Computational protocol: Quantitative Trait Loci for Light Sensitivity, Body Weight, Body Size, and Morphological Eye Parameters in the Bumblebee, Bombus terrestris

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Protocol publication

[…] First, we performed the Kruskal-Wallis (KW) test, a single marker non-parametric method imbedded in the software program MapQTL5.0 [] to detect possible QTLs as done in several other studies (e.g., [,]). Secondly, we performed a composite Interval Mapping analysis (IM) with MapQTL 5 []. The LOD thresholds for declaring a suggestive QTL (linkage group wide) or a significant QTL (genome wide) were obtained by standard permutation tests (1000 iterations) with MapQTL 5.0 [] for the significance level p = 0.05 and p = 0.01. These permutation tests are less dependent on normal distributions to calculate significance thresholds. Third, we performed also a multiple QTL model mapping (MQM) within MapQTL 5.0. The selection of obtained suggestive QTLs in IM were used as cofactors during the MQM-mapping which allowed for the detecting of additional QTLs[]. When the LOD value of the QTL, assigned as cofactor, dropped during the MQM mapping below the threshold value, then the QTL was removed as cofactor and MQM was run again. We repeated this procedure until the list of cofactors remained stable. For both IM and MQM, the traits need to follow a normal distribution. Most traits were significantly different from normality (). However, the Box-Cox transformation had none or only very small effects on the size of the observed QTL regions. For the graphical presentation of the QTLs and markers we employed the software MapChart version 2.2 []. […]

Pipeline specifications

Software tools MapQTL, JoinMap
Application WGS analysis
Organisms Bombus terrestris, Solanum lycopersicum