Estudos genômicos de características indicadoras de eficiência alimentar em duas populações de bovinos da raça Nelore
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Data
2018-07-31
Autores
Santos, Samuel Wallace Boer dos
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Universidade Estadual Paulista (Unesp)
Resumo
Características de eficiência alimentar estão diretamente associadas com a lucratividade e sustentabilidade da bovinocultura de corte. Conversão alimentar, consumo alimentar residual, consumo de matéria seca, eficiência alimentar e ganho em peso, são características importantes para a seleção de animais mais eficientes dentro de um sistema de produção, porém, com exceção do ganho em peso, as demais não vêm sendo consideradas como critérios de seleção devido à dificuldade de obtenção de fenótipos para as mesmas. Com o avanço nas tecnologias de genotipagem e sequenciamento, foram desenvolvidos chips de alta densidade de marcadores do tipo SNP (Single Nucleotide Polymorphism) espalhados pelo genoma. Estas informações moleculares vêm sendo utilizadas em estudos de associação genômica ampla (GWAS) e de seleção genômica (SG). Basicamente, o GWAS permite a identificação de variações genéticas de maior efeito sobre a expressão fenotípica de características de interesse, enquanto a SG visa a predição do valor genômico direto dos candidatos à seleção utilizando apenas a informação molecular, o que tem revolucionado o melhoramento genético por proporcionar a diminuição do intervalo de geração e o aumento da acurácia de predição dos valores genéticos dos animais. Assim sendo, os objetivos do presente trabalho foram: 1) encontrar regiões cromossômicas de maior efeito sobre características de eficiência alimentar em animais Nelore provenientes de dois programas de melhoramento (Instituto de Zootecnia - IZ e Nelore Qualitas), visando encontrar possíveis diferenças/semelhanças entre as populações; 2) avaliar a existência de genes candidatos comum às populações; e 3) avaliar a possibilidade e os benefícios de combinar estas duas populações Nelore em estudos de seleção genômica. Foram utilizadas informações fenotípicas e genotípicas de 1.137 animais do IZ e 817 animais do Qualitas. Os animais foram genotipados com painel de alta densidade (Illumina BovineHD chip) ou tiveram seus genótipos imputados para HD através do software FImpute. Após o controle de qualidade dos genótipos, permaneceram para análise 408.161 SNPs para o IZ e 428.621 SNPs para o Qualitas. O GWAS foi realizado para cada população individualmente, considerando a metodologia GBLUP. Modelos unicaracterísticos foram empregados nas análises, incluindo, além dos efeitos aleatórios de animal e resíduo, os efeitos sistemáticos de grupos de contemporâneos (GC), os quais foram definidos como: sexo, ano de nascimento e instalação (IZ) e ano do teste e baia (Qualitas). Para o IZ também foram incluídos, para todas as características, os efeitos fixos de mês de nascimento, e, como covariáveis, idade do animal (linear), idade da mãe (linear e quadrática) e os dois primeiros componentes principais (obtidos a partir da matriz G). O efeito quadrático da idade do animal foi incluído no modelo apenas para o consumo de matéria seca e ganho médio diário. Para o Qualitas, foi considerado, para todas as características, o efeito linear da idade do animal como covariável. No GWAS, foram encontradas algumas regiões cromossômicas de maior efeito para cada característica nas duas populações, porém, não foram encontradas regiões em comum. No estudo de seleção genômica (SG), foram utilizados dez diferentes abordagens e esquemas envolvendo as duas populações para comparar a acurácia de predição. Em geral, a combinação das populações pode gerar benefícios para a seleção genômica, porém, tais benefícios dependem da característica e do esquema de validação.
