Computational protocol: Genetic Architecture of Natural Variation Underlying Adult Foraging Behavior That Is Essential for Survival of Drosophila melanogaster

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Protocol publication

[…] We used single nucleotide polymorphisms (SNPs), SNPs annotations, and inversion status reported in DGRP freeze 2 (), which is based on D. melanogaster genome release 5. Coordinates and gene names reported in our study are also based on release 5. We used GCTA 1.02 () to estimate genetic covariance matrix of SNPs, followed by using REML (restricted maximum likelihood) implemented in GCTA to estimate narrow sense heritability (VG/VP). To evaluate the influence of population structures on our observed phenotype, we used the SmartPCA program of Eigensoft 5.0.2 () to identify top principle components (PCs) from the SNP data. We then used the projection length of each strain on the first and second PCs to test if our observed phenotypic variation is due to cryptic population structures.We used PLINK () to perform association analysis for SNPs that have minor allele frequency above 15% (1,023,674 SNPs). Day5 survival rates in foraging assay (foraging index) and Day 2 survival rate in starvation assay (starvation resistance index) were regressed on each SNPs and covariates. Covariates include starvation resistance index and inversion status (In(2L)t and In(3R)Mo). See Result sections for reasons of including different covariates. Regression model used includes:Foraging index ∼ genotype,Foraging index ∼ genotype + starvation resistance index,Foraging index ∼ genotype + inversion status,Foraging index ∼ genotype + starvation resistance index + inversion status, andStarvation resistance index ∼ genotype.Foraging index ∼ genotype,Foraging index ∼ genotype + starvation resistance index,Foraging index ∼ genotype + inversion status,Foraging index ∼ genotype + starvation resistance index + inversion status, andStarvation resistance index ∼ genotype.Go enrichment analysis was performed using GOWINDA (). GOWINDA was run with “gene” mode, including SNPs upstream/downstream 2,000 bp to a gene, minimum gene number 3, and with 100,000 simulations. Functional annotations of genes were downloaded from FuncAssociate (http://llama.mshri.on.ca/funcassociate/ (last accessed July 2015), ). […]

Pipeline specifications

Software tools GCTA, EIGENSOFT, PLINK, FuncAssociate
Applications Population genetic analysis, GWAS
Organisms Drosophila melanogaster