Coat Color Research Articles

Assessment of the adaptive capacity of Morada Nova ewes with different coat coloration.

Coat color is a factor affecting heat tolerance in tropical ruminant and a particular coat color can determine which is more resilient to environmental changes. The aim of this study was to measure the level of adaptation of Morada Nova sheep with different coat color by using an Adaptability Index (AI). Adult ewes were used, including two different coat colors of Morada Nova sheep (red and white) with mean of body weight of 28.02 ± 5.70kg and 31.47 ± 3.41kg, respectively. Physiology parameters, hematology, electrolytes, acid-base status, mineral, renal functions, metabolites, enzymes, and proteins were measured. AI was designed using a multivariate approach (principal component analysis) to "weigh" the influence of each variable in the animal responses. The variables more important for adaptive aspects of Red Morada Nova were: haematology, electrolytes and acid-base status. The hemoglobin (HG), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), sodium (Na+), oxygen pressure (PO2), glucose (GLU) and albumin (ALB) were significantly higher in Red Morada Nova sheep and hydrogen carbonate (HCO3), base excess (BE), total carbon dioxide concentration (TCO2) and URE were significantly higher in the white phenotype. The variables more important for adaptive aspects of White Morada Nova sheep were: (K+), total protein (TP), PO2, HG, cholesterol (CHO), rectal temperature (RT) and glucose (GLU). Both phenotypes showed a high adaptation level, however, a higher value was generated for the Red Morada Nova sheep (81.97). This study concludes that both phenotypes of the Morada Nova sheep breed are well adapted to the climatic condition of the Brazilian tropical region using different adaptive mechanisms.

Genomic regions associated with coat color in Gir cattle.

Indicine cattle breeds are adapted to the tropical climate, and their coat plays an important role in this process. Coat color influences thermoregulation and the adhesion of ectoparasites and may be associated with productive and reproductive traits. Furthermore, coat color is used for breed qualification, with breeders preferring certain colors. The Gir cattle is characterized by a wide variety of coat colors. Therefore, we performed genome-wide association studies to identify candidate genes for coat color in Gir cattle. Different phenotype scenarios were considered in the analyses and regions were identified on eight chromosomes. Some regions and many candidate genes are influencing coat color in the Gir cattle, which was found to be a polygenic trait. The candidate genes identified have been associated with white spotting patterns and base coat color in cattle and other species. In addition, a possible epistatic effect on coat color determination in the Gir cattle was suggested. This is the first published study that identified genomic regions and listed candidate genes associated with coat color in Gir cattle. The findings provided a better understanding of the genetic architecture of the trait in the breed and will allow to guide future fine-mapping studies for the development of genetic markers for selection.

Haofa dog – An indigenous canine germplasm from Manipur, India

A study on Haofa dog was carried out at its breeding tract in Ukhrul and Kamjong districts of Manipur to find out its origin, distribution and phenotypic characteristics. A total of 100 adult Haofa dogs (50 male and 50 female) were recorded for studying physical characters and body measurement. Further, 69 number of observation were also recorded for studying body weights of adult male and female. In addition, 100 Haofa owners were interviewed to study the reproductive characteristics, management practices followed and their utility, etc. The study revealed that Haofa were of medium size with a compact body, broad chest, straight top line and slightly tucked up abdomen. The coat colour is usually black with grey skin while some dogs have black coat colour with white markings in ventral parts and tips of legs. The head of a Haofa dog is medium in size with a slightly trapezoid shape, while the forehead is usually prominent with the straight nasal bridge. Eyes are oval shaped with golden colour. Ears are erect and usually cropped at an early age. The dogs have short coats and their tails are usually semi-curved and docked usually at a young age. The adult body weight and average litter size at birth ranges from 22-31 kg and 3-8, respectively. Haofa is morphologically different from the other exotic breeds, crossbreeds or local dogs found in the state. Hence, it deserves to be recognized as a distinct breed of dog.

Assessing the performance of Moghani crossbred lambs derived from different mating systems with Texel and Booroola sheep.

