Coat Color Research Articles

Genome-based analysis of the genetic pattern of black sheep in Qira sheep

ObjectiveBlack wool can effectively prevent sheep from DNA damage as well as fungal infection, and can improve reproductive performance. In order to explore the candidate genes related to black wool formation in Qira sheep.MethodsWe selected 123 adult healthy ewes with different coat colors in Qira sheep groups (black (B), brown (Y) and grey (G)) and extracted DNA from their venous blood to obtain Illumina Ovine SNP 50K chip data. Subsequently, our PCA, NJ-tree, and Admixture population structure analyses of the 3 wool color Qira sheep populations showed that the 3 middle wool color populations exhibited the same genetic traits. Fst, xp-EHH, iHS, and π were detected for selection signals, and the 5% SNPs loci positively selected from the analyses were annotated based on SheepOar_v4.0. The region of exon 1 of the TYRP1 gene was further screened, amplified and sequenced through the DNA of the Qira sheep and associated with goodness-of-fit using the chi-square test.ResultsThe results showed that 71 SNPs associated with black wool traits, among which TYRP1, PARD3 and CDH2 genes were strongly associated with black wool production. Three mutations were detected in the exon 1 region of the TYRP1 gene that were significantly associated with coat color variation inQira sheep (2:81,183,168, 2:81,183,281 and 2:81,183,284).ConclusionIn this paper, Qira sheep could not differentiate the genetic structure of this population by wool color, and obtained 71 SNPs related to black wool. Detection of mutation sites on the TYRP1 gene affecting hair color change provides a basis for black sheep line selection as well as breed conservation.

Resequencing Composite Kazakh Whiteheaded Cattle: Insights into Ancestral Breed Contributions, Selection Signatures, and Candidate Genetic Variants

This study investigates the genetic architecture of the Kazakh Whiteheaded (KWH) cattle, applying population genetics approaches to resequenced genomes. FST analysis of 66 cattle breeds identified breeds for admixture analysis. At K = 19, the composite KWH breed showed contributions from Hereford, Altai, and Kalmyk cattle. Principal component analysis and ancestry inference confirmed these patterns, with KWH genomes comprising 45% Hereford, 30% Altai, and 25% Kalmyk ancestries. Haplotype analysis revealed 73 regions under putative selection in KWH, some shared with Hereford (e.g., with the gene DCUN1D4) and some KWH-specific (e.g., with the gene SCMH1). FST analysis identified 105 putative intervals under selection, with key genes (KITLG, SLC9C1, and SCMH1) involved in coat colour and physiological adaptations. Functional enrichment using The Database for Annotation, Visualization, and Integrated Discovery (DAVID) in selected regions highlighted clusters associated with developmental processes, ubiquitination, and fatty acid metabolism. Point FST identified 42 missense variants in genes enriched in functions related to economically important traits. Local ancestry inference revealed genomic intervals with predominantly non-Hereford ancestry, including high Altai (e.g., SCAPER) and Kalmyk (e.g., SRD5A2) contributions, while Hereford-dominated regions included genes ENO1 and RERE. This work elucidates the genomic contributions and adaptive signatures of selection shaping the KWH breed, providing candidate genetic variants for breeding program improvement and enhanced genome predictions.

Genome-wide association scan and candidate gene analysis for seed coat color in sesame (Sesamum indicum L.)

IntroductionSeed coat color in sesame is a crucial trait for breeding programs as it is closely associated with important characteristics such as oil content, protein levels, and disease resistance, which directly influence seed quality and market value.MethodsThis study investigates the genetic basis of seed coat color in 200 Sudanese sesame genotypes grown for two consecutive years through comprehensive phenotyping, genomic diversity analysis, genome-wide association studies (GWAS), and candidate gene discovery.Results and discussionPhenotypic analysis across two growing seasons revealed high heritability and significant correlations among color parameters (L*, a*, and b*), indicating strong genetic control over seed coat color. The genomic analysis identified distinct clusters among sesame accessions, with rapid linkage disequilibrium decay suggesting a high level of recombination. GWAS identified significant SNPs associated with seed coat color traits, revealing key genomic regions on chromosomes 3, 6, 9, 12, and 13. Candidate gene analysis highlighted several genes, including DOF zinc finger proteins and WRKY transcription factors, which may play essential roles in pigment biosynthesis pathways. These findings provide valuable insights for breeding programs to enhance desirable seed coat color traits in sesame.

Evaluation of phenotypic risk indicators for the development of alopecia X (hair cycle arrest) in Pomeranian dogs in the Netherlands and Belgium.

