Comparative transcriptome analysis reveals genes related to the yolk ratio of duck eggs

Yolk ratio is an important production index in the salted duck egg industry. Yolk constituents are deposited during development of follicles. However, the molecular mechanism responsible for different yolk ratios in laying ducks remains elusive. In this study, Shaoxing ducks laying eggs with different yolk ratios were chosen for an analysis of liver and ovary transcriptome information. Twelve libraries were constructed and generated an average of 58.5 million clean reads per library, of which 69% of clean reads from liver and 65% of clean reads from ovary were mapped to a reference genome. Between cross-phenotype groups, a total of 250 and 230 differently expressed genes (DEGs) were identified in liver and ovary respectively, of which 101 and 50 DEGs respectively were characterized. Several DEGs were detected, among which HMGCS1, HMGCR, FDFT1, (DHCR7), (STARD4), CYP46A1 and LPIN3 are involved in cholesterol metabolism-related pathways; KIAA0319, STARD4, AP1S3, SH3GL2 and CAV2 are involved in vesicular transport in the liver; and ELOVL2 and PSD2 are involved in fatty acid elongation and endocytosis in the ovary. High yolk-ratio ducks had higher activity for cholesterol synthesis and molecular trafficking. The identification of candidate genes greatly advances the understanding of the genetic basis of the formation of different yolk ratios.