Biology subjects

Swinnen, G.

Publications and source records attributed to Swinnen, G..

4 recordsLinked to original sources

bioRxiv2026

Cryptic variation alters gene dosage sensitivity to shape inflorescence architecture in tomato

Phenotypic diversity arises in large part from genetic variants at multiple interacting loci, many of which alter gene dosage rather than abolish gene function. Dosage-sensitive variants, which often produce nonlinear phenotypic outcomes, can be exploited to fine-tune quantitative traits for crop improvement using genome editing. However, the phenotypic outcomes of individual variants can differ substantially across genetic backgrounds, as segregating alleles may modulate allelic effects in unexpected ways. Yet, how genetic background shapes gene dosage effects remains underexplored. Here, we show that MADS-box gene dosage effects, which can be used to tune tomato inflorescence architecture for optimal fruit yield, differ profoundly between distinct genetic backgrounds. We mapped the genetic basis of this background dependency and identified the cryptic modifier locus suppressor of branching 2 (sb2), which contains the conserved floral identity gene ANANTHA. We show that natural variation at sb2 modulates how inflorescence architecture responds to MADS-box dosage effects from natural and engineered loss-of-function mutations. Our findings illustrate how cryptic genetic variants can reshape gene dosage relationships and underscore the importance of characterizing such hidden variation for predictive engineering of quantitative traits using genome editing. Significance StatementAdvances in crop genome editing enable precise modifications of gene dosage to fine-tune quantitative traits in crop improvement, but the predictability of such strategies remains limited. We show that hidden genetic differences, known as cryptic variation, can alter how gene dosage changes influence plant growth and development. Using tomato inflorescence architecture as a model, we characterize a natural cryptic modifier locus, suppressor of branching 2 (sb2), that modifies the effects of natural and engineered mutations in dosage-sensitive MADS-box genes. Our findings demonstrate that gene dosage effects depend on genetic background and highlight an often-unrecognized constraint on precision breeding by genome editing. Accounting for similar cases of cryptic variation will be essential for predictable engineering of quantitative traits in crops.

plant biology↗

bioRxiv2024

Application of a GRF-GIF chimera enhances plant regeneration for genome editing in tomato

Genome editing has become a routine tool for functionally characterizing plant and animal genomes. However, stable genome editing in plants remains limited by the time- and labor- intensive process of generating transgenic plants, as well as by the efficient isolation of desired heritable edits. In this study, we evaluated the impact of the morphogenic regulator GRF-GIF on plant regeneration and genome editing outcomes in tomato. We demonstrate that expressing a tomato GRF-GIF chimera reliably accelerates the onset of shoot regeneration from callus tissue culture by approximately one month and nearly doubles the number of recovered transgenic plants. Consequently, the GRF-GIF chimera enables the recovery of a broader range of edited haplotypes and simplifies the isolation of mutants harboring heritable edits, but without markedly interfering with plant growth and development. Based on these findings, we outline strategies that employ basic or advanced diagnostic pipelines for efficient isolation of single and higher-order mutants in tomato. Our work represents a technical advantage for tomato transformation and genome editing, with potential applications across other Solanaceae species.

plant biology↗

bioRxiv2020

KIX8 and KIX9 are conserved repressors of organ size in the asterid species tomato

Plant organ size and shape are major agronomic traits that depend on cell division and expansion, which are both regulated by complex gene networks. In several eudicot species belonging to the rosid clade, organ growth is controlled by a repressor complex consisting of PEAPOD (PPD) and KINASE-INDUCIBLE DOMAIN INTERACTING (KIX) proteins. The role of these proteins in asterids, which together with the rosids constitute most of the core eudicot species, is still unknown. We used CRISPR-Cas9 genome editing to target SlKIX8 and SlKIX9 in the asterid model species tomato (Solanum lycopersicum) and analyzed loss-of-function phenotypes. We found that loss of function of SlKIX8 and SlKIX9 led to the production of enlarged, dome-shaped leaves and that these leaves exhibited increased expression of putative SlPPD target genes. Unexpectedly, kix8 kix9 mutants carried enlarged fruits with increased pericarp thickness due to cell expansion. At the molecular level, protein interaction assays indicated that SlKIX8 and SlKIX9 act as adaptors between the SlPPD and SlTOPLESS co-repressor proteins. Our results show that KIX8 and KIX9 are regulators of organ growth in asterids and can provide strategies to improve important traits in produce such as thickness of the fruit flesh. One sentence summaryTwo transcriptional repressors negatively regulate organ growth in tomato with loss-of-function lines producing enlarged fruits due to an appearance of more expanded cells in the fruit flesh.

plant biology↗

bioRxiv2020

Constitutive Steroidal Glycoalkaloid Biosynthesis in Tomato is Regulated by the Clade IIIe Basic Helix-Loop-Helix Transcription Factors MYC1 and MYC2

Specialized metabolites are produced by plants to fend off biotic enemies. Across the plant kingdom, the biosynthesis of these defense compounds is promoted by jasmonate signaling in which clade IIIe basic helix-loop-helix (bHLH) transcription factors take on a central role. Tomato (Solanum lycopersicum) produces cholesterol-derived steroidal glycoalkaloids (SGAs) that act as phytoanticipins against a broad variety of herbivores and pathogens. The biosynthesis of SGAs from cholesterol occurs constitutively in tomato plants and can be further stimulated by jasmonates. Here, we demonstrate that the two tomato clade IIIe bHLH transcription factors, MYC1 and MYC2, redundantly and specifically control the constitutive biosynthesis of SGAs. Double myc1 myc2 loss-of-function tomato hairy roots displayed suppressed constitutive expression of cholesterol and SGA biosynthesis genes, and consequently severely reduced levels of the main tomato SGAs -tomatine and dehydrotomatine. In contrast, basal expression of genes involved in canonical jasmonate signaling or in the biosynthesis of highly jasmonate-inducible phenylpropanoid-polyamine conjugates was not affected. Furthermore, CRISPR-Cas9(VQR)-mediated genome editing of a specific cis-regulatory element, targeted by MYC1/2, in the promoter of a cholesterol biosynthesis gene led to decreased constitutive expression of this gene, but did not affect its jasmonate inducibility. Our results demonstrate that clade IIIe bHLH transcriptional regulators might have evolved to regulate the biosynthesis of specific constitutively accumulating specialized metabolites independent of jasmonate signaling. One sentence summaryThe clade IIIe basic helix-loop-helix transcription factors MYC1 and MYC2 control the constitutive biosynthesis of tomato steroidal glycoalkaloids and might do so independently of jasmonate signaling.

plant biology↗