Structural variation underlies functional diversity at methyl salicylate loci in tomato

Abstract

Methyl salicylate is an important inter- and intra-plant signaling molecule, but is deemed undesirable by humans when it accumulates to high levels in ripe fruits. Balancing the tradeoff between consumer satisfaction and overall plant health is challenging as the mechanisms regulating volatile levels have not yet been fully elucidated. In this study, we investigated the accumulation of methyl salicylate in ripe fruits of tomatoes that belong to the red-fruited clade. We determine the genetic diversity and the interaction of four known loci controlling methyl salicylate levels in ripe fruits. In addition to Non-Smoky Glucosyl Transferase 1 (NSGT1), we uncovered extensive genome structural variation (SV) at the Methylesterase (MES) locus. This locus contains four tandemly duplicated Methylesterase genes and genome sequence investigations at the locus identified nine distinct haplotypes. Based on gene expression and results from biparental crosses, functional and non-functional haplotypes for MES were identified. The combination of the non-functional MES haplotype 2 and the non-functional NSGT1 haplotype IV or V in a GWAS panel showed high methyl salicylate levels in ripe fruits, particularly in accessions from Ecuador, demonstrating a strong interaction between these two loci and suggesting an ecological advantage. The genetic variation at the other two known loci, Salicylic Acid Methyl Transferase 1 (SAMT1) and tomato UDP Glycosyl Transferase 5 (SlUGT5), did not explain volatile variation in the red-fruited tomato germplasm, suggesting a minor role in methyl salicylate production in red-fruited tomato. Lastly, we found that most heirloom and modern tomato accessions carried a functional MES and a non-functional NSGT1 haplotype, ensuring acceptable levels of methyl salicylate in fruits. Yet, future selection of the functional NSGT1 allele could potentially improve flavor in the modern germplasm.

Genetic diversity, population structure, and taxonomic confirmation in annual medic (Medicago spp.) collections from Crimea, Ukraine

“…The presence of missing marker loci can be attributed to various factors, including variations in primer sites and the potential presence of structural variations in the targeted regions. Structural variations, such as insertions, deletions, or duplications, can significantly impact gene expression and protein functions, leading to variations in phenotype ( Alonge et al., 2020 ; Sapkota et al., 2023 ). Therefore, the observed missing marker loci are possibly associated with the phenotypic natural variation observed in the species being evaluated, providing valuable insights into the underlying genomic variation contributing to the diverse phenotypes within the collection.…”

Multi-omic applications for understanding and enhancing tropical fruit flavour

“…Genomics data may further advance tropical fruit flavour through targeted breeding and genetic selection strategies or gene-editing technology (Mathiazhagan et al 2021 ). Genome-wide association studies (GWAS) and quantitative trait loci (QTL) mapping approaches have previously identified genome regions responsible for the regulation of fruit flavour compounds in tomato (Gai et al 2023 ; Sapkota et al 2023 ), grape (Koyama et al 2022 ; Bosman et al 2023 ) and apple (Yang et al 2023 ).…”