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1.
Genet Sel Evol ; 51(1): 37, 2019 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-31269896

RESUMO

BACKGROUND: This study aimed at identifying genomic regions that underlie genetic variation of worm egg count, as an indicator trait for parasite resistance in a large population of Australian sheep, which was genotyped with the high-density 600 K Ovine single nucleotide polymorphism array. This study included 7539 sheep from different locations across Australia that underwent a field challenge with mixed gastrointestinal parasite species. Faecal samples were collected and worm egg counts for three strongyle species, i.e. Teladorsagia circumcincta, Haemonchus contortus and Trichostrongylus colubriformis were determined. Data were analysed using genome-wide association studies (GWAS) and regional heritability mapping (RHM). RESULTS: Both RHM and GWAS detected a region on Ovis aries (OAR) chromosome 2 that was highly significantly associated with parasite resistance at a genome-wise false discovery rate of 5%. RHM revealed additional significant regions on OAR6, 18, and 24. Pathway analysis revealed 13 genes within these significant regions (SH3RF1, HERC2, MAP3K, CYFIP1, PTPN1, BIN1, HERC3, HERC5, HERC6, IBSP, SPP1, ISG20, and DET1), which have various roles in innate and acquired immune response mechanisms, as well as cytokine signalling. Other genes involved in haemostasis regulation and mucosal defence were also detected, which are important for protection of sheep against invading parasites. CONCLUSIONS: This study identified significant genomic regions on OAR2, 6, 18, and 24 that are associated with parasite resistance in sheep. RHM was more powerful in detecting regions that affect parasite resistance than GWAS. Our results support the hypothesis that parasite resistance is a complex trait and is determined by a large number of genes with small effects, rather than by a few major genes with large effects.


Assuntos
Enteropatias Parasitárias/veterinária , Doenças dos Ovinos/genética , Doenças dos Ovinos/parasitologia , Animais , Austrália , Mapeamento Cromossômico/veterinária , Resistência à Doença/genética , Fezes/parasitologia , Estudo de Associação Genômica Ampla/veterinária , Hereditariedade , Enteropatias Parasitárias/genética , Ovinos/genética
2.
Genet Sel Evol ; 51(1): 34, 2019 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-31262251

RESUMO

BACKGROUND: Milk quality in dairy cattle is routinely assessed via analysis of mid-infrared (MIR) spectra; this approach can also be used to predict the milk's cheese-making properties (CMP) and composition. When this method of high-throughput phenotyping is combined with efficient imputations of whole-genome sequence data from cows' genotyping data, it provides a unique and powerful framework with which to carry out genomic analyses. The goal of this study was to use this approach to identify genes and gene networks associated with milk CMP and composition in the Montbéliarde breed. RESULTS: Milk cheese yields, coagulation traits, milk pH and contents of proteins, fatty acids, minerals, citrate, and lactose were predicted from MIR spectra. Thirty-six phenotypes from primiparous Montbéliarde cows (1,442,371 test-day records from 189,817 cows) were adjusted for non-genetic effects and averaged per cow. 50 K genotypes, which were available for a subset of 19,586 cows, were imputed at the sequence level using Run6 of the 1000 Bull Genomes Project (comprising 2333 animals). The individual effects of 8.5 million variants were evaluated in a genome-wide association study (GWAS) which led to the detection of 59 QTL regions, most of which had highly significant effects on CMP and milk composition. The results of the GWAS were further subjected to an association weight matrix and the partial correlation and information theory approach and we identified a set of 736 co-associated genes. Among these, the well-known caseins, PAEP and DGAT1, together with dozens of other genes such as SLC37A1, ALPL, MGST1, SEL1L3, GPT, BRI3BP, SCD, GPAT4, FASN, and ANKH, explained from 12 to 30% of the phenotypic variance of CMP traits. We were further able to identify metabolic pathways (e.g., phosphate and phospholipid metabolism and inorganic anion transport) and key regulator genes, such as PPARA, ASXL3, and bta-mir-200c that are functionally linked to milk composition. CONCLUSIONS: By using an approach that integrated GWAS with network and pathway analyses at the whole-genome sequence level, we propose candidate variants that explain a substantial proportion of the phenotypic variance of CMP traits and could thus be included in genomic evaluation models to improve milk CMP in Montbéliarde cows.


Assuntos
Bovinos/genética , Queijo , Estudo de Associação Genômica Ampla/veterinária , Leite/química , Animais , Simulação por Computador , Conjuntos de Dados como Assunto , Feminino , Regulação da Expressão Gênica , Redes Reguladoras de Genes , Masculino , Locos de Características Quantitativas , Sequenciamento Completo do Genoma/veterinária
3.
J Anim Sci ; 97(8): 3253-3261, 2019 Jul 30.
Artigo em Inglês | MEDLINE | ID: mdl-31150538

RESUMO

Porcine reproductive and respiratory syndrome virus (PRRSV) is an economically important pathogen that continues to threaten swine industry sustainability. The complexity and high genetic diversity of PRRSV has prevented vaccines from conferring adequate protection against disease outbreaks. Genome-wide association analyses of PRRSV experimentally infected pigs representing two genetic lines (n = 174 to 176) revealed two major genomic regions accounting for ~1.2% of the genetic variation in PRRSV-specific antibody level in serum or lung. The major region for serum antibody was mapped to SSC7 near the SLAII complex, which has also been implicated in susceptibility to other swine viral pathogens. Haplotype substitution analysis uncovered potential DQB1 haplotypes associated with divergent effects. A novel major region for lung antibody was mapped to the proximal end of SSC17 with the top SNP overlapping two genes, PRAG1 and LONRF1. Sequencing LONRF1 uncovered polymorphisms within the coding region that may play a role in regulating PRRSV-specific antibody production in lung tissue following PRRSV infection. These data implicate novel host genomic regions (SSC17) that influence PRRSV-specific immune response as well as a common region (SSC7) potentially involved in susceptibility to multiple viral pathogens.


