title: Identification and profiling of microRNAs associated with white and black plumage pigmentation in the white and black feather bulbs of ducks by RNA sequencing.
abstract: MicroRNAs (miRNAs) play important roles in many biological processes by regulating gene expression at the post-transcriptional level. However, the mechanism by which specific miRNAs may regulate plumage pigmentation has remained largely elusive. In this study, we sequenced miRNAs using Solexa sequencing and then performed a detailed analysis of their expression profiles between the black and white feather bulbs of ducks from Cui Hei, Kaiya, Liancheng pure breeds and a Kaiya-Liancheng F2 population. mirdeep2 software identified 121 conserved and eight novel miRNAs. Five differentially expressed miRNAs between the two tissues types were also identified by degseq software. Notably, miR-204 was predominantly expressed in black feather bulbs. To further validate the sequencing data, we applied stem-loop quantitative PCR of ten known miRNAs based on the identified sequences. Furthermore, in exploring the temporal expression pattern of miR-204, we performed profiling in nine duck tissues. The targets of these miRNAs were predicted using a PITA algorithm and were later grouped based on Gene Ontology and KEGG pathway analysis using the DAVID website. The melanogenesis pathway was among the identified signalling pathways, implying key roles of these miRNAs in plumage pigmentation. Expression analysis of the target genes in the melanogenesis pathways was also performed. This study provides the foundation for subsequent studies on the prospective practical role for such miRNAs in post-transcriptional gene regulation linked to plumage pigmentation.
authors.affiliation: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China.
authors.forename: S
authors.initials: S
authors.lastname: Apopo
authors.affiliation: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China.
authors.forename: H
authors.initials: H
authors.lastname: Liu
authors.affiliation: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China.
authors.forename: L
authors.initials: L
authors.lastname: Jing
authors.affiliation: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China.|College of Informatics, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China.
authors.forename: X
authors.initials: X
authors.lastname: Du
authors.affiliation: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China.
authors.forename: S
authors.initials: S
authors.lastname: Xie
authors.affiliation: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China.
authors.forename: Y
authors.initials: Y
authors.lastname: Gong
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, Jilin, China.
authors.forename: R
authors.initials: R
authors.lastname: Xu
authors.affiliation: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China.
authors.forename: S
authors.initials: S
authors.lastname: Li
mesh_terms: D000818:Animals; D004372:Ducks / Q000235:genetics*; D005241:Feathers; D020869:Gene Expression Profiling; D035683:MicroRNAs / Q000235:genetics*; D010858:Pigmentation / Q000235:genetics*; D017423:Sequence Analysis, RNA
chemical_list: D035683:MicroRNAs
keywords: Solexa sequencing; duck; miRNA; plumage colour