RESUMO
The identification of the presence of genotype by environment interaction effects on important traits in Holstein cattle allows for the use of international genetic evaluations and a more efficient design of regional genetic evaluation programmes. The aim of this study was to determine the genotype × environment interaction effects in Chilean Holstein dairy cattle through the analysis of records corresponding to calvings between 1998 and 2015. Herds were classified in the central and southern regions of Chile based on herd location as well as by high and low levels of production environments based on the fat plus protein yield averages per herd within each region. The central region has a Mediterranean climate and a confined production system while the southern region has a humid temperate climate and a production system based on grazing with supplementation. Traits studied were milk yield (MY), fat yield (FY), protein yield (PY), fat content (FC) and protein content (PC) by lactation, age at first calving (AFC) and calving interval (CI). Several four-trait mixed animal models were applied to environmental category data as different traits, which included herd-year-calving season (herd-year-birth season for AFC) and lactation number as fixed effects, and animal additive genetic, sire-herd, permanent environment and residual effects as random effects. Genetic correlations (rg) for MY, FY, FC, PC and CI were found to decrease as differences between environmental categories increased. The rg between the most extreme environmental categories considered in this study for AFC (0.26) was the only one found statistically lower than 0.60. Genetic correlation values statistically lower than 0.80 (P < 0.05) were observed for AFC, CI, MY, FY and PY between some environmental categories. If separate genetic evaluations are adopted as practical criteria when the value of rg is lower than 0.60, the consequence of improving a multi-trait economic breeding objective in this population is likely to be small unless extreme environmental categories are considered. However, a moderate decrease in selection response and re-ranking of selection candidates is expected for AFC, CI and yield traits when selection is performed in different environmental conditions. Genotype × environment interaction effects involving production systems in a Mediterranean climate and confinement vs. Temperate Oceanic climate and grazing with supplementation, and between two fat plus protein yield level categories within each environment, were at most moderate for the studied traits.
Assuntos
Lactação , Leite , Animais , Bovinos/genética , Feminino , Genótipo , Parto , Fenótipo , GravidezRESUMO
The aim of this study was to evaluate the effect of including calving age (CA) on genetic evaluation models for Holstein cattle. The evaluated models included the permanent environment, the sire-herd interactions, and the animals and residual effects as random. The fixed effects included the average production of milk, fat, and protein and the herd-year-season effect. The analyzed data included 603,521 records of milk production (in kg) corresponding to 438,098 animals from 527 herds. Additionally, there were 179,122 records of fat and protein components, corresponding to 148,930 animals from 137 herds. The records were classified by first lactation only (FL) and all available lactations (AL) for validation test (VT). The FL records corresponded to 275,487 milk production records with a mean of 10,874.1 ± 2773.9 kg at a mean CA of 25.6 ± 4.2 months. For FL, the milk components consisted of 78,955 records with a mean fat production of 392.86 ± 89.9 kg, a mean protein production of 362.8 ± 74.9 kg and a mean CA of 25.2 ± 4.1 months. For AL, the number of records was 603,521 for milk production with a mean of 10,802.8 ± 2905.9 kg and a mean CA of 35.6 ± 11.5 months. For the milk components, there were 179,122 records with a mean of 36.1 ± 9.5 months for CA and 388.3 ± 98.4 kg and 356.7 ± 82.6 kg for fat and protein, respectively. Three models were compared: the base model (M0) described above, and two alternative models that included CA in a linear and quadratic form (M1 and M2, respectively). Estimations of the variance components (VC) and breeding value (BV) were obtained using a repeatability animal model, with the same phenotypic and pedigree information used for all models. To select the best fit model for the data, a likelihood ratio test (LRtest) was used. A validation test (VT) was also applied to each model to evaluate the consistency of the genetic trends for females with information on AL and FL. The inclusion of CA in its linear form (M1) was the model that achieved the best results in the LRtest and an acceptable value for the VT. These results show that CA improves the model fit for BV prediction and reliability.