Assuntos
Anticorpos Antivirais/genética , Suscetibilidade a Doenças/veterinária , Estudo de Associação Genômica Ampla/veterinária , Genoma/genética , Síndrome Respiratória e Reprodutiva Suína/imunologia , Vírus da Síndrome Respiratória e Reprodutiva Suína/imunologia , Animais , Anticorpos Antivirais/sangue , Feminino , Variação Genética , Genética Populacional , Haplótipos , Imunidade Humoral , Pulmão/imunologia , Pulmão/virologia , Masculino , Fenótipo , Síndrome Respiratória e Reprodutiva Suína/virologia , Distribuição Aleatória , Suínos
4.
J Dairy Sci ; 102(8): 7237-7247, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31155255

RESUMO

Relatedness between reference and test animals has an important effect on the reliability of genomic prediction for test animals. Because genomic prediction has been widely applied in practical cattle breeding and bulls have been selected according to genomic breeding value without progeny testing, the sires or grandsires of candidates might not have phenotypic information and might not be in the reference population when the candidates are selected. The objective of this study was to investigate the decreasing trend of the reliability of genomic prediction given distant reference populations, using genomic best linear unbiased prediction (GBLUP) and Bayesian variable selection models with or without including the quantitative trait locus (QTL) markers detected from sequencing data. The data used in this study consisted of 22,242 bulls genotyped using the 54K SNP array from EuroGenomics. Among them, 1,444 Danish bulls born from 2006 to 2010 were selected as test animals. Different reference populations with varying relationships to test animals were created according to pedigree-based relationships. The reference individuals having a relationship with one or more test animals higher than 0.4 (scenario ρ < 0.4), 0.2 (ρ < 0.2), or 0.1 (ρ < 0.1, where ρ = relationship coefficient) were removed from reference sets; these represented the distance between reference and test animals being 2 generations, 3 generations, and 4 generations, respectively. Imputed whole-genome sequencing data of bulls from Denmark were used to conduct a genome-wide association study (GWAS). A small number of significant variants (QTL markers) from the GWAS were added to the array data. To compare the effects of different models, the basic GBLUP model, a Bayesian selection variable model, a GBLUP model with 2 components of genetic effects, and a Bayesian model with pooled array data and QTL markers were used for estimating genomic estimated breeding values (GEBV) of test animals. The reliability of genomic prediction decreased when the test animals were more generations away from the reference population. The reliability of genomic prediction was 0.461 for 1 generation away and 0.396 for 3 generations away, with the same number of individuals in the reference set, using a GBLUP model with chip markers only. The results showed that using the Bayesian method and QTL markers improved the reliability of genomic prediction in all scenarios of relationship between test and reference animals, in a range of 1.3% and 65.1% (4 generations away with only 841 individuals in the reference set). However, most gains were for predictions of milk yield and fat yield. There was little improvement for predictions of protein yield and mastitis, and no improvement for prediction of fertility, except for scenario ρ < 0.1, in which there was a large improvement for predictions of all traits. On the other hand, models including more than 10% polygenic effect decreased prediction reliability when the relationship between test and reference animals was distant.


Assuntos
Teorema de Bayes , Bovinos/genética , Estudo de Associação Genômica Ampla/veterinária , Mastite Bovina/genética , Leite/metabolismo , Locos de Características Quantitativas/genética , Animais , Cruzamento , Dinamarca , Feminino , Fertilidade/genética , Marcadores Genéticos/genética , Genômica , Genótipo , Masculino , Herança Multifatorial/genética , Linhagem , Fenótipo , Reprodutibilidade dos Testes
5.
J Dairy Sci ; 102(8): 7263-7276, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31155265

RESUMO

Genetic effects on milk production traits in dairy cattle might change during lactation. However, most genome-wide association studies (GWAS) for milk production traits assume that genetic effects are constant during lactation. This assumption might lead to missing these quantitative trait loci (QTL) whose effects change during lactation. This study aimed to screen the whole genome specifically for QTL whose effects change during lactation. For this purpose, 4 different GWAS approaches were performed using test-day milk protein content records: (1) separate GWAS for specific lactation stages, (2) GWAS for estimated Wilmink lactation curve parameters, (3) a GWAS using a repeatability model where SNP effects are assumed constant during lactation, and (4) a GWAS for genotype by lactation stage interaction using a repeatability model and accounting for changing genetic effects during lactation. Separate GWAS for specific lactation stages suggested that the detection power greatly differs between lactation stages and that genetic effects of some QTL change during lactation. The GWAS for estimated Wilmink lactation curve parameters detected many chromosomal regions for Wilmink parameter a (protein content level), whereas 2 regions for Wilmink parameter b (decrease in protein content toward nadir) and no regions for Wilmink parameter c (increase in protein content after nadir) were detected. Twenty chromosomal regions were detected with effects on milk protein content; however, there was no evidence that their effects changed during lactation. For 5 chromosomal regions located on chromosomes 3, 9, 10, 14, and 27, significant evidence was observed for a genotype by lactation stage interaction and thus their effects on milk protein content changed during lactation. Three of these 5 regions were only identified using a GWAS for genotype by lactation stage interaction. Our study demonstrated that GWAS for genotype by lactation stage interaction offers new possibilities to identify QTL involved in milk protein content. The performed approaches can be applied to other milk production traits. Identification of QTL whose genetic effects change during lactation will help elucidate the genetic and biological background of milk production.


