A non-synonymous variant of C21R in the <i>ABCG2</i> gene is significantly associated with brown eggshell color of Lueyang black-boned chicken.

Eggshell colors have a significant effect on sale of eggs. The aim of this study is to identify sequence variants associated with color variation of chicken brown eggs in the <i>ABCG2</i>, a protoporphyrin transport-related gene. Three successive eggs were collected from each of 381 Lueyang black-boned hens at the 31 weeks old. Eggshell color was quantified via the L*a*b color space. g.18378442T>C (a non-synonymous mutation C21R), g.18383682A>G and g.18391548A>T were genotyped <i>via</i> the MassARRAY platform. The associations of genotypes with color indexes were tested by one-way ANOVA. The conservation of the C21R locus was analyzed by multiple alignment of 52 avian genomes from the UCSC database. We predicted 3D structures of ABCG2 with C²¹ and R²¹ by homology modelling using the MODELLER program to analyze effect of C21R on protein structures. Results showed that g.18378442T>C was significantly associated with L and b values. The L value (75.3±4.0) of CC was significantly lower than ones of CT (76.6±4.3) and TT (78.0±4.4) genotypes. The b value (16.2±3.5) of CC was significantly higher than ones of CT (15.7±3.6) and TT (15.7±3.6). g.18383682A>G was only associated with the L value (<i>P</i><0.05). There was no any association between g.18391548A>T and three color indexes (<i>P</i>>0.05)。The C²¹ was completely conserved among 45 bird species. In contrast, the R²¹ was only present in two species of Psittaciformes. Structure comparisons showed that C21R potentially cause 468 structure alternations, of which 49.6% belong to hydrogen bond alternations, 38.8% for solvent accessible, 8.1% for positive φ angle and 3.5% for changes of secondary structures. In conclusion, this study identifies C21R as a molecular marker that is associated with color variation of chicken brown eggs and has a potential effect on protein structures. The CC genotype of C21R is associated with dark brown color and the TT for light brown.