Coat Color Research Articles

Survey of ocular abnormalities in a population of Turkmen horses.

The aim of this study was to detect and describe ocular abnormalities in a population of Turkmen horses. A total of 55 Turkmen horses (33 mares and 22 stallions) from one herd were evaluated in this study. Demographic data (Age, Sex, Coat color) were recorded. All animals underwent complete ophthalmic examination. The Schirmer tear test -I (STT-I) was performed for all horses prior to other diagnostic tests. Neuro-ophthalmic examinations (menace response, dazzle reflex, pupillary light reflex, maze test, and visual tracking) were carried out in different lighting situations (bright and dim lights). Slit lamp biomicroscopy, direct and indirect ophthalmoscopy, fluorescein staining, and tonometry were performed for each horse. The mean (standard deviation) age of horses was 5.7 (4.6) years (range of 1-17 years). In total, 18 horses (32.7%) had ocular-related lesions. Cataract, iris hyperpigmentation and corneal edema were the most identified conditions in the horses of this study. About one-third of studied horses had at least one ocular abnormality. No ocular abnormalities attributed to the distinct cream/gold coat color were identified, which the Turkmen horse is known for.

PSIV-9 Pedigree tracing to determine the origin of the golden coat phenotype within the Golden American Saddlebred horse

Abstract With the incorporation of the Golden American Saddlebred Horse Association (GASHA) into the American Saddlebred Horse Association (ASHA), breeding specifically for coat color within the breed registry became less of an emphasis for horse breeders. Nevertheless, historical documentation of the horses making up the foundation of the GASHA through the application of pedigree tracing holds value in understanding the origin of the breed and its coat color. This can be of value to horse breeders targeting a specific coat color as the study of coat colors is a relatively new field of research within equine science. Thus, the objective of this study was to document the historical origins of the GASHA through pedigree tracing to determine the influence of the dilution genes that produce the golden coat phenotype. A random sample of 550 horses was obtained from the Official Directory of GASHA. Using the All-Breed Data Base, sampled horses were entered and examined for pedigrees suitable for analysis of color inheritance, and of these, 507 were found to have extended pedigrees with documented coat colors that were used for this study. Results determined that 43% of traced pedigrees carried the champagne gene, 36.1% carried the cream gene, and 20% had pedigrees that were non-informative as these pedigrees went to unknown ancestors or were found to be incorrect as to ancestry. Another 0.9% were determined to be obligate carriers for the cream gene; as the pedigrees presented conflict concerning color designation so that accurate conclusion of coat color phenotype associated with the cream dilution gene could not be verified. Of the 507, all traced back to 6 foundation mares and most of the breed traced back to 2 of these mares; with one mare, Maud, being a champagne mutation and the other, Allens Queen, a cream mutation (Table 1). In conclusion, through pedigree tracing the GASHA origins were documented giving an understanding as to the genetic contributions for today’s GASHA golden coat color. Further, these results will give breeders more input on how they might select for certain coat color phenotypes.

PSI-1 Genetic and non-genetic factors influencing beef cattle attractiveness to horn fly

Abstract Horn flies are the most common summer pests of cattle, leading to substantial economic losses due to impaired production and decreased animal welfare. Genetic and non-genetic factors have been reported to influence cattle susceptibility to horn flies. However, the wide range of heritability estimates, and few identified genomic regions associated with cattle resistance to horn fly may be due to subjective assessment in collecting the fly load phenotype and the small size of the population assessed. Here, beef calves from the UF purebred Brahman (BRA) and Multibreed Angus-Brahman (MAB) populations were video recorded at weaning using a GoPro camera mounted on the top of the chute. Fly infestation was determined as the average fly count obtained from five longitudinal images of each animal using ImageJ software. A total of 748 crossbred and 415 purebred calves born from 2021 to 2023 were evaluated during summer (August or September). Analysis of variance (ANOVA) was performed within herd by fitting linear models that included collection date, age, skin color, coat color, and pre-weaning average daily gain (ADG) as fixed effects, and residual as a random effect. For MAB calves, breed groups (BG) determined based on the percentage of Brahman breed, with BG1 ranging from 0 to 19%, BG2 from 20 to 39%, BG3 from 40 to 59%, BG4 from 60 to 79%, BG5 from 80 to 100%, were also fit in the model. Fly count was transformed to a natural log value (log[count +1]) ensuring normally distribute residuals. As expected, darker colors were significantly more attractive to horn flies, while animals with greaterr percentage of Brahman were less susceptible than animals with greater percentage of Angus breed. Considerable variability in fly load was observed within purebred Brahmans, indicating that additional genetic factors, other than breed, influence cattle resistance to flies. Positive estimates were observed between horn fly load and average daily gain in both herds, which can be due to the fly load below the previously reported economic injury level of 200 flies (BRA: 28.78 ± 38.20, MAB: 19.31 ± 26.72). Variance components were estimated within herds by fitting the same aforementioned effects and a genomic-based relationship matrix (G) constructed with genotypes from the GeneSeek Genomic Profiler F250 SNP chip. The moderate heritability estimate demonstrates the feasibility of selecting cattle resistant to horn flies. Overall, our findings have the potential to contribute to reducing losses and costs in beef cattle operations, while reducing the impact on the environment of overuse of insecticides.

