Characterization of intronic SNP located in candidate genes influencing cattle temperament

The objective of this study was to evaluate the effect of intronic single nucleotide polymorphisms (SNP) on temperament traits in a Brahman cattle population. The SNP located in CACNG4, EXOC4, NRXN3, and SLC9A4 candidate genes were genotyped in 250 animals with temperament records of exit velocity, pen score, and temperament score. Rs3423464051:G>A in the CACNG4 gene was associated with exit velocity and temperament score. An in silico analysis of the five intronic SNP showed that alternative alleles of CACNG4-rs3423464051, EXOC4-rs109393235, and SLC9A4-rs109722627 SNP could alter branch point sites during splicing, while a protein-protein interaction network analysis demonstrated a GRIA2 gene-mediated interaction between CACNG4 and NRXN3. The present results support previously reported evidence regarding bovine temperament-related candidate genes, particularly CACNG4, which is a confirmed candidate gene in need of more detailed analyses to reveal its role in temperament-related traits.(AU)

Performance of the tetra-primer PCR technique compared to PCR-RFLP in the search for rs12979860 (C/T) and rs8099917 (T/G) single nucleotide polymorphisms (SNPs) in the IFNL4 gene / Desempenho da técnica tetra-primer PCR em relação a PCR-RFLP na pesquisa de polimorfismos de nucleotídeos únicos (SNPs) rs12979860 (C/T) e rs8099917 (T/G) no gene IFNL4

Single nucleotide polymorphisms (SNPs, rs12979860 e rs8099917) in the Interferon Lambda 4 gene (IFNL4, formerly IFNL3and/or IL28B) has been associated with failure in the innate immune response, sustained virological response in hepatitis C, and HTLV-1-associated myelopathy (HAM) development. To search for these polymorphisms several methodologies can be employed, such as sequencing, real-time or quantitative polymerase chain reaction (qPCR), restriction fragment length polymorphism analysis in PCR products (PCR-RFLP), and tetra-primer PCR. The present study compared the performance of the tetra-primer PCR in relation to the PCR-RFLP, both optimized in the Research HTLV Laboratory of the Center of Immunology of Instituto Adolfo Lutz in São Paulo. One hundred DNA samples obtained from patients of STD/Aids Reference Centre in São Paulo, previously analyzed for IL28B SNPs by PCR-RFLP were selected for analysis, after confirming that they represent all IL28B SNPs patterns described in the literature. The results obtained showed concordance between the PCR-RFLP and the tetra-primer PCR SNPs results, and because of the low cost, easy to perform, and minor employment of biological specimen and reagents, the tetra-primer PCR is of choice to be used in routine. (AU)

Polimorfismos de nucleotídeos únicos (single nucleotide polymorphisms, SNPs rs12979860 e rs8099917) no gene que codifica o Interferon Lambda 4 (IFNL4, antigamente IFNL3 e/ou IL28B) têm sido associados às falhas na resposta imune inata e resposta virológica sustentada na hepatite C, e a mielopatia associada ao HTLV-1 (HTLV-1-associated myelopathy, HAM). A pesquisa destes polimorfismos pode empregar diversas metodologias: sequenciamento, reação em cadeia da polimerase em tempo real ou quantitativa (quantitative polymerase chain reaction, qPCR), análise de fragmentos de restrição enzimática em produtos de PCR (restriction fragment length polymorphism in PCR products, PCR-RFLP) e a tetra-primer PCR. Este estudo comparou o desempenho da tetra-primer PCR em relação a PCR-RFLP, ambas otimizadas no Laboratório de Pesquisa em HTLV do Centro de Imunologia do Instituto Adolfo Lutz de São Paulo. Foram selecionadas 100 amostras de DNA obtidas de pacientes do Centro de Referência e Treinamento em DST/Aids de São Paulo cujos SNPs na IL28B foram anteriormente determinados por PCR-RFLP e representaram todos os perfis descritos em literatura. Os resultados obtidos mostraram concordância entre elas, e pelo fato da tetra-primer PCR ter menor custo, ser de fácil execução, empregar menos tempo, insumos e material biológico, é a técnica de escolha para uso em rotina. (AU)

Overview of the use of genomic data in animal breeding / Panorama do uso de dados genômicos no melhoramento genético animal

The use of molecular information in breeding programs contributed to important advances in the improvement of traits of economic interest in livestock production. The advent of single nucleotide polymorphism (SNP) panels applied to genome-wide selection (GWS) and genome-wide association studies (GWAS), along with computational advances (e.g., use of powerful software and robust analyses) allowed a better understanding of the genetic architecture of farm animals and increased the selection efficiency. In this context, the statistic method single-step GBLUP has been frequently used to perform GWS, and more recently GWAS analyses, providing accurate predictions and QTL detection, respectively. Nevertheless, in developing countries, species such as sheep and goats, whose genomic data are more difficult to be obtained, the use of data simulation has been efficient in the study of the major factors involved in the selection process, such as size of training population, density of SNP chips, and genotyping strategies. The effects of these factors are directly associated with the prediction accuracy of genomic breeding values. In this review we showed important aspects of the use of genomics in the genetic improvement of production traits of animals, the main methods currently used for prediction and estimation of molecular marker effects, the importance of data simulation for validation of those methods, as well as the advantages, challenges and limitations of the use of GWS and GWAS in the current scenario of livestock production.