Assuntos
Bovinos/genética , Estudo de Associação Genômica Ampla/veterinária , Proteínas do Leite/metabolismo , Polimorfismo de Nucleotídeo Único/genética , Locos de Características Quantitativas/genética , Animais , Bovinos/fisiologia , Feminino , Genótipo , Lactação/genética , Fenótipo
6.
J Dairy Sci ; 102(8): 7189-7203, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31178181

RESUMO

The aim of this study was to investigate the feasibility of using mid-infrared (MIR) spectroscopy analysis of milk samples to increase the power and precision of genome-wide association studies (GWAS) for milk composition and to better distinguish linked quantitative trait loci (QTL). To achieve this goal, we analyzed phenotypic data of milk composition traits, related MIR spectra, and genotypic data comprising 626,777 SNP on 5,202 Holstein, Jersey, and crossbred cows. We performed a conventional GWAS on protein, lactose, fat, and fatty acid concentrations in milk, a GWAS on individual MIR wavenumbers, and a partial least squares regression (PLS), which is equivalent to a multi-trait GWAS, exploiting MIR data simultaneously to predict SNP genotypes. The PLS detected most of the QTL identified using single-trait GWAS, usually with a higher significance value, as well as previously undetected QTL for milk composition. Each QTL tends to have a different pattern of effects across the MIR spectrum and this explains the increased power. Because SNP tracking different QTL tend to have different patterns of effect, it was possible to distinguish closely linked QTL. Overall, the results of this study suggest that using MIR data through either GWAS or PLS analysis applied to genomic data can provide a powerful tool to distinguish milk composition QTL.


Assuntos
Bovinos/fisiologia , Estudo de Associação Genômica Ampla/veterinária , Leite/química , Locos de Características Quantitativas/genética , Animais , Bovinos/genética , Ácidos Graxos/análise , Feminino , Genótipo , Glicolipídeos/análise , Glicoproteínas/análise , Raios Infravermelhos , Lactose/análise , Leite/efeitos da radiação , Proteínas do Leite/análise , Fenótipo
7.
Genet Sel Evol ; 51(1): 29, 2019 Jun 20.
Artigo em Inglês | MEDLINE | ID: mdl-31221081

RESUMO

BACKGROUND: Selection of cattle that are less sensitive to environmental variation in unfavorable environments and more adapted to harsh conditions is of primary importance for tropical beef cattle production systems. Understanding the genetic background of sensitivity to environmental variation is necessary for developing strategies and tools to increase efficiency and sustainability of beef production. We evaluated the degree of sensitivity of beef cattle performance to environmental variation, at the animal and molecular marker levels (412 K single nucleotide polymorphisms), by fitting and comparing the results of different reaction norm models (RNM), using a comprehensive dataset of Nellore cattle raised under diverse environmental conditions. RESULTS: Heteroscedastic RNM (with different residual variances for environmental level) provided better fit than homoscedastic RNM. In addition, spline and quadratic RNM outperformed linear RNM, which suggests the existence of a nonlinear genetic component affecting the performance of Nellore cattle. This nonlinearity indicates that within-animal sensitivity depends on the environmental gradient (EG) level and that animals may present different patterns of sensitivity according to the range of environmental variations. The spline RNM showed that sensitivity to environmental variation from harsh to average EG is lowly correlated with sensitivity from average to good EG, at both the animal and molecular marker levels. Although the genomic regions that affect sensitivity in harsher environments were not the same as those associated with less challenging environments, the candidate genes within those regions participate in common biological processes such as those related to inflammatory and immune response. Some plausible candidate genes were identified. CONCLUSIONS: Sensitivity of tropical beef cattle to environmental variation is not continuous along the environmental gradient, which implies that animals that are less sensitive to harsher conditions are not necessarily less responsive to variations in better environmental conditions, and vice versa. The same pattern was observed at the molecular marker level, i.e. genomic regions and, consequently, candidate genes associated with sensitivity to harsh conditions were not the same as those associated with sensitivity to less challenging conditions.