Alopecia X (AX) is a common noninflammatory alopecic condition of Pomeranian dogs with an unknown cause. While a genetic aetiology is suspected, no current tests can predict the development of this disorder or confirm the aetiology. Therefore, identifying potential risk indicators for the development of AX would be of value in this breed. This study aimed to identify risk indicators for AX in Pomeranians in the Netherlands and Belgium. A retrospective epidemiological study was conducted in the Netherlands and the Dutch-speaking parts of Belgium between March 2022 and August 2023, using an online survey of Pomeranian owners. Variables such as sex, birth season, neutering status, coat type, coat colour, grooming frequency and whether the dog experienced an 'ugly stage' of hair coat growth or not were recorded, along with the presence or absence of alopecia and the age of onset of the condition. Of 234 completed surveys, 211 were eligible for analysis. Statistical analysis with a Cox proportional-hazard model indicated that the risk of developing alopecia was greater for a woolly versus shiny coat and for males versus females. A woolly hair coat type and male sex were identified as risk indicators for developing AX in Pomeranian dogs in this study.

Unveiling the genetic potential and diversity of rice landraces for grain Fe content

Addressing micronutrient deficiency is increasingly recognized as a critical aspect of food and nutrition security in developing nations. Leveraging diverse genetic resources offers a promising avenue for identifying and enhancing micronutrient-rich genotypes through breeding strategies, thus providing sustainable solutions to this pressing challenge. The study aimed to identify rice genotypes with high Fe content and to study the extent of genetic divergence based on morphological and grain quality traits in a set of 50 native rice landraces over 2 different locations. A wide range of variation for grain Fe content was observed among the studied genotypes, which varied from 9.28–14.45 mg kg-1 and 1.88–4.87 mg kg-1 in brown and polished rice respectively. Results showed that the genotypes Jaya, Kalanamak, Kottara Samba, Gandakasala and Gopalbhog recorded high grain Fe content before polishing whereas Kottara Samba, Kalapathi Black, Jyothi, Chinnar and Kalanamak were found to have high Fe content after polishing. Interestingly, landraces possessing red seed coat color and medium slender grain group were identified to possess high grain Fe content. This was further substantiated by the correlation study where kernel breadth recorded a negative association with Fe content after polishing. Clustering resulted in 5 groups where the high Fe content possessing genotypes were grouped into clusters 2 and 4. Thus, these genotypes could be utilized as donors in further bio-fortification breeding programs.

Morphological diversity variation of seed traits among 587 germplasm resources of Medicago Genus and 32 germplasm resources of Trigonella Genus

Germplasm resources within the Medicago genus are highly regarded for their value as forage crops and their critical roles in nitrogen cycling, ecosystem restoration, and soil structure improvement. Therefore, understanding the diversity of seed morphology in this genus is essential for advancing its development and utilization. This study analyzed seed samples from 587 germplasm accessions representing 77 species within Medicago genus, as well as 32 accessions from 21 species within the closely related genus Trigonella. A statistical analysis was conducted on twelve traits, including seven quantitative traits-straight length (SL), straight width (SW), width-to-length ratio (WL), perimeter (PE), radicle length (RL), hilum length (HL), and 100-seed weight (SY)-and five qualitative traits, including seed coat condition, radicle characteristics, seed size, shape, and color. The results revealed that: (1) there was significant diversity (P < 0.05) in SL, SW, WL, PE, RL, HL, and SY across Medicago species; (2) principal component analysis of the 587 Medicago accessions identified SL, SW, PE, HL, RL, and SY as the primary contributors to morphological diversity; and (3) high-resolution images of seeds from various accessions were captured for future research. This study provides a solid foundation for the establishment of seed banks and the enhancement of germplasm resources through the systematic analysis of these morphological traits.

Genomic insights into genetic diversity and seed coat color change in common bean composite populations

