title: 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.
authors.affiliation: 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.
authors.forename: Feng
authors.initials: F
authors.lastname: Zhu
authors.affiliation: Department of Animal Nutrition, China Agricultural University, Beijing, 100193, China.
authors.forename: Jian-Ming
authors.initials: JM
authors.lastname: Yuan
authors.affiliation: 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.
authors.forename: Zhen-He
authors.initials: ZH
authors.lastname: Zhang
authors.affiliation: Beijing Jinxing Golden Star Duck Center, Beijing, 100076, China.
authors.forename: Jin-Ping
authors.initials: JP
authors.lastname: Hao
authors.affiliation: Beijing General Station of Animal Husbandry, Beijing, 100107, China.
authors.forename: Yu-Ze
authors.initials: YZ
authors.lastname: Yang
authors.affiliation: Beijing Jinxing Golden Star Duck Center, Beijing, 100076, China.
authors.forename: Shen-Qiang
authors.initials: SQ
authors.lastname: Hu
authors.affiliation: Beijing Jinxing Golden Star Duck Center, Beijing, 100076, China.
authors.forename: Fang-Xi
authors.initials: FX
authors.lastname: Yang
authors.affiliation: 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.
authors.forename: Lu-Jiang
authors.initials: LJ
authors.lastname: Qu
authors.affiliation: 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.
authors.forename: Zhuo-Cheng
authors.initials: ZC
authors.lastname: Hou
mesh_terms: D000821:Animal Feed; D000818:Animals; D000829:Animals, Domestic / Q000235:genetics / Q000254:growth & development; D030541:Databases, Genetic; D004372:Ducks / Q000235:genetics* / Q000254:growth & development; D007583:Jejunum / Q000254:growth & development*; D008297:Male; D008460:Meat; D018482:Muscle, Skeletal / Q000254:growth & development*; D059467:Transcriptome
keywords: Peking duck; duck breeding; fat deposition; feed conversion efficiency