Assuntos
Bovinos/genética , Interação Gene-Ambiente , Animais , Feminino , Estudo de Associação Genômica Ampla/veterinária , Masculino , Polimorfismo de Nucleotídeo Único , Clima Tropical , Ganho de Peso/genética
8.
Genet Sel Evol ; 51(1): 28, 2019 Jun 20.
Artigo em Inglês | MEDLINE | ID: mdl-31221101

RESUMO

BACKGROUND: Single-step genomic best linear unbiased prediction (SSGBLUP) is a comprehensive method for genomic prediction. Point estimates of marker effects from SSGBLUP are often used for genome-wide association studies (GWAS) without a formal framework of hypothesis testing. Our objective was to implement p-values for single-marker GWAS studies within the single-step GWAS (SSGWAS) framework by deriving computational algorithms and procedures, and by applying these to a large beef cattle population. METHODS: P-values were obtained based on the prediction error (co)variances for single nucleotide polymorphisms (SNPs), which were obtained from the prediction error (co)variances of genomic predictions based on the inverse of the coefficient matrix and formulas to estimate SNP effects. RESULTS: Computation of p-values took a negligible time for a dataset with almost 2 million animals in the pedigree and 1424 genotyped sires, and no inflation of statistics was observed. The SNPs that passed the Bonferroni threshold of 10-5.9 were the same as those that explained the highest proportion of additive genetic variance, but even at the same significance levels and effects, some of them explained less genetic variance due to lower allele frequency. CONCLUSIONS: The use of a p-value for SSGWAS is a very general and efficient strategy to identify quantitative trait loci (QTL). It can be used for complex datasets such as those used in animal breeding, where only a proportion of the pedigreed animals are genotyped.


Assuntos
Peso ao Nascer/genética , Bovinos/genética , Marcadores Genéticos , Estudo de Associação Genômica Ampla/veterinária , Algoritmos , Animais , Conjuntos de Dados como Assunto , Feminino , Masculino , Modelos Genéticos , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas
9.
Genet Sel Evol ; 51(1): 32, 2019 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-31242855

RESUMO

BACKGROUND: This study aimed at (1) comparing the accuracies of genomic prediction for parasite resistance in sheep based on whole-genome sequence (WGS) data to those based on 50k and high-density (HD) single nucleotide polymorphism (SNP) panels; (2) investigating whether the use of variants within quantitative trait loci (QTL) regions that were selected from regional heritability mapping (RHM) in an independent dataset improved the accuracy more than variants selected from genome-wide association studies (GWAS); and (3) comparing the prediction accuracies between variants selected from WGS data to variants selected from the HD SNP panel. RESULTS: The accuracy of genomic prediction improved marginally from 0.16 ± 0.02 and 0.18 ± 0.01 when using all the variants from 50k and HD genotypes, respectively, to 0.19 ± 0.01 when using all the variants from WGS data. Fitting a GRM from the selected variants alongside a GRM from the 50k SNP genotypes improved the prediction accuracy substantially compared to fitting the 50k SNP genotypes alone. The gain in prediction accuracy was slightly more pronounced when variants were selected from WGS data compared to when variants were selected from the HD panel. When sequence variants that passed the GWAS [Formula: see text] threshold of 3 across the entire genome were selected, the prediction accuracy improved by 5% (up to 0.21 ± 0.01), whereas when selection was limited to sequence variants that passed the same GWAS [Formula: see text] threshold of 3 in regions identified by RHM, the accuracy improved by 9% (up to 0.25 ± 0.01). CONCLUSIONS: Our results show that through careful selection of sequence variants from the QTL regions, the accuracy of genomic prediction for parasite resistance in sheep can be improved. These findings have important implications for genomic prediction in sheep.


Assuntos
Doenças dos Ovinos/genética , Doenças dos Ovinos/parasitologia , Sequenciamento Completo do Genoma/veterinária , Animais , Austrália , Resistência à Doença/genética , Feminino , Marcadores Genéticos , Testes Genéticos/veterinária , Variação Genética , Estudo de Associação Genômica Ampla/veterinária , Masculino , Contagem de Ovos de Parasitas/veterinária , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Ovinos
10.
J Dairy Sci ; 102(7): 6296-6305, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31056319

RESUMO

A healthy sucking reflex is essential for newborn calves to ensure sufficient colostrum intake in the first few hours postpartum. In recent decades, European Brown Swiss breeders have repeatedly reported that some calves lack the ability to consume colostrum directly after birth due to an absent sucking reflex. In this study, we collected the phenotypes of more than 5,500 German Brown Swiss calves and performed variance component estimation with sire threshold models using Markov chain Monte Carlo algorithms. The 50K (777K) genotypes of nearly 2,000 (200) calves were collected, and an imputation was performed for all 50K genotypes up to 777K. Genome-wide association studies (GWAS) for the trait sucking reflex were conducted for all 777K genotypes. Depending on the trait coding, a low heritability was estimated to range from 0.08 to 0.11. The GWAS results identified 34 trait-associated SNP on 6 different chromosomes. Post-GWAS analyses showed significant overrepresentation of Gene Ontologies for central nervous development and several regulative processes. Functional annotation clustering and pathway analysis revealed relations to lipid metabolism, immune and endocrine systems, and signal transduction. The results of this study suggest that breeding for an improved sucking reflex is possible but requires large data sets for the estimation of reliable breeding values (either large progeny testing groups or a large reference genome in a genomic selection program).


