Genetics and dietary calcium (Ca) are each critical regulators of peak bone mass but it is unclear how genetics alters the physiologic response of bone to dietary Ca restriction (RCR). Here, we conducted genetic mapping in C57BL/6J × DBA/2J (BXD) recombinant inbred mouse lines to identify environmentally sensitive loci controlling whole‐bone mass (bone mineral density [BMD], bone mineral content [BMC]), distal trabecular bone, and cortical bone midshaft of the femur. Mice were fed adequate (basal) or low Ca diets from 4–12 weeks of age. Femurs were then examined by dual‐energy X‐ray absorptiometry (DXA) and micro‐computed tomography (μCT). Body size–corrected residuals were used for statistical analysis, genetic mapping, and to estimate narrow sense heritability (h 2 ). Genetics had a strong impact on femoral traits (eg, bone volume fraction [BV/TV] basal Ca, h 2 = 0.60) as well as their RCR (eg, BV/TV, h 2 = 0.32). Quantitative trait locus (QTL) mapping identified up to six loci affecting each bone trait. A subset of loci was detected in both diet groups, providing replication of environmentally robust genetic effects. Several loci control multiple bone phenotypes suggesting the existence of genetic pleiotropy. QTL controlling the bone RCR did not overlap with basal diet QTL, demonstrating genetic independence of those traits. Candidate genes underlying select multi‐trait loci were prioritized by protein coding effects or gene expression differences in bone cells. These include candidate alleles in Rictor (chromosome [chr] 15) and Egfl7 (chr 2) at loci affecting bone in the basal or low Ca groups and in Msr1 (chr 8), Apc , and Camk4 (chr 18) at loci affecting RCR. By carefully controlling dietary Ca and measuring traits in age‐matched mice we identified novel genetic loci determining bone mass/microarchitecture of the distal femur as well as their physiologic adaptation to inadequate dietary Ca intake. © 2022 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.

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