Plumage Traits Research Articles

Joint Genomic and Transcriptomic Analysis Reveals Candidate Genes Associated with Plumage Color Traits in Matahu Ducks.

Plumage color is a key trait for identifying waterfowl breeds with significant economic importance. A white-feathered group has recently emerged within the native Matahu duck population, presenting an opportunity for breeding new lines. However, the genetic basis for this plumage variation is still unknown, necessitating further research. This study aims to identify the genetic mechanisms underlying the emergence of white-feathered individuals in the Matahu duck population through combined genome and transcriptome analysis, providing insights for selective breeding and the development of new white-feathered lines. In this study, a total of 1344 selected genes and 1406 significantly differentially expressed genes were identified through selection signal analysis and transcriptomic analysis, respectively. The functional enrichment of these genes revealed several key signaling pathways, including those related to cGMP-PKG, cAMP, PI3K-Akt, and MAPK. Furthermore, important candidate genes involved in melanin biosynthesis, such as MITF, MC1R, TYR, TYRP1, and ABCB6, were identified. Notably, 107 genes were detected by both methods, and, among these, DGKI, GPRC5B, HMX1, STS, ADGRA1, PRKAR2B, and HOXB9 are suggested to play a role in melanin formation and potentially influence plumage traits. Through the integrative approach combining genomic selection signals and transcriptomic analyses, we identified several candidate genes directly associated with plumage color, including MITF, TYR, TYRP1, and MC1R, along with multiple signaling pathways linked to melanin formation. We hypothesize that the expression of DGKI, GPRC5B, HMX1, STS, ADGRA1, PRKAR2B, and HOXB9, detected by both methods, may be closely related to the regulation of plumage color traits. These findings provide a foundational basis for further research aimed at elucidating the genetic mechanisms governing plumage color variation in ducks.

Divergent ornamentation within a single population of the barn swallow.

Differential migration strategies favour different sets of characteristics, including sexually selected ornamentation. Such phenotypic variation is particularly evident in a population with partial migration, where migrants and non-migrants co-exist. Partial migration provides insights into the link between migration, local environment and ornamentation, although empirical studies remain scarce. Here, we studied the plumage traits of barn swallows (Hirundo rustica) in southern Japan, where both winterings and migrants breed sympatrically. We further examined this relationship with multiple isotopes (δ2H, δ13C, δ15N and δ34S), which provides insight into their moulting habitat. Among males, winterings and migrants differed in their morphological traits: wintering males had shorter wings, which suggests the high demand for flight apparatus in migratory birds. Moreover, wintering males had larger white tail spots and less colourful throat patches than migratory males, indicating ornament divergence between them. Wintering males had a significantly smaller isotopic space when examining the combinations of δ34S with the other isotopes compared to migratory males, which indicates a differential geographic range between them, perhaps because of the limited variation in the distance to the sea in wintering males. As in males, wintering females had a significantly smaller isotopic space than migrant females, but there were few morphological differences between migratory and wintering females. Instead, some morphological traits were related to isotope values in females. These results indicate sex-specific linkage between migration, local environment, and ornamentation.

Trait Variation and Spatiotemporal Dynamics across Avian Secondary Contact Zones.

A secondary contact zone (SCZ) is an area where incipient species or divergent populations may meet, mate, and hybridize. Due to the diverse patterns of interspecific hybridization, SCZs function as field labs for illuminating the on-going evolutionary processes of speciation and the establishment of reproductive isolation. Interspecific hybridization is widely present in avian populations, making them an ideal system for SCZ studies. This review exhaustively summarizes the variations in unique traits within avian SCZs (vocalization, plumage, beak, and migratory traits) and the various movement patterns of SCZs observed in previous publications. It also highlights several potential future research directions in the genomic era, such as the relationship between phenotypic and genomic differentiation in SCZs, the genomic basis of trait differentiation, SCZs shared by multiple species, and accurate predictive models for forecasting future movements under climate change and human disturbances. This review aims to provide a more comprehensive understanding of speciation processes and offers a theoretical foundation for species conservation.