Assuntos
Bovinos/fisiologia , Lactação/genética , Leite/metabolismo , Reprodução , Fatores Etários , Animais , Bovinos/genética , Feminino , México , Modelos Teóricos , Reprodutibilidade dos TestesRESUMO
Genomic selection has been proposed for the mitigation of methane (CH4) emissions by cattle because there is considerable variability in CH4 emissions between individuals fed on the same diet. The genome-wide association study (GWAS) represents an important tool for the detection of candidate genes, haplotypes or single nucleotide polymorphisms (SNP) markers related to characteristics of economic interest. The present study included information for 280 cows in three dairy production systems in Mexico: 1) Dual Purpose (n = 100), 2) Specialized Tropical Dairy (n = 76), 3) Familiar Production System (n = 104). Concentrations of CH4 in a breath of individual cows at the time of milking (MEIm) were estimated through a system of infrared sensors. After quality control analyses, 21,958 SNPs were included. Associations of markers were made using a linear regression model, corrected with principal component analyses. In total, 46 SNPs were identified as significant for CH4 production. Several SNPs associated with CH4 production were found at regions previously described for quantitative trait loci of composition characteristics of meat, milk fatty acids and characteristics related to feed intake. It was concluded that the SNPs identified could be used in genomic selection programs in developing countries and combined with other datasets for global selection.
Assuntos
Ração Animal , Bovinos/genética , Metano/metabolismo , Modelos Genéticos , Polimorfismo de Nucleotídeo Único , Animais , Marcadores Genéticos , Estudo de Associação Genômica AmplaRESUMO
Genealogical information is an essential tool for carrying out any genetic improvement program. The objective of this study was to determine the accuracy of pedigree information in the Mexican registered Holstein population using genomic data available in Mexico and for the US Holstein population. The study included 7,508 animals (158 sires and 7,350 cows) that were born from 2002 through 2014, registered with Holstein de México, and genotyped with single nucleotide polymorphism arrays of different densities. Parentage could not be validated for 17% of sires of cows and 12% of sires of bulls. Most (79%) of the dams of cows and the dams of bulls had no genotype available and could not be validated. A parentage test was possible for only 6,104 sires of cows, 139 sires of bulls, 1,519 dams of cows, and 33 dams of bulls. Of the animals with a parentage test, parent assignment was confirmed for 89% of sires of cows, 92% of dams of cows, 95% of sires of bulls, and 97% of dams of bulls. Parent discovery was possible for some animals without confirmed parents: 17% for sires of cows, 2.5% for dams of cows, 43% for sires of bulls, and 0% for dams of bulls. Of the 7,795 progeny tests, 777 had parent conflicts, which is an error rate of 9.97% for parental recording in the population, a rate that is similar to those recently reported for other populations. True parents for some progeny conflicts (15%) were discovered for the Mexican population, and the remaining parents were assigned as unknown. Expected effects of misidentification on rate of genetic gain could be decreased by half if genealogical errors were decreased to 5%. This study indicates that genotyping and genealogy recovery may help in increasing rates of genetic improvement in the Mexican registered Holstein population.
Assuntos
Bovinos/genética , Animais , Cruzamento , Bovinos/fisiologia , Feminino , Genoma , Genômica , Genótipo , Masculino , México , Parto , Linhagem , GravidezRESUMO
BACKGROUND: Copy number variations are genome polymorphism that influence phenotypic variation and are an important source of genetic variation in populations. The aim of this study was to investigate genetic variability in the Mexican Creole chicken population using CNVs. RESULTS: The Hidden Markov Model of the PennCNV software detected a total of 1924 CNVs in the genome of the 256 samples processed with Axiom® Genome-Wide Chicken Genotyping Array (Affymetrix). The mapped CNVs comprised 1538 gains and 386 losses, resulting at population level in 1216 CNV regions (CNVRs), of which 959 gains, 226 losses and 31 complex (i.e. containing both losses and gains). The CNVRs covered a total of 47 Mb of the whole genome sequence length, corresponding to 5.12% of the chicken galGal4 autosome assembly. CONCLUSIONS: This study allowed a deep insight into the structural variation in the genome of unselected Mexican chicken population, which up to now has not been genetically characterized. The genomic study disclosed that the population, even if presenting extreme morphological variation, cannot be organized in differentiated genetic subpopulations. Finally this study provides a chicken CNV map based on the 600 K SNP chip array jointly with a genome-wide gene copy number estimates in a native unselected for more than 500 years chicken population.