Em programas de melhoramento genético, o uso de informações moleculares garantiu importantes avanços para a melhoria de características de interesse econômico, no âmbito da produção animal. O advento da tecnologia de painéis de SNPs aplicados à seleção genômica ampla (GWS) e associação genômica ampla (GWAS), aliado ao avanço computacional, com o uso de softwares e análises robustas, permitiram melhor compreensão sobre a arquitetura genética dos animais de produção e, consequentemente, maior eficiência na seleção. Nesse contexto, o método estatístico single-step GBLUP tem sido utilizado, frequentemente, na execução da GWS e, mais recentemente, em GWAS, possibilitando predições acuradas e detecção de QTLs, respectivamente. No entanto, em países em desenvolvimento e, em espécies como os ovinos e caprinos, que existe maior dificuldade para a aquisição de dados genômicos, o uso da simulação de dados tem se mostrado eficiente para estudar os principais fatores envolvidos no processo de seleção, como o tamanho da população de treinamento, densidade de chipde SNPs e estratégias de genotipagem, cujos efeitos estão diretamente associados à acurácia da predição de valores genéticos genômicos. Nesta revisão, serão abordados pontos importantes sobre o uso da genômica no melhoramento genético de características produtivas em animais, principais métodos de predição e estimação de efeitos de marcadores moleculares na atualidade, a importância da simulação de dados para a validação desses métodos, bem como as vantagens, os desafios e as limitações no cenário atual da produção animal com o uso da seleção e associação genômica ampla.

Genome-enabled prediction through quantile random forest for complex traits / Predição genômica por meio do random forest quantílitico para características complexas

ABSTRACT: Quantile Random Forest (QRF) is a non-parametric methodology that combines the advantages of Random Forest (RF) and Quantile Regression (QR). Specifically, this approach can explore non-linear functions, determining the probability distribution of a response variable and extracting information from different quantiles instead of just predicting the mean. This evaluated the performance of the QRF in the genomic prediction for complex traits (epistasis and dominance). In addition, compare the accuracies obtained with those derived from the G-BLUP. The simulation created an F2 population with 1,000 individuals and genotyped for 4,010 SNP markers. Besides, twelve traits were simulated from a model considering additive and non-additive effects, QTL (Quantitative trait loci) numbers ranging from eight to 120, and heritability of 0.3, 0.5, or 0.8. For training and validation, the 5-fold cross-validation approach was used. For each fold, the accuracies of all the proposed models were calculated: QRF in five different quantiles and three G-BLUP models (additive effect, additive and epistatic effects, additive and dominant effects). Finally, the predictive performance of these methodologies was compared. In all scenarios, the QRF accuracies were equal to or greater than the methodologies evaluated and proved to be an alternative tool to predict genetic values in complex traits.

RESUMO: Quantile Random Forest (QRF) é uma metodologia não paramétrica, que combina as vantagens do Random Forest (RF) e da Regressão Quantílica (QR). Especificamente, essa abordagem pode explorar funções não lineares, determinando a distribuição de probabilidade de uma variável resposta e extraindo informações de diferentes quantis em vez de apenas prever a média. O objetivo deste trabalho foi avaliar o desempenho do QRF em predizer o valor genético genômico para características com arquitetura genética não aditiva (epistasia e dominância). Adicionalmente, as acurácias obtidas foram comparadas com aquelas advindas do G-BLUP. A simulação criou uma população F2 com 1.000 indivíduos genotipados para 4.010 marcadores SNP. Além disso, doze características foram simuladas a partir de um modelo considerando efeitos aditivos e não aditivos, com número de QTL (Quantitative trait loci) variando de oito a 120 e herdabilidade de 0,3, 0,5 ou 0,8. Para treinamento e validação foi usada a abordagem da validação cruzada 5-fold. Para cada um dos folds foram calculadas as acurácias de todos os modelos propostos: QRF em cinco quantis diferentes e três modelos do G-BLUP (com efeito aditivo, aditivo e epistático, aditivo e dominante). Por fim, o desempenho preditivo dessas metodologias foi comparado. Em todos os cenários, as acurácias do QRF foram iguais ou superiores às metodologias avaliadas e mostrou ser uma ferramenta alternativa para predizer valores genéticos em características complexas.

Morphometric and molecular differentiation of Pimelodus grosskopfii and Pimelodus yuma (Siluriformes: Pimelodidae)

Pimelodus grosskopfii and Pimelodus yuma, two species endemic to the Magdalena-Cauca basin in Colombia, overlap in the ranges of some of their diagnostic characters, which hampers their correct morphological identification. Aiming to help discriminate these species, this study conducted an integrative analysis using traditional and geometric morphometrics, phylogenetic analysis based on partial sequences of the mitochondrial cytochrome c oxidase subunit 1 gene (COI, cox1) and the identification of diagnostic Single Nucleotide Polymorphism markers (SNP). The species differ significantly in body geometry, allowing 100% discrimination, which was reinforced by a phylogenetic analysis that recovered well-supported monophyly of each species (posterior probability > 0.95). Additionally, the traditional morphometric results corroborated some previously reported diagnostic traits for both species and let us describe one non-overlapping ratio related to the adipose fin length. Three of five SNP markers had reciprocally exclusive alleles suitable for identifying each species. The morphometric and molecular methods conducted in this study constitute alternative tools for the correct discrimination of P. grosskopfii and P. yuma in the wild and in captive populations used for aquaculture.(AU)

