0327 Genome-wide association study for supernumerary teats in Swiss Brown Swiss Cattle reveals LGR5 as a major gene on chromosome 5
Bibliographic record
Abstract
Supernumerary teats (SNT) are any teats present on a cow's udder other than the regular four. In Swiss Brown Swiss cows, 19.9% carry SNT. Different stages of development of SNT are observed from rudimentary appendices to functional and possibly lactating teats. SNT may promote mastitis, impeach good placement of the milking machine and lower the market price of the animals. No genetic analysis of the trait has been done in this cattle population, although SNT have been routinely recorded with other conformation traits since 1995 in Switzerland. This study aimed to investigate the genetic architecture of this trait through genome-wide association studies (GWAS) performed with imputed whole-genome sequence. Two trait definitions were used: Udder Clearance (UCT) considering whether a cow is carrier of any SNT or has a clear udder and Presence of Supernumerary Mammary Gland (PMG) opposing animal carrier of completely developed and possibly functional SNT with animals with a clear udder or carrier of a rudimentary SNT. Breeding values were estimated for Brown Swiss sires of at least 20 daughters with SNT records using an animal model including the random effects expert-by-year, farm-by-year and animal. The animal's dam life stage—heifer or cow—during its parity was fitted as a fixed effect in the same model. Single SNP regression using deregressed proofs of 1519 bulls with genotypes imputed to the variant list of the 5thRun of the 1000 Bulls Genome Project permitted discovery of three important regions on BTA5, BTA17 and BTA20 associated with the presence or the development of SNT. Regions on BTA17 and BTA20 reached clearly lower p-values (10−7 vs. 10−4) when associated to PMG than UCT, while variants on BTA5 were significantly linked to both trait definitions. No candidate genes on BTA 17 and BTA20 were found after functional analysis. On BTA5, however, the leucine-rich repeat-containing G protein coupled receptor 5 (LGR5) can be considered as the major gene for our trait. Encoding a protein known as an up-regulator of the Wnt pathway and having an expression level impacting the mammary gland development, LGR5 also carries a synonymous mutation that is highly associated to SNT. To conclude, GWAS in the Swiss Brown Swiss population revealed LGR5 on BTA5 as a candidate gene influencing the presence and development stage of supernumerary teats.
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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) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.001 | 0.002 |
| 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) | 0.006 | 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".