Assuntos
Bovinos/genética , Reflexo , Algoritmos , Animais , Cruzamento , Bovinos/fisiologia , Feminino , Estudo de Associação Genômica Ampla/veterinária , Genômica , Genótipo , Masculino , Fenótipo , Polimorfismo de Nucleotídeo Único , Característica Quantitativa Herdável
11.
J Dairy Sci ; 102(7): 6276-6287, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31056336

RESUMO

Energy demand for milk production in early lactation exceeds energy intake, especially in high-yielding Holstein cows. Energy deficiency causes increasing susceptibility to metabolic disorders. In addition to several blood parameters, the fat-to-protein ratio (FPR) is suggested as an indicator for ketosis, because a FPR >1.5 refers to high lipolysis. The aim of this study was to analyze phenotypic, quantitative genetic, and genomic associations between FPR and ketosis. In this regard, 8,912 first-lactation Holstein cows were phenotyped for ketosis according to a veterinarian diagnosis key. Ketosis was diagnosed if the cow showed an abnormal carbohydrate metabolism with increased content of ketone bodies in the blood or urine. At least one entry for ketosis in the first 6 wk after calving implied a score = 1 (diseased); otherwise, a score = 0 (healthy) was assigned. The FPR from the first test-day was defined as a Gaussian distributed trait (FPRgauss), and also as a binary response trait (FPRbin), considering a threshold of FPR = 1.5. After imputation and quality controls, 45,613 SNP markers from the 8,912 genotyped cows were used for genomic studies. Phenotypically, an increasing ketosis incidence was associated with significantly higher FPR, and vice versa. Hence, from a practical trait recording perspective, first test-day FPR is suggested as an indicator for ketosis. The ketosis heritability was slightly larger when modeling the pedigree-based relationship matrix (pedigree-based: 0.17; SNP-based: 0.11). For FPRbin, heritabilities were larger when modeling the genomic relationship matrix (pedigree-based: 0.09; SNP-based: 0.15). For FPRgauss, heritabilities were almost identical for both pedigree and genomic relationship matrices (pedigree-based: 0.14; SNP-based: 0.15). Genetic correlations between ketosis with FPRbin and FPRgauss using either pedigree- or genomic-based relationship matrices were in a moderate range from 0.39 to 0.71. Applying genome-wide association studies, we identified the specific SNP rs109896020 (BTA 5, position: 115,456,438 bp) significantly contributing to ketosis. The identified potential candidate gene PARVB in close chromosomal distance is associated with nonalcoholic fatty liver disease in humans. The most important SNP contributing to FPRbin was located within the DGAT1 gene. Different SNP significantly contributed to ketosis and FPRbin, indicating different mechanisms for both traits genomically.


Assuntos
Doenças dos Bovinos/genética , Gorduras/análise , Estudo de Associação Genômica Ampla/veterinária , Cetose/genética , Proteínas/análise , Animais , Bovinos , Doenças dos Bovinos/metabolismo , Gorduras/metabolismo , Feminino , Genoma , Genômica , Genótipo , Cetose/metabolismo , Cetose/veterinária , Lactação/genética , Masculino , Leite/metabolismo , Linhagem , Fenótipo , Polimorfismo de Nucleotídeo Único , Proteínas/metabolismo
12.
J Anim Sci ; 97(7): 2793-2802, 2019 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-31087081

RESUMO

The objectives of this study were to identify informative genomic regions that affect the exterior traits of purebred Korean Yorkshire pigs and to investigate and compare the accuracy of genomic prediction for response variables. Phenotypic data on body height (BH), body length (BL), and total teat number (TTN) from 2,432 Yorkshire pigs were used to obtain breeding values including as response variable the estimated breeding value (EBV) and 2 types of deregressed EBVs-one including the parent average (DEBVincPA) and the other excluding it (DEBVexcPA). A final genotype panel comprising 46,199 SNP markers was retained for analysis after quality control for common SNPs. The BayesB and BayesC methods-with various π and weighted response variables (EBV, DEBVincPA, or DEBVexcPA)-were used to estimate SNP effects, through the genome-wide association study. The significance of genomic windows (1 Mb) was obtained at 1.0% additive genetic variance and was subsequently used to identify informative genomic regions. Furthermore, SNPs with a high model frequency (≥0.90) were considered informative. The accuracy of genomic prediction was estimated using a 5-fold cross-validation with the K-means clustering method. Genomic accuracy was measured as the genomic correlation between the molecular breeding value and the individual weighted response variables (EBV, DEBVincPA, or DEBVexcPA). The number of identified informative windows (1 Mb) for BH, BL, and TTN was 4, 3, and 4, respectively. The number of significant SNPs for BH, BL, and TTN was 6, 4, and 5, respectively. Diversity π did not influence the accuracy of genomic prediction. The BayesB method showed slightly higher genomic accuracy for exterior traits than BayesC method in this study. In addition, the genomic accuracy using DEBVincPA as response variable was higher than that using other response variables. Therefore, the genomic accuracy using BayesB (π = 0.90) with DEBVinPA as a response variable was the most effective in this study. The genomic accuracy values for BH, BL, and TTN were calculated to be 0.52, 0.60, and 0.51, respectively.