Pimelodus grosskopfii y Pimelodus yuma, dos especies endémicas de la Cuenca Magdalena-Cauca en Colombia, se superponen en los rangos de variación de algunos de sus caracteres diagnósticos, lo que dificulta su correcta diferenciación morfológica. Con el objetivo de contribuir a la discriminación de estas especies, se realizó un análisis integrativo utilizando la morfometría geométrica y tradicional, análisis filogenético basado en secuencias parciales del gen mitocondrial citocromo c oxidasa subunidad I (COI, cox1) y la identificación de marcadores diagnósticos de polimorfismo de nucleótido único (SNP). Las especies difieren significativamente en la geometría del cuerpo, permitiendo una discriminación del 100%, lo que fue reforzado por un análisis filogenético que recuperó una monofilia bien soportada para cada especie (probabilidad posterior > 0,95). Además, los resultados de la morfometría tradicional corroboraron algunos rasgos diagnósticos previamente reportados para ambas especies y nos permitieron describir una proporción que no se sobrepone, relacionada con la longitud de la aleta adiposa. Tres de los cinco marcadores SNP poseían alelos recíprocamente exclusivos, adecuados para identificar cada especie. Los métodos morfométricos y moleculares implementados en este estudio constituyen herramientas alternativas para la correcta discriminación de P. grosskopfii y P. yuma tanto en la naturaleza como en poblaciones cautivas utilizadas para la acuicultura.(AU)

Genetic relationships of the Yucatan black hairless pig with Iberian breeds using single nucleotide polymorfisms / Relações genéticas de porcos pretos calvos de Yucatán com raças ibéricas usando Polimorfismo de nucleotídeos isolados

To conduct ex-situ creole pig conservation programs, it is essential to determine which breeding animals will be used, preferentially those with a more significant Iberian genetic component to preserve their origin. This study used a Yucatan black hairless pigs (YBHP) subpopulation to estimate its genetic diversity and population structure. One hundred four adult pigs were selected for the absence of hair, black skin (without spots), black hoof, and straight snout. The porcine-GGP-50K chip was used for SNP genotyping in YBHP, and information on Iberian and Yucatán hairless pigs from the United States (USYU) was taken from databases. All analysis was performed using PLINK v1.9 and v2.1 software. Inbreeding and fixation index values were lower in YBHP, with high observed heterozygosity and allogamy index values, which agree with those obtained in the populations of Canarias and Chato Murciano. According to the clusters generated by the "Genome-Wide Identity by State" analysis, four groups were identified, one of which included pigs from Guadyerbas, USYU, and YBHP. Between populations, YBHP was closely related to the hairless pigs from Guadyerbas, USYU, and Canarias. Principal component analysis showed the same result. According to the results obtained from the runs of homozygosity investigation, aimed to get pools consensus of regions of overlapping, 119 SNPs associated with genes and biological processes were identified. The BMP7 and NSUN2 genes were associated with epithelial cell differentiation, morphogenesis, and epithelial development. For nutrient metabolism: energy, the HADHA, PPARA, ADD1/SREBF1, and FAT 1genes were identified.(AU)

Para realizar programas de conservação ex-situ de suínos crioulos, é importante determinar quais animais serão criados, preferencialmente aqueles com maior componente de genética ibérica, para preservar sua origem. Uma subpopulação de porco preto calvo de Yucatán (YBHP) foi usada para estimar sua diversidade genética e estrutura populacional. Um total de 104 suínos adultos foram selecionados levando-se em consideração características como ausência de pelos, pele preta (sem manchas), casco preto e focinho reto. O painel GGP-50K foi utilizado para a genotipagem dos SNPs em animais YBHP, e informações de porcos sem pelos ibéricos e de Yucatán dos Estados Unidos (USYU) foram retiradas de bancos de dados. Todas as análises foram realizadas com o software PLINK v1.9 e v2.1. Os valores dos índices de endogamia e fixação foram menores em YBHP, com altos valores de índice de heterozigosidade e alogamia observados, que concordam com os obtidos nas populações de Canárias e Chato Murciano. De acordo com os clusters gerados pela análise "Genoma-Wide Identity By State", quatro grupos foram identificados, um dos quais incluiu porcos de Guadyerbas, USYU e YBHP. Entre as populações, YBHP estava intimamente relacionado com os porcos sem pelo de Guadyerbas, USYU e Canárias. A análise de componentes principais mostrou o mesmo resultado. De acordo com os resultados obtidos nas corridas de investigação de homozigose, visando obter consenso de pools de regiões de sobreposição, foram identificados 119 SNPs associados a genes e processos biológicos. Os genes BMP7 e NSUN2 foram associados à diferenciação de células epiteliais, morfogênese e desenvolvimento epitelial. Para metabolismo de nutrientes: energia, os genes HADHA, PPARA, ADD1/SREBF1 e FAT1 foram identificados.(AU)

Overview of the use of genomic data in animal breeding / Panorama do uso de dados genômicos no melhoramento genético animal

ABSTRACT: The use of molecular information in breeding programs contributed to important advances in the improvement of traits of economic interest in livestock production. The advent of single nucleotide polymorphism (SNP) panels applied to genome-wide selection (GWS) and genome-wide association studies (GWAS), along with computational advances (e.g., use of powerful software and robust analyses) allowed a better understanding of the genetic architecture of farm animals and increased the selection efficiency. In this context, the statistic method single-step GBLUP has been frequently used to perform GWS, and more recently GWAS analyses, providing accurate predictions and QTL detection, respectively. Nevertheless, in developing countries, species such as sheep and goats, whose genomic data are more difficult to be obtained, the use of data simulation has been efficient in the study of the major factors involved in the selection process, such as size of training population, density of SNP chips, and genotyping strategies. The effects of these factors are directly associated with the prediction accuracy of genomic breeding values. In this review we showed important aspects of the use of genomics in the genetic improvement of production traits of animals, the main methods currently used for prediction and estimation of molecular marker effects, the importance of data simulation for validation of those methods, as well as the advantages, challenges and limitations of the use of GWS and GWAS in the current scenario of livestock production.

