{"id":"W4414970874","doi":"10.1101/2025.10.08.680093","title":"Positive selection on hotspot and reinforcing regulatory alleles contributed to hexaploid bread wheat improvement","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Wheat and Barley Genetics and Pathology","field":"Agricultural and Biological Sciences","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Agriculture and Agri-Food Canada; University of Guelph","funders":"Natural Sciences and Engineering Research Council of Canada; Genome Canada","keywords":"Allele; Gene; Cultivar; Selection (genetic algorithm); Regulator gene; Genome; Phenotype","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002212476,0.0002369972,0.0002069984,0.0001850914,0.000117169,0.0003425577,0.0001679888,0.0002285991,0.003348571],"category_scores_gemma":[0.0001970728,0.0001174089,0.0001776179,0.0002198995,0.0002017742,0.0001838897,0.0003626305,0.0005375,0.0003709672],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001899748,"about_ca_system_score_gemma":0.0001443014,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002149662,"about_ca_topic_score_gemma":0.0003774596,"domain_scores_codex":[0.9998974,0.00001128067,0.000006466034,0.00005114237,0.00001982813,0.00001399774],"domain_scores_gemma":[0.9998626,0.00003154366,0.00003266549,0.00002232071,0.00001352447,0.00003737988],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0001318927,0.00002647881,0.008033499,0.00005206089,0.00002832516,0.0002231159,0.00004630927,0.0002212756,0.9769168,0.0007792199,0.000171339,0.01336962],"study_design_scores_gemma":[0.0001860414,0.0005277751,0.5158679,0.00005074111,0.0003683485,0.00297059,0.0002898818,0.01268046,0.4456348,0.005552055,0.01581726,0.00005403949],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9922916,0.0003013604,0.005063564,0.0001174887,0.00003004623,0.000009401938,0.0001700847,0.0001375827,0.001878912],"genre_scores_gemma":[0.9936063,0.0001886351,0.00287719,0.000123042,0.00001798578,0.000009077788,0.0002227505,0.00007175388,0.002883126],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.003348571,"threshold_uncertainty_score":0.01120204,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.008877904411804255,"score_gpt":0.2003252187538263,"score_spread":0.1914473143420221,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}