Postharvest seed coat darkening in pinto bean (<i>Phaseolus vulgaris</i>) is regulated by <i>P<sup>sd</sup></i>, an allele of the basic helix‐loop‐helix transcription factor <i>P</i>
Bibliographic record
Abstract
Societal Impact Statement Pinto bean ( Phaseolus vulgaris ) is one of the leading market classes of dry beans that is most affected by postharvest seed coat darkening. The process of seed darkening poses a challenge for bean producers and vendors as they encounter significant losses in crop value due to decreased consumer preference for darker beans. Here, we identified a novel allele of the P gene, P sd , responsible for the slow darkening seed coat in pintos, and identified trait‐specific sequence polymorphisms which are utilized for the development of new gene‐specific molecular markers for breeding. These tools can be deployed to help tackle this economically important issue for bean producers. Summary Postharvest seed coat darkening in pinto bean is an undesirable trait that reduces the market value of the stored crop. Regular darkening (RD) pintos darken faster after harvest and accumulate higher level of proanthocyanidins (PAs) compared to slow darkening (SD) cultivars. Although the markers cosegregating with the SD trait have been known for some time, the SLOW DARKENING ( Sd ) gene identity had not been proven. Here, we identified P sd as a candidate for controlling the trait. Genetic complementation, transcript abundance, metabolite analysis, and inheritance study confirmed that P sd is the Sd gene. P sd is another allele of the P ( Pigment ) gene, whose loss‐of‐function alleles result in a white seed coat. P sd encodes a bHLH transcription factor with two transcript variants but only one is involved in PA biosynthesis. An additional glutamate residue in the activation domain, and/or an arginine to histidine substitution in the bHLH domain of the P sd ‐1 transcript in the SD cultivar is likely responsible for the reduced activity of this allele compared to the allele in a RD cultivar, leading to reduced PA accumulation. Overall, we demonstrate that a novel allele of P , P sd , is responsible for the SD phenotype, and describe the development of new, gene‐specific, markers that could be utilized in breeding to resolve an economically important issue for bean producers.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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 teacher head, 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".