Assuntos
Galinhas/genética , Variações do Número de Cópias de DNA , Polimorfismo de Nucleotídeo Único , Animais , Marcadores Genéticos , Genoma , MéxicoRESUMO
The effects of reference population size and the availability of information from genotyped ancestors on the accuracy of imputation of single nucleotide polymorphisms (SNP) were investigated for Mexican Holstein cattle. Three scenarios for reference population size were examined: (1) a local population of 2,011 genotyped Mexican Holsteins, (2) animals in scenario 1 plus 866 Holsteins in the US genotype database (GDB) with genotyped Mexican daughters, and (3) animals in scenario 1 and all US GDB Holsteins (338,073). Genotypes from 4 chip densities (2 low density, 1 mid density, and 1 high density) were imputed using findhap (version 3) to the 45,195 markers on the mid-density chip. Imputation success was determined by comparing the numbers of SNP with 1 or 2 alleles missing and the numbers of differently predicted SNP (conflicts) among the 3 scenarios. Imputation accuracy improved as chip density and numbers of genotyped ancestors increased, and the percentage of SNP with 1 missing allele was greater than that for 2 missing alleles for all scenarios. The largest numbers of conflicts were found between scenarios 1 and 3. The inclusion of information from direct ancestors (dam or sire) with US GDB genotypes in the imputation of Mexican Holstein genotypes increased imputation accuracy by 1 percentage point for low-density genotypes and by 0.5 percentage points for high-density genotypes, which was about half the gain found with information from all US GDB Holsteins. A larger reference population and the availability of genotyped ancestors improved imputation; animals with genotyped parents in a large reference population had higher imputation accuracy than those with no or few genotyped relatives in a small reference population. For small local populations, including genotypes from other related populations can aid in improving imputation accuracy.
Assuntos
Bovinos/genética , Genótipo , Alelos , Animais , Cruzamento , Bovinos/classificação , México , Análise de Sequência com Séries de Oligonucleotídeos , Polimorfismo de Nucleotídeo Único , Densidade Demográfica , Estados UnidosRESUMO
Genetic and phenotypic parameters for Mexican Holstein cows were estimated for first- to third-parity cows with records from 1998 to 2003 (n=2,971-15,927) for 305-d mature equivalent milk production (MEM), fat production (MEF), and protein production (MEP), somatic cell score (SCS), subsequent calving interval (CAI), and age at first calving (AFC). Genetic parameters were obtained by average information matrix-REML methodology using 6-trait (first-parity data) and 5-trait (second- and third-parity data) animal models. Heritability estimates for production traits were between 0.17+/-0.02 and 0.23+/-0.02 for first- and second-parity cows and between 0.12+/-0.03 and 0.13+/-0.03 for third-parity cows. Heritability estimates for SCS were similar for all parities (0.10+/-0.02 to 0.11+/-0.03). For CAI, estimates of heritability were 0.01+/-0.05 for third-parity cows and 0.02+/-0.02 for second-parity cows. The heritability for AFC was moderate (0.28+/-0.03). No unfavorable estimates of correlations were found among MEM, MEF, MEP, CAI, and SCS. Estimates of environmental and phenotypic correlations were large and positive among production traits; favorable between SCS and CAI; slightly favorable between MEM, MEF, and MEP and SCS, between AFC and SCS, and between SCS and CAI; and small but unfavorable between production traits and CAI. Estimates of genetic variation and heritability indicate that selection would result in genetic improvement of production traits, AFC, and SCS. Estimates of both heritability and genetic variation for CAI were small, which indicates that genetic improvement would be difficult.
Assuntos
Bovinos/genética , Meio Ambiente , Fertilidade/genética , Lactação/genética , Glândulas Mamárias Animais/fisiologia , Leite/metabolismo , Animais , Feminino , Variação Genética , México , Modelos Genéticos , Paridade , Fenótipo , Gravidez , Característica Quantitativa Herdável , Estações do AnoRESUMO
Polynomial regression models of the first, second, and third order were used to fit milk production deviations of daughters in Mexico on Canadian and US predicted transmitting ability values for 305-d mature-equivalent milk production (kg). For the pairs Canada-Mexico and Mexico-United States, 40 and 73 bulls with a minimum reliability of 0.75 were analyzed, respectively. Genetic correlations between pairs of countries were also estimated. The parameters were evaluated for all data, and for sires grouped according to the mean of the average phenotypic milk production (high and low) of their daughters' herd mates. Quadratic and cubic effects were not significant in any analysis. From linear regression models, slopes of Mexican daughter deviations on US and Canadian predicted transmitting abilities were 1.01 and 0.93, respectively. Slopes were greater but intercepts were smaller for the high versus low level of production of the sires' herd mates in Mexico. A greater difference between the genetic correlations was found for the high versus low environmental level than for the low level (0.79 vs. 0.70) for Mexico-US data compared with Canada-Mexico data (0.81 vs. 0.78). Genetic correlations between Mexico and the United States (0.74), and between Mexico and Canada (0.77), were smaller than the genetic correlation between the same Canadian and US sires (0.92), suggesting the presence of a moderate degree of genotype-environment interaction for milk production between Canada and the United States, and Mexico.