Candidate genes
Confidence intervals (CI) of the MAGIC-MET QTLs varied from 0.45Mbp to 87Mbp including a variable number of genes. We thus focused on QTLs presenting CI regions smaller than 2Mbp for CG screening. From 49 (nflw12.1) to 256 (diam4.1) genes were within the regions of the selected QTLs. Taking advantage of the parental allelic effect, the CG were narrowed for each QTL by contrasting the allelic effect of the eight parental lines. The selected candidates after the filtering procedure are presented in Supplemental Table 7, highlighting interesting candidates for further studies. Flowering time QTLs for instance included some CG with consistent matching regarding their functional annotation. For example, the CI of the QTL ppflw11.1 on chromosome 11 included two CG: Solyc11g070100 and Solyc11g071250 corresponding to “Early flowering protein” (ELF) and “EMBYO FLOWERING 1-like protein” (EMF1), respectively. Among other potential flowering candidates, we noticed Solyc12g010490 (AP2-like ERF) for the QTL flw12.1 and Solyc03g114890 and Solyc03g114900 (COBRA-like proteins) for the QTL flw3.2. Aside flowering time, the selected candidate genes for the QTLs diam4.1 and ppSSC1.1 included the Solyc04g081870 (annotated as an Expansin gene) and Solyc01g006740 (annotated as Sucrose phosphate phosphatase) genes, respectively.
We could identify some plasticity QTLs showing sensitivity to the environmental conditions, notably the QTLs detected using the Scv plasticity parameter. Candidate genes were screened for some QTLs falling into this category. The ppfw9.1 QTL CI for example, showing susceptibility to the sum of degree day (SDD), carried a chaperone candidate (solyc09g091180) which might be involved in regulating fruit weight depending on the SDD variation. Similarly, the QTL ppleaf11.1 is affected by the maximal temperature (Supplemental Table 4). Three CG (Solyc11g071830, Solyc11g071930 and Solyc11g071710) belonging to the Chaperone J-domain family, were retained after the filtering procedure in the region of this QTL. Interestingly, the DnaJ-like zinc-finger gene (Solyc11g071710) was among the candidates corresponding to several plasticity QTL including ppflw11.1, ppleaf11.1, ppnflw11.1, ppht11.1 and ppdiam11.2. This gene presented a total of 122 polymorphisms across the eight parental lines among which 35 and 68 are in the up-stream and down-stream gene region. Further investigation regarding this gene is needed to state its potential pleiotropic effect.