In our ongoing project, which focuses on the introgression of Booroola/FecB gene and the myostatin (MSTN) gene into purebred Moghani sheep, we assessed the performance of second-generation Moghani crossbreds such as second crossbreds (F2) and initial backcross generation (BC1). These crossbreds were generated through different mating systems, including in-breeding, outcrossing, first paternal backcrossing (PBC1), and first maternal backcrossing (MBC1). Notably, F2 strains exhibited lean tail, woolly fleece and a higher percentage of white coat color compared to BC1. The impact of mating systems and birth types on pre-weaning survival rates was found to be statistically significant (P < 0.0001), with singleton offspring resulting from paternal backcross showing a particularly substantial effect. The F2 crossbred lambs carrying the Booroola gene did not show a statistically significant difference in survivability compared to those carrying the MSTN gene, implying the Booroola prolificacy gene had no significant impact on survival outcomes. However, the occurrence of multiple births had a significant negative impact on lamb survival (P < 0.0001). The PBC1 sheep strains, specifically Texel Tamlet ram strains carrying the MSTN mutation, exhibited superior growth rates compared to others (P < 0.05). Interestingly, the MSTN mutation in the homozygous variant genotype significantly impacts growth rate before weaning compared to other genotypes and pure Moghani sheep (P < 0.05). In conclusion, this study objectively underscores the pivotal role of genetic factors, specifically through strategic mating systems like paternal backcrossing, in enhancing desired traits and growth rates in Moghani sheep, thereby contributing valuable insights to the field of sheep breeding programs.

BrTTG1 regulates seed coat proanthocyanidin formation through a direct interaction with structural gene promoters of flavonoid pathway and glutathione S-transferases in Brassica rapa L.

Seed coat color is a significant agronomic trait in horticultural crops such as Brassica rapa which is characterized by brown or yellow seed coat coloration. Previous Brassica rapa studies have shown that BrTTG1 is responsible for seed coat proanthocyanidin formation, which is dependent on the MYB-bHLH-WD40 complex, whereas some studies have reported that TRANSPARENT TESTA GLABRA 1 (TTG1) directly interacts with the structural gene promoters of the flavonoid pathway. Herein, the brown-seeded inbred B147 and ttg1 yellow-seeded inbred B80 mutants were used as plant materials for gene expression level analysis, gene promoter clone and transient overexpression. The analysis identified eleven structural genes involved in the flavonoid biosynthesis pathway, which are potentially responsible for BrTTG1- dependent seed coat proanthocyanidin formation. The promoters of these genes were cloned and cis-acting elements were identified. Yeast one-hybrid and dual-luciferase assays confirmed that BrTTG1 directly and independently interacted with proCHS-Bra008792, proDFR-Bra027457, proTT12-Bra003361, proTT19-Bra008570, proTT19-Bra023602 and proAHA10-Bra016610. A TTG1-binding motif (RTWWGTRGM) was also identified. Overexpression of TTG1 in the yellow-seed B. rapa inbred induced proanthocyanidin accumulation by increasing the expression levels of related genes. Our study unveiled, for the first time, the direct interaction between TTG1 and the promoters of the flavonoid biosynthesis pathway structural genes and glutathione S-transferases in Brassica rapa. Additionally, we have identified a novel TTG1-binding motif, providing a basis for further exploration into the function of TTG1 and the accumulation of proanthocyanidins in seed coats.

Non-iridescent magnetite photonic crystal films and pigments with enhanced magnetic coupling effect

Non-iridescent structural color films and pigments with novel enhanced microwave absorption characteristics are successfully fabricated at room temperature for the first time. The quasi-uniform magnetite nanoparticles (CV = 0.10 ∼ 0.20) with high refractive index (n = 2.42) and broad light absorption provide evident low-angle-independent property for the structural color pigments. More importantly, a universal technical protocol is developed for preparation of photonic crystals with inorganic nanoparticles, i.e., through designing of the binding strength between nanoparticles and mediated molecules, the slurry modulus is increased to 105 Pa, which effectively drives the nanoparticles to rapidly assemble into closely packed ordered arrays by our-designed powerful assembly technique. Additionally, the structural color materials are subjected as photonic crystal pigments (∼20 wt%) embedding in a transparent polymer matrix to form color coatings. Remarkably, the photonic crystal pigments exhibit strong magnetic coupling effect and enhanced microwave absorption performance due to the regular arrangement, with superior reflection loss (RLmin) values of −14.97 dB (increase by 65.8 % compared with randomized magnetic nanoparticles), and the effective absorption bandwidth (EAB) of 2.15 GHz. This new kind of photonic crystal pigment, combining visual color and radar wave absorption, provides a novel idea for developing of multi-wave-band high-performance stealth materials.