Assuntos
Estudo de Associação Genômica Ampla/veterinária , Genoma/genética , Genômica , Polimorfismo de Nucleotídeo Único/genética , Locos de Características Quantitativas/genética , Suínos/genética , Animais , Cruzamento , Análise por Conglomerados , Confiabilidade dos Dados , Feminino , Marcadores Genéticos/genética , Testes Genéticos/veterinária , Genótipo , Masculino , Glândulas Mamárias Animais/anatomia & histologia , Fenótipo , Suínos/anatomia & histologia
13.
J Dairy Sci ; 102(7): 6248-6262, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31103307

RESUMO

Selection and breeding can be used to fight transmission of infectious diseases in livestock. The prevalence in a population depends on the susceptibility and infectivity of the animals. Knowledge on the genetic background of those traits would facilitate efficient selection for lower disease prevalence. We investigated the genetic background of host susceptibility and infectivity for digital dermatitis (DD), an endemic infectious claw disease in dairy cattle, with a genome-wide association study (GWAS), using either a simple linear mixed model or a generalized linear mixed model based on epidemiological theory. In total, 1,513 Holstein-Friesian cows of 12 Dutch dairy farms were scored for DD infection status and class (M0 to M4.1) every 2 wk for 11 times; 1,401 of these cows were genotyped with a 75k SNP chip. We performed a GWAS with a linear mixed model on 10 host disease status traits, and with a generalized linear mixed model with a complementary log-log link function (GLMM) on the probability that a cow would get infected between 2 scorings. With the GLMM, we fitted SNP effects for host susceptibility and host infectivity, while taking the variation in exposure of the susceptible cow to infectious herd mates into account. With the linear model we detected 4 suggestive SNP (false discovery rate < 0.20), 2 for the fraction of observations a cow had an active lesion on chromosomes 1 and 14, one for the fraction of observations a cow had an M2 lesion on at least one claw on chromosome 1 (the same SNP as for the fraction of observations with an active lesion), and one for the fraction of observations a cow had an M4.1 lesion on at least one claw on chromosome 10. Heritability estimates ranged from 0.09 to 0.37. With the GLMM we did not detect significant nor suggestive SNP. The SNP effects on disease status analyzed with the linear model had a correlation coefficient of only 0.70 with SNP effects on susceptibility of the GLMM, indicating that both models capture partly different effects. Because the GLMM better accounts for the epidemiological mechanisms determining individual disease status and for the distribution of the y-variable, results of the GLMM may be more reliable, despite the absence of suggestive associations. We expect that with an extended GLMM that better accounts for the full genetic variation in infectivity via the environment, the accuracy of SNP effects may increase.


Assuntos
Doenças dos Bovinos/genética , Dermatite Digital/genética , Estudo de Associação Genômica Ampla/veterinária , Animais , Cruzamento , Bovinos , Doenças dos Bovinos/epidemiologia , Doenças dos Bovinos/transmissão , Dermatite Digital/epidemiologia , Dermatite Digital/transmissão , Feminino , Patrimônio Genético , Predisposição Genética para Doença , Genótipo , Modelos Lineares , Fenótipo , Seleção Genética
14.
J Anim Sci ; 97(7): 3027-3033, 2019 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-30997484

RESUMO

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.


Assuntos
Bovinos/genética , Cromossomos/genética , Estudo de Associação Genômica Ampla/veterinária , Genoma/genética , Polimorfismo de Nucleotídeo Único/genética , Reprodução/genética , Maturidade Sexual/genética , Animais , Cruzamento , Bovinos/crescimento & desenvolvimento , Bovinos/fisiologia , Feminino , Frequência do Gene , Genômica , Genótipo , Desequilíbrio de Ligação , Masculino , Fenótipo , Gravidez , Locos de Características Quantitativas/genética
15.
Anim Genet ; 50(3): 311-314, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30983012

RESUMO

Genome-wide association studies (GWASes) have become a powerful tool for identifying genomic regions associated with important traits in livestock. Milk production traits in dairy sheep are measured at different time points during their life span. Using phenotypic data generated from longitudinal traits could improve the power of association studies but until now have received less attention in GWASes as a methodology and has not been implemented. The aim of this study was to carry out a GWAS for milk production traits in Valle del Belice sheep using repeated measures. After quality control, 469 ewes and 37 228 SNPs were retained for the analysis, and phenotypic data included 5586 test-day records for five milk production traits (milk yield, MY; fat yield and percentage, FY and F%; protein yield and percentage, PY and P%). Nine SNPs located within or close to known genes were found to be associated with milk production traits. In particular, rs398340969, associated with both milk yield and protein yield, is located within the DCPS gene. In addition, rs425417915 and rs417079368, both associated with both fat percentage and protein percentage, are located within the TTC7B gene and at 0.37 Mb within the SUCNR1 gene respectively. In summary, the use of repeated records was beneficial for mapping genomic regions affecting milk production traits in the Valle del Belice sheep.


Assuntos
Estudo de Associação Genômica Ampla/veterinária , Leite , Carneiro Doméstico/genética , Carneiro Doméstico/fisiologia , Animais , Feminino , Polimorfismo de Nucleotídeo Único , Carneiro Doméstico/classificação
16.
Genet Sel Evol ; 51(1): 15, 2019 Apr 18.
Artigo em Inglês | MEDLINE | ID: mdl-30999842

