LRR-RLPs are modular proteins anchored in the cell membrane, with an ectodomain built from tandem leucine-rich repeats that grips pathogen-derived molecules, and a short membrane-proximal region that connects to intracellular signalling complexes. Unlike the better-known LRR receptor-like kinases, which carry an internal kinase domain, RLPs rely on partner kinases to transmit their signal. This architecture makes them exquisitely adaptable: the repeat region can evolve to recognize new pathogen ligands while the signalling module stays intact. Many famous disease-resistance traits in crops trace back to RLP-type receptors, including the Cf proteins that protect tomatoes against leaf mold fungus. Yet despite their agricultural importance, no one had systematically traced how RLP lineages, their domain architectures, their copy numbers and their chromosomal arrangements differ across the whole tomato clade, which includes cultivated tomato and a dozen or so wild species from the Andean region.

To fill that gap, the team took a pan-genome approach. Rather than studying a single reference genome, they compiled the primary proteomes of 76 accessions spanning the tomato clade and used the clustering tool OrthoFinder to group RLP candidates into orthogroups, sets of genes descended from a common ancestor. The result was a pan-gene family of 3,798 candidates distributed across 97 orthogroups. Strikingly, no single orthogroup was detected in every accession under the study’s annotation, detection and clustering criteria. Even when the analysis was restricted to the 72 accessions from tomato’s home section, Lycopersicon, no strict core orthogroup emerged. Instead, the family split into 14 soft-core groups present in most accessions, 42 shell groups present in some, six cloud groups present in few, and 35 private groups found only in individual lineages.

The dominance of the shell category is the headline statistic of the study. Shell orthogroups accounted for 43.3 percent of all orthogroups but a remarkable 61.8 percent of all candidate genes, meaning that most RLP sequences in any given tomato genome belong to lineages that come and go across the species panel. This is a hallmark of genes under pathogen-driven selection: immune receptors are gained, lost and reshuffled as plants and their enemies race to outmaneuver one another. The authors were careful about verification. Independent reciprocal-best-hit searches and synteny checks, which compare the chromosomal neighborhoods of genes to confirm true orthology, supported the gene pairs in 40 orthogroups, while flagging six nominally private orthogroups whose apparent uniqueness may reflect annotation or clustering artifacts rather than genuine lineage-specific invention.

Beyond counting genes, the researchers dissected the architecture of the receptors themselves. A distinctive feature of many plant LRR receptors is the island domain, a non-leucine-rich insertion embedded within the repeat array that often serves as the actual ligand-binding surface. Across the panel the team identified 6,024 island domains, and a recurring pattern emerged: an island domain followed by four leucine-rich repeats at the terminal end of the ectodomain, a configuration that extends earlier cross-species observations and appears to be a favored structural solution in this receptor family. When the researchers clustered island-domain events by the comparison groups in which they occurred, communities spanning four or five groups contained 93.6 percent of all events, suggesting that most architectural variation is shared across related lineages rather than invented de novo in each species.

The modular composition of the receptors also told an evolutionary story. The team built phylogenetic trees from two regions: the C3 module and the combined endomembrane-juxtamembrane, transmembrane and cytoplasmic juxtamembrane region, abbreviated eJM-TM-cJM. Comparing the two trees revealed partial topological discordance, meaning that different parts of the same receptor family appear to have followed somewhat different evolutionary histories, perhaps through ancient recombination or domain shuffling. The authors note, however, that two of the classification boundaries separating module types had weak bootstrap support, a caution that the precise number of module classes should be interpreted with care. Such methodological honesty is increasingly valued in pan-genome research, where clustering thresholds can materially change conclusions.

Copy-number variation proved to be another axis of diversity. Different tomato accessions carried comparable burdens of multi-copy orthogroups, but the specific receptor lineages involved differed from accession to accession, meaning that each genome has expanded its own subset of immune receptors. Tandem duplications, where a gene is copied next to its original, together with proximal duplications nearby, accounted for 86.5 percent of the within-orthogroup duplication pairs detected, pointing to local replication events as the dominant engine of RLP expansion. Relative to the reference cultivar Heinz, local structural variants affected 28 of the 3,539 callable candidates, a reminder that even reference-relative comparisons reveal meaningful genomic rearrangements in these receptor-rich regions.

