Sources of bias in genetic association studies in cattle: A review

Abstract Background: Genetic association studies have been increasingly used in cattle breeding programs. However, inconsistent results -such as positive, negative, or absence of association- across studies restrain reproducibility and proper implementation, propitiating the occurrence of bias. Objective: To identify and classify potential sources of bias and determine possible strategies to avoid it in genetic association studies in cattle. Source of bias in genetic association studies: Genetic and genomic sources of bias include effects associated with the gene loci governing expression. Sampling-related and statistical biases are related with factors such as stratification and database size. Strategies to correct bias in genetic association studies: Correction strategies differ in nature. Genetic and genomic strategies are based on determining the appropriate approach to obtain and report the genetic information. Sampling-related and statistical strategies are based on grouping individuals with certain traits that lead to a reduction in heterogeneity. Conclusion: It is necessary to consider the methodology used in previous studies to establish a hierarchy of sources of bias and facilitate decisions on the use of tools to reduce inconsistencies in the results of future studies.Resumo Antecedentes: Nos programas de criação de bovinos, os estudos de associação genética têm sido cada vez mais utilizados. No entanto, resultados inconsistentes, como positivos, negativos ou ausência de associação entre os estudos, restringem a reprodutibilidade e sua adequada implementação, propiciando o aparecimento de viés. Objetivo: Identificar e classificar potenciais fontes de viés e determinar estratégias possíveis para evitá-lo nos estudos de associação genética em bovinos. Fonte de viés em estudos de associação genética: Fontes genéticas e genômicas do viés incluem os efeitos associados aos genes que relacionam a expressão. Os vícios estatísticos e de amostragem estão relacionados a fatores como a estratificação e o tamanho do banco de dados. Estratégias para corrigir os viéses nos estudos de associação genética: As estratégias de correção diferem na natureza. As estratégias genéticas e genômicas são baseadas na determinação da abordagem apropriada para obter e relatar a informação genética. As estratégias estatísticas e de amostragem baseiam-se no agrupamento de indivíduos com certos traços que levam a uma redução na heterogeneidade. Conclusão: É necessário considerar a metodologia utilizada em estudos anteriores para estabelecer uma hierarquia de fontes de viés e facilitar decisões sobre o uso de ferramentas para reduzir inconsistências nos resultados de estudos futuros.Resumen Antecedentes: Los estudios de asociación genética son cada vez más usados en los programas de mejoramiento genético. Sin embargo, resultados inconsistentes de los estudios -como positivos, negativos o ausencia de asociación- restringen la reproducibilidad y su aplicación adecuada, propiciando la aparición de sesgos. Objetivo: Identificar y clasificar las fuentes potenciales de sesgo y determinar posibles estrategias para evitarlo en estudios de asociación genética en ganado. Fuentes de sesgo en estudios de asociación genética: Las fuentes genéticas y genómicas de sesgo incluyen los efectos asociados con la expresión que gobierna los loci. Los sesgos estadísticos y de muestreo están relacionados con factores como la estratificación y el tamaño de la base de datos. Estrategias para corregir sesgos en estudios de asociación genética: Las estrategias de corrección difieren en naturaleza. Las estrategias genéticas y genómicas se basan en determinar el enfoque apropiado para obtener la información genética. Las estrategias estadísticas y relacionadas con el muestreo se basan en la agrupación de individuos con ciertos rasgos que conducen a una reducción de la heterogeneidad. Conclusión. Se deben considerar las metodologías utilizadas en estudios previos para jerarquizar las fuentes de sesgo y facilitar las decisiones sobre el uso de herramientas para reducir inconsistencias en resultados futuros

Sources of bias in genetic association studies in cattle: A review

Abstract Background: Genetic association studies have been increasingly used in cattle breeding programs. However, inconsistent results -such as positive, negative, or absence of association- across studies restrain reproducibility and proper implementation, propitiating the occurrence of bias. Objective: To identify and classify potential sources of bias and determine possible strategies to avoid it in genetic association studies in cattle. Source of bias in genetic association studies: Genetic and genomic sources of bias include effects associated with the gene loci governing expression. Sampling-related and statistical biases are related with factors such as stratification and database size. Strategies to correct bias in genetic association studies: Correction strategies differ in nature. Genetic and genomic strategies are based on determining the appropriate approach to obtain and report the genetic information. Sampling-related and statistical strategies are based on grouping individuals with certain traits that lead to a reduction in heterogeneity. Conclusion: It is necessary to consider the methodology used in previous studies to establish a hierarchy of sources of bias and facilitate decisions on the use of tools to reduce inconsistencies in the results of future studies