A selection breeding pattern for sexually dimorphic breast plumage color in Guangxi Yao chickens

The breast plumage color of Guangxi Yao chickens shows obvious sexual dimorphism, with roosters showing black and black with red, and hens displaying partridge and red. Black plumage in roosters is considered a sign of quality, necessitating the purification of plumage color. Here, we developed an effective method based on genetic variations within MC1R and plumage characteristics. We clarified the distribution of 5 single nucleotide polymorphisms (SNP) and 3 haplotypes (H1, H2, and H3) of MC1R gene, and revealed potential associations between haplotype H1 and black breast plumage in the F2 resource population derived from a backcross between Guangxi Yao and Yellow chickens. Subsequently, using H1/H1 diplotype roosters and hens to construct families (n = 1,244) notably increased the proportion of offspring with black plumage. Further analysis suggested that red plumage in hens may be the putative phenotype of black plumage in roosters, driven by haplotype H1 of the MC1R gene, as verified by genotype and phenotype analysis. As expected, we found that almost all male offspring of hens with red breast plumage showed black plumage. In short, we established a selection pattern based on the combination of black-plumage roosters and red-plumage hens can significantly purify the sexually dimorphic plumage color and improve the efficiency of breeding programs in Guangxi Yao chickens. Our findings provide a novel technical framework to accelerate the breeding process for plumage trait in poultry.

Ant-following behavior is correlated with plumage traits in African understory birds

Ant-following behavior is a common phenomenon in birds of Neotropical and Afrotropical rainforests but yet little is known from Central Africa. We here report on the phenomenon in lowland rainforest in Cameroon, quantifying the strength of the interaction of different ant-following bird species with driver ants and test the hypothesis that higher levels of specialization in ant-following behavior are associated with dominance or aggression-dependent plumage and other morphological traits. Flock size varied between 1 and 11 individuals with a mean size of 5.34 ± 2.68 (mean ± SD) individuals occurring at the same time. The maximum number of species present during one raid observed was ten, whereas the minimum number was four with an overall species richness of 6.89 ± 2.1 species. The 21 attending bird species strongly varied in the degree of ant-following behavior. In an interspecific comparison, plumage traits such as the presence of a colored crown, eyespots, and bare skin around the eye, in combination with metatarsus length and weight, were significantly correlated with ant-following behavior. These results suggest that—in size and identity of species—ant-following bird assemblages in Central Africa are similar to those reported from East Africa. They also suggest that ant following favors the selection of traits that signal dominance in interactions between individuals struggling for valuable food resources in the forest understory.

Investigation into the association of FNDC1 and ADAMTS12 gene expression with plumage coloration in Muscovy ducks.

To elucidate the molecular genetic mechanisms underpinning feather color in Muscovy ducks. A cohort of 100 Muscovy ducks was meticulously selected for this research. Follicular tissues from ducks exhibiting black and white plumage served as the experimental samples. From these tissues, RNA and proteins were extracted for further analysis. The RNA underwent reverse transcription polymerase chain reaction amplification, followed by validation through western blot assays. The data revealed a significant upregulation in the expression of FN domain-containing protein 1 (FNDC1) and ADAMTS12 genes in Muscovy ducks with white plumage traits as opposed to those with black plumage traits. Specifically, individuals with pure white plumage demonstrated a markedly elevated expression of the FNDC1 gene in comparison to their pure black counterparts. Conversely, expression levels of the ADAMTS12 gene were found to be reduced in ducks with pure black plumage relative to those with pure white plumage. Notably, the expression patterns of FNDC1 and ADAMTS12 genes exhibited inconsistencies between mRNA and protein levels. This study offers significant insights into the molecular genetic mechanisms underlying feather color variation in Muscovy ducks. FNDC1 and ADAMTS12 could be considered potential targets for genetic manipulation or selective breeding strategies aimed at achieving specific feather color phenotypes in Muscovy ducks.

Ongoing introgression of a secondary sexual plumage trait in a stable avian hybrid zone.

Hybrid zones are dynamic systems where natural selection, sexual selection, and other evolutionary forces can act on reshuffled combinations of distinct genomes. The movement of hybrid zones, individual traits, or both are of particular interest for understanding the interplay between selective processes. In a hybrid zone involving two lek-breeding birds, secondary sexual plumage traits of Manacus vitellinus, including bright yellow collar and olive belly color, have introgressed ~50 km asymmetrically across the genomic center of the zone into populations more genetically similar to Manacus candei. Males with yellow collars are preferred by females and are more aggressive than parental M. candei, suggesting that sexual selection was responsible for the introgression of male traits. We assessed the spatial and temporal dynamics of this hybrid zone using historical (1989-1994) and contemporary (2017-2020) transect samples to survey both morphological and genetic variation. Genome-wide single nucleotide polymorphism data and several male phenotypic traits show that the genomic center of the zone has remained spatially stable, whereas the olive belly color of male M. vitellinus has continued to introgress over this time period. Our data suggest that sexual selection can continue to shape phenotypes dynamically, independent of a stable genomic transition between species.

