Comparative transcriptome analysis provides clues to molecular mechanisms underlying blue-green eggshell color in the Jinding duck (Anas platyrhynchos)

Abstract

BackgroundIn birds, blue-green eggshell color (BGEC) is caused by biliverdin, a bile pigment derived from the degradation of heme and secreted in the eggshell by the shell gland. Functionally, BGEC might promote the paternal investment of males in the nest and eggs. However, little is known about its formation mechanisms. Jinding ducks (Anas platyrhynchos) are an ideal breed for research into the mechanisms, in which major birds lay BGEC eggs with minor individuals laying white eggs. Using this breed, this study aimed to provide insight into the mechanisms via comparative transcriptome analysis.ResultsBlue-shelled ducks (BSD) and white-shelled ducks (WSD) were selected from two populations, forming 4 groups (3 ducks/group): BSD1 and WSD1 from population 1 and BSD2 and WSD2 from population 2. Twelve libraries from shell glands were sequenced using the Illumina RNA-seq platform, generating an average of 41 million clean reads per library, of which 55.9% were mapped to the duck reference genome and assembled into 31,542 transcripts. Expression levels of 11,698 genes were successfully compared between all pairs of 4 groups. Of these, 464 candidate genes were differentially expressed between cross-phenotype groups, but not for between same-phenotype groups. Gene Ontology (GO) annotation showed that 390 candidate genes were annotated with 2234 GO terms. No candidate genes were directly involved in biosynthesis or transport of biliverdin. However, the integral components of membrane, metal ion transport, cholesterol biosynthesis, signal transduction, skeletal system development, and chemotaxis were significantly (P < 0.05) overrepresented by candidate genes.ConclusionsThis study identified 464 candidate genes associated with duck BGEC, providing valuable information for a better understanding of the mechanisms underlying this trait. Given the involvement of membrane cholesterol contents, ions and ATP levels in modulating the transport activity of bile pigment transporters, the data suggest a potential association between duck BGEC and the transport activity of the related transporters.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4135-2) contains supplementary material, which is available to authorized users.

Transcriptomic analysis of the liver in aged laying hens with different intensity of brown eggshell color

“…Regarding eggshell quality, previous studies have focused primarily on transcriptomic analysis in the uterus, which can reveal the molecular mechanisms that may cause laying hens with different eggshell quality [9,10]. For the eggshell color, Wang et al [11] conducted transcriptomic analysis to identify molecular factors affecting blue coloration in the uterus of duck with blue-green eggshells and reported a large difference in cholesterol biosynthesis and ion levels involved in the modulation of the transporting activity of bile pigment transporters. In laying hens, most of previous experiments have studied protoporphyrin IX (PP9) synthesis and transport to eggshells, specifically in the uterus because PP9 is the main pigment of brown color in eggshells and its synthesis and deposition occur in the uterine [12,13].…”

Comparative liver transcriptome analysis in ducklings infected with duck hepatitis A virus 3 (DHAV-3) at 12 and 48 hours post-infection through RNA-seq

“…To date, many studies have reported on transcriptome sequencing in ducks. It is being widely used in the studies on duck-pathogens [ 10 – 15 ], duck-phenotypes [ 16 , 17 ] and duck-performance interaction [ 18 ]. In 2013, Tang et al carried out transcriptome sequencing to explore and compare the gene expression patterns of normal and DHAV-3 infected duckling livers at 24 hours post-infection (hpi) [ 10 ].…”

Genetic Parameters for Yolk Cholesterol and Transcriptional Evidence Indicate a Role of Lipoprotein Lipase in the Cholesterol Metabolism of the Chinese Wenchang Chicken

“…Six libraries from each group ( n = 3) were sequenced. First, raw reads in FASTQ format were filtered to generate clean reads by removing reads containing adapters or ambiguous nucleotides and reads of low quality, as described by Wang et al (2017a). Then, the filtered reads were mapped to the chicken reference genome (Gallus_gallus-5.0) using the spliced mapping algorithm of Tophat (version 2.0.9) with no more than two mismatches.…”