Potential influence of κ-casein and β-lactoglobulin genes in genetic association studies of milk quality traits

Objective From a review of published information on genetic association studies, a meta-analysis was conducted to determine the influence of the genes κ-casein (CSN3) and β-lactoglobulin (LGB) on milk yield traits in Holstein, Jersey, Brown Swiss, and Fleckvieh. Methods The GLIMMIX procedure was used to analyze milk production and percentage of protein and fat in milk. Models included the main effects and all their possible two-way interactions; not estimable effects and non-significant (p>0.05) two-way interactions were dropped from the models. The three traits analyzed used Poisson distribution and a log link function and were determined with the Interactive Data Analysis of SAS software. Least square means and multiple mean comparisons were obtained and performed for significant main effects and their interactions (p<0.0255). Results Interaction of breed by gene showed that Holstein and Fleckvieh were the breeds on which CSN3 (6.01%±0.19% and 5.98%±0.22%), and LGB (6.02%±0.19% and 5.70%±0.22%) have the greatest influence. Interaction of breed by genotype nested in the analyzed gene indicated that Holstein and Jersey showed greater influence of the CSN3 AA genotype, 6.04%±0.22% and 5.59%±0.31% than the other genotypes, while LGB AA genotype had the largest influence on the traits analyzed, 6.05%±0.20% and 5.60%±0.19%, respectively. Furthermore, interaction of type of statistical model by genotype nested in the analyzed gene indicated that CSN3 and LGB genes had similar behavior, maintaining a difference of more than 7% across analyzed genotypes. These results could indicate that both Holstein and Jersey have had lower substitution allele effect in selection programs that include CSN3 and LGB genes than Brown Swiss and Fleckvieh. Conclusion Breed determined which genotypes had the greatest association with analyzed traits. The mixed model based in Bayesian or Ridge Regression was the best alternative to analyze CSN3 and LGB gene effects on milk yield and protein and fat percentages

Polymorphism of three milk protein genes in Mexican Jersey cattle

The objective was to estimate the allelic and genotypic frequencies, genetic diversity and polymorphic information content for the β-casein, κ-casein and β-lactoglobulin genes. Blood and frozen semen samples were collected from 453 Jersey individuals registered by the Mexican Jersey Cattle Association. Twenty eight breed specific SNP primers for whole genes were used. The B allele of κ-casein had higher frequency (0.69) than the A (0.26) and E (0.05). For β-lactoglobulin, the highest frequency was for B (0.72), followed by A and C alleles (0.26 and 0.02, respectively). The β-casein allele with the highest frequency was A2 (0.71), followed by A1 (0.19), A3 (0.05), B (0.04) and C (0.01). The average genetic diversity (He) was 0.53. The average locus effective allele number was 1.79. These results indicate a high allelic diversity for κ-caseín, β-casein and β-lactoglobulin that could be included in breeding programs in the population studied, aimed to improve the milk quality traits of economic importance

Modificación del método de tiocianato de guanidina para extraer ADN de semen para análisis genómico en mamíferos

