Graphical representation of the experimental strategy.

<p>The oviposition cycle of all birds was measured daily, and birds were slaughtered 18 h after ovulation. This stage generally represents the fast growth stage during the eggshell calcification. Individuals from the same sire family that laid eggs with one of two extremely different eggshell qualities were selected. We selected eight birds with normal eggshell strength (NES) and eight birds with very low eggshell strength (LES) for further study. Two biological replicate samples from each group were selected for transcriptome sequencing, and one pooled DNA library for each group was made for whole genome re-sequencing. Finally, we integrated transcriptome and whole genome re-sequencing data to discover the genetic information related to eggshell quality.