RESUMO: Em programas de melhoramento genético, o uso de informações moleculares garantiu importantes avanços para a melhoria de características de interesse econômico, no âmbito da produção animal. O advento da tecnologia de painéis de SNPs aplicados à seleção genômica ampla (GWS) e associação genômica ampla (GWAS), aliado ao avanço computacional, com o uso de softwares e análises robustas, permitiram melhor compreensão sobre a arquitetura genética dos animais de produção e, consequentemente, maior eficiência na seleção. Nesse contexto, o método estatístico single-step GBLUP tem sido utilizado, frequentemente, na execução da GWS e, mais recentemente, em GWAS, possibilitando predições acuradas e detecção de QTLs, respectivamente. No entanto, em países em desenvolvimento e, em espécies como os ovinos e caprinos, que existe maior dificuldade para a aquisição de dados genômicos, o uso da simulação de dados tem se mostrado eficiente para estudar os principais fatores envolvidos no processo de seleção, como o tamanho da população de treinamento, densidade de chipde SNPs e estratégias de genotipagem, cujos efeitos estão diretamente associados à acurácia da predição de valores genéticos genômicos. Nesta revisão, serão abordados pontos importantes sobre o uso da genômica no melhoramento genético de características produtivas em animais, principais métodos de predição e estimação de efeitos de marcadores moleculares na atualidade, a importância da simulação de dados para a validação desses métodos, bem como as vantagens, os desafios e as limitações no cenário atual da produção animal com o uso da seleção e associação genômica ampla.

Genome-enabled prediction through quantile random forest for complex traits / Predição genômica por meio do random forest quantílitico para características complexas

Quantile Random Forest (QRF) is a non-parametric methodology that combines the advantages of Random Forest (RF) and Quantile Regression (QR). Specifically, this approach can explore non-linear functions, determining the probability distribution of a response variable and extracting information from different quantiles instead of just predicting the mean. This evaluated the performance of the QRF in the genomic prediction for complex traits (epistasis and dominance). In addition, compare the accuracies obtained with those derived from the G-BLUP. The simulation created an F2 population with 1,000 individuals and genotyped for 4,010 SNP markers. Besides, twelve traits were simulated from a model considering additive and non-additive effects, QTL (Quantitative trait loci) numbers ranging from eight to 120, and heritability of 0.3, 0.5, or 0.8. For training and validation, the 5-fold cross-validation approach was used. For each fold, the accuracies of all the proposed models were calculated: QRF in five different quantiles and three G-BLUP models (additive effect, additive and epistatic effects, additive and dominant effects). Finally, the predictive performance of these methodologies was compared. In all scenarios, the QRF accuracies were equal to or greater than the methodologies evaluated and proved to be an alternative tool to predict genetic values in complex traits.

Quantile Random Forest (QRF) é uma metodologia não paramétrica, que combina as vantagens do Random Forest (RF) e da Regressão Quantílica (QR). Especificamente, essa abordagem pode explorar funções não lineares, determinando a distribuição de probabilidade de uma variável resposta e extraindo informações de diferentes quantis em vez de apenas prever a média. O objetivo deste trabalho foi avaliar o desempenho do QRF em predizer o valor genético genômico para características com arquitetura genética não aditiva (epistasia e dominância). Adicionalmente, as acurácias obtidas foram comparadas com aquelas advindas do G-BLUP. A simulação criou uma população F2 com 1.000 indivíduos genotipados para 4.010 marcadores SNP. Além disso, doze características foram simuladas a partir de um modelo considerando efeitos aditivos e não aditivos, com número de QTL (Quantitative trait loci) variando de oito a 120 e herdabilidade de 0,3, 0,5 ou 0,8. Para treinamento e validação foi usada a abordagem da validação cruzada 5-fold. Para cada um dos folds foram calculadas as acurácias de todos os modelos propostos: QRF em cinco quantis diferentes e três modelos do G-BLUP (com efeito aditivo, aditivo e epistático, aditivo e dominante). Por fim, o desempenho preditivo dessas metodologias foi comparado. Em todos os cenários, as acurácias do QRF foram iguais ou superiores às metodologias avaliadas e mostrou ser uma ferramenta alternativa para predizer valores genéticos em características complexas.

Identification of Polymorphism in the MC1R Gene and Its Association with the Melanin Content in Feathers of Chinese Yellow Quails

MC1R plays a crucial role in controlling the type of melanin synthesized in the melanocytes, which greatly affects plumage color in birds. One g.16796362G/T SNP was found in the MC1R gene coding region, which caused a Met120Ile mutation in the amino acid sequence. The Met120Ile mutation was located in the third transmembrane domain of the MC1R protein and decreased protein stability. The g.16796362G/T locus achieved medium polymorphism and had significant association with feather melanin content in Chinese yellow quails. The contents of total melanin and pheomelanin with AA genotype were significant lower than those with AB or BB genotypes in skin tissues, while the expression levels of MC1R mRNA had no significant difference in feathers with different genotypes. This experiment indicated that the Met120Ile mutation could affect the function of the MC1R protein and change the biosynthesis of melanin in Chinese yellow quails.(AU)

