Genome-Wide Analysis Identifies Candidate Genes Encoding Beak Color of Duck

Whole-genome resequencing reveals melanin deposition candidate genes of Luning chicken

BACKGROUND

Melanin in the black-bone chicken's body is considered the material basis for its medicinal effects and is an economically important trait. Therefore, improving the melanin content is a crucial focus in the breeding process of black-bone chickens. Luning chickens are black-bone chickens, with black beaks, skin, and meat. To investigate the genetic diversity and molecular mechanisms of melanin deposition in Luning chickens, we conducted whole-genome resequencing to analyze their breeding history and identify candidate genes influencing their black phenotype, along with transcriptome sequencing of dorsal skin tissues of male Luning chickens.

RESULTS

Population structure analysis revealed that Luning chickens tend to cluster independently and are closely related to Tibetan chickens. Runs of homozygosity analysis suggested potential inbreeding in the Luning chicken and Tibetan chicken population. By combining genetic differentiation index (Fst) and nucleotide diversity (θπ) ratios, we pinpointed selected regions associated with melanin deposition. Gene annotation identified 540 genes with the highest Fst value in LOC101750371 and LOC121108313, located on the 68.24-68.58 Mb interval of chromosome Z. Combining genomic and transcriptomic data, we identified ATP5E, EDN3, and LOC101750371 as candidate genes influencing skin color traits in black-bone chickens.

CONCLUSIONS

This study characterized the evolutionary history of Luning chickens and preliminarily excavated candidate genes influencing the genetic mechanism of pigmentation in black-bone chickens, providing valuable insights for the study of animal melanin deposition.

Transcriptome analysis of sexual dimorphism in dorsal down coloration in goslings

BACKGROUND

In day-old Hungarian white goose goslings, there is a noticeable difference in dorsal down coloration between males and females, with females having darker dorsal plumage and males having lighter plumage. The ability to autosex day-old goslings based on their dorsal down coloration is important for managing them efficiently and planning their nutrition in the poultry industry. The aim of this study was to determine the biological and genetic factors underlying this difference in dorsal down colorationthrough histological analysis, biochemical assays, transcriptomic profiling, and q‒PCR analysis.

RESULTS

Tissue analysis and biochemical assays revealed that compared with males, 17-day-old embryos and day-old goslings of female geese exhibited a greater density of melanin-containing feather follicles and a greater melanin concentration in these follicles during development. Both female and male goslings had lower melanin concentrations in their dorsal skin compared to 17-day-old embryos. Transcriptome analysis identified a set of differentially expressed genes (DEGs) (MC1R, TYR, TYRP1, DCT and MITF) associated with melanogenesis pathways that were downregulated or silenced specifically in the dorsal skin of day-old goslings compared to 17-day-old embryos, affecting melanin synthesis in feather follicles. Additionally, two key genes (MC1R and MITF) associated with feather coloration showed differences between males and females, with females having higher expression levels correlated with increased melanin synthesis and darker plumage.

CONCLUSION

The expression of multiple melanogenesis genes determines melanin synthesis in goose feather follicles. The dorsal down coloration of day-old Hungarian white goose goslings shows sexual dimorphism, likely due to differences in the expression of the MC1R and MITF genes between males and females. These results could help us better understand why male and female goslings exhibit different plumage patterns.

Study on changing disciplinarian of beak colors in ducks and the regulation network based on transcriptome sequencing

Beak color in ducks is a primary characteristic of local breeds and genetic resources. Among them, black beaks, a rare packaging trait of high-quality duck products, have attracted much attention. In this study, Runzhou White Created ducks (black beak) and white-feathered Putian black ducks (yellow beak) were used to construct the F2 generation resource population to study the changing discipline of beak color combined with the beak color statistics of gray-beaked ducklings of Runzhou White Created ducks. Subsequently, transcriptome sequencing was performed to identify genetic markers related to beak color. To explore the rules of beak color change and its regulatory network, trends, and trend analysis and weighted gene co-expression network analysis（WGCNA）were performed. The screening results were verified by real-time quantitative polymerase chain reaction. A large difference was observed between the beak colors of birds from the F1 generation at 0 and 42 d of age. The F2 generation results show that nearly half of the black-beaked ducklings become green-beaked; the proportion of black spots for gray- and patterned-beaked ducklings increases with age, with most becoming green-beaked. Moreover, the beak color darkened from the first day, and the gray color value decreased significantly from the second day. Transcriptome sequencing indicated that TYR was differentially expressed between black and yellow beaks at 4 to 6 wk of age, and trend and WGCNA analyses showed that EDNRB signaling pathway genes and MITF were highly expressed in the first week, and TYR, TYRP1, and DCT were highly expressed at 4 to 6 wk of age. Therefore, there is melanin synthesis and deposition after hatching for gray- and patterned-beaked ducklings, while the yellow pigment might be deposited in the epidermis of beaks for black-beaked ducklings. The EDNRB signaling pathway is probably involved in early melanosome maturation and melanin formation in duck beaks, and genes such as TYR can maintain the black-beak phenotype.

