Structural variations in the phytoene synthase 1 gene affect carotenoid accumulation in tomato fruits and result in bicolor and yellow phenotypes
Bibliographic record
Abstract
Abstract Tomato fruits normally accumulate large amounts of the red pigment lycopene in their chromoplasts. Some tomato cultivars ( Solanum lycopersicum ) show however distinct phenotypes, from a pure yellow hue to bicolor fruits with red and yellow sections. In this study, we show that alleles of the phytoene synthase 1 gene (PSY1), the first gene of carotenoid synthesis pathway, are responsible for the yellow, but also the bicolor phenotype. Introgression lines with the PSY1 allele from the green-fruited species S. habrochaites express less the enzyme, resulting in a bicolor phenotype. On the other hand, in tomato bicolor cultivars, the same coloration pattern is caused by a 3789 bp-deletion in the promoter region of PSY1 . Since the deletion contains part of the 5’UTR region of PSY1 , translation efficiency is likely decreased resulting in a reduction of lycopene accumulation. Furthermore, we identified that the yellow r y phenotype is caused by a duplication and an inversion implicating PSY1 and the downstream neighbor gene. The genomic rearrangement change the end of PSY1 amino acid sequence. The fruits of yellow r y cultivars are still able in certain conditions to accumulate lycopene near the blossom-end of the fruit, though to a lesser extent than in bicolor cultivars. In contrast, fruits of the yellow r cultivars never present fleshy red sections. These cultivars have an insertion of a single long terminal repeat from the Rider transposon in the first exon of PSY1 resulting in a non-functional protein. These results demonstrate how multiple phenotypes can arise from structural variations in a key gene.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".