Transcriptome profiles of the skin associated with the color of the black and white coat of Angora goats

The coat color of mammals, determined by the distribution of melanin, particularly eumelanin and pheomelanin, reflects intricate genetic and molecular processes. However, our understanding of the relationship between coat color, gene expression, and polymorphisms in goats remains nascent. This study investigates transcriptomic differences between black and white Angora goats across three distinct hair growth phases. Skin tissue samples from both colored and white Angora goats were analyzed using mRNA expression profiling. Three skin samples were taken from each goat as biological duplicates at every stage of hair follicle growth (September, January, and March). In total, 36 samples were analyzed in this study, including samples from two Angora goat varieties, three developmental stages (three biological replicates), and two technical replicates for RNA sequencing. Significant differences in gene expression were observed between black and white goats at each growth phase, particularly in genes associated with the melanogenesis pathway. Specifically, several pigmentation genes were identified solely in black goats, indicating phase-specific and breed-specific regulation. Noteworthy genes, such as SLC2A1, STAR, and SLC7A5, exhibited differential expression patterns across growth phases in black goats, further highlighting the complexity of melanogenesis regulation. This is the first study to use mRNA expression profiling of skin tissues to analyze coat color differences between black and white coated Angora goats at the anagen, catagen, and telogen stages. The identification of phase-specific and black goat-specific pigmentation genes provides valuable insights into the complex mechanisms governing coat color formation.

275 Frequency of chronic passive congestive livers at harvest in the Texas Panhandle and the association with carcass outcomes

Abstract Chronic passive congestive (CPC) livers are reported as one of the most common clinical signs of right-sided Bovine Congestive Heart Failure (BCHF). Frequency of CPC livers at harvest and the associated loss of offal and carcass value does not appear in the literature. Our objectives were to 1) quantify the frequency of CPC livers at harvest within the Texas Panhandle, and 2) evaluate the association with offal and carcass outcomes. Audits were performed over the duration of a production week (both harvest shifts) per each large commercial beef processing facility (4 total) in the Texas Panhandle. West Texas A&M University trained personnel identified CPC (large blue) livers at evisceration and documented heart score (HS; scale 1 = normal to 5 = extreme structural changes), liver weight, USDA-FSIS inspection fate (U.S. Inspected & Passed; U.S. Condemned) of the liver, remaining viscera, and carcass. Other visual observations (sex, predominant black hair coat color, carcass/visceral edema, liver abscesses) were noted. 1) Frequency data were documented among cattle-type populations: sex (steers, heifers, cows, bulls), and phenotype [native, dairy-cross, dairy, category-B (Mexico-origin)]. 2) Carcass and lot identification were collected for the purpose of tracking and obtaining carcass grading data. Of carcasses deemed wholesome-U.S. Inspected & Passed, USDA yield and quality metrics [hot carcass weight (HCW), 12th-rib fat thickness (FT), ribeye area (REA), marbling score (MS)] of those identified with CPC, as well as data for the balance of respective lots were collected. Carcass outcomes of those exhibiting a CPC liver were compared with the outcomes of remaining lot. Frequency data were analyzed via chi-square. Carcass data were analyzed using mixed models, where occurrence of CPC liver was the fixed effect; facility, cattle type, and sex were random effects. A total of 83,527 animals were audited, with a CPC liver frequency of 0.17% (n = 144). Frequencies among sex (steer = 0.16%; heifer = 0.17%; cow = 0.33%; P < 0.01) and phenotypes (native = 0.15%; category-B = 0.04%; dairy cross = 0.14%; P = 0.01) were documented. Heart scores ranged from 1 to 4, with HS 3 occurring most frequently [HS 1 (n = 2); HS 2 (n = 39); HS 3 (n = 62); HS 4 (n = 17)]. Weights of CPC livers ranged from 7.3 kg to 34.4 kg; the heaviest CPC livers were recorded in cows (mean = 17.2 kg; P < 0.01). Despite USDA-FSIS guidelines, 2.08% of CPC livers were U.S. Inspected & Passed, along with 16.90% of viscera and 84.03% of carcasses. Cow carcasses encountered the greatest U.S. Condemn-rates (38.24%) among the sex categories. Within the fed-beef population, natives were the only category resulting in U.S. Condemned carcasses (10.64%). All carcass outcomes were decreased (P ≤ 0.01) by CPC livers.

