Genome-wide association study considering genotype-by-environment interaction for productive and reproductive traits using whole-genome sequencing in Nellore cattle

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Filho, Ivan Carvalho ; Arikawa, Leonardo M. ; Mota, Lucio F. M. ; Campos, Gabriel S. ; Fonseca, Larissa F. S. ; Fernandes, Gerardo A. ; Schenkel, Flavio S. ; Lourenco, Daniela ; Silva, Delvan A. ; Teixeira, Caio S. ; Silva, Thales L. ; Albuquerque, Lucia G. ; Carvalheiro, Roberto

• Tipo de documento: Artigo Científico
• Fonte: BMC Genomics; v. 25, n. 1, p. 16-pg., 2024-06-20.

Resumo

Background The genotype-by-environment interaction (GxE) in beef cattle can be investigated using reaction norm models to assess environmental sensitivity and, combined with genome-wide association studies (GWAS), to map genomic regions related to animal adaptation. Including genetic markers from whole-genome sequencing in reaction norm (RN) models allows us to identify high-resolution candidate genes across environmental gradients through GWAS. Hence, we performed a GWAS via the RN approach using whole-genome sequencing data, focusing on mapping candidate genes associated with the expression of reproductive and growth traits in Nellore cattle. For this purpose, we used phenotypic data for age at first calving (AFC), scrotal circumference (SC), post-weaning weight gain (PWG), and yearling weight (YW). A total of 20,000 males and 7,159 females genotyped with 770k were imputed to the whole sequence (29 M). After quality control and linkage disequilibrium (LD) pruning, there remained similar to 2.41 M SNPs for SC, PWG, and YW and similar to 5.06 M SNPs for AFC.Results Significant SNPs were identified on Bos taurus autosomes (BTA) 10, 11, 14, 18, 19, 20, 21, 24, 25 and 27 for AFC and on BTA 4, 5 and 8 for SC. For growth traits, significant SNP markers were identified on BTA 3, 5 and 20 for YW and PWG. A total of 56 positional candidate genes were identified for AFC, 9 for SC, 3 for PWG, and 24 for YW. The significant SNPs detected for the reaction norm coefficients in Nellore cattle were found to be associated with growth, adaptative, and reproductive traits. These candidate genes are involved in biological mechanisms related to lipid metabolism, immune response, mitogen-activated protein kinase (MAPK) signaling pathway, and energy and phosphate metabolism.Conclusions GWAS results highlighted differences in the physiological processes linked to lipid metabolism, immune response, MAPK signaling pathway, and energy and phosphate metabolism, providing insights into how different environmental conditions interact with specific genes affecting animal adaptation, productivity, and reproductive performance. The shared genomic regions between the intercept and slope are directly implicated in the regulation of growth and reproductive traits in Nellore cattle raised under different environmental conditions. (AU)

• Processo FAPESP: 17/10630-2 - Aspectos genéticos da qualidade, eficiência e sustentabilidade da produção de carne em animais da raça Nelore
• Beneficiário: Lucia Galvão de Albuquerque
• Modalidade de apoio: Auxílio à Pesquisa - Temático
• Processo FAPESP: 18/20026-8 - EMU concedido no processo 2017/10630-2: servidor
• Beneficiário: Lucia Galvão de Albuquerque
• Modalidade de apoio: Auxílio à Pesquisa - Programa Equipamentos Multiusuários
• Processo FAPESP: 20/14846-2 - Estudos de associação genômica com sequência completa do genoma para características de crescimento em Nelore usando normas de reação
• Beneficiário: Ivan Carvalho Filho
• Modalidade de apoio: Bolsas no Exterior - Estágio de Pesquisa - Doutorado
• Processo FAPESP: 19/06361-1 - Interação genótipo-ambiente em bovinos Nelore para características de crescimento e escores visuais com utilização de dados de sequência
• Beneficiário: Ivan Carvalho Filho
• Modalidade de apoio: Bolsas no Brasil - Doutorado
• Processo FAPESP: 22/11852-7 - Modelo de equação estrutural como uma ferramenta para interpretar a interação genótipo-ambiente e estudos de associação genômica (GWAS) para características de crescimento e reprodução em novilhas da raça Nelore usando dados de sequência completa
• Beneficiário: Lúcio Flávio Macedo Mota
• Modalidade de apoio: Bolsas no Brasil - Pós-Doutorado