The genomic and transcriptomic analyses for selection and genetic improvement require DNA or RNA of hig concentration and purity, coming from different tissues, including semen. The DNA may be from hair, saliva, cartilage, blood, or semen. The methods usually used to extract DNA from semen have low efficiency in terms of quantity and quality. This is due to the solvents and dilutors used for semen conservation, physical and chemical characteristics of sperms, and non-cellular fraction of ejaculate. In this study, modifications to the guanidinium thiocyanate method are proposed, including a second washing of the sample using a phosphate buffer solution, and two washing with organic solvents, one strong (phenol:chloroform:Isoamyl alcohol), and one weak (chloroform:isoamyl alcohol), to get rid of the protein and dilutors present in the sample. Additionally, it is proposed a separate incubation with RNA-ase to reduce contamination of nucleic acids during measurement and dilution preparation for PCR amplification. The precipitation added to the isopropanol of the original method 3 M sodium acetate to separate the residuals of potential PCR inhibitors. Finally, there were included high-speed centrifugation and decantation to avoid the need for mechanical separation of the DNA and protein. The DNA extracted with the modified method did not present degradation, and the quality and quantity were better (P<0.0001) than the original, with a mean of 1.84±0.09 in the range of 260/ 280 and 156.99±7.29 ng/l for concentration. The present method of extraction is a viable low-cost alternative to obtain DNA from semen with the necessary characteristics for genomic analysis in mammals.The genomic and transcriptomic analyses for selection and genetic improvement require DNA or RNA of hig concentration and purity, coming from different tissues, including semen. The DNA may be from hair, saliva, cartilage, blood, or semen. The methods usually used to extract DNA from semen have low efficiency in terms of quantity and quality. This is due to the solvents and dilutors used for semen conservation, physical and chemical characteristics of sperms, and non-cellular fraction of ejaculate. In this study, modifications to the guanidinium thiocyanate method are proposed, including a second washing of the sample using a phosphate buffer solution, and two washing with organic solvents, one strong (phenol:chloroform:Isoamyl alcohol), and one weak (chloroform:isoamyl alcohol), to get rid of the protein and dilutors present in the sample. Additionally, it is proposed a separate incubation with RNA-ase to reduce contamination of nucleic acids during measurement and dilution preparation for PCR amplification. The precipitation added to the isopropanol of the original method 3 M sodium acetate to separate the residuals of potential PCR inhibitors. Finally, there were included high-speed centrifugation and decantation to avoid the need for mechanical separation of the DNA and protein. The DNA extracted with the modified method did not present degradation, and the quality and quantity were better (P<0.0001) than the original, with a mean of 1.84±0.09 in the range of 260/ 280 and 156.99±7.29 ng/l for concentration. The present method of extraction is a viable low-cost alternative to obtain DNA from semen with the necessary characteristics for genomic analysis in mammals.Los análisis genómicos y transcriptómicos para selección y mejoramiento genético animal requieren ADN o ARN de alta concentración y pureza, proveniente de diferentes tejidos incluyendo semen. Los métodos usualmente utilizados para extraer ADN de semen son menos efectivos en cantidad y calidad de ADN, debido a los solventes y diluyente utilizados para la conservación, características físico-químicas de los espermatozoides, y fracción no celular del eyaculado. En este estudio, se proponen modificaciones al método de tiocianato de guanidina, incluyendo un segundo lavado de la muestra con solución buffer fosfato, y dos lavados con solventes orgánicos, uno fuerte (fenol:cloroformo:alcohol isoamílico) y uno débil (cloroformo:alcohol isoamílico), para retirar la proteína y diluyente presentes en la muestra. Además, se propone una incubación por separado con ARNasa para reducir contaminación de ácidos nucleicos en la medición y elaboración de diluciones para amplificación por PCR. La precipitación agregó al isopropanol de la metodología original 3 M de acetato de sodio para retirar restos de posibles inhibidores de la PCR. Finalmente, se incluyeron centrifugaciones de alta velocidad y decantaciones para evitar la necesidad de separación mecánica del ADN y la proteína. El ADN extraído con el método propuesto no presentó degradación, y la calidad y cantidad fueron mejores (P<0.0001), encontrándose una media de 1.84±0.09 en el rango 260/280 y 156.99±7.29 ng/ꟺ para la variable de concentración. El presente método de extracción es una alternativa de bajo costo, viable para obtener ADN de semen con características necesarias para análisis genómicos en mamíferos.

