Zhu Feng, Yuan Jian-Ming, Zhang Zhen-He, Hao Jin-Ping, Yang Yu-Ze, Hu Shen-Qiang, Yang Fang-Xi, Qu Lu-Jiang, Hou Zhuo-Cheng
Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China.
Department of Animal Nutrition, China Agricultural University, Beijing, 100193, China.
Anim Genet. 2015 Dec;46(6):636-45. doi: 10.1111/age.12361. Epub 2015 Oct 12.
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.
胸肌产量和饲料转化效率是鸭育种中的主要育种目标。了解特定转录本在肌肉和小肠中的作用可能有助于阐明相关的生物学过程。在本研究中，我们从两株北京鸭中获取了空肠和胸肌样本，这两株北京鸭根据饲料转化率（FCR）和胸肌百分比被分为两个尾端群体。从混合样本中构建了10个RNA-Seq文库，并使用Hiseq2000平台进行测序。我们使用从头组装方法创建了一个参考鸭转录本数据库，其中包括16663个非冗余重叠群，N50长度为1530 bp。这个新的鸭参考cDNA数据集显著提高了RNA-Seq数据的映射率，从50%提高到70%。映射和注释之后进行基因本体分析，结果表明低FCR组和高FCR组之间有许多基因差异表达。空肠中差异表达的基因富集在与免疫反应和免疫反应激活相关的生物学过程中，而胸肌中的差异表达基因则显著富集在与肌肉细胞分化和器官发育相关的生物学过程中。我们鉴定出了用于提高鸭FCR和胸肌产量的新候选基因，即PCK1，并获得了更好的鸭参考转录本。本研究表明，在将转录组分析应用于基因组不完整的物种时，从头组装是必不可少的。