Resistance to natural tick infestation varies with age and coat and hair traits in a tropically adapted beef cattle breed

Rhipicephalus (Boophilus) microplus causes considerable livestock production losses. Knowledge of the traits that influence tick resistance contributes to the development of breeding strategies designed to improve herd productivity. Within this context, this study evaluated the resistance of Caracu, a tropically adapted cattle breed, to R. microplus. Tick count, hair length, coat thickness, and coat color were evaluated in 202 naturally tick-infested females (cows and heifers) over a period of 18 months. Blood samples were collected from all animals during the winter season for hematological analysis. Data were analyzed using Pearson correlations, generalized linear models, and principal component analysis. Correlation coefficients of tick count with coat color, coat thickness, and hair length were estimated within each season. Hematological parameters were only included in the winter season analysis and were analyzed by the restricted maximum likelihood method using log-transformed data. No differences in blood parameters were observed between animals with and without ticks. However, tick count was negatively correlated with erythrocytes (−0.29) and hematocrit (−0.24) and positively correlated with mean corpuscular hemoglobin (0.21) and mean corpuscular hemoglobin concentration (0.25). These findings suggest that higher tick counts lead to a decrease in erythrocytes but also to an increase in the amount of hemoglobin per erythrocyte, which could reduce the damage caused by low erythrocyte levels due to tick hematophagy, delaying or preventing anemia. Although tick infestation on pasture was demonstrated by the infestation of all staff members during herd management, none of the animals exhibited high tick counts, providing evidence of resistance of Caracu animals to R. microplus. Tick infestation was influenced by age class (cows > heifers), season (spring and summer > fall and winter), coat thickness (>1.5 mm > <1.5 mm), and hair length (>6 mm > <6 mm). Three components were extracted by principal component analysis, which accounted for 69.46% of data variance. The findings of this study will contribute to the development of efficient strategies aimed at reducing economic losses due to tick infestation and could be applied in animal breeding to select for tick resistance traits, reducing chemical control strategies and consequently improving sustainable livestock production.

Increasing Knockin Efficiency in Mouse Zygotes by Transient Hypothermia.

Integration of a point mutation to correct or edit a gene requires the repair of the CRISPR-Cas9-induced double-strand break by homology-directed repair (HDR). This repair pathway is more active in late S and G2 phases of the cell cycle, whereas the competing pathway of nonhomologous end-joining (NHEJ) operates throughout the cell cycle. Accordingly, modulation of the cell cycle by chemical perturbation or simply by the timing of gene editing to shift the editing toward the S/G2 phase has been shown to increase HDR rates. Using a traffic light reporter in mouse embryonic stem cells and a fluorescence conversion reporter in human-induced pluripotent stem cells, we confirm that a transient cold shock leads to an increase in the rate of HDR, with a corresponding decrease in the rate of NHEJ repair. We then investigated whether a similar cold shock could lead to an increase in the rate of HDR in the mouse embryo. By analyzing the efficiency of gene editing using single nucleotide polymorphism changes and loxP insertion at three different genetic loci, we found that a transient reduction in temperature after zygote electroporation of CRISPR-Cas9 ribonucleoprotein with a single-stranded oligodeoxynucleotide repair template did indeed increase knockin efficiency, without affecting embryonic development. The efficiency of gene editing with and without the cold shock was first assessed by genotyping blastocysts. As a proof of concept, we then confirmed that the modified embryo culture conditions were compatible with live births by targeting the coat color gene tyrosinase and observing the repair of the albino mutation. Taken together, our data suggest that a transient cold shock could offer a simple and robust way to improve knockin outcomes in both stem cells and zygotes.

Resequencing Analyses Revealed Genetic Diversity and Selection Signatures during Rabbit Breeding and Improvement.