Extreme elevational migration spurred cryptic speciation in giant hummingbirds

The ecoevolutionary drivers of species niche expansion or contraction are critical for biodiversity but challenging to infer. Niche expansion may be promoted by local adaptation or constrained by physiological performance trade-offs. For birds, evolutionary shifts in migratory behavior permit the broadening of the climatic niche by expansion into varied, seasonal environments. Broader niches can be short-lived if diversifying selection and geography promote speciation and niche subdivision across climatic gradients. To illuminate niche breadth dynamics, we can ask how "outlier" species defy constraints. Of the 363 hummingbird species, the giant hummingbird (Patagona gigas) has the broadest climatic niche by a large margin. To test the roles of migratory behavior, performance trade-offs, and genetic structure in maintaining its exceptional niche breadth, we studied its movements, respiratory traits, and population genomics. Satellite and light-level geolocator tracks revealed an >8,300-km loop migration over the Central Andean Plateau. This migration included a 3-wk, ~4,100-m ascent punctuated by upward bursts and pauses, resembling the acclimatization routines of human mountain climbers, and accompanied by surging blood-hemoglobin concentrations. Extreme migration was accompanied by deep genomic divergence from high-elevation resident populations, with decisive postzygotic barriers to gene flow. The two forms occur side-by-side but differ almost imperceptibly in size, plumage, and respiratory traits. The high-elevation resident taxon is the world's largest hummingbird, a previously undiscovered species that we describe and name here. The giant hummingbirds demonstrate evolutionary limits on niche breadth: when the ancestral niche expanded due to evolution (or loss) of an extreme migratory behavior, speciation followed.

Färgvariation hos vattenpiplärka Anthus spinoletta i vinterdräkt

This study of colour variation on Water Pipit Anthus spinoletta in winter plumage, is based on photos of 93 individuals from southern Sweden. Using moulting criteria, the birds were aged from the photographs, and the presence or absence of five specific plumage characteristics were recorded. Twelve individuals in this study confirm the hypothesis that adult Water Pipits show a distinct combination of plumage traits during winter. However, the presence of these plumage traits varied in younger birds in their first winter plumage. Among the 81 individuals classified as first winter plumage, 23 (28%) displayed all “adult characteristics”, 32 (40%) one to four of the characteristics, while 26 (32%) lacked all “adult characteristics”. The latter group thus lacked a gray nape/crown, whitish supercilium, and lighter brown colouration of the mantle/scapulars. Ever since the first Swedish records in the mid-1990s, there have been ongoing discussions regarding species-specific characters in Water Pipits. The present quantification of colour variation in different age groups complements previous criteria for a reliable species identification of Water Pipits in winter plumage.

Abnormal Feather Phenotype Associated with a Fatal Stress Response and Unusual Tolerance to Human Contact in the Zebra Finch (Taeniopygia castanotis).

The zebra finch (Taeniopygia castanotis) is a songbird sold in the pet trade and commonly used in research. In this report, we describe a set of partially overlapping traits shared by 3 birds in 2 broods from the same nest box that included atypical morphologic, developmental, and behavioral characteristics. The most obvious feature of this novel phenotype was feathers exhibiting a clumped appearance, which was accompanied by slow growth, delayed expression of adult plumage traits, and tameness, which we define as a lack of escape response upon handling without behavioral indicators of stress such as rapid breathing. Surprisingly, these birds also displayed a fatal response to nonhuman stressors. In one brood, a male expressed all of these characteristics, 2 females were wild-type, and a male sibling expressed only a hyperactive stress response but was otherwise normal. This indicates that the stress response could be inherited independently of the other abnormalities found in the male nest mate. In a second brood, a male bearing the abnormal feather phenotype behaved similarly to the male in the first brood, supporting the possibility that tameness is genetically associated with the unusual feather phenotype. The 2 other male and 2 female nest mates from this brood were behaviorally and visually normal, although the females developed slowly. Although similar traits have appeared in the aviary previously, such as slow development and small size, these are the first cases documented in detail. This correlated suite of traits suggests a linkage among altered feather growth, developmental rate, and brain and/or physiologic traits influencing normal fear and stress responses in the zebra finch. Awareness and study of the mechanism(s) linking these traits by examination of underlying genetic or environmental factors will allow a better understanding of the relationship between physical and behavioral traits in domesticated laboratory animals.