67 Precision identification and weight assessment of cattle using supervised machine learning on body surface keypoints

Abstract Computer vision systems (CVS) offer identification solutions for animals with distinct coat patterns, but are less effective for solid-colored herds. In addition, they can be used to measure critical phenotypes, such as body weight (BW). Providing both BW and identification for solid-colored animals can help farmers make decisions. This study aimed to 1) develop an automatic CVS capable of identifying using the Euclidean distance between keypoints located at specific anatomical landmarks (e.g., bony prominences), and 2) predict the BW using features extracted from these keypoints. The keypoint model was trained to identify seven keypoints per cow, located at the left and right hips, left and right pin bones, tail head, sacral, and cervical vertebrae. These locations remain constant as body condition score of a cow changes. The Euclidean distance between these keypoints was used to generate biometric features for each cow. The keypoint detection model was trained using 3,928 images over 900 epochs with a batch size of 14 and validated using 391 images. This trained model was used to predict keypoints on a different set of 41 cows over 5 d, resulting in a total of 6,944 images which correspond to the dataset for cow identification. The Random Forest (RF) algorithm for cow identification was trained with the first 4 d (5,376 images), and the last day served as the test set (1,568 images). For the cow identification, a RF algorithm was employed on the Euclidean distance of the keypoints. The hyperparameters were determined through a grid search on the training set, utilizing 5-fold cross-validation. The hyperparameters ‘mtry’ (which ranged from 1 to 10) and ‘ntree’ (which ranged from 250 to 500, in increments of 50) were optimized. For the second objective, due to the completely new environment, the keypoint model was fine-tuned using transfer learning for 240 epochs with a batch size of 14, utilizing 310 images. The model predicted keypoints in 1,593 images from different beef-on-dairy animals. This dataset was used to train the BW prediction model. The Euclidean distances from the predicted images and sex were used as features. A RF model was trained using a leave-one-animal-out cross-validation approach. The hyperparameters were determined through a grid search on the training set, using 10-fold cross-validation. The ‘mtry’ parameter ranged from 2 to 16, in increments of 2. For animal identification, the model achieved an accuracy, precision, recall, and F1-score of 92.7%, 89.0%, 90.2%, and 92.7%, respectively. To predict BW, the RF model achieved an R² of 0.86 and a root mean squared prediction error of 36.9 kg, representing 6.7% of the observed values average. These results suggest that keypoints located on the dorsal body surface can identify and weigh individual animals, even those lacking distinct coat color patterns.

Transcriptome-based screening and validation of key genes for wool color in cashmere goats.

Colored wool from cashmere goats is increasingly popular among consumers, but the transcriptomic differences between coat colors are poorly understood. This study aimed to screen for coat color regulation-associated genes in cashmere goats to ascertain their underlying molecular mechanisms. Transcriptomic sequencing of skin tissues from black (BC), brown (YC), and white cashmere (WC) goats was performed. Immunohistochemistry and western blotting were used to validate SLC24A4 and DCT expression, two essential genes identified for coat color determination. We identified 6,518 differentially expressed genes (DEGs) in the BC vs. WC group (3,919 upregulated, 2,599 downregulated). Next, 5,593 DEGs were identified in the YC vs. WC group (3,629 upregulated, 1,964 downregulated). Finally, 4,538 DEGs were expressed in both groups, with 1,980 and 1,055 DEGs exclusively expressed in either group. Functions and pathways associated with hair color were enriched, including melanosomes, melanocyte migration, melanin biosynthesis processes and functions, and melanogenesis pathways. TYRP1, SLC24A4, PMEL, OCA2, and DCT were significantly upregulated in BC goat skin, while ASIP was significantly upregulated in YC skin. Additionally, KIT, POMC, SLC24A5, Wnt3a, and EDN3 were DEGs for different coat colors. Immunohistochemistry revealed SLC24A4 and DCT expression in dermal papillae, inner and outer root sheaths, and the hair follicle matrix. Western blotting showed that SLC24A4 protein levels were highest in BC goat skin. DCT protein levels were also highest in BC goat skin, albeit not significantly. These results further our understanding of coat color regulation in cashmere goats, establishing a foundation for their molecular breeding.

