Background: Skeletal damage is a challenge for laying hens because the physiological adaptations required for egg
laying make them susceptible to osteoporosis. Previously, we showed that genetic factors explain 40% of the variation
in end of lay bone quality and we detected a quantitative trait locus (QTL) of large effect on chicken chromosome 1.
The aim of this study was to combine data from the commercial founder White Leghorn population and the F2 map‑
ping population to fine-map this QTL and understand its function in terms of gene expression and physiology.Results: Several single nucleotide polymorphisms on chromosome 1 between 104 and 110 Mb (galGal6) had highly
significant associations with tibial breaking strength. The alternative genotypes of markers of large effect that flanked
the region had tibial breaking strengths of 200.4 vs. 218.1 Newton (P<0.002) and, in a subsequent founder generation, the higher breaking strength genotype was again associated with higher breaking strength. In a subsequent
generation, cortical bone density and volume were increased in individuals with the better bone genotype but with
significantly reduced medullary bone quality. The effects on cortical bone density were confirmed in a further generation and was accompanied by increased mineral maturity of the cortical bone as measured by infrared spectrometry
and there was evidence of better collagen cross-linking in the cortical bone. Comparing the transcriptome of the tibia
from individuals with good or poor bone quality genotypes indicated four differentially-expressed genes at the locus,
one gene, cystathionine beta synthase (CBS), having a nine-fold higher expression in the genotype for low bone quality. The mechanism was cis-acting and although there was an amino-acid difference in the CBS protein between the
genotypes, there was no difference in the activity of the enzyme. Plasma homocysteine concentration, the substrate
of CBS, was higher in the poor bone quality genotype. Conclusions: Validated markers that predict bone strength have been defined for selective breeding and a gene was
identified that may suggest alternative ways to improve bone health in addition to genetic selection. The identification of how genetic variants affect different aspects of bone turnover shows potential for translational medicine.