PANTOTHENATE KINASE4, LOSS OF GDU2, and TRANSPOSON PROTEIN1 affect the canalization of tomato fruit metabolism

Abstract

Most studies investigating quantitative traits focus on mean levels per genotype rather than the variation between different individuals of one genotype or the variation elicited by different environments. Consequently, the genes that govern this effect are not well understood. The concept, named canalization, which describes a lack of variation, is well-known in the context of developmental processes but is poorly studied for quantitative traits such as metabolism. In this study, we selected eight putative candidate genes from previously identified canalized metabolic quantitative trait loci (cmQTL) and created genome-edited tomato (Solanum lycopersicum) mutants of these genes for experimental validation. Most lines showed wild-type morphology, except for an ADP-ribosylation factor (ARLB) mutant showing aberrant phenotypes in the form of scarred fruit cuticles. In greenhouse trials with different irrigation conditions, whole-plant traits showed a general increase of their level towards the more optimal irrigation conditions, whereas most metabolic traits showed an increase towards the other end of the gradient. Mutants of a PANTOTHENATE KINASE 4 (PANK4), the AIRP ubiquitin gene LOSS OF GDU2 (LOG2), and TRANSPOSON PROTEIN 1 (TRANSP1) grown under these conditions showed an overall improved plant performance. Additional effects, on both target and other metabolites in tomato fruits, regarding the mean level at specific conditions and, ergo, the cross-environment coefficient of variation (CV), were observed. However, variation between individuals remained unaffected. In conclusion, this study supports the idea of distinct sets of genes regulating different types of variation.

Characterization of tomatocanal-1mutant using a multi-omics approach

“…Consecutive experiments were conducted at the MPIMP in Potsdam-Golm, Germany and plants were grown as described previously (Wijesingha Ahchige et al ., 2023). Plants were grown 2018 and 2019 in a greenhouse.…”

“…A similar study looked at the genetic canalization of flowering time on Boechera stricta (Lee et al ., 2014), while treatment of Arabidopsis ecotypes and RILs with pharmacological inhibitors of Hsp70 has been taken to suggest that it acts as a capacitor of phenotypic variation in plants (Queitsch et al ., 2002). In addition to these developmental studies, the concept has recently been applied to describe metabolic quantitative traits (Alseekh et al ., 2017, Wijesingha Ahchige et al ., 2023).…”

Plant biochemical genetics in the multiomics era

“…While this has been done in some cases ( Schauer et al , 2006 ; Wentzell et al , 2007 ; Schauer et al , 2008 ; Jimenez-Gomez et al , 2011 ; Alseekh et al , 2017 ), this resource of legacy data is still underutilized. Together with new data generated through the high-throughput platforms of the multiomics era, it can be used to study canalization and variation more comprehensively ( Wijesingha Ahchige et al , 2023 ).…”