Chronic social defeat stress gives rise to social avoidance through fear learning

Chronic social defeat stress (CSDS), a widely used rodent model of stress, reliably leads to decreased social interaction in stress susceptible animals. Here, we investigate a role for fear learning in this response using male 129 Sv/Ev mice, a strain that is more vulnerable to CSDS than the commonly used C57BL/6 strain. We first demonstrate that defeated 129 Sv/Ev mice avoid a CD-1 mouse, but not a conspecific, indicating that motivation to socialize is intact in this strain. CD-1 avoidance is characterized by approach behavior that results in running in the opposite direction, activity that is consistent with a threat response. We next test whether CD-1 avoidance is subject to the same behavioral changes found in traditional models of Pavlovian fear conditioning. We find that associative learning occurs across 10 days CSDS, with defeated mice learning to associate the color of the CD-1 coat with threat. This leads to the gradual acquisition of avoidance behavior, a conditioned response that can be extinguished with 7 days of repeated social interaction testing (5 tests/day). Pairing a CD-1 with a tone leads to second-order conditioning, resulting in avoidance of an enclosure without a social target. Finally, we show that social interaction with a conspecific is a highly variable response in defeated mice that may reflect individual differences in generalization of fear to other social targets. Our data indicate that fear conditioning to a social target is a key component of CSDS, implicating the involvement of fear circuits in social avoidance.

Influence of variable valence metal oxides on physico-chemical and antibacterial properties of semi-coated glazes

The paper presents the results of studies on the production of semi-coated glazes with antibacterial activity by introducing variable valence oxides CeO2, WO3, Bi2O3, Fe2O3, MnO2 and MoO3 into their composition. The raw polycomponent compositions were comprised of aluminosilicate multi-calcium glass frit, dolomite powder, feldspar, alumina, quartz sand, wet-enriched kaolin and refractory clay. The coatings were obtained by single firing on a ceramic-based porcelain stoneware at a temperature of 1 200 ± 5 °C in a high-speed mode for 60 ± 2 minutes. The study focused on the processes of glaze formation of coatings and the influence of the components of glaze charges on decorative and aesthetic characteristics of coatings (color, texture, gloss and whiteness). Parameters of physical and chemical properties were determined in accordance with the existing specification for the products, i. e. temperature coefficient of linear expansion, heat resistance, chemical resistance, microhardness, frost resistance, wear resistance, etc. Antibacterial activity of the coatings towards Escherichia coli ATCC 8739 and Staphylococcus aureus ATCC 6538 test strains was studied.

Video-based compilation of acute pain behaviours in cats.

The aim of this work was to create a video-based compilation of acute pain behaviours in cats as an open-access online resource for training of veterinary health professionals. A database comprising 60 h of video recordings of cats was used. Videos were previously recorded after ethical approval and written client consent forms, and involved cats with different types (eg, medical, surgical, trauma, orofacial) and degrees (eg, from no pain to severe pain) of acute pain, before and after surgery or the administration of analgesia. The database included videos of cats of different coat colours, ages, sex and breeds. Video selection was based on a published ethogram of acute pain behaviours in cats. Videos were selected by one observer (SM) according to their definition and quality, followed by a second round of screening by two observers (SM and PVS). Video editing included a standardised template (ie, watermark and titles). A total of 24 videos (mean length 33 ± 17 s) with each acute pain-related behaviour described in the ethogram were uploaded to an open-access online video-sharing platform (http://www.youtube.com/@Steagalllaboratory) with an individual hyperlink. Videos were provided with a short description of the behaviour for the public. This video-based compilation may promote better training of veterinary health professionals on acute pain assessment while improving feline health and welfare and the understanding of cat behaviours.

Rhipicephalus (Boophilus) microplus Infestation and its Implications in Anaplasma marginale Infection among Cattle in South Gujarat, India

