Deep RNA Sequencing of Pectoralis Muscle Transcriptomes during Late-term Embryonic to Neonatal Development in Indigenous Chinese Duck Breeds

In this project we try to character potential candidate genes and signaling pathways related to PM development during late-term embryonic to neonatal development in indigenous chinese duck breeds. We use RNA-seq to analyse PM samples selected at embryonic days (E) 21 and 27 and 5 days post-hatch (dph) in Gaoyou and Jinding ducks. There were about 45 million clean reads, the total mapped rate was 58.58%–64.82%, and the uniquely mapped rate was 56.21%–63.55%.The results of cluster analysis of DEGs are shown that with the same developmental time nodes superimposed. There were 522 DEGs between Gaoyou and Jinding ducks at E21, including 146 novel genes. There were 299 DEGs and 81 novel genes at E27, and 510 DEGs and 118 novel genes at 5 dph. A total of 43 DEGs were shared by both breeds at all time points, including 19 novel genes.We further considered the 393 genes with expression patterns in line with the muscle development curve in both breeds. these DEGs may be involved in the mechanisms responsible for the phenomenon of static or decreased breast muscle growth in duck breeds during the late embryonic period. Overall design: Constructed eighteen polyA mRNA-seq libraries, including nine from Gaoyou duck PM at E21 and E27, and at 5 days post-hatching (dph) (three libraries at each developmental stage), and nine libraries from Jinding duck PM at the same time points (three libraries at each developmental stage). We performed an integrated analysis of the DEGs detected in this work to identify key genes affecting early PM development in ducks.