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chunyan159金虫 (小有名气)
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[求助]
QTL mapping analysis
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| A high-density genetic map was created with 1,046 molecular markers that included 937 SFPs and 109 SSRs, with an average marker separation of less than 2 cM. The interval mapping (IM) method was conducted to predict QTLs, followed by composite interval mapping (CIM) using Qgene v4.3.6 ,with permutations of 1000 iterations to declare the QTL as significant. For CIM, stepwise cofactor selection was used with markers as cofactors and the maximum number of cofactors was selected automatically (F to add=0.01 and F to drop=0.01). The permutation LOD value at p ≤ 0.05 was used as the threshold to declare the significance of the QTLs. The interactions among QTLs were identified using QTLNetwork-v2.1 software, with a mixed linear model based on CIM with a 10 cM window size and 1 cM walking speed. Permutation tests with 1,000 runs were used to determine the threshold of the F-value for the significance of QTLs to control genome-wide type I errors. Digenic interactions were also analyzed using a mixed-model approach. Significance levels for the genome scans for candidate intervals, QTL detection, and effects were set at 0.05, 0.001, and 0.001, respectively. The epistatic interaction between QTLs was illustrated using the Circos software. |
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