Domestication has shaped the diverse characteristics of rabbits, including coat color, fur structure, body size, and various physiological traits. Utilizing whole-genome resequencing (DNBSEQ-T7), we analyzed the genetic diversity, population structure, and genomic selection across 180 rabbits from 17 distinct breeds to uncover the genetic basis of these traits. We conducted whole-genome sequencing on 17 rabbit breeds, identifying 17,430,184 high-quality SNPs and analyzing genomic diversity, patterns of genomic variation, population structure, and selection signatures related to coat color, coat structure, long hair, body size, reproductive capacity, and disease resistance. Through PCA and NJ tree analyses, distinct clusters emerged among Chinese indigenous rabbits, suggesting varied origins and domestication histories. Selective sweep testing pinpointed regions and genes linked to domestication and key morphological and economic traits, including those affecting coat color (TYR, ASIP), structure (LIPH), body size (INSIG2, GLI3), fertility (EDNRA, SRD5A2), heat stress adaptation (PLCB1), and immune response (SEC31A, CD86, LAP3). Our study identified key genomic signatures of selection related to traits such as coat color, fur structure, body size, and fertility; these findings highlight the genetic basis underlying phenotypic diversification in rabbits and have implications for breeding programs aiming to improve productive, reproductive, and adaptive traits. The detected genomic signatures of selection also provide insights into rabbit domestication and can aid conservation efforts for indigenous breeds.

Colorization strategy for carbon-based electrochromic devices: Achieving visible and mid-infrared regions modulation

Carbon-based materials exhibit unrivaled ability to modulate electromagnetic waves in the infrared band. However, the black appearance restricts the application in the visible light camouflage. This work combines color coatings (consisting mainly of pigments and thermochromic microcapsules) with carbon-based devices and overcomes the high absorption of the color coatings in the mid-infrared band. Ultimately, the obtained white carbon film (W-CNT) device exhibits tunable thermal emissivity from 0.453 to 0.833, maintains a residual modulation range up to 71.7%. In addition, the expansion of the coloration layer to thermochromic microcapsules enables the devices to independently modulate the visible and mid-infrared spectra, further expanding the applicability. We believe that the carbon-based device is valuable for a wide range of applications in camouflage and personal thermal management, which may provide some ideas for designing multispectral independent modulation devices.

Evaluation of print mottle of double coated paper by octave band filtering technique

The effects of the pre-coating color formulation, dwell time, and coat weights of pre- and top- coating layers on print mottle of double-coated paper were investigated using an octave band filtering image processing technique. To investigate the effect of pre-coating color formulations, six types of coating colors were used. Mottle index and coefficient of variance (COV) of double-coated paper increased as the size of pre-coating pigment particles decreased, which was attributed to the reduction in relative pore size of the pre-coating layer. Decreasing the dwell time decreased transfer time from the coating head to dryer of a Maiyoh coater. As the transfer time to dryer decreased, the mottle index and COV increased because of uneven distribution of latex within the coating layer. Pre-coat weight was found to have a greater impact on print mottle than the top-coat weight.

Determination of combining ability and heritability for canning quality traits in common bean

Breeding for common bean (Phaseolus vulgaris L.) genotypes with optimal canning quality holds the potential for increased dry bean consumption among middle-class income urban dwellers in sub-Saharan Africa (SSA). Understanding the genetic control of canning quality traits is central for the improvement of common bean genotypes for desired canning quality. The objective of this study was to determine the combining ability and heritability of canning quality traits (CQTs) in common bean; and to establish entry points for effective breeding for these traits. A population from two contrasting parents for canning quality traits was developed and progressed to F2. The F2:F4 seed was evaluated for CQTs at three months post-harvest. Substantial variation was observed among the canning quality traits tested, including the general appearance of the canned beans, seed coat colour retention namely, clumping, free starch, splitting, and hydration coefficient. Canning quality traits encompassed a spectrum of both additive and non-additive effects. Promising combiners for CQTs were identified among the parents, KK8 and MAC 13, suggesting their potential for utilisation in breeding programmes. Moderate to high Baker’s ratio (BR = 0.41-0.94) values were observed for some CQTs and narrow sense heritability (h2 = 0.47-0.66). Canning quality traits exhibited substantial broad sense heritability (H2) values, ranging from 0.6 to 0.92. These findings provide valuable entry points for breeding programmes focused on improving common bean for canning quality.

