Copy number variations and genome-wide associations reveal putative genes and metabolic pathways involved with the feed conversion ratio in beef cattle

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de Almeida Santana, Miguel Henrique ; Oliveira Junior, Gerson Antonio ; Mello Cesar, Aline Silva ; Freua, Mateus Castelani ; Gomes, Rodrigo da Costa ; da Luz e Silva, Saulo ; Leme, Paulo Roberto ; Fukumasu, Heidge ; Carvalho, Minos Esperandio ; Ventura, Ricardo Vieira ; Coutinho, Luiz Lehmann ; Kadarmideen, Haja N. ; Sterman Ferraz, Jose Bento

• Tipo de documento: Artigo Científico
• Fonte: JOURNAL OF APPLIED GENETICS; v. 57, n. 4, p. 495-504, NOV 2016.
• Citações Web of Science: 19

Resumo

The use of genome-wide association results combined with other genomic approaches may uncover genes and metabolic pathways related to complex traits. In this study, the phenotypic and genotypic data of 1475 Nellore (Bos indicus) cattle and 941,033 single nucleotide polymorphisms (SNPs) were used for genome-wide association study (GWAS) and copy number variations (CNVs) analysis in order to identify candidate genes and putative pathways involved with the feed conversion ratio (FCR). The GWAS was based on the Bayes B approach analyzing genomic windows with multiple regression models to estimate the proportion of genetic variance explained by each window. The CNVs were detected with PennCNV software using the log R ratio and B allele frequency data. CNV regions (CNVRs) were identified with CNVRuler and a linear regression was used to associate CNVRs and the FCR. Functional annotation of associated genomic regions was performed with the Database for Annotation, Visualization and Integrated Discovery (DAVID) and the metabolic pathways were obtained from the Kyoto Encyclopedia of Genes and Genomes (KEGG). We showed five genomic windows distributed over chromosomes 4, 6, 7, 8, and 24 that explain 12 % of the total genetic variance for FCR, and detected 12 CNVRs (chromosomes 1, 5, 7, 10, and 12) significantly associated {[}false discovery rate (FDR) < 0.05] with the FCR. Significant genomic regions (GWAS and CNV) harbor candidate genes involved in pathways related to energetic, lipid, and protein metabolism. The metabolic pathways found in this study are related to processes directly connected to feed efficiency in beef cattle. It was observed that, even though different genomic regions and genes were found between the two approaches (GWAS and CNV), the metabolic processes covered were related to each other. Therefore, a combination of the approaches complement each other and lead to a better understanding of the FCR. (AU)

• Processo FAPESP: 12/02039-9 - Estudo genômico da ingestão e eficiência alimentar em bovinos da raça Nelore
• Beneficiário: José Bento Sterman Ferraz
• Modalidade de apoio: Auxílio à Pesquisa - Regular
• Processo FAPESP: 13/20571-2 - Genômica funcional da ingestão e eficiência alimentar de bovinos da raça Nelore
• Beneficiário: Miguel Henrique de Almeida Santana
• Modalidade de apoio: Bolsas no Brasil - Pós-Doutorado
• Processo FAPESP: 14/14121-7 - Estudos de genética de sistemas de medidas de confinamento usando painel de SNP super-denso
• Beneficiário: Miguel Henrique de Almeida Santana
• Modalidade de apoio: Bolsas no Exterior - Estágio de Pesquisa - Pós-Doutorado