Discovering Key Transcripts Of Regulating Feed Conversion And Breast Muscle Growth Using RNA-Seq

Breast muscle growth and feed conversion are received much attention in duck breeding, which could embody production performance and commercial value of meat duck. Understanding the role of specific transcripts in muscle and intestine is conducive to study interrelated biological processes. However analysis of duck transcriptome is tough as a result of low-quality reference genome.In this study, we took jejunum and breast muscle from two-tailed population of Peking duck and Maple-Leaf duck sorted by feed conversion rate (FCR) and breast muscle rate (BMR). Libraries were made from the pooled samples and were sequenced using Hiseq2000 platform. Here for improving follow-up analysis, a reference transcriptome was generated by de novo assembly and we applied reciprocal-best blast algorithm to annotate contigs with chicken transcripts information. Final ref-transcript database has 16,663 contigs with N50 length of 1530 after eliminating low-quality sequences and redundancies. Totally,11960 (72%) contigs had a one-to-one relationship with chicken transcripts and the rest (28%) were denoted as uncertain. Most uncertain sequences (4498,27%) had no coding potentiality except only one. Other 167 (1%) sequence were not detected reading framework. After mapping and annotation, in breast muscle, there are 274 genes show significant differential expression between high FCR term and low FCR term in Pekin duck, and 314 significantly differentially expressed genes in Maple-Leaf duck,44 genes are shared in both strains. We found a great amount of differentially expressed transcripts were enriched in 6 biological process about cell differentiation, transmembrane transportation, muscle development, immunization and glycoprotein metabolic process. Especially, the most significant enriched genes were showed in the nuclear receptor peroxisome proliferator-activated receptor β (PPARβ signal pathway) which was the master regulator of fat-cell formation among 5 biological pathways.In jejunum, there are 632 genes show significant differential expression between high FCR term and low FCR term in Pekin duck, and 240 significantly differentially expressed genes in Leaf duck,101 genes are shared in both strains. We found a great amount of differentially expressed transcripts were enriched in 9 biological process about immune response, activation of immune response process. The most significant enriched genes were showed in the CCR interaction pathways which are related to cellular immunity and apoptosis among 4 biological pathways. Our results showed fat metabolism related and immune response related genes have an important role in breast muscle growth and feed conversion of duck. We provided new candidate genes for improving feed conversion and breast muscle.