Branching out: Tomato genes point to new medicines
Cold Spring Harbor Laboratory
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Tomatoes grow on the vine at Uplands Farm, about a mile east of Cold Spring Harbor Laboratory’s main campus on Long Island. The agricultural research station offers a shared resource for CSHL scientists studying various topics, from plant genetics to quantitative biology and cancer.
view moreCredit: Lippman lab/CSHL
Picture juicy red tomatoes on the vine. What do you see? Some tomato varieties have straight vines. Others are branched. The question is why. New research from Cold Spring Harbor Laboratory (CSHL) provides the strongest evidence to date that the answer lies in what are called cryptic mutations. The findings have implications for agriculture and medicine, as they could help scientists fine-tune plant breeding techniques and clinical therapeutics.
Cryptic mutations are differences in DNA that don’t affect physical traits unless certain other genetic changes occur at the same time. CSHL Professor & HHMI Investigator Zachary Lippman has been researching cryptic mutations’ effects on plant traits alongside CSHL Associate Professor David McCandlish and Weizmann Institute Professor Yuval Eshed. Their latest study, published in Nature, reveals how interactions between cryptic mutations can increase or decrease the number of reproductive branches on tomato plants. Such changes result in more or fewer fruits, seeds, and flowers. The interactions in question involve genes known as paralogs.
“Paralogs emerge across evolution through gene duplication and are major features of genetic networks,” Lippman explains. “We know paralogs can buffer against each other to prevent gene mutations from affecting traits. Here, we found that collections of natural and engineered cryptic mutations in two pairs of paralogs can impact tomato branching in myriad ways.”
One crucial component of the project was the pan-genome Lippman and colleagues completed for Solanum plants around the globe, including cultivated and wild tomato species. Where genomes typically encompass one species, pan-genomes capture DNA sequences and traits across many species. The pan-genome pointed Lippman’s lab toward natural cryptic mutations in key genes controlling branching. Lippman lab postdoc Sophia Zebell then engineered other cryptic mutations using CRISPR. That enabled Lippman’s lab to count the branches on more than 35,000 flower clusters with 216 combinations of gene mutations. From there, McCandlish lab postdoc Carlos Martí-Gómez used computer models to predict how interactions between specific combinations of mutations in the plants would change the number of branches.
“We can now engineer cryptic mutations in tomatoes and other crops to modify important agricultural traits, like yield,” Lippman says.
Additionally, the kind of modeling done here could have many other applications. McCandlish explains: “When making mutations or using a drug that mimics the effects of a mutation, you often see side effects. By being able to map them out, you can choose the manner of controlling your trait of interest that has the least undesirable side effects.”
In other words, this research points not only to better crops but also better medicines. So, you see tomatoes? Science sees tomorrow.
Journal
Nature
Article Publication Date
9-Jul-2025
IPK research team unlocks potential of barley’s closest wild relative, Hordeum bulbosum
Leibniz Institute of Plant Genetics and Crop Plant Research
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A spike of Hordeum bulbosum in Israel
view moreCredit: Amir Sharon, Tel Aviv University
Wild relatives of cultivated plants are a vital source of genetic diversity for improving crops and provide a valuable reservoir of resistance against biotic and abiotic stressors. Although their value has been recognised for decades, technological obstacles have long hindered their exploration. Thanks to advances in high-throughput genomic research, the same tools can now be used in crops and their wild relatives.
An international research team led by the IPK Leibniz Institute studied structural genome evolution in barley (Hordeum vulgare) and Hordeum bulbosum. For this study, Dr. Frank Blattner collected H. bulbosum genotypes in natural populations all over the Mediterranean, which, combined with accessions from genebanks, resulted in a panel of 263 diverse genotypes. This collection comprises both diploid and tetraploid cytotypes. After analysing their population structure, the research team assembled and annotated ten reference-quality chromosome-scale genomes of bulbous barleys.
“The tetraploid forms have two origins, one in Greece and one in southwestern Asia. In Asia they originated already between one and two million years ago, while in Greece tetraploids arose only within the last 100,000 years”, explains Jia-Wu Feng, first author of the study. “We found evidence that both types are now interbreeding, which provides a way for polyploids to enrich their genomic diversity through multiple origins”, Dr. Frank Blattner adds.
Although H. bulbosum is barley’s closest wild relative, with an estimated divergence time of 4.5 million years, the species has evolved quite differently genetically. The most obvious difference is the expansion of the barley genome. “Quite surprising, we showed that this expansion did not occur uniformly across the genome, but mainly at the ends of the chromosomes”, says Jia-Wu Feng.
A common way of transferring genes from wild relatives into domesticated plants is through introgression lines. These are derived from crosses between crops and their wild relatives and contain a small proportion of the wild parent’s genes within a cultivated genomic background. Based on the reference genomes, the research team has decoded the Ryd4 resistance locus's structure approximately 40 years after its introgression from H. bulbosum into barley. "This is without question the most promising crop-wild introgression in barley to date, and the only one close to being deployed in commercial varieties. It provides qualitative resistance to the devastating barley yellow dwarf virus, which affects several cereal crops”, explains Dr. Martin Mascher, head of IPK’s “Domestication Genomics” research group and a member of the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig.
“Having genome sequences for crop wild relatives will be useful for more targeted introgression breeding in the future”, says Dr. Martin Mascher. “The systematic genomic characterisation of crop plants and their wild relatives is important foundational research to make plant genetic resources better accessible for crop improvement”, emphasises Prof. Dr. Nils Stein, head of the Federal Ex situ Genebank for agricultural and horticultural crops at IPK Leibniz Institute, “and it is the driver to evolve the genebank from a seedstore into a biodigital resources centre”.
Journal
Nature
Article Title
A haplotype-resolved pangenome of the barley wild relative Hordeum bulbosum
Article Publication Date
9-Jul-2025
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