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.