Genetic variation in the MITF promoter affects skin colour and transcriptional activity in black-boned chickens

Skin colour: A window into human phenotypic evolution and environmental adaptation

As modern humans ventured out of Africa and dispersed around the world, they faced novel environmental challenges that led to geographic adaptations including skin colour. Over the long history of human evolution, skin colour has changed dramatically, showing tremendous diversity across different geographical regions, for example, the majority of individuals from the expansive lands of Africa have darker skin, whereas the majority of people from Eurasia exhibit lighter skin. What adaptations did lighter skin confer upon modern humans as they migrated from Africa to Eurasia? What genetic mechanisms underlie the diversity of skin colour observed in different populations? In recent years, scientists have gradually gained a deeper understanding of the interactions between pigmentation gene and skin colour through population-based genomic studies of different groups around the world, particularly in East Asia and Africa. In this review, we summarize our current understanding of 26 skin colour-related pigmentation genes and 48 SNPs that influence skin colour. Important pigmentation genes across three major populations are described in detail: MFSD12, SLC24A5, PDPK1 and DDB1/CYB561A3/TMEM138 influence skin colour in African populations; OCA2, KITLG, SLC24A2, GNPAT and PAH are key to the evolution of skin pigmentation in East Asian populations; and SLC24A5, SLC45A2, TYR, TYRP1, ASIP, MC1R and IRF4 significantly contribute to the lightening of skin colour in European populations. We summarized recent findings in genomic studies of skin colour in populations that implicate diverse geographic environments, local adaptation among populations, gene flow and multi-gene interactions as factors influencing skin colour diversity.

Videla Rodriguez E, Smith VA, van den Brand H, Rodenburg TB, Visser B. A two-step Bayesian network approach to identify key SNPs associated to multiple phenotypic traits in four purebred laying hen lines

When purebred laying hen chicks hatch, they remain at a rearing farm until approximately 17 weeks of age, after which they are transferred to a laying farm. Chicks or pullets are removed from the flocks during these 17 weeks if they display any rearing abnormality. The aim of this study was to investigate associations between single nucleotide polymorphisms (SNPs) and rearing success of 4 purebred White Leghorns layer lines by implementing a Bayesian network approach. Phenotypic traits and SNPs of four purebred genetic White Leghorn layer lines were available for 23,000 rearing batches obtained between 2010 and 2020. Associations between incubation traits (clutch size, embryo mortality), rearing traits (genetic line, first week mortality, rearing abnormalities, natural death, rearing success, pullet flock age, and season) and SNPs were analyzed, using a two-step Bayesian Network (BN) approach. Furthermore, the SNPs were connected to their corresponding genes, which were further explored in bioinformatics databases. BN analysis revealed a total of 28 SNPs associated with some of the traits: ten SNPs were associated with clutch size, another 10 with rearing abnormalities, a single SNP with natural death, and seven SNPs with first week mortality. Exploration via bioinformatics databases showed that one of the SNPs (ENAH) had a protein predicted network composed of 11 other proteins. The major hub of this SNP was CDC42 protein, which has a role in egg production and reproduction. The results highlight the power of BNs in knowledge discovery and how their application in complex biological systems can help getting a deeper understanding of functionality underlying genetic variation of rearing success in laying hens. Improved welfare and production might result from the identified SNPs. Selecting for these SNPs through breeding could reduce stress and increase livability during rearing.

Genetic mapping identifies SNP mutations in MITF-M promoter associated with melanin formation in Putian black duck

