Avaliação genômica em bovinos da raça Gir de Brasil e Colômbia
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Data
2020-05-06
Autores
Toro, Alejandra Maria ospina
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Universidade Estadual Paulista (Unesp)
Resumo
A raça Gir (Bos indicus) é importante recurso genético para produção de carne e leite no Brasil e em países tropicais. Estudos genômicos entre populações são de interesse para identificar regiões genômicas importantes e aplicar na seleção de caraterísticas de produção. As corridas de homozigose (ROH) são regiões homozigotas contíguas do genoma, utilizadas na identificação de genes associados a características de interesse econômico, bem como na obtenção dos coeficientes de endogamia. A interação genótipo ambiente (IGA), também representa papel importante no estudo de populações de bovinos e na seleção dos melhores reprodutores para os diferentes ambientes. Com isto, os objetivos do presente estudo foram analisar o comprimento e a distribuição das ilhas ROH do genoma, com identificação dos gene presentes, além de avaliar a acurácia da imputação utilizando diferentes painéis comerciais e a interação genótipo ambiente da produção de leite em bovinos da raça Gir do Brasil e Colômbia. Na avaliação das ilhas ROH foram utilizados dados genotípicos de 173 animais selecionados para produção de carne e 291 animais selecionados para produção leiteira e obtidos os resultados via programa Plink. Análise da acurácia utilizando diferentes painéis de SNPs (GGP Bovine 30K, GGP indicus 35K e HD 777K) de 464 animais do Brasil e da Colômbia foram avaliados e os resultados comparados via correlação simples (CS) e taxa de concordância (CR). Na análise da IGA foi utilizado modelo de norma de reação bi-característica para produção de leite até 305 dias no Brasil (PL305BR) e Colômbia (PL305COL) usando os programas GIBBS3F90 e POSTGSf90, e incluía dados genotípicos (27.505 SNPs) de 464 animais. A análise ROH apresentou diferenças no número de ROH curto (ROH1-2 Mb) entre as duas populações, enquanto o número de ROH longo (ROH> 16 Mb) foi semelhante. As ilhas ROH com frequência maior que 0,5 sobrepuseram vários segmentos do genoma das duas populações. Os genes identificados foram associados à produção de leite, crescimento, reprodução, resposta imune e características de resistência. A maior porcentagem de acurácia dos quatro cenários estudados, demonstrou o painel de 30K com maiores valores de CS (94%) e CR (96%), portanto, a densidade de 30K foi indicada para ser utilizada na imputação dos dados das análises posteriores que incluía dados do Brasil e Colômbia. No modelo de norma de reação, os resultados das caraterísticas PL305BR e PL305COL evidenciaram IGA pela reclassificação dos touros entre os dois países, demonstrando diferenças ambientais e a importância da aplicação desta metodologia na avaliação e seleção dos touros. Além disto, foram identificadas regiões genômicas afetando o intercepto e inclinação da norma de reação e influenciando a expressão de genes relacionados à produção de leite, imunidade e fertilidade. Os resultados contribuem no entendimento da seleção para diferentes fins (leite e carne) moldando segmentos do genoma e aumentando a frequência de regiões em homozigose. Quanto a imputação, se verificou a importância da escolha do painel para posterior imputação dos dados genotípicos de animais da raça Gir. O uso de metodologia adequada considerando a IGA se faz necessário em análise incluindo dados de PL305 do Brasil e Colômbia, e evita reclassificação dos touros nos diferentes ambientes. Conclui-se, aplicação de programa de melhoramento em animais da raça Gir com informações genômicas permite controlar os coeficientes de endogamia e identificar alterações de frequência e tamanho de regiões relacionadas as características de interesse econômico, devido ao direcionamento da seleção, além da importância da escolha de painéis de forma a obter a maior acurácia da imputação e da aplicação de modelos considerando a IGA, possibilitando maior precisão na escolha dos reprodutores.