One orthogroup stood out for its evolutionary signal. RLP-OG0013 showed the highest median pairwise ratio of nonsynonymous to synonymous substitution rates, Ka/Ks, at 1.55, a value above one that is conventionally read as a sign of positive selection, where amino-acid changes are favored over silent mutations. The authors are appropriately measured here, describing the figure as a descriptive divergence signal that requires lineage-aware selection tests before firm conclusions can be drawn, since averaging Ka/Ks across divergent lineages can obscure the true pattern of selection acting on individual branches. Still, the result marks RLP-OG0013 as a prime candidate for deeper evolutionary analysis, and potentially for functional studies of pathogen recognition.

The study did not stop at genomes. In two separate time-course experiments in which plants were inoculated with the necrotrophic fungus Botrytis cinerea, the gray mold pathogen that devastates tomatoes worldwide, 43 candidate receptor genes from 27 orthogroups were differentially expressed, linking a substantial slice of the pan-gene family to actual immune responses. One technical nuance deserves attention: reads from the wild accession LA2574 were quantified against reference genes from LA1777, another wild species, which permitted integration of expression data at the orthogroup level but did not allow any inference of LA2574’s own genomic copy number. This kind of cross-reference quantification is common in non-model wild species but constrains interpretation, and the authors flag it explicitly.

What emerges from the study is a portrait of the tomato immune receptor repertoire as a dynamic, patchwork system: recurrent receptor architectures shared across the clade, combined with accession-dependent lineage representation and copy expansion shaped by tandem duplication. For breeders, the orthogroup-level genomic and expression summaries provide a ranked shortlist of candidates for genotype-matched tests of pathogen recognition and resistance, particularly against threats like gray mold where cell-surface perception is a first line of defense. As wild relatives continue to supply resistance genes for cultivated tomato, knowing which receptor lineages are private, which are shared, which have expanded locally and which light up after infection turns a haystack of nearly 3,800 genes into a manageable set of leads. The pan-genome framework used here, with its careful attention to clustering artifacts and cross-reference limitations, may well become the template for cataloging immune receptor diversity in other crop clades.

Subject of Research: Pan-genomic diversity of LRR-RLP immune receptor genes in tomato and wild relatives

Article Title: Receptor-module diversity and lineage-specific expansion of the LRR-RLP pan-gene family in tomato and allied wild relatives

Article References: Jiang, T., Yang, W., Tang, B., Wang, Q., Ao, N., Mo, C., Deng, Y., & Zhang, B. (2026). Receptor-module diversity and lineage-specific expansion of the LRR-RLP pan-gene family in tomato and allied wild relatives. BMC Plant Biology. https://doi.org/10.1186/s12870-026-10132-5

Image Credits: AI Generated

DOI: 10.1186/s12870-026-10132-5

Keywords: tomato, wild relatives, LRR-RLP, pan-gene family, island domain, receptor modules, copy-number variation, coding-sequence divergence, pathogen response, Botrytis cinerea, orthogroups, tandem duplication

The study, published in Genome Biology, was led by Senior Research Associate Carmen Catala and Professor Zhangjun Fei, together with adjunct professor and USDA scientist James Giovannoni. The team set out to answer a question that has frustrated tomato breeders for generations: which genetic controls produce the striking differences in color, sweetness, bitterness, and aroma between cultivated tomatoes and their wild cousins, and which of those controls are worth reintroducing into modern varieties? The answer required the researchers to look not just at which genes differ between species, but at how those genes are switched on and off as a fruit grows, ripens, and develops its final chemistry.