RESUMO

BACKGROUND: Quantitative genetic studies suggest the existence of variation at the genome level that affects the ability of cattle to resist to parasitic diseases. The objective of the current study was to identify regions of the bovine genome that are associated with resistance to endo-parasites. METHODS: Individual cattle records were available for Fasciola hepatica-damaged liver from 18 abattoirs. Deregressed estimated breeding values (EBV) for F. hepatica-damaged liver were generated for genotyped animals with a record for F. hepatica-damaged liver and for genotyped sires with a least one progeny record for F. hepatica-damaged liver; 3702 animals were available. In addition, individual cow records for antibody response to F. hepatica on 6388 genotyped dairy cows, antibody response to Ostertagia ostertagi on 8334 genotyped dairy cows and antibody response to Neospora caninum on 4597 genotyped dairy cows were adjusted for non-genetic effects. Genotypes were imputed to whole-sequence; after edits, 14,190,141 single nucleotide polymorphisms (SNPs) and 16,603,644 SNPs were available for cattle with deregressed EBV for F. hepatica-damaged liver and cows with an antibody response to a parasitic disease, respectively. Association analyses were undertaken using linear regression on one SNP at a time, in which a genomic relationship matrix accounted for the relationships between animals. RESULTS: Genomic regions for F. hepatica-damaged liver were located on Bos taurus autosomes (BTA) 1, 8, 11, 16, 17 and 18; each region included at least one SNP with a p value lower than 10-6. Five SNPs were identified as significant (q value < 0.05) for antibody response to N. caninum and were located on BTA21 or 25. For antibody response to F. hepatica and O. ostertagi, six and nine quantitative trait loci (QTL) regions that included at least one SNP with a p value lower than 10-6 were identified, respectively. Gene set enrichment analysis revealed a significant association between functional annotations related to the olfactory system and QTL that were suggestively associated with endo-parasite phenotypes. CONCLUSIONS: A number of novel genomic regions were suggestively associated with endo-parasite phenotypes across the bovine genome and two genomic regions on BTA21 and 25 were associated with antibody response to N. caninum.


Assuntos
Doenças dos Bovinos/genética , Bovinos/genética , Interações Hospedeiro-Parasita/genética , Animais , Cruzamento , Fasciola hepatica/patogenicidade , Fertilidade/genética , Variação Genética/genética , Estudo de Associação Genômica Ampla/veterinária , Genótipo , Parasitos/genética , Parasitos/patogenicidade , Fenótipo , Polimorfismo de Nucleotídeo Único/genética , Locos de Características Quantitativas/genética , Sequenciamento Completo do Genoma/métodos
17.
Genet Sel Evol ; 51(1): 9, 2019 Mar 05.
Artigo em Inglês | MEDLINE | ID: mdl-30836944

RESUMO

BACKGROUND: In livestock, deleterious recessive alleles can result in reduced economic performance of homozygous individuals in multiple ways, e.g. early embryonic death, death soon after birth, or semi-lethality with incomplete penetrance causing reduced viability. While death is an easy phenotype to score, reduced viability is not as easy to identify. However, it can sometimes be observed as reduced conception rates, longer calving intervals, or lower survival for live born animals. METHODS: In this paper, we searched for haplotypes that carry putatively recessive lethal or semi-lethal alleles in 132,725 genotyped Irish beef cattle from five breeds: Aberdeen Angus, Charolais, Hereford, Limousin, and Simmental. We phased the genotypes in sliding windows along the genome and used five tests to identify haplotypes with absence of or reduced homozygosity. Then, we associated the identified haplotypes with 44,351 insemination records that indicated early embryonic death, and postnatal survival records. Finally, we assessed haplotype pleiotropy by estimating substitution effects on estimates of breeding value for 15 economically important traits in beef production. RESULTS: We found support for one haplotype that carries a putatively recessive lethal (chromosome 16 in Simmental) and two haplotypes that carry semi-lethal alleles (chromosome 14 in Aberdeen Angus and chromosome 19 in Charolais), with population frequencies of 8.8, 15.2, and 14.4%, respectively. These three haplotypes showed pleiotropic effects on economically important traits for beef production. Their allele substitution effects are €2.30, €3.42, and €1.47 for the terminal index and €1.03, - €3.11, and - €0.88 for the replacement index, where the standard deviations for the terminal index are €22.52, €18.65, and €22.70 and for the replacement index they are €31.35, €29.82, and €35.79. We identified ZFAT as the candidate gene for semi-lethality in Aberdeen Angus, several candidate genes for the lethal Simmental haplotype, and no candidate genes for the semi-lethal Charolais haplotype. CONCLUSIONS: We analysed genotype, reproduction, survival, and production data to detect haplotypes that carry putatively recessive lethal or semi-lethal alleles in Irish beef cattle and identified one lethal and two semi-lethal haplotypes, which have pleiotropic effects on economically important traits in beef production.


Assuntos
Bovinos/genética , Frequência do Gene , Genes Recessivos , Pleiotropia Genética , Haplótipos , Carne Vermelha/normas , Animais , Estudo de Associação Genômica Ampla/veterinária , Genótipo , Característica Quantitativa Herdável
18.
J Dairy Sci ; 102(6): 5254-5265, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30904297

