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Methyl salicylate imparts a potent flavor and aroma described as medicinal and wintergreen that is undesirable in tomato (Solanum lycopersicum) fruit. Plants control the quantities of methyl salicylate through a variety of biosynthetic pathways, including the methylation of salicylic acid to form methyl salicylate and subsequent glycosylation to prevent methyl salicylate emission. Here, we identified a subclade of tomato methyl esterases, SALICYLIC ACID METHYL ESTERASE1-4, responsible for demethylation of methyl salicylate to form salicylic acid in fruits. This family was identified by proximity to a highly significant methyl salicylate genome-wide association study locus on chromosome 2. Genetic mapping studies in a biparental population confirmed a major methyl salicylate locus on chromosome 2. Fruits from SlMES1 knockout lines emitted significantly (P < 0,05, t test) higher amounts of methyl salicylate than wild-type fruits. Double and triple mutants of SlMES2, SlMES3, and SlMES4 emitted even more methyl salicylate than SlMES1 single knockouts—but not at statistically distinguishable levels—compared to the single mutant. Heterologously expressed SlMES1 and SlMES3 acted on methyl salicylate in vitro, with SlMES1 having a higher affinity for methyl salicylate than SlMES3. The SlMES locus has undergone major rearrangement, as demonstrated by genome structure analysis in the parents of the biparental population. Analysis of accessions that produce high or low levels of methyl salicylate showed that SlMES1 and SlMES3 genes expressed the highest in the low methyl salicylate lines. None of the MES genes were appreciably expressed in the high methyl salicylate-producing lines. We concluded that the SlMES gene family encodes tomato methyl esterases that convert methyl salicylate to salicylic acid in ripe tomato fruit. Their ability to decrease methyl salicylate levels by conversion to salicylic acid is an attractive breeding target to lower the level of a negative contributor to flavor.

 

Fruit flavor is defined as the perception of the food by the olfactory and gustatory systems, and is one of the main determinants of fruit quality. Tomato flavor is largely determined by the balance of sugars, acids and volatile compounds. Several genes controlling the levels of these metabolites in tomato fruit have been cloned, including LIN5 , ALMT9 , AAT1 , CXE1 , and LoxC . The aim of this study was to identify any association of these genes with trait variation and to describe the genetic diversity at these loci in the red-fruited tomato clade comprised of the wild ancestor Solanum pimpinellifolium , the semi-domesticated species Solanum lycopersicum cerasiforme and early domesticated Solanum lycopersicum . High genetic diversity was observed at these five loci, including novel haplotypes that could be incorporated into breeding programs to improve fruit quality of modern tomatoes. Using newly available high-quality genome assemblies, we assayed each gene for potential functional causative polymorphisms and resolved a duplication at the LoxC locus found in several wild and semi-domesticated accessions which caused lower accumulation of lipid derived volatiles. In addition, we explored gene expression of the five genes in nine phylogenetically diverse tomato accessions. In general, the expression patterns of these genes increased during fruit ripening but diverged between accessions without clear relationship between expression and metabolite levels. 

The mechanisms that regulate the vast diversity of plant organ shapes such as the fruit remain to be fully elucidated. TONNEAU1 Recruiting Motif proteins (TRMs) have been implicated in the control of organ shapes in a number of plant species, including tomato. However, the role of many of them is unknown. TRMs interact with Ovate Family Proteins (OFPs) via the M8 domain. However, thein plantafunction of the TRM‐OFP interaction in regulating shape is unknown.

We used CRISPR/Cas9 to generate knockout mutants in TRM proteins from different subclades and in‐frame mutants within the M8 domain to investigate their roles in organ shape and interactions with OFPs.

Our findings indicate that TRMs impact organ shape along both the mediolateral and proximo‐distal axes of growth. Mutations inSltrm3/4andSltrm5act additively to rescue the elongated fruit phenotype ofovate/Slofp20(o/s) to a round shape. Contrary, mutations inSltrm19andSltrm17/20aresult in fruit elongation and further enhance the obovoid phenotype in theo/smutant.

This study supports a combinatorial role of the TRM‐OFP regulon where OFPs and TRMs expressed throughout development have both redundant and opposing roles in regulating organ shape.