Table 2.
Quantitative trait loci identified in the genomewide association analyses for the presence or absence of lung consolidation (LC), lung lesions (LL), or hyperinflated lungs (HIF) in 920 Colorado feedlot steers
| Chromosome (location in Mb)1 | Lead SNP (no. SNP)2 | Phenotype | P-value of lead SNP3 | Positional candidate genes4 |
|---|---|---|---|---|
| unassigned | rs109299286 (1) | LC | 2.87 × 10−6 | NA |
| 1 (49–50) | rs136506519 (1) | HIF | 2.86 × 10−6 | – |
| 2 (54–55) | rs133243829 (1) | HIF | 3.01 × 10−6 | – |
| 3 (112–113) | rs43365726 (1) | HIF | 3.83 × 10−10 | – |
| 4 (102–103)5 | rs137372462 (1) | HIF | 7.72 × 10−6 | – |
| 4 (102–103)5 | rs135680653 (1) | HIF | 1.64 × 10−6 | CREB3L2 |
| 4 (102–103)5 | rs136731537 (5) | HIF | 2.33 × 10−7 | AKR1D1 |
| 4 (102–103)5 | rs133846461 (1) | HIF | 9.54 × 10−6 | – |
| 4 (102–103)5 | rs135535135 (1) | HIF | 1.44 × 10−6 | – |
| 4 (102–103)5 | rs137634412 (1) | HIF | 8.50 × 10−6 | – |
| 5 (30–31) | rs133157293 (2) | HIF | 2.64 × 10−6 | TUBA1A and TUBA1B |
| 6 (72–73) | rs109673399 (1) | HIF | 2.38 × 10−6 | KDR |
| 8 (0–1) | rs133944973 (5) | HIF | 2.55 × 10−8 | ANXA10 |
| 8 (81–82) | rs134212138 (1) | LL | 5.55 × 10−6 | – |
| 11 (0–1) | rs134761437 (1) | HIF | 4.73 × 10−6 | ENSBTAG00000038257 |
| 11 (96–97) | rs134730725 (1) | LC | 9.98 × 10−6 | MAPKAP1 |
| 14 (64–65) | rs135662870 (2) | LC | 4.13 × 10−6 | NCALD |
| rs110429664 (4) | LL | 4.24 × 10−6 | ||
| 15 (47–48) | rs135937397 (1) | HIF | 7.02 × 10−6 | APBB1, HPX, and TRIM3 |
| 18 (44–45) | rs136844537 (1) | LC | 7.25 × 10−6 | – |
| 20 (70–71) | rs135580824 (1) | LC | 6.61 × 10−6 | – |
| 23 (7–8) | rs136808471 (1) | HIF | 8.34 × 10−7 | ITPR3 and IP6K3 |
| 28 (0–1) | rs109312685 (1) | LL | 5.87 × 10−6 | – |
1Chromosome location of the QTL followed by the location of SNP in megabases, in parentheses, as measured by numbered nucleotides in the UMD 3.1 reference genome assembly (http://bovinegenome.org/?q=node/61; accessed 11 August 2016).
2The most significant SNP tagging the QTL was identified by the rs number, which is a reference number assigned to markers submitted to the National Center for Biotechnology Information SNP database (https://www.ncbi.nlm.nih.gov/projects/SNP/; accessed 1 September 2016). The number of SNP associated with each QTL is listed in parentheses.
3Significance (P-value) for the SNP with the strongest evidence for an association (lead SNP) with LC, LL or HIF.
4NA = Not applicable. Positional candidate genes were defined as genes located within 12 kb on either side of the associated SNP. Bold gene names represent genes where SNP within the QTL are located within an intron of the gene.
5Haplotypes defined using the method described by Gabriel et al. (2002) and a r2 > 0.9 resulted in these being in different haplotype blocks, although loci were located within 351.6 kb from one another.