IntroductionThe color of the seed coat of common bean (Phaseolus vulgaris L.) is an important trait influencing marketability and consumer preferences. An understanding of the genetic mechanisms underlying seed coat color variation can aid in breeding programs aimed at improving esthetic and agronomic traits. This study investigates the genetic diversity and molecular mechanisms associated with seed coat color change in composite bean populations through phenotypic analysis and whole genome sequencing (WGS).MethodsFour composite populations and two standard varieties of common bean were cultivated over a two-year period and seed coat color and morphological traits were assessed. WGS was performed on 19 phenotypes and yielded 427 GB of data with an average sequencing depth of 30×. More than 8.6 million high-confidence single nucleotide polymorphisms (SNPs) were identified. Genetic diversity metrics such as nucleotide diversity (π), observed heterozygosity (Ho), expected heterozygosity (He) and allelic richness (Ar) were calculated. Population structure was analyzed using Fst, principal component analysis (PCA) and clustering. Cross-population statistics (XP-CLR and XP-EHH) were used to identify selection signals associated with seed coat color change. Gene Ontology (GO) and KEGG enrichment analyzes were performed for candidate genomic regions.ResultsPhenotypic analysis revealed significant differences in seed coat color among the four composite populations, with notable changes among years. The populations exhibited different growth habits and plant types, especially KIS_Amand and SRGB_00366, which showed the highest phenotypic diversity in seed coat color. WGS identified 8.6 million SNPs, with chromosomes 4 and 1 having the highest SNP density (11% each), while chromosomes 3 and 6 had the lowest. KIS_Amand had the highest genetic diversity (π = 0.222, Ar = 1.380) and SRGB_00189 the lowest (π = 0.067, Ar = 1.327). SRGB_00366 showed moderate genetic diversity (π = 0.173, Ar = 1.338) and INCBN_03048 showed medium diversity (π = 0.124, Ar = 1.047). The Fst values indicated a strong genetic differentiation, especially between the two standard varieties ETNA and Golden_Gate (Fst = 0.704) and the composite populations. Selective sweep analysis with XP-CLR and XP-EHH identified 118 significant regions associated with seed coat color change, with most regions located on chromosomes 4, 9, 10 and 11. Phosphatidylinositol signaling pathways were highly enriched in candidate regions, indicating that cellular transport mechanisms play a critical role in seed coat pigmentation. Key GO terms included phosphatidylinositol-biphosphate binding, exocytosis, and vesicle-mediated transport, suggesting a link between cellular transport and pigment deposition in the seed coat.DiscussionThe study demonstrates significant genetic diversity within and among common bean composite populations, with KIS_Amand and SRGB_00366 exhibiting the highest phenotypic and genetic variability. The identification of selective sweeps and the enrichment of phosphatidylinositol-related pathways provide new insights into the molecular mechanisms controlling seed coat color variation. The strong genetic differentiation between standard varieties and composite populations highlights the role of selective breeding in shaping the genetic landscape of common bean. The results suggest that variation in seed coat color is controlled by both regulatory and structural genetic changes, providing valuable information for breeding programs.ConclusionThis study provides a detailed analysis of the genetic architecture of seed coat color variation in common bean. The identification of key genomic regions and pathways associated with seed pigmentation improves our understanding of the complex genetic interactions underlying this trait. These results provide valuable genomic resources for future breeding efforts aimed at improving seed color and other important traits in common bean.

PSC1, a basic/helix-loop-helix transcription factor controlling the purplish-red testa trait in peanut.

Seed color is a key agronomic trait in crops such as peanut, where it is a vital indicator of both nutritional and commercial value. In recent years, peanuts with darker seed coats have gained market attention due to their high anthocyanin content. Here, we used bulk segregant analysis to identify the gene associated with the purplish-red coat trait and identified a novel gene encoding a basic/helix-loop-helix transcription factor,PURPLE REDSEEDCOAT1 (PSC1), which regulates the accumulation of anthocyanins in the seed coat. Specifically, we found that a 35-bp insertion in the PSC1 promoter increased the abundance of PSC1 mRNA. Transcriptomic and metabolomic analyses indicated that the purplish-red color of the seed coat was the result of decreased expression of anthocyanidin reductase (ANR), leading to increased accumulation of delphinidin, cyanidin, and pelargonidin derivatives. Further analysis revealed that PSC1 interacts with AhMYB7 to form a complex that specifically binds to the ANR promoter to suppress its expression, resulting in increased anthocyanin accumulation. Moreover, overexpression of PSC1 increased anthocyanin content in Arabidopsis thaliana and peanut callus. Our study reveals a new gene that controls seed coat color by regulating anthocyanin metabolism and provides a valuable genetic resource for breeding peanuts with a purplish-red seed coat.