When colors mislead: Genomics and bioacoustics prompt re-classification of Asian flycatcher radiation (Aves: Niltavinae)

Traditional classification of many animals, including birds, has been highly dependent on external morphological characters like plumage coloration. However, both bioacoustics and genetic or genomic data have revolutionized our understanding of the relationships of certain lineages and led to sweeping taxonomic re-organizations. In this study, we present a case of erroneous delimitation of genus boundaries in the species-rich flycatcher subfamily Niltavinae. Genera within this subfamily have historically been delineated based on blue versus brown male body plumage until recent studies based on a few mitochondrial and nuclear loci unearthed several cases of generic misclassification. Here we use extensive bioacoustic data from 43 species and genomic data from 28 species for a fundamental reclassification of species in the Niltavinae. Our study reveals that song is an important trait to classify these birds even at the genus level, whereas plumage traits exhibit ample convergence and have led to numerous historic misattributions. Our taxonomic re-organization leads to new biogeographic limits of major genera, such that the genus Cyornis now only extends as far east as the islands of Sulawesi, Sula, and Banggai, whereas Eumyias is redefined to extend far beyond Wallace’s Line to the islands of Seram and Timor. Our conclusions advise against an over-reliance on morphological traits and underscore the importance of integrative datasets.

Digest: Understanding the evolution of sexual dichromatism also requires a female perspective.

The study of sexual dichromatism has generally focused on sexual selection for conspicuous males, ignoring the potential role played by selection in females. To address this problem, Price et al. took into account evolutionary changes in both males and females when investigating the evolution of plumage dichromatism across the New World blackbirds (Icteridae). They found that sexual dichromatism was repeatedly and rapidly lost as females evolved male-like plumage traits. The evolutionary dynamics in plumage coloration were drastically different in males and females, highlighting the importance of considering both perspectives in trait evolution.

Stabilizing selection on a plumage-based foraging adaptation: hooded warblers with average-sized white tail spots live longer.

Avian flush-pursuit insectivores typically use contrasting white plumage patches in their tails or wings to startle potential prey. Although experimental evidence indicates that the extent of white has been fine-tuned by natural selection to optimize foraging performance, the hypothesis that within-population plumage variation directly influences survival or lifetime reproduction and is subject to stabilizing selection has not been tested. Here, I provide such a test using data collected as part of a 14-year study of a colour-ringed breeding population of the hooded warbler (Setophaga citrina), a migratory flush-pursuit insectivore that shows inter-individual variation in the extent of white in the tail that is highly repeatable across moults and probably heritable. As expected under stabilizing selection, warblers with average-sized white tail patches achieved significantly higher apparent long-term survival than individuals with either a lesser or greater extent of white in the tail. Evidence of stabilizing selection was especially strong in males, an observation that is probably related to pronounced sexual habitat segregation on the wintering range. My results provide infrequently observed evidence of stabilizing selection operating in a natural population, and also illustrate how stabilizing selection can act on avian plumage traits outside the context of sexual and social signalling.

Phenotypic characterization and genetic diversity of indigenous chickens of Jordan in comparison with native and commercial breeds ‎for conservation and breeding purposes

Indigenous chickens of Jordan are facing extinction and need genetic conservation because they were unable to commercially compete in poultry industry because of low genetic ability ‎compared to commercial layers. The study aimed to investigate phenotypic and genetic diversity ‎of village chickens in the Jordan using discriminant analyses procedures to provide a basis for ‎sustainable genetic conservation and utilization program to overcome any possible extinction. The ‎sampled chicken population of 578 one-year old chickens (125 males and 433 females) was ‎phenotypically characterized for 15 biometric and plumage traits from major cities of the three ‎regions; Middle, North, and South. The traits variations within and between breeds were detected ‎statistically by stepwise discriminant and canonical-discriminant of uni- and multivariate analyses. ‎The results showed the sampled population as village chickens in Jordan is comprised of ‎indigenous (Baladi) breed (85%) and few exotic and commercial breeds. The breeds were distinct ‎and differentiated based on phenotypic traits indicating high genetic variability. The major ‎phenotypic traits that showed significant power to differentiate breeds were comb type, body ‎weight, comb size, earlobe color, wattle size, face color and breast size in males and comb type and ‎size, body weight, face and breast size, leg color and wattle size in females. Recent and past ‎crossings, admixture or migration from exotic and commercial breeds were noted. Moreover, low ‎levels of phylogeographic structure were observed across the studied breeds. In conclusion, there is need to conserve the indigenous breed in situ and in vivo for its adaptive gene pool in coming ‎days of persisted climate change and diseases threats.

