Linkage mapping on the genotypic mean and plasticity phenotypes
Linkage mapping was carried out with a set of 1345 SNP markers selected from the genome resequencing of the eight parental lines. All the MAGIC lines were genotyped for those SNPs and at each SNP position, the founder haplotype probability was predicted with the functioncalc_genoprob from R/qtl2 package (Broman et al., 2019). Founder probabilities were then used with the Haley-Knott regression model implemented in R/qtl2 for QTL detection. The response variables were the genotypic means, slope, VAR and SCv for each trait. To attest for significance, the threshold for all phenotypes was set to a LOD threshold of -log10 (α/number of SNPs) where α was fixed at 5% risk level. The VAR plasticity parameter was log transformed for all traits except fset (sqrt transformation) to meet normality assumption before QTL analysis. The function find_peaks () of R/qtl2 package was used to detect all peaks exceeding the defined threshold and the LOD score was dropped of two and one units to separate two significant peaks as distinct QTLs and to define the confidence interval of the QTLs, respectively.