RESUMO

The aim of this study was to perform genetic, genome-wide association (GWAS), and gene-set enrichment analyses with latent variables related to milk fatty acid profile (i.e., fatty acids factor scores; FAF), milk composition, and udder health in a cohort of 1,158 Italian Brown Swiss cows. The phenotypes under study were 12 FAF previously identified through factor analysis and classified as follows: de novo FA (F1), branched-chain FA-milk yield (F2), biohydrogenation (F3), long-chain fatty acids (F4), desaturation (F5), short-chain fatty acids (F6), milk protein and fat contents (F7), odd fatty acids (F8), conjugated linoleic acids (F9), linoleic acid (F10), udder health (F11) and vaccelenic acid (F12). (Co)variance components were estimated for factor scores using a Bayesian linear animal model via Gibbs sampling. The animals were genotyped with the Illumina BovineSNP50 BeadChip v.2 (Illumina Inc., San Diego, CA). A single marker regression model was fitted for GWAS analysis. The gene-set enrichment analysis was run on the GWAS results using the Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes pathway databases to identify the ontologies and pathways associated with the FAF. Marginal posterior means of the heritabilities of the aforementioned FAF ranged from 0.048 for F12 to 0.310 for F5. Factors F1 and F6 had the highest number of relevant genetic correlations with the other traits. The genomic analysis detected a total of 39 significant SNP located on 17 Bos taurus autosomes. All latent variables produced signals except for F2 and F10. The traits with the highest number of significant associations were F11 (17) and F12 (7). Gene-set enrichment analyses identified significant pathways (false discovery rate 5%) for F3 and F7. In particular, systemic lupus erythematosus was enriched for F3, whereas the MAPK (mitogen-activated protein kinase) signaling pathway was overrepresented for F7. The results support the existence of important and exploitable genetic and genomic variation in these latent explanatory phenotypes. Information acquired might be exploited in selection programs and when designing further studies on the role of the putative candidate genes identified in the regulation of milk composition and udder health.


Assuntos
Estudo de Associação Genômica Ampla/veterinária , Genômica , Glândulas Mamárias Animais/fisiologia , Mastite Bovina/genética , Leite/química , Animais , Teorema de Bayes , Bovinos , Estudos de Coortes , Ácidos Graxos/metabolismo , Feminino , Predisposição Genética para Doença , Genótipo , Itália , Ácido Linoleico/metabolismo , Leite/metabolismo , Proteínas do Leite/metabolismo
19.
J Dairy Sci ; 102(6): 5305-5314, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30904307

RESUMO

Advances in the molecular area of selection have expanded knowledge of the genetic architecture of complex traits through genome-wide association studies (GWAS). Several GWAS have been performed so far, but confirming these results is not always possible due to several factors, including environmental conditions. Thus, our objective was to identify genomic regions associated with traditional milk production traits, including milk yield, somatic cell score, fat, protein and lactose percentages, and fatty acid composition in a Holstein cattle population producing under tropical conditions. For this, 75,228 phenotypic records from 5,981 cows and genotypic data of 56,256 SNP from 1,067 cows were used in a weighted single-step GWAS. A total of 46 windows of 10 SNP explaining more than 1% of the genetic variance across 10 Bos taurus autosomes (BTA) harbored well-known and novel genes. The MGST1 (BTA5), ABCG2 (BTA6), DGAT1 (BTA14), and PAEP (BTA11) genes were confirmed within some of the regions identified in our study. Potential novel genes involved in tissue damage and repair of the mammary gland (COL18A1), immune response (LTTC19), glucose homeostasis (SLC37A1), synthesis of unsaturated fatty acids (LTBP1), and sugar transport (SLC37A1 and MFSD4A) were found for milk yield, somatic cell score, fat percentage, and fatty acid composition. Our findings may assist genomic selection by using these regions to design a customized SNP array to improve milk production traits on farms with similar environmental conditions.


Assuntos
Bovinos/genética , Estudo de Associação Genômica Ampla/veterinária , Genótipo , Polimorfismo de Nucleotídeo Único , Animais , Brasil , Bovinos/fisiologia , Ácidos Graxos/metabolismo , Feminino , Genoma , Genômica , Leite/metabolismo
20.
Anim Genet ; 50(2): 154-156, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30815891

RESUMO

In this study we aimed to identify genomic regions associated with muscle pH, meat colour and water-holding capacity in a population of 280 Italian Duroc pigs genotyped by the Illumina PorcineSNP60 v2 Genotyping BeadChip. After quality control, the remaining 32 597 SNPs and 278 subjects were used to perform a genome-wide association study with the genabel package, using a kinship matrix in a model with the effects of sex, age and slaughter day. Bonferroni correction was applied, and the significant markers and regions were then further investigated to identify the nearest genes and the linkage disequilibrium (LD) between markers. Four markers (ASGA0082344, ASGA0095635, DBWU0000985 and CASI0005117) were significantly associated with ultimate pH (pHu ); no significant association was detected for the other traits. The four significant variants, located from 16.841 to 17.643 Mb on chromosome 3, were found within or close to the sequences of the sulfatase modifying factor 2 (SUMF2), lysine acetyltransferase 8 (KAT8), serine protease 8 (PRSS8) and phosphorylase kinase catalytic subunit gamma 2 (PHKG2) genes. The four associated markers lie in two LD blocks, suggesting that the observed effect is related to mutations located in two regions: the first one where SUMF2 is mapped and the second one where genes KAT8, PRSS8 and PHKG2 are located.


Assuntos
Marcadores Genéticos , Estudo de Associação Genômica Ampla/veterinária , Carne/análise , Polimorfismo de Nucleotídeo Único , Sus scrofa/fisiologia , Animais , Cor , Feminino , Concentração de Íons de Hidrogênio , Desequilíbrio de Ligação , Masculino , Músculos/química , Sus scrofa/genética , Água/fisiologia
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