Urbanisation impacts plumage colouration in a songbird across Europe: Evidence from a correlational, experimental and meta-analytical approach.

Urbanisation is accelerating across the globe, transforming landscapes, presenting organisms with novel challenges, shaping phenotypes and impacting fitness. Urban individuals are claimed to have duller carotenoid-based colouration, compared to their non-urban counterparts, the so-called 'urban dullness' phenomenon. However, at the intraspecific level, this generalisation is surprisingly inconsistent and often based on comparisons of single urban/non-urban populations or studies from a limited geographical area. Here, we combine correlational, experimental and meta-analytical data on a common songbird, the great tit Parus major, to investigate carotenoid-based plumage colouration in urban and forest populations across Europe. We find that, as predicted, urban individuals are paler than forest individuals, although there are large population-specific differences in the magnitude of the urban-forest contrast in colouration. Using one focal region (Malmö, Sweden), we reveal population-specific processes behind plumage colouration differences, which are unlikely to be the result of genetic or early-life conditions, but instead a consequence of environmental factors acting after fledging. Finally, our meta-analysis indicates that the urban dullness phenomenon is well established in the literature, for great tits, with consistent changes in carotenoid-based plumage traits, particularly carotenoid chroma, in response to anthropogenic disturbances. Overall, our results provide evidence for uniformity in the 'urban dullness' phenomenon but also highlight that the magnitude of the effect on colouration depends on local urban characteristics. Future long-term replicated studies, covering a wider range of species and feeding guilds, will be essential to further our understanding of the eco-evolutionary implications of this phenomenon.

Variability of a consistent trait: The size of the white wing patch in European Stonechats (Saxicola rubicola rubicola)

Numerous bird species exhibit striking white patches on their plumages that have been reported as signals of individual quality in the context of sexual selection. Whereas differences in white plumage traits between individuals have been well studied, phenotypic variation and the factors affecting their consistency within the individual have received less attention. Here, we studied the consistency in the size of the white wing patch and its components of variation in a Spanish population of European Stonechats Saxicola rubicola rubicola monitored over 6 years (2007–2012). The wing patch was larger in males than in females for all age‐classes, and first‐year individuals exhibited smaller wing patches than older birds, particularly males. This trait also varied within the plumage‐year at both population and individual level, with slight changes from the moulting period to the breeding season and a sharp decrease afterwards. In addition, patch size varied both between and within individuals across years. The daily mean temperature experienced in the month immediately prior to the moult (i.e. May) had a positive effect on male wing patch size. In females, however, no variable was found to explain wing patch variation satisfactorily. Despite being a dynamic trait throughout the moults, baseline and adjusted repeatabilities indicated a moderately high consistency for white wing patch size in both sexes. Therefore, the white wing patch in Stonechats is a dynamic trait that changes throughout individuals' lives, but is also a consistent trait at the individual level. These results indicate that this depigmented patch could convey information about both the long‐term quality and the current state of individuals, harmonizing the existence of intra‐individual changes in the size of sexual traits with its potential role as a genetic quality indicator.

Community-sourced sightings of atypical birds can be used to understand the evolution of plumage color and pattern

AbstractBirds are known for their brilliant colors and extraordinary patterns. Sightings of individuals with atypical plumage often cause considerable excitement in the birding public, but receive little attention beyond reporting one-off sightings by the scientific community. In this Perspective, we argue that sightings of individuals with atypical plumage submitted to community science platforms hold the potential to further our understanding of the evolution of plumage color and patterning in birds. As a demonstration, we outline two examples using sightings of leucistic individuals—those that lack melanin across the body or in certain feather patches. First, we discuss the potential for understanding carotenoid pigmentation with these sightings. Leucism influences melanins, but not carotenoids, and so the extent and distribution of carotenoids across the body are unmasked. In a leucistic individual, carotenoids may or may not be more extensive than what is typically visible and this could help to understand the energetic costs and constraints involved in obtaining, processing, and depositing carotenoids in different species. Second, we discuss how partial leucism could provide insights into plumage pattern evolution. We demonstrate that one can use the many observations present on community science platforms to identify repeated patterns in different partially leucistic individuals of the same species, and match these to patches present in related species. These patterns could be the result of shared underlying genetic variation that controls plumage patterning in birds over long evolutionary timescales. With these examples, we outline a few potential lines of inquiry possible with atypical sightings submitted to community science platforms and note that other plumage aberrations provide additional opportunities. We encourage researchers to take full advantage of these chance sightings when they occur and database managers to make it possible to more easily tag photos of individuals with atypical plumage or other traits.

