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.

Identifying and profiling the microRNAs associated with skin colour in the Muchuan black-bone chicken

“…These include gga-miR-204, which is a miRNA known to be associated with melanogenesis. The expression of gga-miR-204 is significantly different between black and white feather bulbs in ducks (Apopo et al 2015), and is also associated with skin colour in fish (Yan et al 2013). In our study, gga-miR-204 was up-regulated in chickens with black skin, similar to results from previous studies (Adijanto et al 2012b;Apopo et al 2015).…”

“…Previous research has indicated that miRNAs can target genes or pathways involved in melanocyte biology (Mione and Bosserhoff 2015). In other vertebrates, such as ducks (Apopo et al 2015), alpacas (Xue et al 2012), goats (Wu et al 2014), mice (Dynoodt et al 2013), and fish (Yan et al 2013), miRNAs are known to be responsible for pigmentation. However, no studies to date have reported on the role of miRNAs in determining skin colour in chickens.…”

MicroRNA-340 is involved in ultraviolet B-induced pigmentation by regulating the MITF/TYRP1 axis

“…31,32 To date, studies have shown a close connection between miRNA, UVB irradiation, 33 and skin. [15][16][17] Although several studies have examined functional roles for miRNAs in the regulation of pigmentation of different species, [34][35][36] to our knowledge, such a role for miRNAs in the regulation of genes critical to pigmentation has not been demonstrated in normal adult melanocytes. Moreover, in melanoma cells, miR-340 can bind to the 3 0 -UTR of MITF mRNA and mediate the degradation of its mRNA, reducing the expression and activity of MITF protein.…”

Development and application of genome sequencing in studies on poultry production traits and health

“…Thanks to DNA sequencing, it is possible to analyze genetic variability of production traits and phenotypic characteristics of animals. Analysis at the molecular level will facilitate selection of the animals resistant to pathogens or carrying favorable production traits (3).…”