The Dominant white mutation in the PMEL17 gene does not cause visual impairment in chickens

Functional Domains and Evolutionary History of the PMEL and GPNMB Family Proteins

The ancient paralogs premelanosome protein (PMEL) and glycoprotein nonmetastatic melanoma protein B (GPNMB) have independently emerged as intriguing disease loci in recent years. Both proteins possess common functional domains and variants that cause a shared spectrum of overlapping phenotypes and disease associations: melanin-based pigmentation, cancer, neurodegenerative disease and glaucoma. Surprisingly, these proteins have yet to be shown to physically or genetically interact within the same cellular pathway. This juxtaposition inspired us to compare and contrast this family across a breadth of species to better understand the divergent evolutionary trajectories of two related, but distinct, genes. In this study, we investigated the evolutionary history of PMEL and GPNMB in clade-representative species and identified TMEM130 as the most ancient paralog of the family. By curating the functional domains in each paralog, we identified many commonalities dating back to the emergence of the gene family in basal metazoans. PMEL and GPNMB have gained functional domains since their divergence from TMEM130, including the core amyloid fragment (CAF) that is critical for the amyloid potential of PMEL. Additionally, the PMEL gene has acquired the enigmatic repeat domain (RPT), composed of a variable number of imperfect tandem repeats; this domain acts in an accessory role to control amyloid formation. Our analyses revealed the vast variability in sequence, length and repeat number in homologous RPT domains between craniates, even within the same taxonomic class. We hope that these analyses inspire further investigation into a gene family that is remarkable from the evolutionary, pathological and cell biology perspectives.

Comparative Transcriptome Analysis Identifies Candidate Genes Related to Black-Spotted Pattern Formation in Spotted Scat (Scatophagus argus)

Simple Summary

Spotted scat (Scatophagus argus) is a commercially important marine aquaculture and ornamental fish species in China and East Asian countries. There are dozens of black spots on each side of the body, and the caudal fin, which is yellow and black, is appreciated in ornamental fish markets. To explore the genetic mechanisms of its pattern formation, we found 2357 differentially expressed genes (DEGs) by comparing the transcriptome in the black-spotted skin, non-spotted skin and caudal fin in S. argus. The results will expand our knowledge about the molecular mechanism of important genes and pathways associated with pigment pattern formation and provide a certain theoretical basis for the molecular breeding in S. argus.

Abstract

Spotted scat (Scatophagus argus) is an economically important marine aquaculture and ornamental fish species in Asia, especially in southeast China. In this study, skin transcriptomes of S. argus were obtained for three types of skin, including black-spotted skin (A), non-spotted skin (B) and caudal fin (C). A total of nine complementary DNA (cDNA) libraries were obtained by Illumina sequencing. Bioinformatics analysis revealed that 1358, 2086 and 487 genes were differentially expressed between A and B, A and C, and B and C, respectively. The results revealed that there were 134 common significantly differentially expressed genes (DEGs) and several key genes related to pigment synthesis and pigmentation, including tyrp1, mitf, pmel, slc7a2, tjp1, hsp70 and mart-1. Of these, some DEGs were associated with pigmentation-related Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, such as tyrosine metabolism, melanogenesis, the Wnt signaling pathway and the mitogen-activated protein kinase (MAPK) signaling pathway. The results will facilitate understanding the molecular mechanisms of skin pigmentation differentiation in S. argus and provide valuable information for skin coloration, especially the formation of spotted patterns on other marine fish species.

Comparative transcriptome analysis reveals the genetic basis of skin color variation in common carp

Background

The common carp is an important aquaculture species that is widely distributed across the world. During the long history of carp domestication, numerous carp strains with diverse skin colors have been established. Skin color is used as a visual criterion to determine the market value of carp. However, the genetic basis of common carp skin color has not been extensively studied.

Methodology/Principal Findings

In this study, we performed Illumina sequencing on two common carp strains: the reddish Xingguo red carp and the brownish-black Yellow River carp. A total of 435,348,868 reads were generated, resulting in 198,781 assembled contigs that were used as reference sequences. Comparisons of skin transcriptome files revealed 2,012 unigenes with significantly different expression in the two common carp strains, including 874 genes that were up-regulated in Xingguo red carp and 1,138 genes that were up-regulated in Yellow River carp. The expression patterns of 20 randomly selected differentially expressed genes were validated using quantitative RT-PCR. Gene pathway analysis of the differentially expressed genes indicated that melanin biosynthesis, along with the Wnt and MAPK signaling pathways, is highly likely to affect the skin pigmentation process. Several key genes involved in the skin pigmentation process, including TYRP1, SILV, ASIP and xCT, showed significant differences in their expression patterns between the two strains.

Conclusions

In this study, we conducted a comparative transcriptome analysis of Xingguo red carp and Yellow River carp skins, and we detected key genes involved in the common carp skin pigmentation process. We propose that common carp skin pigmentation depends upon at least three pathways. Understanding fish skin color genetics will facilitate future molecular selection of the fish skin colors with high market values.

