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

• Document type: Journal article
• Source: BMC Genomics; v. 25, n. 1, p. 16-pg., 2024-06-20.

Abstract

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)

• FAPESP's process: 17/10630-2 - Genetic aspects of meat production quality, efficiency and sustainability in Nelore breed animals
• Grantee: Lucia Galvão de Albuquerque
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 18/20026-8 - Multi-user equipment approved in grant 2017/10630-2: server
• Grantee: Lucia Galvão de Albuquerque
• Support Opportunities: Multi-user Equipment Program
• FAPESP's process: 20/14846-2 - Genome-wide association studies with whole genome sequence for growth traits in Nelore cattle using reaction norm models
• Grantee: Ivan Carvalho Filho
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate
• FAPESP's process: 19/06361-1 - Genotype-environment interaction in Nellore cattle for growth traits and visual scores using sequence data
• Grantee: Ivan Carvalho Filho
• Support Opportunities: Scholarships in Brazil - Doctorate
• FAPESP's process: 22/11852-7 - Structural equation modeling as a tool to interpret genotype-environment interaction and genome-wide association (GWAS) for growth and reproductive traits in Nellore heifers using whole-genome sequence data
• Grantee: Lúcio Flávio Macedo Mota
• Support Opportunities: Scholarships in Brazil - Post-Doctoral