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Genome-wide analysis of single-locus and epistatic SNP effects on subcutaneous fat thickness trait in angus beef cattle [electronic resource].

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Abdel Ghaffar, M. A

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Agricultural research journal, Suez Canal University, 2012 v.12(1) [electronic resource].

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In: Agricultural Research Journal, Suez Canal University 2012 v.12(1)Summary: The goal of this study was to identify the single-locus and epistasis effects of 38499 single-nucleotide polymorphism (SNP) markers on subcutaneous fat thickness. Phenotypic data were collected from 1066 head of Angus bulls, steers and heifers from two resources. The epiSNP computer package was used for genome-wide analysis of single-locus and epistasis SNP effects. Models defined gender within harvest date as a fixed effect and harvest age was a covariate in the epiSNP analysis. One single locus was significantly (p < 0.423x10⁻⁶; Bonferroni correction) associated with Subcutaneous Fat Thickness. The epistasis analysis tested five effects for each pair of SNPs: two-locus interaction, additive x additive, additive x dominance, dominance x additive, and dominance x dominance effects.

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The goal of this study was to identify the single-locus and epistasis effects of 38499 single-nucleotide polymorphism (SNP) markers on subcutaneous fat thickness. Phenotypic data were collected from 1066 head of Angus bulls, steers and heifers from two resources. The epiSNP computer package was used for genome-wide analysis of single-locus and epistasis SNP effects. Models defined gender within harvest date as a fixed effect and harvest age was a covariate in the epiSNP analysis. One single locus was significantly (p < 0.423x10⁻⁶; Bonferroni correction) associated with Subcutaneous Fat Thickness. The epistasis analysis tested five effects for each pair of SNPs: two-locus interaction, additive x additive, additive x dominance, dominance x additive, and dominance x dominance effects.

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