Parâmetros genéticos e identicação de regiões regulatórias para características ponderais em bovinos Nelore
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Data
2023-02-28
Autores
Teodoro, Miller de Jesus
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Universidade Estadual Paulista (Unesp)
Resumo
Características ponderais têm sido amplamente usadas na seleção de bovinos Nelore no Brasil, estando diretamente associadas com a produtividade e lucratividade dos rebanhos. Estudos de associação genômica ampla (GWAS) tem sido utilizados para investigar variantes presentes no genoma bovino que estão associadas a fenótipos de interesse. Entretanto, devido algumas limitações do GWAS, a anotação de classes funcionais para identificação de regiões candidatas pode ser usada para aumentar o poder de detecção do GWAS. Considerando os poucos estudos de classes funcionais associadas com características ponderais na raça Nelore, os objetivos deste estudo foram realizar GWAS para identificar regiões do cromossomo 14 associadas com características ponderais de bovinos da raça Nelore, e verificar quais classes funcionais explicam maior proporção da variância, buscando auxiliar o processo de seleção em características de crescimento. Para isso, foi empregado um banco de dados de genótipos e fenótipos para as características peso ao nascimento (PN), peso a desmama (PD) e peso ao sobreano (PS). Duas abordagens do GWAS foram conduzidas, associação genômica ampla em passo único ponderada (WssGWAS) e outra com base na matriz genômica de parentesco (GRM) única para cada classe funcional. As herdabilidades aditivas diretas obtidas para PN e PD foram de moderada magnitude, sendo 0,24 e 0,20, respectivamente, e para PS foi de alta magnitude, sendo 0,48. Já as herdabilidades materna obtidas foram de baixa magnitude para PN (0,06) e PD (0,12). Os resultados mostram que existem variantes associadas com as características ponderais distribuídas por diversas regiões do cromossomo 14, reafirmando a importância deste cromossomo na seleção destas características. Os genes CSMD3, PCMTD1, PLAG1 e STK3 estão associados com crescimento e desenvolvimento corporal. Os resultados das classes funcionais demonstram a importância de classes regulatórias e splice sites na proporção da variância capturada e explicada pelas variantes nessas classes. As análises das classes funcionais complementam o GWAS, contribuindo para o entendimento da atuação das variantes nas características ponderais da raça Nelore.
Weight traits have been widely used in the selection of Nellore cattle in Brazil, being directly associated with herd productivity and profitability. Genome-wide association studies (GWAS) have been used to investigate variants in the bovine genome that are associated with target phenotypes. However, due to some limitations of GWAS, functional classes annotation for identifying candidate regions can be used to increase GWAS detection power. As few studies were published regarding functional classes associated with weight traits in the Nellore cattle, the objectives of this study were to perform GWAS to identify chromosome 14 regions associated with weight traits in Nellore cattle, and to verify which functional classes explain the greater proportion of variance, seeking to assist the selection process on growth traits. For this, a database of genotypes and phenotypes was analyzed for birth weight (BW), weaning weight (WW) and yearling weight (YW). Two GWAS approaches were conducted, weighted single-step genome-wide association (WssGWAS) and another based on the genomic relationship matrix (GRM) unique to each functional class. The direct additive heritabilities obtained for BW and WW were moderate (0.24 and 0.20, respectively) and for YW was high (0.48). The maternal heritabilities obtained were of low magnitude for BW (0.06) and WW (0.12). The results show that there are variants associated with weight traits distributed across different regions of chromosome 14, reaffirming the importance of this chromosome in the selection of these traits. The CSMD3, PCMTD1, PLAG1 and STK3 genes are associated with growth and development. The results of the functional classes demonstrate the importance of regulatory classes and splice sites in the proportion of the variance captured and explained by the variants in these classes. The analyzes of the functional classes complement the GWAS, contributing to the understanding of the performance of the variants in the weight traits in Nelore cattle.
Weight traits have been widely used in the selection of Nellore cattle in Brazil, being directly associated with herd productivity and profitability. Genome-wide association studies (GWAS) have been used to investigate variants in the bovine genome that are associated with target phenotypes. However, due to some limitations of GWAS, functional classes annotation for identifying candidate regions can be used to increase GWAS detection power. As few studies were published regarding functional classes associated with weight traits in the Nellore cattle, the objectives of this study were to perform GWAS to identify chromosome 14 regions associated with weight traits in Nellore cattle, and to verify which functional classes explain the greater proportion of variance, seeking to assist the selection process on growth traits. For this, a database of genotypes and phenotypes was analyzed for birth weight (BW), weaning weight (WW) and yearling weight (YW). Two GWAS approaches were conducted, weighted single-step genome-wide association (WssGWAS) and another based on the genomic relationship matrix (GRM) unique to each functional class. The direct additive heritabilities obtained for BW and WW were moderate (0.24 and 0.20, respectively) and for YW was high (0.48). The maternal heritabilities obtained were of low magnitude for BW (0.06) and WW (0.12). The results show that there are variants associated with weight traits distributed across different regions of chromosome 14, reaffirming the importance of this chromosome in the selection of these traits. The CSMD3, PCMTD1, PLAG1 and STK3 genes are associated with growth and development. The results of the functional classes demonstrate the importance of regulatory classes and splice sites in the proportion of the variance captured and explained by the variants in these classes. The analyzes of the functional classes complement the GWAS, contributing to the understanding of the performance of the variants in the weight traits in Nelore cattle.
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Palavras-chave
Bovinos de corte, Genes, Peso corporal, Polimorfismo de nucleotídeo único, Beef cattle, Body weight, Single nucleotide polymorphism