Candidate genes
Multi-parental populations are powerful for QTL mapping studies (Huang et al. 2012; Kover et al. 2009) and are besides interesting for fine mapping and candidate gene screening. Barrero et al. (2015) for instance considered the variation of the QTL effect estimated for the different parental lines, combined with transcriptomic analyses to efficiently identify candidate genes. Similarly, Septiani et al. (2019) narrowed candidate genes for Fusarium resistance in a maize MAGIC population using allelic effect of the MAGIC parents.
A number of candidate genes were proposed in our study, affecting both genotypic means and plasticity variation. These candidate genes were selected based on the parental allelic effect and represent valuable targets for future studies attempting to characterize the molecular mechanisms underlying plasticity in tomato. Indeed, relevant candidate genes were proposed for plasticity of flowering time including the Solyc11g071250 which corresponds to an “EMBYO FLOWERING 1-like protein” (EMF1). The implication of EMF1 in flowering time has been observed in Arabidopsis by Aubert et al., (2001) who highlighted an indirect effect of EMF1 on flowering time and inflorescence. More recently, Luo et al., (2018) outlined the role of EMF1 interacting with CONSTANS proteins in a complex pathway to regulate the expression of flowering time genes in Arabidopsis. Solyc11g070100 which is annotated as “Early flowering protein” (ELF) gene is also an interesting candidate for flowering time regulation. It was observed across species that a consistent expression of ELF3 can extend the rapid transition to flowering (Huang et al., 2017). ELF3 loss of function is therefore expected to trigger early flowering according to these authors. Interestingly, Solyc11g070100 was affected by 69 SNPs and 14 INDELs polymorphisms, among which only one SNP showed polymorphism variation in line with the estimated allelic effect for the eight parental lines at this QTL. This SNP was localized at the position 54,632,225 bp in chromosome 11, upstream the gene Solyc11g070100. The parent LA1420 carried the reference allele at this SNP while the remaining parents held the alternative allele. Considering the estimated allelic effects at this QTL, we could assume that the LA1420 allele variant might induce an early flowering phenotype comparatively to the other parents.