Improvement of Ruminal Neutral Detergent Fiber Degradability by Obtaining and Using Exogenous Fibrolytic Enzymes from White-Rot Fungi

The present review examines the factors and variables that should be considered to obtain, design, and evaluate EFEs that might enhance ruminal NDF degradability. Different combinations of words were introduced in Google Scholar, then scientific articles were examined and included if the reported factors and variables addressed the objective of this review. One-hundred-and-sixteen articles were included. The fungal strains and culture media used to grow white-rot fungi induced the production of specific isoforms of cellulases and xylanases; therefore, EFE products for ruminant feed applications should be obtained in cultures that include the high-fibrous forages used in the diets of those animals. Additionally, the temperature, pH, osmolarity conditions, and EFE synergisms and interactions with ruminal microbiota and endogenous fibrolytic enzymes should be considered. More consistent results have been observed in studies that correlate the cellulase-to-xylanase ratio with ruminant productive behavior. EFE protection (immobilization) allows researchers to obtain enzymatic products that may act under ruminal pH and temperature conditions. It is possible to generate multi-enzyme cocktails that act at different times, re-associate enzymes, and simulate natural protective structures such as cellulosomes. Some EFEs could consistently improve ruminal NDF degradability if we consider fungal cultures and ruminal environmental conditions variables, and include biotechnological tools that might be useful to design novel enzymatic products

Improvement of Ruminal Neutral Detergent Fiber Degradability by Obtaining and Using Exogenous Fibrolytic Enzymes from White-Rot Fungi

The present review examines the factors and variables that should be considered to obtain, design, and evaluate EFEs that might enhance ruminal NDF degradability. Different combinations of words were introduced in Google Scholar, then scientific articles were examined and included if the reported factors and variables addressed the objective of this review. One-hundred-and-sixteen articles were included. The fungal strains and culture media used to grow white-rot fungi induced the production of specific isoforms of cellulases and xylanases; therefore, EFE products for ruminant feed applications should be obtained in cultures that include the high-fibrous forages used in the diets of those animals. Additionally, the temperature, pH, osmolarity conditions, and EFE synergisms and interactions with ruminal microbiota and endogenous fibrolytic enzymes should be considered. More consistent results have been observed in studies that correlate the cellulase-to-xylanase ratio with ruminant productive behavior. EFE protection (immobilization) allows researchers to obtain enzymatic products that may act under ruminal pH and temperature conditions. It is possible to generate multi-enzyme cocktails that act at different times, re-associate enzymes, and simulate natural protective structures such as cellulosomes. Some EFEs could consistently improve ruminal NDF degradability if we consider fungal cultures and ruminal environmental conditions variables, and include biotechnological tools that might be useful to design novel enzymatic products

Design and implementation of the AMIGA embedded system for data acquisition

International audienceThe Auger Muon Infill Ground Array (AMIGA) is part of the AugerPrime upgrade of the Pierre Auger Observatory. It consists of particle counters buried 2.3 m underground next to the water-Cherenkov stations that form the 23.5 km2 large infilled array. The reduced distance between detectors in this denser area allows the lowering of the energy threshold for primary cosmic ray reconstruction down to about 1017 eV. At the depth of 2.3 m the electromagnetic component of cosmic ray showers is almost entirely absorbed so that the buried scintillators provide an independent and direct measurement of the air showers muon content. This work describes the design and implementation of the AMIGA embedded system, which provides centralized control, data acquisition and environment monitoring to its detectors. The presented system was firstly tested in the engineering array phase ended in 2017, and lately selected as the final design to be installed in all new detectors of the production phase. The system was proven to be robust and reliable and has worked in a stable manner since its first deployment

Measurement of quarkonium production cross sections in pp collisions at s=\sqrt{s}= 13 TeV

Differential production cross sections of prompt J/ψ and ψ(2S) charmonium and ϒ(nS) ( n=1,2,3 ) bottomonium states are measured in proton–proton collisions at s=13TeV , with data collected by the CMS detector at the LHC, corresponding to an integrated luminosity of 2.3 fb$^{−1}$ for the J/ψ and 2.7 fb$^{−1}$ for the other mesons. The five quarkonium states are reconstructed in the dimuon decay channel, for dimuon rapidity |y|<1.2 . The double-differential cross sections for each state are measured as a function of y and transverse momentum, and compared to theoretical expectations. In addition, ratios are presented of cross sections for prompt ψ(2S) to J/ψ , ϒ(2S) to ϒ(1S) , and ϒ(3S) to ϒ(1S) production