QTL-by-environment analysis (QEI)
Multi-environment forward-backward models were used to assess the
significance and the strength of the QTL effects across environments.
The QEI analysis was conducted in two steps using the same set of 1345
SNP markers that were also used for linkage mapping analysis. This
analysis yielded 28 QEI (only those showing significant interaction) for
the 10 traits (Supplemental Table 4). The number of QEI varied from 0
QEI for nfr to 6 QEI for flw. These two traits also demonstrated the
lowest and highest \(H^{2}\).
All QEI identified in this step were confronted to the plasticity and
genotypic means QTLs using the physical positions of the QTLs and their
confidence intervals. Interestingly, this comparison revealed that all
the detected QEI were also identified using either genotypic means or
plasticity parameters, in the linkage mapping analysis, except two QEI
located on the same region of chromosome 6 (flw6.1 and firm6.1). Among
the 106 unique QTLs identified on genotypic means, PP and QEI, a notable
number of QTLs were specific representing 30 and 32% for plasticity and
genotypic means, respectively (Figure 4). Eight QTLs involving five
different traits (flw1.1, fw2.1, fw2.2, fw11.2, leaf6.1, nflw11.2,
SSC1.2 and SSC9.1) were identified with all the three approaches
highlighting their robustness and susceptibility to environmental
variation.