Animal factors affecting the cheese-making properties and the heat coagulation time of milk from dairy sheep in a New Zealand flock

ABSTRACT The objective of this study was to evaluate the effect of animal factors on the cheese-making properties and on the heat coagulation time of milk from individual dairy sheep in a New Zealand flock. A total of 521 individual records were obtained from a seasonal pasture-based flock of 169 ewes milked once-a-day, from 50 to 182 days in milk. A statistical model was used to quantify the effects of animal factors (coat colour variety, age, litter size and stage of lactation) on the studied traits. Stage of lactation, confounded with seasonality, strongly influenced all properties of milk investigated. With the advancement of lactation, the milk took longer to coagulate after rennet addition, and the curd was softer. Higher relative cheese yield was achieved towards the end of lactation. The milk was also less stable to high-temperature treatment in late lactation. Coefficient of variation for processability traits was high and ranged from 20.2% to 58%, which can be largely attributed to stage of lactation but could also indicate room for genetic improvement of traits. Further genetic studies are underway to define animal genetic variance, heritability, and the phenotypic and genetic correlations between these processability and milk composition traits.

A new strategy for structural color fabrics: Transfer of photonic crystal coatings from slides to fabrics

The construction of three-dimensional photonic crystals on textile surfaces has emerged as a highly effective method to create fabrics with structural color, generating significant interest among researchers. However, the strict requirements of the substrate fabrics and the challenges associated with patterning coatings for bright structural colors have hindered the widespread application of photonic crystal materials in the textile industry. In this study, we present a strategy for obtaining patterned structural color coatings on fabrics made of different materials. Pre-crystallized poly(styrene-methyl methacrylate-acrylic acid) (P(St-MMA-AA)) liquid photonic crystals (LPCs) are used as raw material for the rapid preparation of solid photonic crystals (SPCs). These SPCs with structural colors are used as templates and transferred to various fabrics through transfer printing techniques. Importantly, the SPCs maintain an ordered face-centered cubic structure both before and after transfer. Such a feature ensures that the processed structural color fabrics exhibit vibrant and iridescent structural colors. This result is achieved by modification of the substrate fabric with viscous polymer and the intact retention of SPCs. The sandwich structure formed by the adhesive polymer on the base fabric and the encapsulation of the film-forming material on the SPCs imparts good stability to the structural color fabric. It is worth noting that patterned photonic crystal coatings can be easily obtained on the fabrics made of different materials (cotton, linen, wool, and silk fabrics) by manipulating the shape of the viscous polymer. Additionally, a wide range of common materials, such as paper, wood, steel, and others, can be used as target substrates. This novel dyeing strategy not only offers new ideas for preparing patterned structural color fabrics but also further promotes the application of photonic crystal materials in textile printing or display.

Morphological Characterization of Kage and Baruwal Sheep (Ovis aries Linnaeus, 1758) Breeds in Nepal

Sheep farming in Nepal is closely linked to its agricultural heritage and contributes to livelihoods and the socio-economic fabric. This study synthesizes the morphological characterization of Kage and Baruwal (Ovis aries Linnaeus, 1758) sheep, highlighting their genetic and functional attributes, including body size, conformation, coat color, horn morphology, and reproductive parameters. This study synthesizes the morphological characterization of Kage and Baruwal (O. aries) sheep, highlighting their genetic and functional attributes, including body size, conformation, coat color, horn morphology, and reproductive parameters. The analysis revealed a significant difference (P ≤ 0.01**) in quantitative traits between the two breeds. The Baruwal sheep exhibited higher mean values for tail length (12.96 ± 0.47 cm), ear length (10.67±0.20 cm), neck length (21.75±0.38 cm), chest girth (67.14±0.50), height at hip bone (64.78±0.44 cm), body weight (33.04±0.65 Kg), and height below withers (67.10±0.56). Additionally, correlation analysis of different quantitative traits was found to be significant at the 0.01 level on a two-tailed test. The study's results indicate significant quantitative variations, which suggest genetic adaptations and selective pressures. The analysis of qualitative traits highlights differences in horn presence, shape, fleece, head color, neckline, and tail shape, providing insights into genetic diversity and functional adaptations. The study concludes that comprehending such phenotypic traits helps with breed management, conservation, and sustainable agriculture. The preservation of genetic diversity and adaptability is underscored by indigenous sheep breeds, which requires further research to elucidate the genetic mechanisms underlying these traits.