Embryo biopsies for genomic selection in tropical dairy cattle

Genomic selection has transformed the livestock industry, enabling early-life selection of animals. Biopsy sampling of pre-implantation embryos has been described since 1968. However, it was only after 2010, with the advancement of molecular biology techniques such as whole genomic amplification and SNP Chips, that next-generation sequencing became commercially available for bovine embryos. It is now possible to make decisions about which embryos to transfer not only based on recipients' availability or embryo morphology but also on genomic estimates. This technology can be implemented for a wide spectrum of applications in livestock. In this review, we discuss the use of embryo biopsy for genomic selection and share our experience with Gir and Girolando Brazilian breeding programs, as well as future goals for implementing it in Brazilian bovine in vitro embryo production practices.(AU)

Heterozygosity as a factor of increasing the meat productivity of kalmyk steers / Heterozigosidade como fator de aumento da produtividade da carne de bois kalmyk

The present work carried out full-genome SNP genotyping of 16-month-old Kalmyk steers to study their productive characteristics and beef quality indicators in the leading farms of the Republic of Kalmykia (Group I was located at the Agrofirma Aduchi farm; Group II at the Kirovsky breeding plant, and Group III at the Plodovitoye agricultural cooperative). As a result of investigating the frequencies of some homozygous alleles, the study established that the heterozygous allele A/A varied considerably along the lines from 0.2785 to 0.3146, while B/B varied from 0.3697 to 0.4125. Meanwhile, the heterozygous allele A/B varied from 0.2986 to 0.3197. Estimated inbreeding coefficients were 1.35, 1.28 and 1.27%. The conducted studies established a higher natural resistance determined by lysozyme, bactericidal and phagocytic activities of steers raised at the Agrofirma Aduchi as farm than their counterparts at the other agricultural enterprises. Over the entire period of the experiment, the steers from 8 to 16 months of age in Group I exceeded the indices of their counterparts in Groups II and III by 30.46g, or 3.31% and 38.04g, or 4.16%, respectively. It is concluded that an increase in the heterozygosity of the studied Kalmyk steers not only results in higher meat productivity, but also improves the quality of carcass and beef quality, increases the yield of more valuable meat grades, and optimizes the fractional composition of proteins.

O presente trabalho realizou a genotipagem de bois Kalmyk de 16 meses de idade para estudar suas características produtivas e indicadores de qualidade da carne bovina nas principais fazendas da República de Kalmykia (o Grupo I estava localizado na fazenda Agrofirma Aduchi; Grupo II - na planta de criação Kirovsky; Grupo III - na cooperativa agrícola Plodovitoye). Como resultado da investigação das freqüências de alguns alelos homozigotos, o estudo estabeleceu que o alelo heterozigotos A/A variou consideravelmente de 0,2785 a 0,3146, enquanto o B/B variou de 0,3697 a 0,4125. Enquanto isso, o alelo heterozigoto A/B variou de 0,2986 a 0,3197. Os coeficientes estimados de consanguinidade foram de 1,35, 1,28 e 1,27%. Os estudos realizados estabeleceram uma maior resistência natural determinada pelas atividades lisozóides, bactericidas e fagocitárias dos bois criados na Agrofirma Aduchi como fazenda do que suas contrapartes nas outras empresas agrícolas. Durante todo o período do experimento, os bois de 8 a 16 meses de idade no Grupo I excederam os índices de suas contrapartes nos Grupos II e III em 30,46g, ou 3,31% e 38,04g, ou 4,16%, respectivamente. Conclui-se que um aumento na heterozigosidade dos bois Kalmyk estudados não só resulta em maior produtividade da carne, mas também melhora a qualidade da carcaça e da carne bovina, aumenta o rendimento das carnes de maior valor e otimiza a composição fracionária das proteínas.

The relationship between IL-4 polymorphisms and asthma: a systematic review / A relação entre polimorfismos de IL-4 e asma: uma revisão sistemática

Asthma is a chronic and heterogeneous disease of the airways that begins in childhood and persists, in many cases, into adulthood. The disease is the result of environmental, epigenetic and genetic interactions. This work aims to review the polymorphisms described in the literature in the IL-4 gene associated with susceptibility or protection to the development of asthma. This is a systematic literature review, carried out in PubMed, MEDLINE and Science Direct databases in the time frame from 2000 to July 2021, revealing the following key points: IL-4, Polymorphisms and Asthma. The search resulted in 29 articles, all in English. Despite some divergent studies, the SNP rs2243250, which was the most studied in populations from different countries, was also the one that found the most correlations of susceptibility with the disease. It is concluded that although there is controversial data on IL-4 SNPs related to the disease, the association of pangenomic studies has brought a list of genes and their variations associated with the risk of developing asthma, such as the rs2243250 SNP that was well related in populations of several countries analyzed. (AU)

A asma é uma doença crônica e heterogênea das vias aéreas que tem início na infância e persiste em muitos casos até a vida adulta. A doença é resultado de interações ambientais, epigenéticas e genéticas. Este trabalho tem como objetivo revisar sobre os polimorfismos descritos na literatura no gene IL-4 associados à susceptibilidade ou proteção ao desenvolvimento da asma. Trata-se de uma revisão sistemática da literatura, feita nos bancos de dados PubMed, MEDLINE e Science Direct no corte temporal de 2000 a julho de 2021, ressaltando os seguintes pontos-chave: IL-4, Polimorfismos e Asma. A pesquisa resultou em 29 artigos, sendo em sua totalidade em língua inglesa. Apesar de alguns estudos divergentes, o SNP rs2243250, que foi o mais estudado em populações de diversos países, também foi o que mais encontrou correlações de susceptibilidade com a doença. Conclui-se que, apesar de haver dados controversos sobre os SNPs de IL-4 relacionados à doença, a associação dos estudos pangenômicos tem trazido uma lista de genes e variações deles associados com o risco de desenvolver a asma, como o SNP rs2243250 que foi bem relacionado em populações de vários países analisados (AU).

