Genome-wide association study for backfat thickness in Canchim beef cattle using Random Forest approach

Abstract

BackgroundMeat quality involves many traits, such as marbling, tenderness, juiciness, and backfat thickness, all of which require attention from livestock producers. Backfat thickness improvement by means of traditional selection techniques in Canchim beef cattle has been challenging due to its low heritability, and it is measured late in an animal’s life. Therefore, the implementation of new methodologies for identification of single nucleotide polymorphisms (SNPs) linked to backfat thickness are an important strategy for genetic improvement of carcass and meat quality.ResultsThe set of SNPs identified by the random forest approach explained as much as 50% of the deregressed estimated breeding value (dEBV) variance associated with backfat thickness, and a small set of 5 SNPs were able to explain 34% of the dEBV for backfat thickness. Several quantitative trait loci (QTL) for fat-related traits were found in the surrounding areas of the SNPs, as well as many genes with roles in lipid metabolism.ConclusionsThese results provided a better understanding of the backfat deposition and regulation pathways, and can be considered a starting point for future implementation of a genomic selection program for backfat thickness in Canchim beef cattle.

Integration of Random Forest with population‐based outlier analyses provides insight on the genomic basis and evolution of run timing in Chinook salmon (Oncorhynchus tshawytscha)

“…; Mokry et al . ). Random Forest has recently been used in a conservation context to identify SNPs associated with traits relevant to climate adaptation in conifers (Holliday et al .…”

Associations between single nucleotide polymorphisms and carcass traits in Nellore cattle using high-density panels

“…Although chromosome 7 exhibited a larger number of significant SNPs (P < 0.001), chromosomes 1 and 2 contained regions of less dispersed significant SNPs (P < 0.001) (Figure 1 and Table 3). Using the BovineHD BeadChip to genotype 400 Canchim animals, Mokry et al (2013) also identified significant SNPs for BF on chromosome 1, in addition to chromosomes 3, 10, 13, and 19. QTLs for BF have been identified on chromosomes 2, 3, 7, and 14 of crossbred cattle (Brahman x Hereford) (Casas et al, 2003).…”

“…Using a chip with a higher density of markers (BovineSNP50 BeadChip), Nishimura et al (2012) identified SNPs associated with carcass weight on chromosomes 6, 8, and 14 of Japanese Black cattle. Mokry et al (2013) genotyped 400 Canchim cattle using the BovineHD BeadChip. The authors found an association between SNPs and BF, indicating regions with potential QTLs for this trait on chromosomes 1, 3, 13, and 19.…”

Metodologia baseada em técnicas de mineração de dados para suporte à certificação de raças de ovinos

“…Dentre eles, MOKRY et al (2013) utilizaram Random Forest para a identificação de marcadores SNP ligados à espessura de gordura de gados Canchim. LEWIS et al (2011) aplicaram Análise de Componentes Principais (PCA) para a identificação de SNP relevantes na rastreabilidade de bovinos.…”

“…Outros trabalhos abordaram seleção de atributos em suínos (CORDEIRO et al, 2012) e humanos (WU et al, 2012), porém são raros os trabalhos envolvendo dados de ovinos. De forma geral, observou-se que os trabalhos relacionados selecionaram um número menor que 100 marcadores SNP em seus resultados finais (MOKRY et al, 2013;SASAZAKI et al, 2011;SUEKAWA et al, 2010), número a que este trabalho buscou referenciar-se como limite para a seleção dos SNPs mais informativos. Além disso, considerou-se o possível desenvolvimento de um microarranjo de baixa densidade, que aloca múltiplos de 48 marcadores SNP em sua superfície (ROORKIWAL et al, 2013).…”