Association of SNP in the CCL2, IL8, CCR2, and CXCR1 genes with health and production traits in Canadian Holsteins
Bibliographic record
Abstract
Chemokines and their receptors contribute to leukocyte trafficking to the mammary gland, and may play an important role in the host immune response during acute and chronic intramammary infections. Therefore, identification of SNP in coding and regulatory sequences from chemokine genes is fundamental for understanding chemokine function and gene expression in response to infectious diseases. The aim of this study was to identify the presence of SNP in chemokine and chemokine receptor genes and their 5' regulatory regions, to assess their potential contribution to variation in estimated breeding values (EBV) for somatic cell score (SCS) and production traits of Holstein bulls. A DNA pool was constructed for SNP detection by sequencing using equal amounts of DNA from bulls with high (H) and low (L) EBV for SCS. Using this approach, we were able to detect SNP with a frequency as low as 1%, and 16 SNP in various chemokines and chemokines receptor genes. The SNP in 'CCL2' (n = 2), 'CXCL8' (n = 5), 'CXCR1' (n = 4) and ' CCR2' (n = 1) were genotyped in Canadian Holstein bulls (n = 338) using Tetra Primer ARMS-PCR. Average allele substitution effects were estimated to investigate associations between the 12 SNP and EBV for SCS and production traits. The SNP 'CXCR1c.-1768T>A' was found the most significantly associated with EBV for SCS in the first ('P' = 0.019) and second ('P' = 0.035) lactations at comparison-wise level, and across all lactations ('P' = 0.007) at experimental-wise level. Given the location of SNP 'CXCR1c.-1768T>A,' it may be implicated in gene regulation. To test this hypothesis, we evaluated the impact of ' CXCR1c.-1768T>A' SNP on 'CXCR1' expression by quantitative real-time PCR. Neutrophils were isolated from whole blood challenged with lipopolysaccharide (LPS) from cows with genotypes (AA n = 4, AT n = 5, and TT n = 5) at 0, 3 and 5h post 'in vitro' challenge. ' CXCR1' expression was significantly different in cows with the AA genotype, when compared to the AT and TT genotypes. Further analysis of the associtation between 'CXCR1c.'-1768T>A SNP and SCS is warranted before this genetic marker can be implemented in a selective breeding program.
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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 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 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".