Genome-Wide Association Study on Two Immune-Related Traits in Jinghai Yellow Chicken

This study was designed to discover molecular marker associated with the interferon INF-γ and avian influenza (AI) antibody titer traits in Jinghai Yellow chicken (Gallus gallus). Serum samples were taken from 400 female chickens and the INF-γ concentrations and AI antibody titer levels were measured. A genome-wide association study was carried out using specific-locus amplified fragment (SLAF) sequencing. Bioinformatics analysis was applied to detect single-nucleotide polymorphisms (SNPs) associated with the two traits. After sequencing and quality control, 103,680 SLAFs and 90,961 SNPs were obtained. The 400 samples were divided into 10 subgroups to reduce the effects of group stratification. The Bonferroni adjusted P-value of genome-wide significance was set at 1.87E−06 according to the number of independent SNP markers and linkage disequilibrium blocks. A SNP that was significantly associated with INF-γ concentration was detected in the myomesin 1 (MYOM1) gene on chromosome 2, and another SNPthat was significantly associated with the AI antibody titer level was detected in an RNA methyltransferase gene (Nsun7), which was found to have an important biological function. We propose that MYOM1 and Nsun7 are valuable candidate genes that influence the disease resistance characters of chicken. However, in-depth investigations are needed to determine the essential roles of these genes in poultry disease resistance and their possible application in breeding disease resistant poultry.(AU)

Novel missense variant L46Q of fatty acid synthase gene and fatty acids content in Awassi sheep

This study was conducted to investigate the association between the polymorphism of the FASN gene with fatty acid content in Awassi sheep. A total of 100 male Awassi sheep between the ages of one and two and a half years old were used in this study. Phenotypic measurement was recorded at slaughter, and from each animal, the longissimus dorsi (LD) muscle samples were taken to analyze the fatty acid profile. Genotyping, sequencing reactions, and in silico tools were performed to confirm the variants in amplified fragments. The result of genotyping revealed two genotypes (AA and AB) of the ovine FASN gene (exon 3). Novel SNP (L46Q) was discovered only within the FASN gene (AB genotype). All utilized in silico tools revealed remarkably deleterious effects for the L46Q on the mutant protein structure, function, and stability. Association analysis revealed that the AB genotype has significantly (p < 0.05) higher levels of animal length and monounsaturated fatty acids (MUFA) with lower amounts of saturated fatty acids (SFA) content than the AA genotype. In conclusion, novel SNP (L46Q) was discovered within the FASN gene (AB genotype), made the animals that has the AB genotype associated with good meat quality traits and this polymorphism may serve as markers for meat quality.(AU)

Association between somatotropic axis gene polymorphisms and reproductive efficiency of bovine females: a review / Associação entre polimorfismos de genes do eixo somatotrópico e eficiência reprodutiva de fêmeas bovinas: revisão de literatura

Reproductive characteristics directly reflect on productive performance, as they determine the number of calves born annually and the interval between generations, thereby affecting the selection intensity. This allows for the determination of the most important economic variables that directly affect the production system. The present study is a literature review of somatotropic axis gene polymorphisms that are associated with reproductive functions in heifers and cows (Bos taurus taurus and Bos taurus indicus). The following characteristics were analyzed from the various studies reviewed: number of services per pregnancy (Nº services/ pregnancy), age at first calving (AFC), calving interval (CI), and period of service calving conception interval (CCI). The research was conducted during the period from 2011 to 2021, and associations were found among all indicators of reproductive efficiency evaluated in heifers and cows, with 27 single nucleotide polymorphisms (SNPs): 18 in GHR, 5 in IGF-I, and 4 in STAT5A. This study revealed the relationships between SNPs and the reproductive efficiency indicators and demonstrated that molecular genetic techniques enhance the animal selection process, resulting in more profitable systems that are sustainable in the long term.

Características reprodutivas refletem diretamente no desempenho produtivo visto que são capazes de determinar o número de bezerros nascidos anualmente, além de afetar o intervalo entre gerações e, consequentemente, a intensidade de seleção, fazendo com o que tais atributos sejam apontados como variáveis econômicas das mais importantes que afetam diretamente o sistema de produção. O presente estudo propõe realizar uma revisão de literatura de polimorfismos de genes do eixo somatotrópico associados a funções reprodutivas em novilhas e vacas (Bos taurus taurus e Bos taurus indicus), indicadas pelos índices: número de serviços por gestação (Nº serviços/gestação), idade ao primeiro parto (IPP), intervalo de partos (IP) e período de serviço, como também denominado de intervalo parto-concepção (IPC). As pesquisas encontradas durante o período de 2011 a 2021 demonstraram associações entre todos os indicadores de eficiência reprodutiva analisados de novilhas e vacas com 27 polimorfismos de nucleotídeo único (SNPs), sendo 18 em GHR, 5 em IGF-I e 4 em STAT5A. Dessa forma, este estudo mostrou relação entre os SNPs e os indicadores de eficiência reprodutiva, demonstrando que técnicas de genética molecular potencializam o processo de seleção dos animais, resultando em sistemas mais lucrativos e que se sustentam a longo prazo.

