Biology subjects

Wijesingha Ahchige, M.

Publications and source records attributed to Wijesingha Ahchige, M..

3 recordsLinked to original sources

bioRxiv2026

High-resolution mapping and epistatic QTL of tomato fruit metabolism

Tomato wild relatives are valuable genetic resources for trait discovery and understanding the genetic basis of fruit metabolism and quality. Yet, only a fraction of naturally occurring variation has been exploited. Here, we performed metabolite profiling of two large Backcross Inbred Line populations derived from crosses between the wild species S. pennellii accession LA5240 (Lost) and cultivated genotypes LEA (determinate) and TOP (indeterminate), including [~]1400 and [~]500 lines, respectively. High-resolution mapping identified enormous metabolic quantitative trait loci (mQTL), including a new locus on chromosome 12 associated with fruit sucrose accumulation that harbours INVERTASE INHIBITOR 3 (SlINVINH3) protein. Comparative analysis indicated that SlINVINH3 is highly expressed in wild S. pennellii 0716 fruit, whereas a six-amino acid deletion is present in its coding sequence compared with S.pennellii LA5240 and S. lycopersicum. We further demonstrated that in SlINVINH3-overexpressing tomato plants, only the S. pennellii LA5240 allele led to increased sucrose, accompanied by reduced fructose and glucose levels. Furthermore, the large population size enabled us to assess the epistatic interactions, with approximately 40% of interactions being more-than-additive and 60% less-than-additive. Our results demonstrate the power of permanent exotic populations to reveal hidden metabolic diversity and provide an approach for improving fruit quality through targeted breeding and metabolic engineering.

plant biology↗

bioRxiv2026

Endogenous short enhancer sequences increase expression of soybean and cowpea RUBP regeneration genes

Improving regeneration of ribulose-1,5-bisphosphate (RUBP) is a promising approach to improve photosynthesis and plant growth. In addition to transgenic overexpression of target genes, it could be possible to directly overexpress endogenous target genes, through transcriptional enhancements. As shown by the recent discovery of a short sequence motif, that resembles the known octopine synthase (ocs) enhancer, transcriptional enhancement is achievable by relatively short endogenous sequences. In this study, we query the genome of several model and crop plant genomes for the presence of short enhancer motifs. We find hits across all genomes including some in promoter regions of genes. By using derivatives of these motifs in a transient fluorescence assay, we show that several of these are capable of inducing target gene expression in different promoter contexts. A motif scan of the created constructs, for the presence of known transcription factor binding sites, shows that the insertion of these motifs has created binding sites for different TGA-, NAC- and bZIP-transcription factors. Taken together our study shows the feasibility of finding enhancer sequences in the genomes of different plants. With advancement in gene-editing technologies, like prime editing, using such endogenous enhancer sequences, could allow for precise cisgenic promoter engineering of target genes.

plant biology↗

bioRxiv2024

Genetic architecture of the tomato fruit lipidome; new insights link lipid and volatile compounds

Tomato (Solanum lycopersicum L.) fruit flavor is determined by a combination of multiple volatile compounds, including several derived from lipids and fatty acids. Although fruit flavor has been intensively studied, the linkage between lipid metabolism and flavor remains largely undefined. Here, we performed a genome-wide association study (GWAS) and QTL mapping for the fruit lipid content from 550 tomato accessions and 107 backcross inbred lines (BILs) in two consecutive seasons. Over 130 lipid compounds were identified and mapped, allowing for the identification of over 600 metabolic QTL (mQTL). We further described and validated candidate genes associated with lipid content. Among them is a lipase-like protein (TomLLP) whose function was validated in vivo using overexpression lines in tomato and knockout mutants in Arabidopsis. We also identified functions for three enzymes: a class III lipase (Sl-LIP8), a cyclopropane-fatty-acyl-phospholipid synthase (CFAPS1), and Lipoxygenase C (TomLoxC). By utilizing knockout lines for CFAPS1 and CRISPR-Cas9 loss-of-function lines for Sl-LIP8 and TomLoxC, we demonstrated the functional importance of these enzymes in fruit lipid metabolism. Our study provides a comprehensive analysis of the tomato fruit lipidome and insights into key genes that shaped the natural variation in tomato lipid content and their links to flavor-associated volatile compounds.

molecular biology↗