Equine multiple congenital ocular anomalies and silver coat colour result from the pleiotropic effects of mutant PMEL

Equine Multiple Congenital Ocular Anomalies (MCOA) syndrome is a heritable eye disorder mainly affecting silver colored horses. Clinically, the disease manifests in two distinct classes depending on the horse genotype. Horses homozygous for the mutant allele present with a wide range of ocular defects, such as iris stromal hypoplasia, abnormal pectinate ligaments, megaloglobus, iridociliary cysts and cataracts. The phenotype of heterozygous horses is less severe and predominantly includes iridociliary cysts, which occasionally extend into the temporal retina. In order to determine the genetic cause of MCOA syndrome we sequenced the entire previously characterized 208 kilobase region on chromosome 6 in ten individuals; five MCOA affected horses from three different breeds, one horse with the intermediate Cyst phenotype and four unaffected controls from two different breeds. This was performed using Illumina TruSeq technology with paired-end reads. Through the systematic exclusion of all polymorphisms barring two SNPs in PMEL, a missense mutation previously reported to be associated with the silver coat colour and a non-conserved intronic SNP, we establish that this gene is responsible for MCOA syndrome. Our finding, together with recent advances that show aberrant protein function due to the coding mutation, suggests that the missense mutation is causative and has pleiotrophic effect, causing both the horse silver coat color and MCOA syndrome.

Using electroretinograms to assess flicker fusion frequency in domestic hens Gallus gallus domesticus

The assessment of flicker fusion frequency (FFF), the stimulus frequency at which a flickering light stimulus can no longer be resolved and appears continuous, and critical flicker fusion frequency (CFF; the highest frequency at any light intensity that an observer can resolve flicker) are useful methods for comparing temporal resolution capabilities between animals. Behavioural experiments have found that average CFFs in domestic chickens (Gallus gallus domesticus) are in the range of ca. 75-87 Hz, measured in response to full spectrum (i.e. white light plus UV) stimuli. In order to examine whether the chicken retina is able to detect flicker at higher frequencies, we used electroretinograms (ERGs) to assess FFF/CFF in adult hens from two commercial genotypes, Lohmann Selected Leghorns (LSLs) and Lohmann Browns (LBs). ERGs were recorded in response to flickering light at ten full spectrum light intensities ranging from 0.7 to 2740 cd m(-2). Two methods were used to determine FFF/CFF from the ERG recordings and these methods yielded very similar results, with average FFF ranging from ca. 20Hz at 0.7 cd m(-2) to an average CFF of ca. 105 Hz at 2740 cd m(-2). In some individuals, CFFs of 118-119 Hz were recorded. The Intensity/FFF (I/FFF) curves are double-branched with a break point representing the rod-cone transition occurring between 2.5 and 5.9 cd m(-2). No significant differences in the I/FFF curves were found between the two genotypes. At stimulus light intensities >250 cd m(-2), the ERG-derived FFF and CFF values are all higher than those from behavioural studies using the same stimuli. Although hens do not appear to be able to consciously perceive flicker above approximately 90 Hz, the finding that the ERG responses are able to remain in phase with light flickering at frequencies >100 Hz means that the retinae of domestic poultry housed in artificial light conditions may be able to resolve flicker from fluorescent lamps. As range of detrimental effects have been reported in humans as a result of exposure to such "invisible flicker", the possibility exists that flicker from fluorescent lamps also acts as stressor in domesticated birds.

Inactivation of Pmel alters melanosome shape but has only a subtle effect on visible pigmentation

PMEL is an amyloidogenic protein that appears to be exclusively expressed in pigment cells and forms intralumenal fibrils within early stage melanosomes upon which eumelanins deposit in later stages. PMEL is well conserved among vertebrates, and allelic variants in several species are associated with reduced levels of eumelanin in epidermal tissues. However, in most of these cases it is not clear whether the allelic variants reflect gain-of-function or loss-of-function, and no complete PMEL loss-of-function has been reported in a mammal. Here, we have created a mouse line in which the Pmel gene has been inactivated (Pmel^−/−). These mice are fully viable, fertile, and display no obvious developmental defects. Melanosomes within Pmel^−/− melanocytes are spherical in contrast to the oblong shape present in wild-type animals. This feature was documented in primary cultures of skin-derived melanocytes as well as in retinal pigment epithelium cells and in uveal melanocytes. Inactivation of Pmel has only a mild effect on the coat color phenotype in four different genetic backgrounds, with the clearest effect in mice also carrying the brown/Tyrp1 mutation. This phenotype, which is similar to that observed with the spontaneous silver mutation in mice, strongly suggests that other previously described alleles in vertebrates with more striking effects on pigmentation are dominant-negative mutations. Despite a mild effect on visible pigmentation, inactivation of Pmel led to a substantial reduction in eumelanin content in hair, which demonstrates that PMEL has a critical role for maintaining efficient epidermal pigmentation.