The wild relatives of tomato remain an extraordinary reservoir of traits that domestication left behind. Some wild species pack their fruit with high levels of lycopene, the red pigment that gives ripe tomatoes their characteristic color and contributes much of their nutritional value. Others store sugar in forms and concentrations that cultivated fruit no longer achieves. And some, notably Solanum pennellii and Solanum neorickii, never turn red at all, producing fruit that stays green through maturity. Breeders have long suspected that these species hold the raw material for tastier, more nutritious tomatoes, but importing wild traits into elite lines has always been a gamble, because the same wild chromosomes that carry desirable genes often carry undesirable ones as well.

That tension is at the heart of why wild diversity has been so hard to exploit. As Catala explained, wild tomatoes offer an enormous reservoir of diversity for flavor, nutrition, and resilience, but bringing those traits into modern varieties can come at the expense of characteristics that breeders have spent decades improving, such as yield, fruit size, or shelf life. The way around that trade-off, she argued, is precise information about how the genes responsible for each trait are controlled. If breeders know exactly which genetic switches govern sweetness or pigment, they can move those switches without dragging along the rest of the wild genome.

To build that precision, the research team turned to a classic genetic trick with a modern analytical twist. Imagine every gene as a lamp whose brightness shapes how a fruit grows, ripens, and tastes. A lamp can be dimmed in two ways. One is a dimmer built into the lamp itself—a change in the stretch of DNA sitting immediately next to the gene that controls how strongly that single gene is expressed. Biologists call this a cis effect. The other is a change in the building’s wiring: a trans effect, in which an alteration somewhere else in the genome changes the regulatory signals reaching many genes at once. From the outside, the two look identical, because either one changes a gene’s activity. Telling them apart, however, makes an enormous difference to anyone trying to breed with the underlying DNA.

The way to separate the two is to plug both lamps into the same outlet. The researchers crossed cultivated tomato with each of three wild relatives to produce hybrid plants. A hybrid carries one copy of every gene from each parent, and both copies operate inside the same cells, bathed in the same regulatory environment. If the cultivated copy and the wild copy of a gene behave differently under those identical conditions, the difference must be written into the DNA adjacent to the gene itself—a cis effect. As Fei put it, the hybrid gives researchers a natural controlled experiment: both versions of each gene sit in the same cells and receive the same signals, so any difference in their activity points directly to local regulatory change.

With that framework in place, the team measured gene activity with remarkable granularity. They examined three distinct fruit tissues—the fleshy outer wall, the placenta, and the jelly-like tissue surrounding the seeds—at up to four stages spanning early fruit development through ripening. This tissue-by-tissue, stage-by-stage design matters because a gene that influences sweetness may only act in the placenta, while a pigment gene may only matter in the outer wall during ripening. Averaging across whole fruits would blur exactly the signals breeders need to see.

The results were strikingly lopsided. In every species, every tissue, and every developmental stage examined, cis changes were the dominant driver of differences in gene activity, affecting up to 23.5 percent of active genes. Trans changes, by contrast, affected no more than 4.6 percent. The number of genes showing regulatory differences roughly doubled in the more distant wild relatives compared with Solanum pimpinellifolium, the closest wild cousin of cultivated tomato, consistent with the idea that regulatory divergence accumulates as species drift apart. Many of the identified switches were also highly specific, operating in only one tissue at one particular moment of fruit development—a specificity that could prove invaluable for breeders hoping to alter one trait without disturbing the rest of the fruit.

The regulatory map also illuminates several familiar fruit traits with new clarity. In the green-fruited species, cis changes boost genes that steer the pigment pathway away from lycopene, explaining why those fruits never develop the red color and associated nutritional profile of ripe cultivated tomatoes. Sweetness follows a matched pair of sugar-related genes: one gene that breaks down sucrose and another that blocks that breakdown are regulated in a coordinated way in the green-fruited species, allowing those fruits to retain more of the sucrose that cultivated tomatoes convert. Bitterness, meanwhile, reveals a developmental program the researchers describe as defense early, edibility at maturity. Early in fruit development, trans regulation helps maintain high levels of glycoalkaloids, the bitter defensive compounds that deter herbivores in young fruit. Later, cis changes in cultivated tomato redirect those compounds into non-bitter forms as the fruit ripens, converting a chemical shield into a palatable food.