The coloration of plumage in poultry species has substantial economic significance. Putian black ducks encompass 2 distinct strains characterized by black and white plumage variations resulting from selective breeding. This study aimed to identify the molecular mechanisms responsible for plumage coloration in these 2 distinct strains. A comprehensive genome-wide association study was conducted using DNA data sourced from a F2 segregating population, consisting of 71 individuals with black plumage and 39 individuals with white plumage, derived from these distinct 2 strains. This analysis revealed that 894 nucleotide polymorphisms and identified 58 candidate genes. Subsequent Gene Ontology and Kyoto Encyclopedia of Genes and Genomes coenrichment analyses identified MITF as a key candidate gene implicated in melanin biosynthesis. Furthermore, extensive screening of significant polymorphic loci within MITF was carried out via mass spectrometry in 3 distinct populations: 100 individuals with black plumage and 100 individuals with white plumage from the F0 generation; and 50 with black plumage form the F1 generation). Eighteen candidate polymorphic loci were identified demonstrating significant associations with variations in black and white plumage. Notably, 8 of these loci were located within the 2,000 bp region upstream of MITF-M. To validate the critical regulatory role of MITF-M in black and white plumage formation, a dual-fluorescence reporter system was constructed, and dual-fluorescence activity was assessed. The results revealed that the fluorescence activity at wild-type sites (corresponding to black plumage) was significantly higher than that at the mutant-type sites (associated with white plumage) (P < 0.01). To corroborate the pivotal role of MITF-M in black and white plumage formation, qPCR was employed to evaluate the expression levels of various MITF variants in black and white feather bulbs. This analysis demonstrated that only MITF-M exhibited specific expression in black feather bulbs. These results elucidate the central role of polymorphic mutations within the MITF promoter region in the regulation of black and white plumage coloration in Putian black ducks. This study extends our understanding of mechanisms governing duck plumage coloration and provides valuable molecular markers for future research in duck production and breeding based on plumage coloration.

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.

Ancestry-inclusive dog genomics challenges popular breed stereotypes

Behavioral genetics in dogs has focused on modern breeds, which are isolated subgroups with distinctive physical and, purportedly, behavioral characteristics. We interrogated breed stereotypes by surveying owners of 18,385 purebred and mixed-breed dogs and genotyping 2155 dogs. Most behavioral traits are heritable [heritability (h²) > 25%], and admixture patterns in mixed-breed dogs reveal breed propensities. Breed explains just 9% of behavioral variation in individuals. Genome-wide association analyses identify 11 loci that are significantly associated with behavior, and characteristic breed behaviors exhibit genetic complexity. Behavioral loci are not unusually differentiated in breeds, but breed propensities align, albeit weakly, with ancestral function. We propose that behaviors perceived as characteristic of modern breeds derive from thousands of years of polygenic adaptation that predates breed formation, with modern breeds distinguished primarily by aesthetic traits.

Deubiquitination of MITF-M Regulates Melanocytes Proliferation and Apoptosis

Microphthalmia-associated transcription factor-M (MITF-M) is the key gene in the proliferation and differentiation of melanocytes, which undergoes an array of post-translation modifications. As shown in our previous study, deubiquitinase USP13 is directly involved in melanogenesis. However, it is still ambiguous that the effect of USP13-mediated MITF-M expression on melanocytes proliferation and apoptosis. Herein, we found that MITF-M overexpressing melanocytes showed high cell proliferation, reduced apoptosis, and increased melanin levels. Besides, melanin-related genes, TYR, DCT, GPNMB, and PMEL, were significantly up-regulated in MITF-M overexpressing melanocytes. Furthermore, Exogenous USP13 significantly upregulated the endogenous MITF-M protein level, downregulated USP13 significantly inhibited MITF-M protein levels, without altering MITF-M mRNA expression. In addition, USP13 upregulation mitigated the MITF-M degradation and significantly increased the half-life of MITF-M. Also, USP13 stabilized the exogenous MITF protein levels. In conclusion, the MITF-M level was regulated by USP13 deubiquitinase in melanocytes, affecting melanocytes proliferation and apoptosis. This study provides the theoretical basis for coat color transformation that could be useful in the development of the new breed in fur animals.

Comparative transcriptome and histological analyses provide insights into the skin pigmentation in Minxian black fur sheep (Ovis aries)

Background

Minxian black fur (MBF) sheep are found in the northwestern parts of China. These sheep have developed several special traits. Skin color is a phenotype subject to strong natural selection and diverse skin colors are likely a consequence of differences in gene regulation.

