Computational protocol: Genetic Architecture of Flowering-Time Variation in Arabidopsis thaliana

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Protocol publication

[…] Raw genotype data were converted to the appropriate genotype format A, B, H (A being a marker homozygous for parent A; B homozygous for parent B; H a heterozygous marker). Genotype and phenotype data were merged and saved as .csv files. QTL analysis was performed using R/qtl, with simple and composite interval mapping (). The confidence intervals around each significant QTL peak were determined with the baysint function, at 95% confidence levels. Additional information on the extent of variation explained by each QTL, as well as the effect associated with each parental allele, was gathered using the sim.geno, makeqtl, fitqtl, effectplot, and effectscan functions. Epistatic interactions between QTL were identified by using the qb.scantwo function in R/qtlbim ().For joint QTL analysis, all F2 plants were combined into a single population, the genotype of each chromosome at any given SNP taking on 1 of the 18 possible identities (from our founding accessions). Evidence for a QTL is given as log P, P being the probability that a QTL is segregating at a given SNP ().QTL data on flowering time obtained from RIL analysis were taken from published studies (; ; ; , ; ; ; ). […]

Pipeline specifications

Software tools R/qtl, QTLBIM
Application WGS analysis
Organisms Arabidopsis thaliana, Zea mays