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1. Idiosyncratic and dose-dependent epistasis drives variation in tomato fruit size

   https://doi.org/10.1126/science.adi5222  

   Aguirre, Lyndsey; Hendelman, Anat; Hutton, Samuel F; McCandlish, David M; Lippman, Zachary B (October 2023, Science)

   Epistasis between genes is traditionally studied with mutations that eliminate protein activity, but most natural genetic variation is in cis-regulatory DNA and influences gene expression and function quantitatively. In this study, we used natural and engineered cis-regulatory alleles in a plant stem-cell circuit to systematically evaluate epistatic relationships controlling tomato fruit size. Combining a promoter allelic series with two other loci, we collected over 30,000 phenotypic data points from 46 genotypes to quantify how allele strength transforms epistasis. We revealed a saturating dose-dependent relationship but also allele-specific idiosyncratic interactions, including between alleles driving a step change in fruit size during domestication. Our approach and findings expose an underexplored dimension of epistasis, in which cis-regulatory allelic diversity within gene regulatory networks elicits nonlinear, unpredictable interactions that shape phenotypes. 

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2. Fruit-FIT: Drone Interfaced Multiplexed Sensor Suite to Determine the Fruit Ripeness

   https://doi.org/10.1109/SENSORS52175.2022.9967097  

   Hossain, Nafize Ishtiaque; Tabassum, Shawana (October 2022, 2022 IEEE Sensors)
3. Metabolomic selection for enhanced fruit flavor

   https://doi.org/10.1073/pnas.2115865119  

   Colantonio, Vincent; Ferrão, Luis Felipe; Tieman, Denise M.; Bliznyuk, Nikolay; Sims, Charles; Klee, Harry J.; Munoz, Patricio; Resende, Marcio F. (February 2022, Proceedings of the National Academy of Sciences)

   Although they are staple foods in cuisines globally, many commercial fruit varieties have become progressively less flavorful over time. Due to the cost and difficulty associated with flavor phenotyping, breeding programs have long been challenged in selecting for this complex trait. To address this issue, we leveraged targeted metabolomics of diverse tomato and blueberry accessions and their corresponding consumer panel ratings to create statistical and machine learning models that can predict sensory perceptions of fruit flavor. Using these models, a breeding program can assess flavor ratings for a large number of genotypes, previously limited by the low throughput of consumer sensory panels. The ability to predict consumer ratings of liking, sweet, sour, umami, and flavor intensity was evaluated by a 10-fold cross-validation, and the accuracies of 18 different models were assessed. The prediction accuracies were high for most attributes and ranged from 0.87 for sourness intensity in blueberry using XGBoost to 0.46 for overall liking in tomato using linear regression. Further, the best-performing models were used to infer the flavor compounds (sugars, acids, and volatiles) that contribute most to each flavor attribute. We found that the variance decomposition of overall liking score estimates that 42% and 56% of the variance was explained by volatile organic compounds in tomato and blueberry, respectively. We expect that these models will enable an earlier incorporation of flavor as breeding targets and encourage selection and release of more flavorful fruit varieties. 

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4. Phytohormones in fruit development and maturation

   https://doi.org/10.1111/tpj.15112  

   Fenn, Matthew A.; Giovannoni, James J. (January 2021, The Plant Journal)

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5. Why is fruit colour so variable? Phylogenetic analyses reveal relationships between fruit‐colour evolution, biogeography and diversification

   https://doi.org/10.1111/geb.12900  

   Lu, Lu; Fritsch, Peter_W; Matzke, Nicholas_J; Wang, Hong; Kron, Kathleen_A; Li, De‐Zhu; Wiens, John_J; Meiri, ed., Shai (March 2019, Global Ecology and Biogeography)

   Abstract AimAre different fruit colours related to large‐scale patterns of dispersal, distribution and diversification? Here, we investigate this question for the first time, using phylogenetic approaches in the tribe Gaultherieae (Ericaceae). We test relationships between fruit colour and (a) biogeographic dispersal, (b) elevational and latitudinal species distributions and (c) rates of diversification. LocationGlobal. Time periodRecent to 30 million years ago. Major taxa studiedThe plant tribe Gaultherieae in the family Ericaceae (blueberries and relatives). MethodsWe estimated a new time‐calibrated phylogeny for Gaultherieae. Data on fruit colours and geographic distributions for each species were compiled from published sources and field observations. Using phylogenetic methods, we estimated major dispersal events across the tree and the most likely fruit colour associated with each dispersal event, and tested whether dispersal between major biogeographic regions was equally likely for different fruit colours, and whether dispersal distances were larger for certain colours. We then tested the relationships between fruit colours and geographic variables (latitude, elevation) and diversification rates. ResultsLarge‐scale dispersal events were significantly associated with red‐fruited lineages, even though red‐fruited species were relatively uncommon. Further, different fruit colours were associated with different elevations and latitudes (e.g. red at lower elevations, violet at lower latitudes, white at higher elevations). Violet colour was related to increased diversification rates, leading to more violet‐fruited species globally. Main conclusionsOverall, we show that different fruit colours can significantly impact the large‐scale dispersal, distribution and diversification of plant clades. Furthermore, the interplay between biogeography and fruit‐colour evolution seems to generate “taxon cycles” in fruit colour that may drive variation in fruit colour over macroevolutionary time‐scales. 

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