Methods

Skin structure, color differences, and gene expression (determined by RNA sequencing) were evaluated the Minxian black fur and Small-tail Han sheep (n = 3 each group), which are both native Chinese sheep breeds.

Results

Small-tail Han sheep have a thicker skin and dermis than the Minxian black fur sheep (P < 0.01); however, the quantity of melanin granules is greater (P < 0.01) in Minxian black fur sheep with a more extensive distribution in skin tissue and hair follicles. One hundred thirty-three differentially expressed genes were significantly associated with 37 ontological terms and two critical KEGG pathways for pigmentation (“tyrosine metabolism” and “melanogenesis” pathways). Important genes from those pathways with known involvement in pigmentation included OCA2 melanosomal transmembrane protein (OCA2), dopachrome tautomerase (DCT), tyrosinase (TYR) and tyrosinase related protein (TYRP1), melanocortin 1 receptor (MC1R), and premelanosome protein (PMEL). The results from our histological and transcriptome analyses will form a foundation for additional investigation into the genetic basis and regulation of pigmentation in these sheep breeds.

Analysis of MC1R, MITF, TYR, TYRP1, and MLPH Genes Polymorphism in Four Rabbit Breeds with Different Coat Colors

Simple Summary

Coat color is an important breed characteristic and economic trait for rabbits, and it is regulated by a few genes. In this study, the gene frequencies of some pigmentation genes were investigated in four Chinese native rabbit breeds with different coat colors. A total of 14 genetic variants were detected in the gene fragments of MC1R, MITF, TYR, TYRP1, and MLPH genes, and there was low-to-moderate polymorphism in the populations. The gene frequency showed significant differences among the four rabbit populations. The above results suggest that these genetic variations play an important role in regulating the coat color of rabbits. This study will provide potential molecular markers for the breeding of coat color traits in rabbits.

Abstract

Pigmentation genes such as MC1R, MITF, TYR, TYRP1, and MLPH play a major role in rabbit coat color. To understand the genotypic profile underlying coat color in indigenous Chinese rabbit breeds, portions of the above-mentioned genes were amplified and variations in them were analyzed by DNA sequencing. Based on the analysis of 24 Tianfu black rabbits, 24 Sichuan white rabbits, 24 Sichuan gray rabbits, and 24 Fujian yellow rabbits, two indels in MC1R, three SNPs in MITF, five SNPs (single nucleotide polymorphisms) in TYR, one SNP in TYRP1, and three SNPs in MLPH were discovered. These variations have low-to-moderate polymorphism, and there are significant differences in their distribution among the different breeds (p < 0.05). These results provide more information regarding the genetic background of these native rabbit breeds and reveal their high-quality genetic resources.

Transcriptome Comparison Reveals Key Components of Nuptial Plumage Coloration in Crested Ibis

Nuptial plumage coloration is critical in the mating choice of the crested ibis. This species has a characteristic nuptial plumage that develops from the application of a black sticky substance, secreted by a patch of skin in the throat and neck region. We aimed to identify the genes regulating its coloring, by comparing skin transcriptomes between ibises during the breeding and nonbreeding seasons. In breeding season skins, key eumelanin synthesis genes, TYR, DCT, and TYRP1 were upregulated. Tyrosine metabolism, which is closely related to melanin synthesis, was also upregulated, as were transporter proteins belonging to multiple SLC families, which might act during melanosome transportation to keratinocytes. These results indicate that eumelanin is likely an important component of the black substance. In addition, we observed upregulation in lipid metabolism in breeding season skins. We suggest that the lipids contribute to an oil base, which imbues the black substance with water insolubility and enhances its adhesion to feather surfaces. In nonbreeding season skins, we observed upregulation in cell adhesion molecules, which play critical roles in cell interactions. A number of molecules involved in innervation and angiogenesis were upregulated, indicating an ongoing expansion of nerves and blood vessels in sampled skins. Feather β keratin, a basic component of avian feather filament, was also upregulated. These results are consistent with feather regeneration in the black skin of nonbreeding season ibises. Our results provide the first molecular evidence indicating that eumelanin is the key component of ibis coloration.