The Gir breed (Bos indicus) is an important genetic resource for meat and milk production in Brazil and in tropical countries. Genomic studies between populations are of interest to identify important genomic regions and apply in the selection of production traits. Runs of Homozygosity (ROH) are contiguous homozygous regions of the genome, used to identify genes associated with characteristics of economic interest, as well as to obtain inbreeding coefficients. The environment genotype (IGA) interaction also plays an important role in the study of bovine populations and in the selection of the best breeders for different environments. Thus, the objectives of the present study were to analyze the length and distribution of the ROH islands of the genome, with identification of the present genes, in addition to assessing the accuracy of imputation using different commercial panels and the environment genotype interaction of milk production in cattle of the Gir breed from Brazil and Colombia. In the evaluation of the ROH islands, genotypic data from 173 animals selected for beef production and 291 animals selected for milk production were used and the results were obtained through the Plink program. Accuracy analysis using different SNP panels (GGP Bovine 30K, GGP indicus 35K and HD 777K) from 464 animals from Brazil and Colombia were evaluated and the results were compared using simple correlation (CS) and concordance rate (CR). The IGA analysis used a bi-traits reaction standard model for milk production up to 305 days in Brazil (PL305BR) and Colombia (PL305COL) using the GIBBS3F90 and POSTGSf90 programs, and included genotypic data (27,505 SNPs) from 464 animals. The ROH analysis showed differences in the number of short ROH (ROH1-2 Mb) between the two populations, while the number of long ROH (ROH> 16 Mb) was similar. ROH islands with a frequency greater than 0.5 overlapped several segments of the genome of the two populations. The identified genes were associated with milk production, growth, reproduction, immune response and resistance characteristics. The highest percentage of accuracy of the four scenarios studied, demonstrated the panel of 30K with higher values of CS (94%) and CR (96%), therefore, the density of 30K was indicated to be used in the imputation of the data of the later analyzes that included data from Brazil and Colombia. In the reaction norm model, the results of the traits PL305BR and PL305COL showed IGA by the reclassification of sires between the two countries, demonstrating environmental differences and the importance of applying this methodology in the evaluation and selection of sires. In addition, genomic regions were identified, affecting the intercept and slope of the reaction norm and influencing the expression of genes related to milk production, immunity and fertility. The results contribute to the understanding of the selection for different purposes (milk and meet) shaping segments of the genome and increasing the frequency of homozygous regions. As for the imputation, it was verified the importance of choosing the panel for later imputation of the genotypic data of Gir animals. The use of appropriate methodology considering the IGA is necessary in analysis including data from PL305 from Brazil and Colombia, and avoids reclassification of bulls in different environments. In conclusion, application of a breeding program in Gir animals with genomic information allows controlling the inbreeding coefficients and identifying changes in frequency and size of regions related to the traits of economic interest, due to the direction of selection, in addition to the importance of choice of panels in order to obtain the highest accuracy of imputation and application of models considering the IGA, enabling greater precision in the choice of sires
The Gir breed (Bos indicus) is an important genetic resource for meat and milk production in Brazil and in tropical countries. Genomic studies between populations are of interest to identify important genomic regions and apply in the selection of production traits. Runs of Homozygosity (ROH) are contiguous homozygous regions of the genome, used to identify genes associated with characteristics of economic interest, as well as to obtain inbreeding coefficients. The environment genotype (IGA) interaction also plays an important role in the study of bovine populations and in the selection of the best breeders for different environments. Thus, the objectives of the present study were to analyze the length and distribution of the ROH islands of the genome, with identification of the present genes, in addition to assessing the accuracy of imputation using different commercial panels and the environment genotype interaction of milk production in cattle of the Gir breed from Brazil and Colombia. In the evaluation of the ROH islands, genotypic data from 173 animals selected for beef production and 291 animals selected for milk production were used and the results were obtained through the Plink program. Accuracy analysis using different SNP panels (GGP Bovine 30K, GGP indicus 35K and HD 777K) from 464 animals from Brazil and Colombia were evaluated and the results were compared using simple correlation (CS) and concordance rate (CR). The IGA analysis used a bi-traits reaction standard model for milk production up to 305 days in Brazil (PL305BR) and Colombia (PL305COL) using the GIBBS3F90 and POSTGSf90 programs, and included genotypic data (27,505 SNPs) from 464 animals. The ROH analysis showed differences in the number of short ROH (ROH1-2 Mb) between the two populations, while the number of long ROH (ROH> 16 Mb) was similar. ROH islands with a frequency greater than 0.5 overlapped several segments of the genome of the two populations. The identified genes were associated with milk production, growth, reproduction, immune response and resistance characteristics. The highest percentage of accuracy of the four scenarios studied, demonstrated the panel of 30K with higher values of CS (94%) and CR (96%), therefore, the density of 30K was indicated to be used in the imputation of the data of the later analyzes that included data from Brazil and Colombia. In the reaction norm model, the results of the traits PL305BR and PL305COL showed IGA by the reclassification of sires between the two countries, demonstrating environmental differences and the importance of applying this methodology in the evaluation and selection of sires. In addition, genomic regions were identified, affecting the intercept and slope of the reaction norm and influencing the expression of genes related to milk production, immunity and fertility. The results contribute to the understanding of the selection for different purposes (milk and meet) shaping segments of the genome and increasing the frequency of homozygous regions. As for the imputation, it was verified the importance of choosing the panel for later imputation of the genotypic data of Gir animals. The use of appropriate methodology considering the IGA is necessary in analysis including data from PL305 from Brazil and Colombia, and avoids reclassification of bulls in different environments. In conclusion, application of a breeding program in Gir animals with genomic information allows controlling the inbreeding coefficients and identifying changes in frequency and size of regions related to the traits of economic interest, due to the direction of selection, in addition to the importance of choice of panels in order to obtain the highest accuracy of imputation and application of models considering the IGA, enabling greater precision in the choice of sires
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Palavras-chave
Bos taurus indicus, Bovinos de corte, Duplo proposito, GWAS, Endogamia, Norma de reação