Hasan  Koyun, Hayrettin  Okut, Seyrani  Koncagül, 
    Genomic Scan to Detect QTL Using SNP Markers for Simulated Data by Regression Analysis in Half-Sib Design,
    Journal of Animal and Veterinary Advances,
    Volume 8,Issue 12,
    2009,
    Pages 2626-2630,
    ISSN 1680-5593,
    javaa.2009.2626.2630,
    (https://makhillpublications.co/view-article.php?doi=javaa.2009.2626.2630)
    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 χ<SUP>2</SUP>-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.
    Keywords: Simulated SNP markers;genome scan;regression;quantitative trait loci;interval mapping