For breeders, the practical payoff is a shift from fishing to targeting. As Giovannoni noted, breeders have always known that wild tomatoes hold valuable traits, but using them introduces undesirable traits as well, forcing time- and labor-intensive cleanup. What has been missing is a way to tell which of thousands of genetic differences lies behind each trait. With this map, researchers can point to specific genes whose effects operate in specific tissues at specific moments of development and ripening, making selection far more deliberate. To spread that advantage, the team has released its full dataset, including two newly assembled wild tomato genomes, freely available to the research community. The work was supported by the USDA National Institute of Food and Agriculture and the U.S. National Science Foundation. The flavor that breeding left behind, it turns out, was never gone—only waiting for a map good enough to lead breeders back to it.

Subject of Research: Regulatory divergence in gene expression underlying fruit traits of cultivated versus wild tomato species

Article Title: Wild tomatoes still hold the flavor we bred away: new map shows breeders where to look

Article References: Wild tomatoes still hold the flavor we bred away: new map shows breeders where to look. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: tomato, wild relatives, cis-regulation, trans-regulation, allele-specific expression, fruit ripening, lycopene, sucrose, glycoalkaloids, Genome Biology, plant breeding, Boyce Thompson Institute

The team tackled a deceptively simple question: when two tomato species look and taste different, how much of that difference comes from the genes themselves versus the molecular switches that control them? To find out, they exploited a clever property of F1 hybrids. When a cultivated tomato is crossed with a wild relative, every cell contains one chromosome set from each parent. Because the two parental copies of each gene sit side by side in the same cellular environment, exposed to identical transcription factors and signaling molecules, any difference in how strongly the two copies are expressed can be attributed to sequences on or near the gene itself. This phenomenon, known as allele-specific expression, allows scientists to separate cis-regulatory effects, which act locally on DNA elements such as promoters and enhancers, from trans-regulatory effects, which arise from diffusible factors encoded elsewhere in the genome.

The scale of the analysis sets the study apart. Rather than examining a single cross at a single moment, the researchers generated hybrids between cultivated tomato and three wild relatives spanning a gradient of evolutionary distances: Solanum pimpinellifolium, the closest wild ancestor; Solanum neorickii at an intermediate distance; and the more distantly related Solanum pennellii. They then profiled gene expression across three distinct fruit tissues and multiple developmental stages, from early cell division through ripening. To support the work, the team assembled new genome sequences and annotations for the parental lines, ensuring that sequencing reads from each hybrid could be assigned accurately to the maternal or paternal copy of every gene.

The resulting dataset delivers an unambiguous headline: cis-regulatory divergence is the dominant force shaping expression differences between tomato species. Across tissues, developmental stages, and levels of relatedness, local regulatory changes consistently explained a larger share of parental expression differences than trans effects. This makes evolutionary sense. Cis-regulatory mutations tend to affect a single gene or small set of genes, allowing fine-tuned changes without catastrophic collateral damage, whereas mutations in trans-acting factors can perturb hundreds of downstream targets simultaneously and are more likely to be deleterious. Natural selection, the authors argue, has repeatedly favored regulatory variants that adjust individual genes without breaking the broader network.

Yet the study also shows how much this simple dichotomy oversimplifies reality. The majority of cis-regulatory effects proved to be tissue-specific, stage-specific, or both. A gene whose wild allele dominates expression in the fruit pericarp may show no such bias in the placenta, or at a different point in ripening. The researchers catalogued genes classified as cis-only, cis-plus-trans, and cis-by-trans, where a cis difference is itself modulated by trans-regulation depending on context. This last category is particularly intriguing, because it implies that local regulatory variants do not act in isolation; their effects can be amplified, suppressed, or reversed depending on the trans environment supplied by the other parent and by the developmental program of the tissue.