Functions of avian elongated tails, with suggestions for future studies

Elongated tails are elaborate plumage traits possessed by a variety of bird species. Sexual selection has long been the dominant hypothesis for explaining why certain species possess such long tails. During the past three decades, however, alternative hypotheses have been proposed and tested. Here, we review evidence, and the lack thereof, for four hypothesised functions of elongated tails in birds: sexual selection, aerodynamic enhancement, anti‐predation signalling and perch balancing. Sexual selection has received the most attention, though with inconsistent support. The other three hypothesised functions, in contrast, have gained less attention, with perch balancing remaining largely speculative. After reviewing and synthesizing information about these functions, we show that our current knowledge of avian elongated tails is not comprehensive. To advance our understanding of this topic, we suggest (1) devising a uniform definition of elongated tails that can be applied to a wide variety of bird species, (2) further investigation of less‐studied functions of such tails, (3) conducting meta‐analyses to discover the origins and trait correlates of elongated tails, (4) considering the possibility that elongated tails serve multiple functions simultaneously, and (5) testing unexplored functions of elongated tails.

Extra‐pair paternity is not repeatable between years in Pied Flycatchers (Ficedula hypoleuca): a role for social context

Extra‐pair paternity (EPP) is the consequence of the interactions between a social pair and extra‐pair males during the female's fertile phase in a specific social context and ecological environment. Although EPP occurs in many avian species, there is a lack of understanding of how environmental factors may impact its frequency. Accordingly, the relative importance of individual characteristics on the one hand, and of their immediate social environment on the other, may affect EPP repeatability and thereby the capacity of this trait to respond to selection. If EPP is an individual genetically based trait that may respond to selection, we expect it to be repeatable across breeding seasons. To check this possibility, we analysed the within‐individual repeatability in EPP of breeding males and females in two natural populations of Pied Flycatchers Ficedula hypoleuca in central Spain during three field seasons. We then studied the relationship between EPP and individual male and female traits (only some of which were themselves repeatable), as well as key context variables such as breeding synchrony and population density. Our results showed no repeatability for EPP in either sex. We found a positive association with laying date and stronger associations of EPP with male plumage and morphological traits than with female characteristics. We suggest that the variable social environment is an important modulator of EPP patterns, and that differences between field EPP studies in this respect may explain contradictory results in the same species, even in the same populations in different years.

Genetic fine-mapping reveals single nucleotide polymorphism mutations in the MC1R regulatory region associated with duck melanism.

Birds are among the most colourful terrestrial vertebrates, with various plumage colours and patterns. We conducted a genome-wide association study (GWAS) on an intercross F2 population of Pekin ducks and mallards (n=722) and identified a 1.57-Mb genetic region (Chr11: 20,176,480-21,750,101 bp) related to duck melanism. Fine mapping by linkage disequilibrium (LD) and FST analysis narrowed the final candidate region to a region of 22,500 bp (Chr11: 20,677,500-20,700,000 bp) including three coding genes, TCF25, MC1R and TUBB3. Combined with transcriptome and qRT-PCR analysis, MC1R was identified as the unique genetic locus responsible for black plumage in ducks, and it was significantly more highly expressed in the feather bulbs of black ducks. We also identified 52G > A (Chr11: 20,696,354G > A) and 376G > A (Chr11: 20,696,678G > A) mutations in the MC1R coding region that have been widely studied in ducks. In addition, structural variations (SVs) were screened by nanopore sequencing, and no significant SV was found to be associated with the duck black plumage trait. However, we identified four novel single nucleotide polymorphisms in the MC1R regulator region (Chr11: 20,678,412G > A, Chr11: 20,679,236G > A, Chr11: 20,692,496 A > G and Chr11: 20,692,791 A > G) that had a strong association with the black plumage phenotype of ducks and combined with potential changes in transcription binding affinities. The luciferase reporter gene assay demonstrated that Chr11: 20,678,412G > A and Chr11: 20,679,236G > A led to significant promoter activity changes. Our research emphasizes the importance of MC1R regulatory region mutation in determining the duck black plumage phenotype, and these results expand our understanding of the genetic mechanism underlying duck plumage colour.