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Genomic Scan to Detect QTL Using SNP Markers for Simulated Data by Regression Analysis in Half-Sib Design

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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.

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