Population genomics reveals that a missense mutation in EDNRB2 contributes to white plumage color in pigeons

Plumage color is an important economic trait for breed feature identification and consumer's requirements in pigeons. The domestic pigeon has multiple types of plumage color, thereby providing a unique opportunity to identify the genetic basis of plumage coloration. White feather color is common for meat and medicinal use. To investigate the genetic variation associated with white plumage color in pigeons, we use genome resequencing and population genomics to identify the genomic regions with strong selective signature between pigeons with brown and white plumage color. Meanwhile, we obtained some candidate genes with melanin or melanosome biosynthesis in selected regions. Finally, we identified a missense mutation p.E256K in the EDNRB2 completely associated with white plumage color. These findings provide a basis for genetic variation in pigeons with plumage color phenotype.

The draft genome of the Temminck's tragopan (Tragopan temminckii) with evolutionary implications

BACKGROUND

High-quality genome data of birds play a significant role in the systematic study of their origin and adaptive evolution. The Temminck's tragopan (Tragopan temminckii) (Galliformes, Phasianidae), a larger pheasant, is one of the most abundant and widely distributed species of the genus Tragopan, and was defined as class II of the list of national key protected wild animals in China. The absence of a sequenced genome has restricted previous evolutionary trait studies of this taxa.

RESULTS

The whole genome of the Temminck's tragopan was sequenced using Illumina and PacBio platform, and then de novo assembled and annotated. The genome size was 1.06 Gb, with a contig N50 of 4.17 Mb. A total of 117.22 Mb (11.00%) repeat sequences were identified. 16,414 genes were predicted using three methods, with 16,099 (98.08%) annotated as functional genes based on five databases. In addition, comparative genome analyses were conducted across 12 Galliformes species. The results indicated that T. temminckii was the first species to branch off from the clade containing Lophura nycthemera, Phasianus colchicus, Chrysolophus pictus, Syrmaticus mikado, Perdix hodgsoniae, and Meleagris gallopavo, with a corresponding divergence time of 31.43 million years ago (MYA). Expanded gene families associated with immune response and energy metabolism were identified. Genes and pathways associated with plumage color and feather development, immune response, and energy metabolism were found in the list of positively selected genes (PSGs).

CONCLUSIONS

A genome draft of the Temminck's tragopan was reported, genome feature and comparative genome analysis were described, and genes and pathways related to plumage color and feather development, immune response, and energy metabolism were identified. The genomic data of the Temminck's tragopan considerably contribute to the genome evolution and phylogeny of the genus Tragopan and the whole Galliformes species underlying ecological adaptation strategies.

Genome-wide association analysis of neck ring traits in NongHua ma male ducks

1. Male NongHua ma ducks have more colourful feathers than females, especially considering that the former have a distinctive neck ring that is different from that of females. This ring development might be influenced by sex selection, the environment, genetics and other elements.2. Genome-wide association analysis (GWAS) was used to locate candidate genes that affect the neck ring formation of male ducks to investigate the genetic basis of this phenomenon.3. In this study, the neck ring area and width of 180 male ducks were assessed at ages 80, 90, 100, 110 and 120 d. GWAS was used to identify associated genes. There were 0, 7, 14, 48 and 21 possible candidate genes annotated around the 0, 12, 25, 76 and 40 SNP loci n corresponding regions. A total of 13 candidate genes were identified around 21 SNP sites at the neck ring width of 120 d.4. These significant genes were annotated and GO and KEGG enrichment analyses were performed. All SNPs that exceeded the significance threshold were annotated and preliminarily screened as candidate genes affecting neck ring formation. From analysis of gene function and enriched KEGG pathways, genes such as THSD1, SLC6A4, DGAT2, PRKDC, B3GAT2, ROR1, GRK7, EXTL3, TXNDC12, COL4A2, PRKG1, ACTR3, were considered important candidate marker sites related to the neck ring. This provided a reference starting point for the genetic mechanism underlying duck feather colour.

Identification of SNPs in MITF associated with beak color of duck

Introduction: Beak color-a pigment-related trait-is an important feature of duck breeds. Recently, little research has addressed genetic mechanism of the beak colors in poultry, whereas the process and the regulation factors of melanin deposition have been well described. Methods: To investigate the genetic mechanism of beak colors, we conducted an integrated analysis of genomic selection signatures to identify a candidate site associated with beak color. For this, we used black-billed (Yiyang I meat duck synthetic line H1, H2, H3&HF) and yellow-billed ducks (Cherry Valley ducks and white feather Putian black duck). Quantitative real-time PCR and genotyping approaches were used to verify the function of the candidate site. Results: We identified 3,895 windows containing 509 genes. After GO and KEGG enrichment analysis, nine genes were selected. Ultimately, MITF was selected by comparing the genomic differentiation (FST). After loci information selection, 41 extreme significantly different loci were selected, which are all located in intron regions of MITF and are in almost complete linkage disequilibrium. Subsequently, the site ASM874695v1:10:g.17814522T > A in MITF was selected as the marker site. Furthermore, we found that MITF expression is significantly higher in black-beaked ducks than in yellow-beaked ducks of the F2 generation (p < 0.01). After genotyping, most yellow-billed individuals are found with homozygous variant; at the same time, there are no birds with homozygous variant in black-billed populations, while the birds with homozygous and heterozygous variant share the same proportion. Conclusion: MITF plays a very critical role in the melanogenesis and melanin deposition of duck beaks, which can effectively affect the beak color. The MITF site, ASM874695v1:10:g.17814522T > A could be selected as a marker site for the duck beak color phenotype.