Genomic signatures of selection in Brangus cattle revealing the genetic foundations of adaptability and production traits using a breed of origin approach

IntroductionThe composite breed Brangus combines the resilience and adaptability of the Bos t. indicus breed Brahman with the superior meat quality and fertility traits of the Bos t. taurus breed Angus. Its diverse genetics not only enables optimal production performance but also adaptability to hot and humid environmental conditions. From a research perspective, this makes Brangus an ideal model for identifying genomic signatures that reveal the effects of both artificial selection and natural adaptation. The aim of this study was to detect genomic signatures of selection by analyzing changes in breed origin of allele (BOA) frequencies across the genome.MethodsUsing a multi-breed Angus and Brahman herd (n = 4,516) as a reference, population structure was measured via principal component analysis and admixture analysis in two commercial Brangus herds (n = 4,720). BOA was estimated in these herds using LAMP-LD, followed by a signature of selection analysis utilizing a median-based Z-score approach and Fst analyses to detect genomic regions under selection.ResultsThe analysis revealed a genome-wide increase in Angus ancestry in both Brangus populations (71.46%, 68.7%), reflecting intense selection for traits associated with this lineage. BOA-based intra- and inter-population analyses identified significant shifts in Brahman and Angus ancestry across the genome, indicating potential selection for breed-specific genetics. Key genomic regions were identified on chromosomes 6, 8, 10, 12, 14, 17, 18, 19, 27, and 28, and were linked to traits such as fertility, growth, heat tolerance, carcass characteristics, and meat quality.DiscussionExpected genes showing signatures of selection included MC1R, responsible for black coat color, and PLAG1, integral to growth, fertility, and carcass traits, underscoring the effectiveness of this methodology. Novel genes under selection, such as CCNB2 (critical for fertility), MTCH2 (associated with meat quality and fertility) and PRLR (associated with coat length and heat tolerance), were also identified. These findings provide deeper insights into the genetic mechanisms driving adaptation and production performance in cattle and offer valuable information for strategic breeding practices aimed at optimizing the strengths of both parental breeds.

Classical and machine learning tools for identifying yellow-seeded Brassica napus by fusion of hyperspectral features.

Due to its favorable traits-such as lower lignin content, higher oil concentration, and increased protein levels-the genetic improvement of yellow-seeded rapeseed has attracted more attention than other rapeseed color variations. Traditionally, yellow-seeded rapeseed has been identified visually, but the complex variability in the seed coat color of Brassica napus has made manual identification challenging and often inaccurate. Another method, using the RGB color system, is frequently employed but is sensitive to photographic conditions, including lighting and camera settings. We present four data-driven models to identify yellow-seeded B. napus using hyperspectral features combined with simple yet intelligent techniques. One model employs partial least squares regression (PLSR) to predict the R, G, and B color channels, effectively distinguishing yellow-seeded varieties from others according to globally accepted yellow-seed classification protocols. Another model uses logistic regression (Logit-R) to produce a probability-based assessment of yellow-seeded status. Additionally, we implement two intelligent models, random forest and support vector classifier to evaluate features selected through lasso-penalized logistic regression. Our findings indicate significant recognition accuracies of 96.55% and 98% for the PLSR and Logit-R models, respectively, aligning closely with the accuracy of previous methods. This approach represents a meaningful advancement in identifying yellow-seeded rapeseed, with high recognition accuracy demonstrating the practical applicability of these models.

Genetic diversity of kaffir sorghum accessions from the VIR collection in kafirin-encoding loci

Background. Sorghum is a universal, highly drought-resistant crop, widely cultivated throughout the world. Sorghum grain has a valuable biochemical composition and is utilized in both food and feed production. Due to the unique structure of endosperm storage proteins, kafirins, adding sorghum flour to dough is promising for producing dietetic nutrition components. Employing polymorphic DNA markers to study the diversity of kaffir sorghum accessions from the VIR collection as potential donors of biological and morphological traits in their grain is relevant for the development of sterile lines and sterility maintainers.Materials and methods. Sixteen kaffir sorghum accessions were phenotyped according to morphological features and kafirin electrophoretic banding patterns in their grain, and genotyped using PCR markers specific for kafirin-encoding genes. The phenotype of mature grains was assessed by seed coat color as well as by the thickness ratio between the vitreous and farinaceous endosperm layers on grain cuts. Proteins were fractionated by polyacrylamide gel electrophoresis. The SSR markers linked to the genes for β- and γ-kafirins, and the STS marker of the coding region of the δ-kafirin gene were used in the PCR analysis.Results and conclusions. The studied accessions differed in grain color and endosperm structure. Three accessions demonstrated a significant thickness of the vitreous layer, while the others had a farinaceous or partially vitreous endosperm. No differences were found among the accessions in the kafirin electrophoretic banding patterns. Meanwhile, the accessions manifested highly polymorphic fragments amplified with primers flanking microsatellite sequences linked to the β- and γ-kafirin genes. Two different versions of the STS marker were detected after amplification with the primers specific to the δ-kafirincoding gene region. The studied accessions were differentiated using the principal coordinates analysis (PCoA).

