Transcriptome Reveals Multi Pigmentation Genes Affecting Dorsoventral Pattern in Avian Body

Abstract

Certain animals exhibit a special dorsoventral pattern with a lighter ventral side compared to the dorsal one and this phenomenon was preserved in the long-term evolution process. Birds also retain this trait. Recently, Inaba et al. (2019) found that ASIP (agouti signal protein) regulated interconversion between different melanocyte types leads to dorsal stripe pattern, which may partly explain the birds' dorsoventral plumage color difference. In this study, we used the embryo samples of LBM (light brown mottling) ducks (Anas platyrhynchos) with white ventral and dark dorsal body parts to investigate the mechanism of dorsoventral color variation. Firstly, melanin deposition process of duck embryos was investigated. The result indicated that E13 and E16 were the active stages of melanin synthesis. Moreover, the melanin deposition on the dorsum of LBM ducks was higher than that on the ventral side throughout. Then, RNA-seq was conducted for the dorsal and ventral skin tissues from E7 (early), E13 (middle) and E19 (late) of LBM ducks. Expression pattern analysis showed that the mRNA expression of most melanin synthesis related genes were at the highest level at E13, which was consistent with the section analysis. A correlation was found between melanogenesis pathway and dorsoventral color difference by co-expression analysis. In the DEG (differentially expressed gene) analysis, we added the dorsal skin transcriptome of embryonic white and black duck of same subspecies (Anas platyrhynchos domestica) for horizontal comparison. The results showed that 8 melanogenesis related genes (TYR, TYRP1, MLANA, RAB38, OCA2, TSPAN10, MC1R, and MSLN) were the common DEGs (Differential expressed genes) in the comparisons of body parts and breeds suggesting that the underlying molecular regulatory mechanism of dorsoventral plumage color difference may be similar to that of albino and melanic duck, which were caused by the different expression of multiple genes in melanin synthesis pathway. In addition, the molecular regulation of melanin synthesis pathway in the dorsal and ventral side of LBM ducks was analyzed. In this pathway, ASIP, MC1R, TYR, and TYRP1 have differential mRNA expression. ASIP, as an upstream gene in this pathway, was likely to play a decisive role in determining the dorsoventral plumage pattern.

Massive genome inversion drives coexistence of divergent morphs in common quails

“…Based on a literature search, we identified 5 genes located in the inverted region that could be potential candidate for pigmentation: TYR, RAB-38, OCA2, DCT and GPR143, 11,[73][74][75][76][77][78] and one related to migratory behavior or restlessness: NPAS2. [79][80][81] To assess if the gene function could be different in quails with and without the inversion, we annotated the SNP dataset with SnpEff v.4.3t 51 using the GTF annotation file from the Japanese quail genome.…”

Genome-wide association analysis reveals that EDNRB2 causes a dose-dependent loss of pigmentation in ducks

“…To investigate the relationship between the phenotype and EDNRB2 mRNA expression level, we examined the RNA-seq results of our previous study about the pigment deposition process during the embryonic period [ 14 ]. The results showed that the expression level of EDNRB2 increased with increasing melanic areas on the body surface of duck embryos (Fig.…”

“…The numbers in the diamond represent R 2 values. d The FPKM (fragments per kilobase of transcript per million mapped reads) values of the EDNRB2 gene in duck embryos with different melanin deposition areas were calculated based on our previous RNA-seq data [ 14 ]. The expression of EDNRB2 showed a significant increasing trend with increasing melanin area.…”

“…The duck embryo models with three levels of spot size variation were from Peking duck (non-pigmented), GF2 duck (moderately pigmented) and Heiwu duck (extensively pigmented). The EDNRB2 expression level in samples with different spot sizes was analyzed using our previous RNA-seq data [ 14 ]. Considering that pigment deposition was almost complete in the embryonic stage and that the phenotypes of the samples in our previous study were basically similar to what we used in the present study, the model should be reliable for studying the expression changes of EDNRB2.…”

Duck pan-genome reveals two transposon-derived structural variations caused bodyweight enlarging and white plumage phenotype formation during evolution

“…Transcriptome data of liver and sebum from mallard and pekin at 2, 4, and 6 weeks of age was downloaded from National Genomics Data Center (China National Center for Bioinformation) from the project number PRJCA002795, PRJCA002803, PRJCA002808, and PRJCA002807 [48]. Transcriptome data of the skin tissue was downloaded from project number PRJCA003516 [79]. Raw reads were filtered using Trimmomatic (v 0.39) [80] and subjected to align the duck pan-genome using STAR (v2.7.1a) [81].…”