Genetic diversity analysis in dairy cows of Nariño, southwestern Colombia / Análise da diversidade genética em vacas leiteiras de Nariño, sudoeste da Colômbia

In Colombia, different dairy breeds were introduced from Europe and the United States, which underwent different crossing and selection processes that generated specific qualities or differences and which likely have their own genomic structure. To characterize genetic diversity, population structure, and admixture, we used genotypes from 23,182 autosomal single nucleotide polymorphisms (SNPs) of 130 animals representing four dairy cattle breed groups from Nariño. In addition, we merged genotypes from 43,043 autosomal SNPs, from 137 animals from the Decker database (Decker et al., 2014) (DRYAD doi:10.5061/dryad.th092). After the quality control process of pruning the merged dataset, we were left with 7,475 autosomal SNPs shared by both databases of Nariño (127 samples) and Decker (135 samples). Genetic diversity levels were moderate in all breeds (average observed heterozygosity = 0.40). Based on the fixation index values, we conclude that Brahman individuals were more differentiated than the taurine breeds (-0.374 to 0.076 for Brown Swiss). Pairs between taurine breeds showed low genetic differentiation (0.011-0.479). Principal component analysis revealed that in both the Nariño and Decker databases, the taurine formed the most compact cluster compared with other breeds known not to share the same ancestry, and Jersey, Brown Swiss, and Normand individuals exhibited high similarity with Holstein individuals. Hierarchical cluster analysis with Admixture revealed that Brahman, Jersey, Normand, and Holstein from the Decker databases most of which were clustered together with the dairy breeds of the Nariño highland tropics are not able to create different groups, thus having greater similarity with each other. This can be explained by the crosses made by farmers to increase milk production volume, always based on the Holstein breed with semen of bulls from America and Canada. Detrimental impacts due to intensive selection might cause some specific traits from the region to be fixed in the offspring, which can influence their adaptive capacity to the highland tropics.

Na Colômbia foram introduzidas diferentes raças leiteiras trazidas da Europa e dos Estados Unidos, que passaram por diferentes processos de cruzamento e seleção, gerando o desenvolvimento de características ou diferenças específicas nas raças bovinas e provavelmente, exibem sua própria estrutura genômica. Para caracterizar a diversidade genética e estrutura populacional foram utilizados genótipos de 23.182 polimorfismos de nucleotídeo único (SNPs) autossômicos de 130 animais, representando quatro grupos de raças de gado leiteiro de Nariño. Além disso, juntamos genótipos de 43.043 SNPs autossômicos, de 137 animais do banco de dados Decker (Decker et al., 2014) (DRYAD doi:10.5061/dryad.th092). Após o processo de controle de qualidade, o conjunto de dados misto ficou com 7.475 SNPs autossômicos compartilhados em ambos os bancos de dados de Nariño (127 amostras) e Decker (135 amostras). Os níveis de diversidade genética foram moderados em todas as raças (heterozigose média observada = 0,40). Com base nos valores do índice de fixação, concluímos que os indivíduos Brahman (zebuínos) foram mais diferenciados em comparação às raças taurinas (-0,374 a 0,076 para Pardo Suíço). Pares entre as raças taurinas apresentaram baixa diferenciação genética (0,011 ­ 0,479). O resultado dos componentes principais mostra que nos dois bancos de dados, Nariño e Decker, os taurinos formaram o cluster mais compacto em comparação com outras raças conhecidas por não compartilharem a mesma ancestralidade; indivíduos Jersey, Pardo Suíço e Normando denotaram alta similaridade com indivíduos Holandeses. A análise de agrupamento hierárquico com Admixture mostrou que Brahman, Jersey, Normando e Holandês da base de dados Decker, a maioria deles também agrupados com as raças leiteiras do alto trópico de Nariño, não são capazes de criar grupos diferentes, portanto, mostram maior semelhança entre eles. Isso pode ser explicado devido aos cruzamentos feitos pelos pecuaristas para aumentar o volume de produção de leite, sempre tendo como base a raça Holandesa com sêmen de touros da América e Canadá. Impactos prejudiciais, devido à seleção intensiva, podem fazer com que algumas características específicas da região sejam fixadas na prole e isso pode influenciar a sua capacidade adaptativa aos trópicos altos.

Polymorphism in the BIEC2-808543 locus and its association with growth curve in Brasileiro de Hipismo horse breed

Our objective was to evaluate whether the single nucleotide polymorphism (SNP) BIEC2-808543, identified in some horse breeds, also occurs in the Brasileiro de Hipismo (BH) breed. In addition, we verified if this SNP is related to the growth curve profile of these animals for the variables body mass, height at withers, and height at croup, using nonlinear mixed models. For the DNA isolation, we collected blood samples from 167 young BH horses. We obtained the genotypes of these animals using the polymerase chain reaction-restriction fragment length polymorphism technique. For the association studies of this polymorphism with the growth curve in foals, we selected three traits: body mass, height at withers, and height at croup. Polymorphism C/T exists in BH horses and is significantly associated with the evaluated traits. Animals that presented the TT genotype were smaller and lighter when compared with animals of the CT and CC genotypes. By the Akaike information criterion, the model that best described the growth curve for the body mass variable is the Brody model associated with the power of the mean variance function. For the height at withers variable, the best-fit model was von Bertalanffy, adjusted without polymorphism effect in parameter b, associated with the asymptotic variance. For the height at croup trait, the model that best described the growth curve was Brody model, associated with asymptotic variance. This polymorphism represents a good molecular marker. Nonlinear models are promising for describing growth curves in horses, particularly by the possibility of associating SNP effects to model parameters.

