Replication and discovery of musculoskeletal QTLs in LG/J and SM/J advanced intercross lines

Abstract

The genetics underlying variation in health-related musculoskeletal phenotypes can be investigated in a mouse model. Quantitative trait loci (QTLs) affecting musculoskeletal traits in the LG/J and SM/J strain lineage remain to be refined and corroborated. The aim of this study was to map muscle and bone traits in males (n = 506) of the 50th filial generation of advanced intercross lines (LG/SM AIL) derived from the two strains. Genetic contribution to variation in all musculoskeletal traits was confirmed; the SNP heritability of muscle mass ranged between 0.46 and 0.56; and the SNP heritability of tibia length was 0.40. We used two analytical software, GEMMA and QTLRel, to map the underlying QTLs. GEMMA required substantially less computation and recovered all the QTLs identified by QTLRel. Seven significant QTLs were identified for muscle weight (Chr 1, 7, 11, 12, 13, 15, and 16), and two for tibia length, (Chr 1 and 13). Each QTL explained 4-5% of phenotypic variation. One muscle and both bone loci replicated previous findings; the remaining six were novel. Positional candidates for the replicated QTLs were prioritized based on in silico analyses and gene expression in muscle tissue. In summary, we replicated existing QTLs and identified novel QTLs affecting muscle weight, and replicated bone length QTLs in LG/SM AIL males. Heritability estimates substantially exceed the cumulative effect of the QTLs, hence a richer genetic architecture contributing to muscle and bone variability could be uncovered with a larger sample size.

Keywords: QTL; Bone; Skeletal muscle; gene expression.

Figure 1

Empirical distribution of traits investigated in LG/SM AIL male mice. Blue histograms represent muscle traits. Tibialis anterior (TA), extensor digitorum longus (EDL), gastrocnemius (Gastroc) and soleus weights differ greater than twofold between the most and least muscular animals. Green histogram represent tibia.

Figure 2

Comparison of LOD scores at all 7236 candidate SNPs computed using QTLRel and GEMMA. Horizontal and vertical dashed lines depict significance thresholds (α = 0.05) for QTLRel and GEMMA LOD scores, respectively.

Figure 3

Genome‐wide scans for TA, EDL, gastrocnemius and soleus muscle weight (blue), and Tibia length (green). The vertical axes show the GEMMA LOD scores for the 7236 polymorphic SNPs arranged by their chromosomal positions in the horizontal axis. The horizontal blue line represents threshold at α = 5%.

Figure 4

Allele‐dependent expression of candidate genes in TA muscle of the LG/SM AIL males. Homozygous carriers of the SM/J and LG/J alleles were compared using Mann–Whitney tests. Mean and SEM. *P < 0.05 (one‐tailed), †P < 0.05 (two‐tailed) compared to SM/J expression. Number indicates sample size within the genotypic group.