Evolutionary distance emerged as a second organizing principle. In hybrids with S. pimpinellifolium, the closest relative, regulatory divergence between the two alleles was comparatively modest and trans effects retained a noticeable share of the action. As the wild parent became more distantly related, cis-regulatory contributions grew progressively larger. The inheritance patterns of expression levels shifted in parallel, indicating that the architecture of regulatory variation is not static across the tomato clade but accumulates and reorganizes over evolutionary time. For crop scientists, this is an encouraging message: the more exotic the germplasm, the greater the reservoir of independent regulatory variants available for breeding.

The practical payoff lies in the pathways the team traced. They found extensive cis-regulatory divergence in genes governing carotenoid biosynthesis, the source of lycopene and beta-carotene that give ripe tomatoes their color and contribute provitamin A; in the phenylpropanoid and flavonoid pathways, which produce antioxidants linked to human health; and in steroidal glycoalkaloid metabolism, which influences bitterness and toxicity in wild fruit. Genes controlling sugar accumulation, a decisive factor in perceived sweetness, and volatile organic compounds, which shape aroma, likewise showed strong allele-specific patterns. In several cases, the wild allele carried regulatory variants that boosted expression of biosynthetic genes in specific tissues or stages, suggesting concrete targets for reintroducing flavor and nutrition into elite cultivars without disrupting yield-related traits.

Among the individual genes highlighted are SlKLUH, a cytochrome P450 involved in fruit growth whose cis-regulation proved strikingly tissue-specific, and ZDS, a key enzyme in the carotenoid pathway. The promoter analysis added a mechanistic layer: a substantial number of differently regulated genes carried structural variations of 30 base pairs or more in the two-kilobase region upstream of the gene, pointing to insertions, deletions, and rearrangements as frequent sources of cis-regulatory novelty. Such structural variants are often invisible to standard SNP-based studies, which may explain why genome-wide association work has undersold the regulatory component of fruit quality variation.

For breeders, the message is that wild tomato relatives are not merely a source of disease-resistance genes but a deep library of regulatory alleles that can tune when, where, and how strongly the fruit’s metabolic genes operate. Because cis-regulatory variants tend to be narrowly scoped, introgressing a wild promoter behind a domesticated gene could, in principle, enhance a specific flavor compound without dragging along the yield penalties that have historically made wild germplasm unattractive. The study’s high-resolution map of which genes are cis-regulated, in which tissue, and at which stage, offers a direct roadmap for such precision breeding, whether through marker-assisted selection or genome editing of regulatory regions.

The work also carries a broader evolutionary lesson about the domestication bottleneck. Decades of selection for size, uniformity, and shelf life narrowed the genetic diversity of cultivated tomato, and with it the diversity of regulatory variants shaping flavor chemistry. By quantifying how much regulatory divergence separates the crop from its wild cousins, and by showing that this divergence concentrates in exactly the pathways that define fruit quality, the study reframes wild relatives as the key to restoring what domestication left behind. As sequencing costs fall and allele-specific analysis becomes routine in crop genomics, the tomato map is likely to become a template for dissecting regulatory variation in other fruits, from pepper to melon, where the difference between a memorable harvest and a forgettable one often comes down to the switches, not the genes.

Subject of Research: Allele-specific gene expression and regulatory divergence between cultivated and wild tomato species

Article Title: Allele-specific expression reveals complex regulatory divergence underlying fruit phenotypic differences between cultivated and wild tomato species

Article References: Zhao, J., Nicolas, P., Xu, Y., Vrebalov, J., Giovannoni, J., Fei, Z., & Catala, C. (2026). Allele-specific expression reveals complex regulatory divergence underlying fruit phenotypic differences between cultivated and wild tomato species. Genome Biology. https://doi.org/10.1186/s13059-026-04279-5

Image Credits: AI Generated

DOI: 10.1186/s13059-026-04279-5

Keywords: tomato, allele-specific expression, cis-regulatory variation, wild relatives, fruit development, flavor, carotenoids, flavonoids, F1 hybrids, gene regulation, Solanum pennellii, crop breeding