidade da carne. Trinta e três cordeiros, contemporâneos, nascidos de parto simples e sem relação de parentesco, foram utilizados no experimento, sendo 13 da raça Santa Inês (SI), sete da raça Somalis Brasileira (SB), seis da raça Morada Nova (MN) e sete ½ Dorper - ½ Morada Nova (F1). Os genótipos SI, SB e F1 apresentaram desempenhos similares quanto ao peso das carcaças quente e fria, cujos valores foram 10,76±0,53kg e 10,46±0,52kg para o SI, 9,20±0,73kg e 8,99±0,71kg para o SB, 9,35±0,73kg e 9,13±0,71kg para o F1, respectivamente. A raça SB apresentou melhor rendimento de carcaça quente (47,10 ±0,88%) e de carcaça fria (46,00±0,87%). Os genótipos SI e F1 apresentaram melhores conformações (2,73±0,12 e 2,50±0,17, respectivamente), enquanto o SB apresentou melhor acabamento (3,29±0,20). As médias para área de olho de lombo (AOL) foram 9,94±0,49cm², 8,66±0,67cm², 7,18±0,72cm² e 9,8±0,67cm² e para o índice de compacidade da carcaça (ICC) foram 0,17±0,01kg/cm, 0,17±0,01kg/cm, 0,11±0,01kg/cm e 0,16±0,01kg/cm, para SI, SB, MN e F1, respectivamente. Não houve diferença significativa entre os genótipos SI, SB e F1 quanto à AOL e ao ICC. Apesar de, no geral, a raça MN apresentar desempenho relativamente inferior aos demais genótipos quanto às características de carcaça analisadas, essa raça apresentou rendimentos de carcaça e espessura de gordura similar ao SI e F1 e conformação e AOL similar ao SB. Não houve um grupo superior ou inferior para todas as características analisadas. Por outro lado, para as condições de manejo empregadas neste estudo, evidenciou-se maior especialização para produção de carne dos genótipos SI, SB e F1 em relação ao grupo MN. Não houve diferenças importantes entre os diferentes genótipos quanto à qualidade da carne.


Assuntos
Animais , Qualidade dos Alimentos , Genótipo , Carne , Ovinos
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