212 Genome-Wide Association Study Investigating the Genomic Components of Efficiency in Beef Cows
Bibliographic record
Abstract
Abstract Efficiency of mature beef cows consuming high-forage diets is not comparable with standard definitions of beef cattle efficiency such as feed conversion or residual feed intake in the feedlot setting. This study aimed to conduct a genome-wide association study (GWAS) to identify regions of the bovine genome associated with efficiency in mature beef cows. Ninety-eight black Angus cows were managed under extensive feeding programs over a two-year period. Using rump fat at calving, calving date, and calf weaning weight as a percentage of the body weight of the dam, a weighted percentile scoring system was used to rank efficiency. Eighty-three of the cows were retained for the GWAS. The 20 most and 20 least efficient cows (HD dataset, n=40) were genotyped with the Illumina BovineHD BeadChip (777,000 SNPs) while the remaining cows were genotyped with the Neogen GGP Bovine 100K chip (LD dataset, n = 43). The LD dataset was imputed to the HD SNP array density using Beagle5.4 (FULL dataset, n = 83). Three separate GWAS were conducted using GAPIT (version3). The first GWAS was performed on the HD dataset using a quantitative phenotype determined by the ranking system. The second GWAS was performed with the HD dataset using a qualitative phenotype (efficient vs non-efficient cows). For the final GWAS, the FULL dataset with ranked phenotypes was used. Five models were evaluated for each GWAS, including the general linear model (GLM), mixed linear model (MLM), multiple loci mixed model (MLMM), fixed and random model circulating probability unification (FarmCPU), and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK). The model that best represented each dataset as determined by quantile-quantile plots was used for downstream analysis. Although results of the GWAS were not significant (Bonferroni threshold), associations were identified on BTA10, 16, 17, 25, 27 and 29. Positional candidate genes in the associated regions include: FOXN3, UPB1, SNX29, DDX54, LOC112444612, RITA1, and TACC1. Further functional analyses are required to confirm these findings; however, this work provides a foundation for identifying genes and gene mutations influencing this newly described phenotype.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.002 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.002 | 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".