{"id":"W4225137805","doi":"10.1186/s12864-022-08555-z","title":"Identifying pleiotropic variants and candidate genes for fertility and reproduction traits in Holstein cattle via association studies based on imputed whole-genome sequence genotypes","year":2022,"lang":"en","type":"article","venue":"BMC Genomics","topic":"Genetic and phenotypic traits in livestock","field":"Biochemistry, Genetics and Molecular Biology","cited_by":63,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Guelph","funders":"Agriculture and Agri-Food Canada; Canadian Dairy Commission; Dairy Farmers of Canada; University of Guelph","keywords":"Biology; Candidate gene; Quantitative trait locus; Genetics; Genome-wide association study; Sire; Single-nucleotide polymorphism; Genetic association; Heritability; Family-based QTL mapping; Gene; Genotype; Gene mapping; Chromosome","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":[0.003002707,0.0003547081,0.000481684,0.001533199,0.0004486717,0.0006862865,0.0005884296,0.0004257052,0.001663859],"category_scores_gemma":[0.002566053,0.0001971401,0.0008061954,0.001706836,0.0004411739,0.0002083987,0.0005339104,0.0004838036,0.0001476981],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000206451,"about_ca_system_score_gemma":0.0003398756,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00255814,"about_ca_topic_score_gemma":0.004308692,"domain_scores_codex":[0.9991978,0.0002961047,0.00005725102,0.0002511388,0.0001112962,0.00008648547],"domain_scores_gemma":[0.997792,0.001500897,0.0003422197,0.0001563078,0.00009349192,0.0001150984],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.002013733,0.0002953442,0.8995388,0.0002154094,0.002783164,0.001069648,0.0005458531,0.005640266,0.046311,0.0005569775,0.0002821018,0.04074767],"study_design_scores_gemma":[0.00009752824,0.0002108572,0.9883065,0.00001972225,0.0007536136,0.0003367946,0.00008498293,0.007173175,0.002099941,0.0003799916,0.0005185567,0.00001845937],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9922368,0.0003740653,0.006733244,0.00003369321,0.000004997124,0.00001336723,0.0004266681,0.00003284517,0.0001443546],"genre_scores_gemma":[0.9892323,0.000170663,0.009069527,0.00004394202,0.00001628716,0.00003087573,0.001217895,0.00001512074,0.0002033783],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.003002707,"threshold_uncertainty_score":0.01587999,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03455730077553842,"score_gpt":0.2757653471126537,"score_spread":0.2412080463371153,"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."}}