Feed efficiency traits are directly associated with the profitability and sustainability of beef cattle. Feed conversion rate, residual feed intake, dry matter intake, feed efficiency and average daily gain are important traits for the selection of more efficiency animals within a production system, but, except for weight gain, the others have not been considered as selection criteria due to the difficulty of obtaining phenotypes. With the advance in genotyping and sequencing technologies, high density chips of SNP (Single Nucleotide Polymorphism) have been developed. This molecular information has been used in genome-wide association (GWAS) and genomic selection (GS) studies. Basically, GWAS allows the identification of genetic variations with major effects on the phenotypic expression of traits of interest, while SG aims at the prediction of direct genomic value for the selection candidates using only their molecular information, which has revolutionized the animal breeding by providing a decrease in generation interval and increases in the prediction accuracies of breeding values. Thus, the objectives of the present study were to: 1) identify chromosomal regions with major effects on feed efficiency traits in animals from two Nellore breeding programs (Instituto de Zootecnia and Nellore Qualitas), in order to find possible differences/similarities between the populations; 2) evaluate the existence of candidate genes in common to populations; and 3) evaluate the possibility and benefits of combining these two Nellore populations in genomic selection studies. Phenotypic and genotypic information of 1,137 animals from IZ and 817 from Qualitas were used. The animals were genotyped with high density panel (Illumina BovineHD chip) or had their genotypes imputed to HD through the FImpute software. After quality control, remained for analysis 408,161 SNPs for IZ and 428.611 SNPs for Qualitas. The GWAS was performed for each population individually, considering the GBLUP methodology. Single-trait models were implemented in the analyzes, including, in addition to the random effects of animal and residual, the systematic effects of contemporary groups (CG), which were defined as: sex, year of birth and pen for the IZ, and year of test and pen for the Qualitas. For IZ, there were also considered, for all traits, the fixed effects of month of birth and, as covariable, age of animal (linear effect), age of dam (linear and quadratic effects) and the first two principal components (calculated based on the G matrix). For ADG and DMI, the quadratic effect of age of animal, as covariable, was added to the model. For Qualitas, it was also included in the model, for all traits, the linear effect of the animal age as covariable. In GWAS, some chromosomal regions of greater effect were found for each trait in both populations. However, no common regions were found. In GS, ten different approach and schemes involving the two Nellore populations were used to compare the accuracy of genomic prediction. In general, genomic predictions combining both populations are feasible, but, the benefits will depend on the trait and validation scheme.
Feed efficiency traits are directly associated with the profitability and sustainability of beef cattle. Feed conversion rate, residual feed intake, dry matter intake, feed efficiency and average daily gain are important traits for the selection of more efficiency animals within a production system, but, except for weight gain, the others have not been considered as selection criteria due to the difficulty of obtaining phenotypes. With the advance in genotyping and sequencing technologies, high density chips of SNP (Single Nucleotide Polymorphism) have been developed. This molecular information has been used in genome-wide association (GWAS) and genomic selection (GS) studies. Basically, GWAS allows the identification of genetic variations with major effects on the phenotypic expression of traits of interest, while SG aims at the prediction of direct genomic value for the selection candidates using only their molecular information, which has revolutionized the animal breeding by providing a decrease in generation interval and increases in the prediction accuracies of breeding values. Thus, the objectives of the present study were to: 1) identify chromosomal regions with major effects on feed efficiency traits in animals from two Nellore breeding programs (Instituto de Zootecnia and Nellore Qualitas), in order to find possible differences/similarities between the populations; 2) evaluate the existence of candidate genes in common to populations; and 3) evaluate the possibility and benefits of combining these two Nellore populations in genomic selection studies. Phenotypic and genotypic information of 1,137 animals from IZ and 817 from Qualitas were used. The animals were genotyped with high density panel (Illumina BovineHD chip) or had their genotypes imputed to HD through the FImpute software. After quality control, remained for analysis 408,161 SNPs for IZ and 428.611 SNPs for Qualitas. The GWAS was performed for each population individually, considering the GBLUP methodology. Single-trait models were implemented in the analyzes, including, in addition to the random effects of animal and residual, the systematic effects of contemporary groups (CG), which were defined as: sex, year of birth and pen for the IZ, and year of test and pen for the Qualitas. For IZ, there were also considered, for all traits, the fixed effects of month of birth and, as covariable, age of animal (linear effect), age of dam (linear and quadratic effects) and the first two principal components (calculated based on the G matrix). For ADG and DMI, the quadratic effect of age of animal, as covariable, was added to the model. For Qualitas, it was also included in the model, for all traits, the linear effect of the animal age as covariable. In GWAS, some chromosomal regions of greater effect were found for each trait in both populations. However, no common regions were found. In GS, ten different approach and schemes involving the two Nellore populations were used to compare the accuracy of genomic prediction. In general, genomic predictions combining both populations are feasible, but, the benefits will depend on the trait and validation scheme.
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Palavras-chave
Associação genômica ampla, Melhoramento genético animal, Seleção genômica, Animal breeding, Genomic selection, Genome wide association studies