ANALIZA ZMIENNOŚCI CECH POKROJU I SKUTECZNOŚCI PRACY HODOWLANEJ U KRÓLIKÓW RAS TERMONDZKI BIAŁY I POPIELNIAŃSKI BIAŁY

The aim of the study was to assess and analyze conformation characteristics and the effectiveness of breeding work in TB and PB rabbits over 10 years. The study determined the variability of conformation traits in two animal herds, as well as their heritability. Additionally, phenotypic trends in conformation traits were estimated. The analysis of variance of conformation traits showed that the year of license had a statistically highly significant impact on: body weight (expressed in grams and points), body structure, breed type, coat color and specific breed characteristics. Gender and race had a statistically significant impact on body weight (g) and coat color. Moreover, race also showed a statistically significant effect on body weight in the scoring. In turn, the farm had a statistically significant impact on: body weight (g), body structure, breed type, coat color and specific breed characteristics. The analysis of conformation characteristics showed that 97.9% of rabbits received positive marks, and 2.1% were disqualified. Only individuals intended for herd improvement were subjected to evaluation. Summarizing the results of the conformation traits analysis, it can be concluded that the rabbits kept on the examined farms underwent proper selection. The animals had very good conformation features. Based on our own research, it was found that rabbit breeding in both of the studied farms was conducted correctly, and the obtained results are satisfactory, both in terms of reproductive and conformatin traits.

Chromosome-level reference genome and resequencing of 322 accessions reveal evolution, genomic imprint and key agronomic traits in adzuki bean.

Adzuki bean (Vigna angularis) is an important legume crop cultivated in over 30 countries worldwide. We developed a high-quality chromosome-level reference genome of adzuki bean cultivar Jingnong6 by combining PacBio Sequel long-read sequencing with short-read and Hi-C technologies. The assembled genome covers 97.8% of the adzuki bean genome with a contig N50 of approximately 16 Mb and a total of 32 738 protein-coding genes. We also generated a comprehensive genome variation map of adzuki bean by whole-genome resequencing (WGRS) of 322 diverse adzuki beans accessions including both wild and cultivated. Furthermore, we have conducted comparative genomics and a genome-wide association study (GWAS) on key agricultural traits to investigate the evolution and domestication. GWAS identified several candidate genes, including VaCycA3;1, VaHB15, VaANR1 and VaBm, that exhibited significant associations with domestication traits. Furthermore, we conducted functional analyses on the roles of VaANR1 and VaBm in regulating seed coat colour. We provided evidence for the highest genetic diversity of wild adzuki (Vigna angularis var. nipponensis) in China with the presence of the most original wild adzuki bean, and the occurrence of domestication process facilitating transition from wild to cultigen. The present study elucidates the genetic basis of adzuki bean domestication traits and provides crucial genomic resources to support future breeding efforts in adzuki bean.

Selection Signatures Reveal Candidate Genes for the Cornish Rex Breed-Specific Phenotype.

Many coat color, behavioral and morphological traits are specific and fixed across cat breeds, with several variants influencing these traits being common among different breeds. In the domestic cat, rexoid mutations have been documented in several breeds. In the Cornish Rex, four bp deletion in the LPAR6 gene has been found to cause a frame shift and a premature stop codon. In addition to the rexoid coat, Cornish Rex cats also have a characteristic head, ear shape and body type. Analysis of the selection signatures in the Cornish Rex genome revealed several regions that are under selective pressure. One of these is located in CFA B4, in the region where the ALX1 gene is located. The ALX1 gene in Burmese cats disrupts the cranial morphogenesis and causes brachycephaly in the heterozygous state. In our study, we confirmed the presence of a deletion in LPAR6 in 20 Cornish Rex and in four F1 hybrids between Cornish Rex and domestic cat. However, we did not confirm the presence of the deletion in ALX1 in Cornish Rex cats. Genome-wide selection signature analysis was performed using ROH islands and integrated haplotype score (iHS) statistics based on publicly available SNP array data of 11 Cornish Rex cats. The selection signatures were detected on chromosomes A1, A3, C2, B1, B4 and D1.

