Project description:In this project we try to character potential candidate genes and signaling pathways related to PM development during late-term embryonic to neonatal development in indigenous chinese duck breeds. We use RNA-seq to analyse PM samples selected at embryonic days (E) 21 and 27 and 5 days post-hatch (dph) in Gaoyou and Jinding ducks. There were about 45 million clean reads, the total mapped rate was 58.58%–64.82%, and the uniquely mapped rate was 56.21%–63.55%.The results of cluster analysis of DEGs are shown that with the same developmental time nodes superimposed. There were 522 DEGs between Gaoyou and Jinding ducks at E21, including 146 novel genes. There were 299 DEGs and 81 novel genes at E27, and 510 DEGs and 118 novel genes at 5 dph. A total of 43 DEGs were shared by both breeds at all time points, including 19 novel genes.We further considered the 393 genes with expression patterns in line with the muscle development curve in both breeds. these DEGs may be involved in the mechanisms responsible for the phenomenon of static or decreased breast muscle growth in duck breeds during the late embryonic period.
Project description:Plumage color plays a prominent role in reproductive isolation and thus understanding the genetic basis of pigmentation patterns can provide critical insight into speciation. Subspecies of the dark-eyed junco (Junco hyemalis) show marked differences in melanic plumage coloration known to have evolved rapidly since the Last Glacial Maximum just 18,000 years ago. To understand this rapid radiation we studied the pigment composition and the genetic basis of coloration in two divergent subspecies, the slate-colored and Oregon juncos. We used HPLC and light microscopy to investigate pigment deposition patterns in feathers from four body areas. RNA-seq data generated under common garden experimental conditions were then used to compare the relative roles of differential gene expression in growing feathers and sequence divergence in loci expressed during feather development. Junco feathers were found to differ in eumelanin and pheomelanin content and distribution, producing a range of black, gray and brown colors. Transcriptomic data revealed marked regulatory differences among subspecies and among body-parts within subspecies in known melanin-pathway genes (including PMEL, TYR, TYRP1, OCA2, MLANA), but also in several novel or poorly known loci (EDAR, VPS33B, HPS1). Within subspecies, lighter feathers expressed less melanin synthesis genes, more ASIP, and showed differential expression of Wnt signaling genes. Feathers from different body regions also showed differential expression of Hox genes. The two subspecies differed in expression of ASIP and three other genes (MFSD12, KCNJ13, HAND2) previously associated with color development. Sequence variation in the expressed genes was not related to color differences between junco subspecies. Our findings suggest that differential expression of a few genes can account for marked differences in plumage color and pattern, a mechanism that can account for the rapid diversification of juncos. Several novel candidate pigmentation genes found in juncos may contribute to the expression of melanic coloration in other vertebrates.
Project description:The objective of this study is to profile microRNA expressed in embryonic breast muscle of duck, analyze the conservation across multiple species and identify candidate microRNAs associated with duck muscle development. microRNA sequencing analysis was performed using female breast muscle samples at embryonic stage 13th day (E13) and embryonic stage 19th day (E19).
Project description:The objective of this study was to identify candidate circular RNAs associated with duck muscle development. circRNA sequencing analysis was employed using female breast muscle samples embryo stage 13th day (E13) and embryo stage 19th day (E19). RNA-seq data and validation experiment in duck myoblast cells showed that circGAS2-2 significantly differential expressed between E13 and E19 group.