Effect of Friesian Dairy Cows’ Coat Color on Their Productive Performance under Heat Stress Conditions

Effect of Friesian Dairy Cows’ Coat Color on Their Productive Performance under Heat Stress Conditions

Bambara groundnut [Vigna subterranea (L.) Verdc.] genetic diversity and population structure assessed through next‐generation sequencing technologies: Restriction‐site‐associated DNA sequencing

AbstractThe importance of underutilized crops in the diversification of diets for both humans and animals, among other uses, has been highlighted in literature in recent times. Underutilized crops are especially important because of their potential to provide nutrient‐packed, climate‐resilient, and sustainable farming practices. One such crop is Bambara groundnut [Vigna subterranea (L.) Verdc], whose genetic potential has not been afforded sufficient research attention. For most of the rural areas in Sub‐Saharan Africa, it is a great source of food and income and is most valued for its nutrient richness and ability to thrive in marginal land. However, farmers grapple with the lack of high agronomic quality seeds where production of the crop is concerned. The aim of this study was to establish an easy basis for selecting seeds that are of favorable agronomic potential by assessing whether a singular characteristic (seed coat color) was sufficient to group landraces. Restriction‐site‐associated DNA (RAD) sequencing was used for the first time to assess the genetic variations and/or similarities in 48 Bambara groundnut landraces. The findings revealed that there are two populations that are genetically variable among the chosen 48 landraces; however, these variations were not as a result of a singular morphological attribute. Therefore, farmers cannot use coat color alone to select for landraces that are of better agronomic quality.

Identifying Candidate Genes Related to Soybean (Glycine max) Seed Coat Color via RNA-Seq and Coexpression Network Analysis.

The quality of soybeans is reflected in the seed coat color, which indicates soybean quality and commercial value. Researchers have identified genes related to seed coat color in various plants. However, research on the regulation of genes related to seed coat color in soybeans is rare. In this study, four lines of seed coats with different colors (medium yellow 14, black, green, and brown) were selected from the F2:5 population, with Beinong 108 as the female parent and green bean as the male parent, and the dynamic changes in the anthocyanins in the seed coat were stained with 4-dimethylaminocinnamaldehyde (DMACA) during the grain maturation process (20 days from grain drum to seed harvest). Through RNA-seq of soybean lines with four different colored seed coats at 30 and 50 days after seeding, we can further understand the key pathways and gene regulation modules between soybean seed coats of different colors. DMACA revealed that black seed coat soybeans produce anthocyanins first and have the deepest staining. Clustering and principal component analysis (PCA) of the RNA-seq data divided the eight samples into two groups, resulting in 16,456 DEGs, including 5359 TFs. GO and KEGG enrichment analyses revealed that the flavonoid biosynthesis, starch and sucrose metabolism, carotenoid biosynthesis, and circadian rhythm pathways were significantly enriched. We also conducted statistical and expression pattern analyses on the differentially expressed transcription factors. Based on weighted gene coexpression network analysis (WGCNA), we identified seven specific modules that were significantly related to the four soybean lines with different seed coat colors. The connectivity and functional annotation of genes within the modules were calculated, and 21 candidate genes related to soybean seed coat color were identified, including six transcription factor (TF) genes and three flavonoid pathway genes. These findings provide a theoretical basis for an in-depth understanding of the molecular mechanisms underlying differences in soybean seed coat color and provide new genetic resources.

Physiological quality of chia seeds as a function of coat color and fungicide treatment

Physiological quality of chia seeds as a function of coat color and fungicide treatment

The genetic basis and origin of coat color in Leiqiong cattle

The genetic basis and origin of coat color in Leiqiong cattle

Metabolomic and Transcriptomic Analyses of Flavonoid Biosynthesis in Different Colors of Soybean Seed Coats.

