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Journal of Animal and Veterinary Advances

Genomic Scan to Detect QTL Using SNP Markers for Simulated Data by Regression Analysis in Half-Sib Design
Hasan Koyun, Hayrettin Okut and Seyrani Koncagül

Abstract: The aim of the present study was to conduct a genome-wide screening for QTL (Quantitative Trait Loci) detection using the simulated phenotype and genotype data sets obtained from the QTL-MAS workshop 12. A genome scan was carried out in 45 half-sib families to identify QTL influencing a hypothetical trait. Among six chromosomes, each chromosome with 1000 SNP loci, 11 informative markers at least 2 cM apart from one another were chosen based on PICs with highest χ2-statistic. Half-sib data were pooled and used simultaneously in the analyses conducted for each chromosome separately. Data were analyzed by generating an F-statistic every 1 cM on a linkage map by regression of phenotypes on the probabilities of inheriting an allele from the sire. Permutation tests at chromosome-wide significance thresholds were carried out over 1000 iterations. Among six chromosomes, significant putative QTL were detected on chromosome 1 (27 cM), 2 (36 cM), 3 (18 cM), 4 (0 cM) and 5 (96 cM) across the families (α = 0.01 and α = 0.05). There was no QTL detected, exceeding chromosome-wide significance level of p<0.05 and p<0.01 on chromosome 6.

How to cite this article
Hasan Koyun, Hayrettin Okut and Seyrani Koncagül, 2009. Genomic Scan to Detect QTL Using SNP Markers for Simulated Data by Regression Analysis in Half-Sib Design. Journal of Animal and Veterinary Advances, 8: 2626-2630.

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