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.