Soybean has outstanding nutritional and medicinal value because of its abundant protein, oil, and flavonoid contents. This crop has rich seed coat colors, such as yellow, green, black, brown, and red, as well as bicolor variants. However, there are limited reports on the synthesis of flavonoids in the soybean seed coats of different colors. Thus, the seed coat metabolomes and transcriptomes of five soybean germplasms with yellow (S141), red (S26), brown (S62), green (S100), and black (S124) seed coats were measured. In this study, 1645 metabolites were detected in the soybean seed coat, including 426 flavonoid compounds. The flavonoids differed among the different-colored seed coats of soybean germplasms, and flavonoids were distributed in all varieties. Procyanidins A1, B1, B6, C1, and B2, cyanidin 3-O-(6″-malonyl-arabinoside), petunidin 3-(6″-p-coumaryl-glucoside) 5-glucoside, and malvidin 3-laminaribioside were significantly upregulated in S26_vs._S141, S62_vs._S141, S100_vs._S141, and S124_vs._S141 groups, with a variation of 1.43-2.97 × 1013 in terms of fold. The differences in the contents of cyanidin 3-O-(6″-malonyl-arabinoside) and proanthocyanidin A1 relate to the seed coat color differences of red soybean. Malvidin 3-laminaribioside, petunidin 3-(6″-p-coumaryl-glucoside) 5-glucoside, cyanidin 3-O-(6″-malonyl-arabinoside), and proanthocyanidin A1 affect the color of black soybean. The difference in the contents of procyanidin B1 and malvidin 3-glucoside-4-vinylphenol might be related to the seed coat color differences of brown soybeans. Cyanidin 3-gentiobioside affects the color of green soybean. The metabolomic-transcriptomic combined analysis showed that flavonoid biosynthesis is the key synthesis pathway for soybean seed color formation. Transcriptome analysis revealed that the upregulation of most flavonoid biosynthesis genes was observed in all groups, except for S62_vs._S141, and promoted flavonoid accumulation. Furthermore, CHS, CHI, DFR, FG3, ANR, FLS, LAR, and UGT88F4 exhibited differential expression in all groups. This study broadens our understanding of the metabolic and transcriptomic changes in soybean seed coats of different colors and provides new insights into developing bioactive substances from soybean seed coats.

Effects of Coat Colour Pattern on Heat Stress Among West African Dwarf Goat

Effects of Coat Colour Pattern on Heat Stress Among West African Dwarf Goat

Qualitative traits characterization of Nigerian West African Dwarf Goat population

The study was conducted to identify and characterize West African Dwarf (WAD) goat genetic resources under smallholder production systems. The goats were sampled from smallholder flocks to collect data on certain qualitative traits. These goats were scored for certain qualitative traits on body, udder and teat. The study showed that goats with black and brown (36.7%), pied coat colour pattern, convex head profile (36.3%), erected ear (51.3%), smooth hair type (68%) were predominant. Low frequencies were obtained for presence of wattle (Waw), light colouration or roan (Ror), beard (Brb), and extra teat (Ete) while all goats have horns. More than half of the goats sampled were with a well-developed, symmetric udder (61.3%) with moderate degree of separation and slightly deep udder. The WAD goats have funnel teat shape (44%) and are mostly with intermediate teat placement (61.3%), teat depth (56.7%), teat length (48%) and teat size (50.7%). The study identified considerable diversities in qualitative attributes of the goats Keywords: Genetic resources, goat, teat, traits, udder

Identification of the Mitf gene mutation causing congenital deafness and pigmentation disorders in porcupines using BSA-Seq

Worldwide, congenital deafness and pigmentation disorders impact millions with their diverse manifestations, and among these genetic conditions, mutations in the Microphthalmia-associated transcription factor (MITF: OMIM#156845) gene are notable for their profound effects on melanocyte development and auditory functions. This study reports a novel porcupine model exhibiting spontaneous deafness and pigmentation abnormalities reminiscent of human Waardenburg Syndrome Type 2 (WS2: OMIM#193510). Through phenotypic characterization, including coat color, skin, eye morphology, and auditory brainstem response (ABR) assessments, we identified hypopigmentation and complete deafness in mutant porcupines. To pinpoint the genetic basis, a breeding program was established, and Bulk Segregant Analysis (BSA) combined with RNA sequencing was conducted. Primers based on the identified candidate genes were designed for PCR amplification, followed by verification through Sanger sequencing. Through BSA analysis, we identified a total of 88 SNP and 336 InDel candidate sites. By annotating the Mitf gene, we obtained four unique transcript sequences. The SNP and InDel sites within the porcupine Mitf gene sequence, identified through BSA screening, were analyzed in conjunction with the gene’s annotation results. This analysis revealed a specific mutation site, Mitf c.875_877delGAA p. (Arg217del), which was subsequently verified by Sanger sequencing. This naturally occurring Mitf mutation in porcupines provides a valuable model for studying the mechanisms underlying WS2 and exploring potential therapeutic strategies for deafness and pigmentation-related disorders.