Pigmentation has since long constituted a prime model to study how genes act and interact. The PMEL gene encodes a protein exclusively found in the melanosomes of pigment-producing cells. Mutations in PMEL underlie some spectacular color phenotypes in animals including Dominant white color in chickens, Silver in horses, and Merle in dogs, but no spontaneous mutation causing a complete inactivation of this gene has yet been found in mammals. We have now developed a PMEL knockout mouse to further study the function of this protein. We show that mice lacking PMEL have almost normal visible pigmentation. However, loss of PMEL has a dramatic effect on the morphology of the melanosomes in skin, hair, and eye, such that the normally rod-shaped melanosomes in wild-type animals are spherical in the knockout mice. The knockout animals also have a substantial reduction in the content of black pigment in hair. The study establishes that PMEL has a critical role for maintaining normal pigment production.

Behavioural assessment of flicker fusion frequency in chicken Gallus gallus domesticus

To interact with its visual environment, an organism needs to perceive objects in both space and time. High temporal resolution is hence important to the fitness of diurnally active animals, not least highly active aerial species such as birds. However, temporal resolution, as assessed by flicker fusion frequency (FFF; the stimulus frequency at which a flickering light stimulus can no longer be resolved and appears continuous) or critical flicker fusion frequency (CFF; the highest flicker fusion frequency at any light intensity) has rarely been assessed in birds. In order to further our understanding of temporal resolution as a function of light intensity in birds we used behavioural experiments with domestic chickens (Gallus gallus domesticus) from an old game breed 'Gammalsvensk dvärghöna' (which is morphologically and behaviourally similar to the wildtype ancestor, the red jungle fowl, G. gallus), to generate an 'Intensity/FFF curve' (I/FFF curve) across full spectrum light intensities ranging from 0.2 to 2812 cd m⁻². The I/FFF curve is double-branched, resembling that of other chordates with a duplex retina of both rods and cones. Assuming that the branches represent rod and cone mediated responses respectively, the break point between them places the transition between scotopic and photopic vision at between 0.8 and 1.9 cd m⁻². Average FFF ranged from 19.8 Hz at the lowest light intensity to a CFF 87.0 Hz at 1375 cd m⁻². FFF dropped slightly at the highest light intensity. There was some individual variation with certain birds displaying CFFs of 90-100 Hz. The FFF values demonstrated by this non-selected breed appear to be considerably higher than other behaviourally derived FFF values for similar stimuli reported for white and brown commercial laying hens, indicating that the domestication process might have influenced temporal resolution in chicken.

Targeted analysis of four breeds narrows equine Multiple Congenital Ocular Anomalies locus to 208 kilobases

The syndrome Multiple Congenital Ocular Anomalies (MCOA) is the collective name ascribed to heritable congenital eye defects in horses. Individuals homozygous for the disease allele (MCOA phenotype) have a wide range of eye anomalies, while heterozygous horses (Cyst phenotype) predominantly have cysts that originate from the temporal ciliary body, iris, and/or peripheral retina. MCOA syndrome is highly prevalent in the Rocky Mountain Horse but the disease is not limited to this breed. Affected horses most often have a Silver coat color; however, a pleiotropic link between these phenotypes is yet to be proven. Locating and possibly isolating these traits would provide invaluable knowledge to scientists and breeders. This would favor maintenance of a desirable coat color while addressing the health concerns of the affected breeds, and would also provide insight into the genetic basis of the disease. Identical-by-descent mapping was used to narrow the previous 4.6-Mb region to a 264-kb interval for the MCOA locus. One haplotype common to four breeds showed complete association to the disease (Cyst phenotype, n = 246; MCOA phenotype, n = 83). Candidate genes from the interval, SMARCC2 and IKZF4, were screened for polymorphisms and genotyped, and segregation analysis allowed the MCOA syndrome region to be shortened to 208 kb. This interval also harbors PMEL17, the gene causative for Silver coat color. However, by shortening the MCOA locus by a factor of 20, 176 other genes have been unlinked from the disease and only 15 genes remain.

The presence of UV wavelengths improves the temporal resolution of the avian visual system

The ability to perceive rapid movement is an essential adaptation in birds, which are involved in rapid flight, pursuing prey and escaping predators. Nevertheless, the temporal resolution of the avian visual systems has been less well explored than spectral sensitivity. There are indications that birds are superior to humans in their ability to detect movement, as suggested by higher critical flicker frequencies (CFFs). It has also been implied, but not properly tested, that properties of CFF, as a function of light intensity, are affected by the spectral composition of light. This study measured CFF in the chicken, Gallus gallus L., using four different light stimuli - white, full-spectrum (white with addition of UV), yellow (590 nm) and UV (400 nm) - and four light intensity levels, adjusted to relative cone sensitivity. The results showed significantly higher CFF values for full-spectrum compared with white light, as well as a steeper rate of increase with intensity. The presence of UV wavelengths, previously demonstrated to affect mate choice and foraging, appears to be important also for detection of rapid movement. The yellow and UV light stimuli yielded rather similar CFFs, indicating no special role for the double cone in flicker detection.