207 Genome-wide association study for beef fatty acid profile using haplotypes in Nellore cattle
Bibliographic record
Abstract
The aim of this study was to identify genomic regions associated with the total amount of saturated (SFA), monounsaturated (MUFA), and polyunsaturated (PUFA) fatty acids in the beef of Nellore cattle. The investigated dataset contained records from 963 Nellore bulls, about two years old, finished in feedlot (90 days). Meat samples of Longissimus dorsi muscle, between the 12th and 13th ribs of the left half-carcasses, were taken to measure the fatty acids (FAs). FAs were quantified by gas chromatography (GC-2010 Plus - Shimadzu AOC 20i autoinjector) using SP-2560 capillary column (100 m × 0.25 mm diameter with 0.02 mm thickness; Supelco, Bellefonte, PA). The animals were genotyped using the high-density SNP panel (BovineHD BeadChip assay 777k, Illumina Inc., San Diego, CA). Those SNP markers with minor allele frequency less than 0.05, call rate less than 90%, monomorphic, located on sex chromosomes, and those with unknown position were removed from the analysis. After genomic quality control, 470,007 SNPs and 868 animals were available for the analyses. Missing genotypes were imputed using FImpute software. Genotypes were phased to haplotypes using fastPHASE software and then haplotype blocks were defined based on linkage disequilibrium using HaploView software. Genome-wide association analyses were performed considering one haplotype at a time. The model included fixed effects of contemporary group (92 levels), haplotype (linear regression on number of copies), and age at slaughter as a linear covariate. Bonferroni correction was applied at 5% significance to adjust for multiple tests. A total of 83,883 haplotypes were included in the genome-wide association analyses. From those haplotypes, 292, 17, and 31 were significantly associated (P < 0.05) with SFA, MUFA, and PUFA, respectively. Most associations were found on BTA17, BTA3, BTA1, BTA8, BTA25, and BTA2. These significant regions harbor genes such as GALNT12, SLC6A7, CAMK2A, SYTL3, EPAS1, PRKCB, EPHA6, MPZL1, UHMK1, KIRREL, FYN, LTBP1, PRKCE, SIK2, TOM1L1, NF1, DNAJA3, SH2B2, AFAP1L2, and AGAP1. These genes are involved in lipid metabolism, reproductive hormone receptors, transport and use of fatty acids and cholesterol, phospholipid and membrane hydrolysis and biosynthesis, energy metabolism, and protein kinase synthesis. Thus, the identification of these associated haplotypes may contribute to further studies to validate these regions and prospect candidate genes that would be useful for breeding programs to improve the beef quality of Nellore cattle.
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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 | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 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) | 0.002 | 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".