De novo transcriptome assembly and identification of genes associated with feed conversion ratio and breast muscle yield in domestic ducks

Abstract

Breast muscle yield and feed conversion efficiency are the major breeding aims in duck breeding. Understanding the role of specific transcripts in the muscle and small intestine might lead to the elucidation of interrelated biological processes. In this study, we obtained jejunum and breast muscle samples from two strains of Peking ducks that were sorted by feed conversion ratio (FCR) and breast muscle percentage into two-tailed populations. Ten RNA-Seq libraries were developed from the pooled samples and sequenced using the Hiseq2000 platform. We created a reference duck transcript database using de novo assembly methods, which included 16 663 irredundant contigs with an N50 length of 1530 bp. This new duck reference cDNA dataset significantly improved the mapping rate for RNA-Seq data, from 50% to 70%. Mapping and annotation were followed by Gene Ontology analysis, which showed that numerous genes were differentially expressed between the low and high FCR groups. The differentially expressed genes in the jejunum were enriched in biological processes related to immune response and immune response activation, whereas those in the breast muscle were significantly enriched in biological processes related to muscle cell differentiation and organ development. We identified new candidate genes, that is, PCK1, for improving the FCR and breast muscle yield of ducks and obtained much better reference duck transcripts. This study suggested that de novo assembly is essential when applying transcriptome analysis to a species with an incomplete genome.

Incorporation of Guava Seeds Powder into a Commercial Diet Improves the Growth Performance, Nutritional and Quality Characteristics of Muscovy Duck’s Meat

“…Similar results had been discussed previously [21,[33][34][35]. In the same context, feeding food-processing wastes resulted in a valuable improvement in FCR and GH in ducks as similarly indicated previously in ducks [20,21,28,[35][36][37]. This might be due to enhancing the GP and strengthening the immunity as observed by Giri et al [38] by using guava leaves whereas no available data on using GSP in poultry diets were recorded.…”

iTRAQ‐Based Quantitative Proteomic Analysis of Duck Eggshell During Biomineralization

“…Amongst the de novo assembled transcripts which we identified, there are several highly abundant proteins that lack annotation information (Table S1, Supporting Information). Our previous work and many other studies have confirmed that it is straightforward to increase the sensitivity of transcriptome data analysis. This study also confirms that transcriptome‐based methods are valid to do proteome analysis.…”

“…As the reference duck protein dataset is not complete, the authors’ own de novo assembled duck transcripts from uterine RNA‐Seq data as a target protein dataset to improve the sensitivity was also added. Uterus tissues were sampled at both 16 and 24 h, and then the uterus transcriptome de novo assembly method was performed as before …”

De novo characterization of placental transcriptome in the Eurasian beaver (Castor fiber L.)

“…In addition, the availability of the reference genome does not always enable full and effective analyses of the transcriptomic data. For example, domestic duck has a reference genome but it is incomplete, which seriously disrupts the precision of analysis and makes a de novo approach also useful for organisms with a known genome (Zhu et al 2015 ).…”