Three HPS5 mutations associated with depigmentation in diverse horse breeds

Depigmentation is a common phenotype in Equus caballus (horse); over 50 identified variants cause white spotting on the skin and coat. HPS5 may influence melanocyte proliferation and mutations in this gene cause depigmentation in humans, mice, and zebrafish. Here we report three equine HPS5 mutations, found in most major breed groups and associated with white spotting. We used a standardized method to quantitatively grade depigmentation, creating a White Score for each horse. We identified associations to each of three variants in HPS5 by comparing the average white score for carriers to that of 41 control horses possessing none of the studied variants. We estimated the functional impact of each mutation using SIFT, GenScan, I-TASSER and cross-species conservation. The first mutation, S1013C termed Eden White 1 (EDXW1), is a missense mutation found to increase average depigmentation by 5.56 points (p = 6.47E-6, n = 70, t-test). Eden White 2 (EDXW2), a missense mutation L560F, increased depigmentation by 9.5 points for individuals with one copy of the variant, but we were unable to phenotype homozygotes (p = 5.55E-16, n = 47, t-test). Eden White 3 (EDXW3), a putative donor splice site mutation at exon 4 + 4, increased white by 5.59 points on average (p = 9.56E-6, n = 101). EDXW1 and EDXW3 are epistatically influenced by MC1R, the gene that controls black vs red coat color in horses. Individuals possessing the dominant E allele produce black pigment, and this allele was associated with higher levels of depigmentation than individuals with the recessive chestnut genotype (e/e) (p = 1.50E-5, p = 1.26E-5 respectively). We tested for epistatic interactions between EDXW1 and Dominant White 20 and found that horses with one copy of each allele had increased average white spotting by 8 points with respect to EDXW1/n or W20/n horses. Compound heterozygotes were significantly more white than horses with one copy of either mutation (p = 7.33E-5), but interactions between other white spotting alleles and EDXW alleles remain to be tested. We propose the convention Eden White (EDXW) for HPS5 mutations in the domestic horse.

Comprehensive whole-genome resequencing unveils genetic diversity and selective signatures of the Xiangdong black goat.

Xiangdong black goats, indigenous to Hunan Province, China, exhibit remarkable adaptation to challenging environments and possess distinct black coat coloration alongside exceptional meat quality attributes. Despite their significance, comprehensive genomic investigations of this breed have been notably lacking. This study involved a comprehensive examination of population structure, genomic diversity, and regions of selection in Xiangdong black goats utilizing whole-genome sequencing data from 20 samples of this breed and 139 published samples from six other Chinese goat breeds. Our genomic analysis revealed a total of 19,133,125 biallelic single nucleotide polymorphisms (SNPs) within the Xiangdong black goat genome, primarily located in intergenic and intronic regions. Population structure analysis indicated that, compared with Jintang, Guizhou and Chengdu goats, Xiangdong black goats exhibit a reduced level of genetic differentiation but exhibit relatively greater divergence from Jining goats. An examination of genetic diversity within Xiangdong black goats revealed a moderate level of diversity, minimal inbreeding, and a substantial effective population size, which are more reflective of random mating patterns than other Chinese goat breeds. Additionally, we applied four distinct selective sweep methods, namely, the composite likelihood ratio (CLR), fixation index (F ST), θ π ratio and cross-population extended haplotype homozygosity (XP-EHH), to identify genomic regions under positive selection and genes associated with fundamental biological processes. The most prominent candidate genes identified in this study are involved in crucial aspects of goat life, including reproduction (CCSER1, PDGFRB, IFT88, LRP1B, STAG1, and SDCCAG8), immunity (DOCK8, IL1R1, and IL7), lactation and milk production (SPP1, TLL1, and ERBB4), hair growth (CHRM2, SDC1, ITCH, and FGF12), and thermoregulation (PDE10A). In summary, our research contributes valuable insights into the genomic characteristics of the Xiangdong black goat, underscoring its importance and utility in future breeding programs and conservation initiatives within the field of animal breeding and genetics.