GSE69301
Identification and profiling of microRNAs associated with white and black plumage pigmentation in the white and black feather bulbs of ducks by RNA-Sequencing
Purpose: 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. 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. Overall design: Methods: Black and white feather bulbs profiles of four ducks namely, Cui Hei, Kaiya, Liancheng pure breeds and Kaiya-Liancheng F2, were generated by illumina solexa sequencing . Three feather bulbs from the same individual duck were pooled as one samples. Samples from the same breed were pooled as one and sent to Beijing Genomics Institute (BGI, China) for small RNA library construction and sequencing. The libraries were prepared with NEBNext® UltraTM RNA Library Prep Kit. Sequencing was performed using Illumina sequencing technology (Illumina HiSeq 2000). The sequence quality was assessed with FastQC software . Clean sequence reads were analysed by miRDeep2 software version 2.1.2 .  We compared the miRNA expression profiles between black and white feather libraries of ducks using the DEGseq software  and our own perl script. miRNAs that adhered to the criteria log2-fold change =1 or = -1 and p-value =0.05 were considered to be differentially expressed. The Student''s t-test was used to compute the value. Validation of 10 conserved miRNAs sequencing data was performed using the SYBR Green assay.