Table 2.
QTL detected and respective statistics for skeletal architecture traits
| Trait | Nearest Marker |
rs | MMU | Peak Position (Mb) |
Naive LOD |
GRAIP LOD |
CI (Mb) | % Variance |
Additive ±SE |
Dominance ±SE |
|---|---|---|---|---|---|---|---|---|---|---|
| Femoral BMD | JAX00098814 | 27504412 | 2 | 113 | 6.0 | 4.1* | 107–115 | 2.2 | −0.0018±0.0004 | −0.001±0.001 |
| JAX00189293 | 50963474 | 3 | 125 | 6.4 | 4.2* | 115–130 | 1.8 | 0.001±0.001 | 0.001±0.001 | |
| JAX00133397 | 29583351 | 5 | 100 | 5.2 | 3.6 | 97–123 | 1.6 | −0.0015±0.0004 | 0.0003±0.0006 | |
| Vertebral BMD | JAX00277411 | 48732938 | 1 | 179 | 7.5 | 4.2* | 172–184 | 7.3 | 0.0022±0.0003† | 0.0003±0.0004 |
| JAX00189293 | 50963474 | 3 | 126 | 7.8 | 4.0* | 121–130 | 3.9 | 0.0014±0.0003 | 0.0013±0.0004 | |
| JAX00581045 | 49523785 | 5 | 47 | 7.5 | 4.0* | 43–52 | 2.9 | −0.0014±0.0003† | 0.0004±0.0004 | |
| Total BMD | JAX00189293 | 50963474 | 3 | 126 | 9.7 | 4.6* | 122–130 | 3.0 | 0.0007±0.0002 | 0.0008±0.0003 |
| Femoral length | JAX00002741 | 31930716 | 1 | 40 | 9.0 | 4.7* | 35–63 | 0.3 | −0.04±0.03 | −0.05±0.04 |
| JAX00582506 | 48305016 | 5 | 53 | 9.9 | 4.7* | 47–60 | 2.1 | 0.11±0.03 | 0.09±0.04 | |
| A-P femoral width | JAX00005495 | 31575493 | 1 | 76 | 16.3 | 4.7* | 72–80‡ | 0.6 | −0.01±0.01 | 0.01±0.01 |
| JAX00567938 | 27582053 | 4 | 135 | 13.7 | 4.6* | 124–139 | 3.5 | 0.02±0.01 | 0.02±0.01 | |
| JAX00153077 | 31789816 | 7 | 76 | 10.0 | 4.4* | 71–80 | 4.7 | 0.03±0.01† | −0.01±0.01 | |
| JAX00165438 | 32321713 | 8 | 103 | 15.7 | 4.7* | 101–107‡ | 7.1 | −0.034±0.004† | −0.0001±0.0068 | |
| JAX00021324 | 13480722 | 10 | 97 | 9.2 | 4.4* | 87–103 | 1.4 | −0.017±0.005 | 0.003±.007 | |
| JAX00041702 | 29736244 | 13 | 10 | 8.1 | 3.9* | −19 | 0.7 | 0.0002±0.0049 | 0.02±0.01 | |
| JAX00395686 | 33859224 | 15 | 24 | 7.8 | 3.9* | −30 | 4.0 | 0.017±0.004 | −0.03±0.01† | |
| M-L femoral width | JAX00100848 | 27189926 | 2 | 140 | 7.1 | 3.6 | 130–159 | 3.1 | −0.03±0.01† | 0.02±0.01 |
| JAX00107680 | 30641053 | 3 | 56 | 8.0 | 4.4* | 46–68 | 1.2 | 0.02±0.01 | −0.003±0.011 | |
| JAX00165438 | 32321713 | 8 | 103 | 12.1 | 4.7* | 100–107‡ | 4.0 | −0.04±0.01† | 0.02±0.01 | |
| JAX00021324 | 13480722 | 10 | 97 | 9.2 | 4.7* | 90–107 | 1.4 | −0.02±0.01 | −0.01±0.01 | |
| JAX00041702 | 29736244 | 13 | 10 | 11.6 | 4.7* | −14‡ | 0.1 | −0.01±0.01 | 0.01±0.01 |
LOD exceeding the 95% (P = 0.05, LOD ≥ 3.9) permutation threshold are denoted by *; other QTL exceeded the 90% (P = 0.1, LOD ≥ 3.5) threshold. Confidence intervals (CIs) for QTL positions were obtained using a 1.0 LOD drop in Mb. Marker positions are based on Mouse Build 36 of the Mouse Diversity Genotyping Array.
Confidence intervals (CI) are relative to the GRAIP permuted LOD score with the exception of those denoted by ‡, which are relative to the naive LOD score. % variance is the percentage of phenotypic variance accounted for by the QTL effect. For additive and dominance effects: positive values indicate increasing effect of the HR allele or increasing effect of the heterozygote, respectively.
†Indicates additive and dominance effects were statistically significant at P < 0.05.