Association Analysis Between Polymorphism of Gonadotrophin Releasing Hormone Genes and Growth Traits of Quail (Coturnix Coturnix)

This study investigated SNP mutation sites of Gonadotrophin releasing hormone (GnRH) gene in China yellow quail, Beijing white quail and Korean quail through PCR amplification and DNA sequencing technologies. Moreover, polymorphism of GnRH gene and its association with growth traits of quail were analyzed, aiming to get molecular markers associated to growth traits of quail, which could provide references for breeding of new quail species. According to research results, a total of 14 SNP mutation sites of GnRH were detected in China yellow quail, Beijing white quail and Korean quail, which were C71T, C108T, C168T, C178T, A184G, C206T, A209C, C215T, A252G, A279T, C281T, C293G, C339T and C458T. Except that only 2 genotypes were detected for A209C and C281T in China yellow quail and Beijing white quail, 3 genotypes were detected for all of the remaining 12 SNP mutation sites in three quail species. Of the 14 SNP sites, C71T, A209C, C215T, C281T, C293G, C339T and C458T were significantly associated with body weight (p 0.05), C71T, C108T, C168T, C178T, A184G, C206T, C215T, A252G, C293G, C339T and C458T were significantly associated with shank length (p 0.05), C71T, C215T, C293G and C458T were significantly associated with breastbone length (p 0.05), A209C and C281T were significantly associated with shank circumference (p 0.05).(AU)

Association Analysis Between Polymorphism of Gonadotrophin Releasing Hormone Genes and Growth Traits of Quail (Coturnix Coturnix)

This study investigated SNP mutation sites of Gonadotrophin releasing hormone (GnRH) gene in China yellow quail, Beijing white quail and Korean quail through PCR amplification and DNA sequencing technologies. Moreover, polymorphism of GnRH gene and its association with growth traits of quail were analyzed, aiming to get molecular markers associated to growth traits of quail, which could provide references for breeding of new quail species. According to research results, a total of 14 SNP mutation sites of GnRH were detected in China yellow quail, Beijing white quail and Korean quail, which were C71T, C108T, C168T, C178T, A184G, C206T, A209C, C215T, A252G, A279T, C281T, C293G, C339T and C458T. Except that only 2 genotypes were detected for A209C and C281T in China yellow quail and Beijing white quail, 3 genotypes were detected for all of the remaining 12 SNP mutation sites in three quail species. Of the 14 SNP sites, C71T, A209C, C215T, C281T, C293G, C339T and C458T were significantly associated with body weight (p 0.05), C71T, C108T, C168T, C178T, A184G, C206T, C215T, A252G, C293G, C339T and C458T were significantly associated with shank length (p 0.05), C71T, C215T, C293G and C458T were significantly associated with breastbone length (p 0.05), A209C and C281T were significantly associated with shank circumference (p 0.05).

Identification of patterns related to linkage groups or disequilibrium by factor analysis / Identificação de padrões relacionados a grupos de ligação ou de desequilíbrio por análise de fatores

Empirical patterns of linkage disequilibrium (LD) can be used to increase the statistical power of genetic mapping. This study was carried out with the objective of verifying the efficacy of factor analysis (AF) applied to data sets of molecular markers of the SNP type, in order to identify linkage groups and haplotypes blocks. The SNPs data set used was derived from a simulation process of an F2 population, containing 2000 marks with information of 500 individuals. The estimation of the factorial loadings of FA was made in two ways, considering the matrix of distances between the markers (A) and considering the correlation matrix (R). The number of factors (k) to be used was established based on the graph scree-plot and based on the proportion of the total variance explained. Results indicated that matrices A and R lead to similar results. Based on the scree-plot we considered k equal to 10 and the factors interpreted as being representative of the bonding groups. The second criterion led to a number of factors equal to 50, and the factors interpreted as being representative of the haplotypes blocks. This showed the potential of the technique, making it possible to obtain results applicable to any type of population, helping or corroborating the interpretation of genomic studies. The study demonstrated that AF was able to identify patterns of association between markers, identifying subgroups of markers that reflect factor binding groups and also linkage disequilibrium groups.(AU)

Padrões empíricos de desequilíbrio de ligação (LD) podem ser utilizados para aumentar o poder estatístico do mapeamento genético. Este trabalho foi realizado com o objetivo de verificar a eficácia da análise de fatores (AF) aplicada a conjuntos de dados de marcadores moleculares do tipo SNP, visando identificar grupos de ligação e blocos de haplótipos. O conjunto de dados SNPs utilizado foi oriundo de um processo de simulação de uma população F2, contendo 2000 marcas com informações de 500 indivíduos. A estimação das cargas fatoriais (loadings) da AF foi feita de duas formas, considerando a matriz de distâncias entre os marcadores (A) e considerando a matriz de correlação (R). O número de fatores (k) a ser utilizado foi estabelecido com base no gráfico scree-plot e com base na proporção da variância total explicada. Os resultados indicam que as matrizes A e R conduzem a resultados similares. Com base no scree-plot considerou-se k igual a 10 e os fatores interpretados como sendo representativos dos grupos de ligação. O segundo critério conduziu a um número de fatores igual a 50, e os fatores interpretados como sendo representativos dos blocos de haplótipos. Isto mostra o potencial da técnica que permite obter resultados aplicáveis a qualquer tipo de população, corroborando a interpretação de estudos genômicos. O trabalho demonstrou que a AF foi capaz de identificar padrões de associação entre marcadores, identificando subgrupos de marcadores que refletem grupos de ligação fatorial e também grupos de desequilíbrio de ligação.(AU)