Computational protocol: Genetic mapping identifies a major locus spanning P450 clusters associated with pyrethroid resistance in kdr free Anopheles arabiensis from Chad

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Protocol publication

[…] The JoinMap 2.0 software package () was used to build genetic linkage maps for each individual family and for the combined genotyping data from both families. Genotype data for each marker were tested for conformity to Mendelian ratios (Hardy–Weinberg equilibrium) with a χ2 goodness-of-fit analysis using the JoinMap JMSLA procedure and a χ2 test for genotype–phenotype association was performed using Haploview 4.2 (). Loci were separated into linkage groups with JMGRP and JMSPL procedures with minimum and maximum logarithm of the odds (LOD) thresholds of 1.0 and 4.0, respectively and LOD increments of 0.1. The JoinMap JMREC was used to estimate pairwise cM distances between all pairs of informative loci in each linkage group and JMMAP to find the maximum likelihood map using the Kosambi distances. Genetic maps were plotted with MapChart 2.1 software ().The JoinMap linkage positions along with the genotype–phenotype data were entered into Windows QTL Cartographer 2.5 (). Interval mapping (IM; ), composite IM (CIM; ) and multiple IM (MIM; ) procedures were performed for each family separately and for the combined data. The MapChart 2.1 software () was used to plot the LOD graphs next to the respective linkage maps. MIM analyzes multiple marker intervals simultaneously to fit multiple putative QTLs. An initial MIM model was estimated by forward and backward marker selection with a probability of a partial r2 set to 0.01. The model was refined by optimising QTL positions, searching for new and testing for existing QTLs. […]

Pipeline specifications

Software tools JoinMap, Haploview
Applications WGS analysis, GWAS
Organisms Anopheles arabiensis
Diseases Malaria
Chemicals Carbamates, DDT, Organophosphates, Piperonyl Butoxide, Pyrethrins