Background: This study aims to identify risk factors for Rhipicephalus (Boophilus) microplus ticks’ infestation in South Gujarat’s cattle and explore its implications on Anaplasma marginale. Methods: An approach was employed to retrieve the crucial insights from the owners and examinations of 2305 cattle (crossbred=1495, indigenous=810) of South Gujarat, India. Species specific PCR was used to detect 576 bp of msp5 gene of A. marginale in the oviposited ticks. Result: Crossbred cattle (73.91%) had higher tick prevalence than indigenous ones (55.80%), with R. (B.) microplus being the dominant species. Highest tick infestation was noted in cattle greater than 3 years (74.43%), followed by less than 1 year (70.23%) and 1-3 years old (55.60%). Ticks collected from crossbred exhibited higher prevalence of A. marginale compared to indigenous cattle. Significantly highest (p greater than 0.05) ticks infestation rate was noted in cattle with pale conjunctiva, poor body condition and black coat colour. Infection rate of both the parasites was highest during summer, followed by monsoon and winter. Kachcha house and earthen floor favoured the survival of the pathogen. Owners in surveyed regions combat tick infestations using mechanical (7.69%), chemical (83.51%) and herbal/no treatments (10.07%). These findings emphasize the intricate link between tick infestations and A. marginale infection, offering crucial insights for cattle health management.

Genetic structure analysis of yak breeds and their response to adaptive evolution

Yaks are crucial genetic resources in the Tibetan Plateau and surrounding regions. Throughout the long process of domestication, natural and artificial selection pressures have enabled yaks to demonstrate adaptive characteristics to the environment in terms of physiological structure and genetic molecules, but no systematic cell analysis has been carried out on this phenomenon of yaks. Here, the population structure and genetic diversity of yak were studied by WGRS, and the genes related to yak adaptability were excavated. Combined with scRNA-seq method, the transcription map of yak lung tissue and skin tissue was constructed, which provided a new comprehensive insight into yak adaptability. The analysis of yak population structure showed that there was obvious genetic differentiation between TZ _ yak and other seven yak populations, while there was significant genetic exchange between PL _ yak and SB _ yak at high altitude. WGRS and scRNA-seq analysis revealed that the gene HIF1A related to high altitude adaptation was expressed in various cell types, while EPAS1 was predominantly expressed in epithelial and endothelial cells of yak lung tissue. Endothelial cells play a critical role in hypoxia-adapted VEGF signaling, which correlates closely with the high expression of KDR and VEGFA genes in endothelial cells and monocytes. Furthermore, in the selection signal of High _ yak vs Low _ yak, 19.8 % of the genes overlapped with the genes screened by skin scRNA-seq, including genes related to coat color such as RORA, BNC2, and KIT. Notably, BNC2 is a gene associated with melanin deposition and shows high expression levels in HS cells. Additionally, GRN in melanocytes and SORT1 in IRS play an important role in cell communication between melanocytes and IRS. These findings offer new insights into the natural polymorphism of yaks and provide a valuable reference for future research on high-altitude mammals, and potentially even human genetics.

Genome-Wide Selection Sweep Analysis to Identify Candidate Genes with Black and Brown Color in Tibetan Sibu Yaks.

Although coat color is an important economic phenotype in domesticated yaks (Bos grunniens), its genetic basis is not yet fully understood. In this study, a genome-wide selective sweep and high-frequency runs of homozygosity (ROH) identification were performed on 50 yaks with different coat colors to investigate candidate genes (CDGs) related to coat color. The results suggested that 2263 CDGs were identified from the 5% interaction windows of the FST and θπ ratio, along with 2801 and 2834 CDGs from black and brown yaks with iHS, respectively. Furthermore, 648 and 691 CDGs from black and brown yaks, which were widely enriched in pathways related to melanogenesis, melanocyte differentiation, and melanosome organization via GO and KEGG functional enrichment, respectively, were confirmed on the basis of the intersection of three parameters. Additionally, the genome of brown yaks presented more ROH, longer ROH fragments, and higher inbreeding levels than those of black yaks. Specifically, a large number of genes related to melanin synthesis and regulation (e.g., UST, TCF25, and AHRR) from the ROH islands were confirmed to be under strong selection. In summary, the results of this study enhance the understanding of the genetic basis for determining yak coat color.

T and Z, partial seed coat patterning genes in common bean, provide insight into the structure and protein interactions of a plant MBW complex.

Flavonoids are secondary metabolites associated with plant seed coat and flower color. These compounds provide health benefits to humans as anti-inflammatory and antioxidant compounds. The expression of the late biosynthetic genes in the flavonoid pathway is controlled by a ternary MBW protein complex consisting of interfacing MYB, beta-helix-loop-helix (bHLH), and WD40 Repeat (WDR) proteins. P, the master regulator gene of the flavonoid expression in common bean (Phaseolus vulgaris L.), was recently determined to encode a bHLH protein. The T and Z genes control the distribution of color in bean seeds and flowers and have historically been considered regulators of the flavonoid gene expression. T and Z candidates were identified using reverse genetics based on genetic mapping, phylogenetic analysis, and mutant analysis. Domain and AlphaFold2 structure analyses determined that T encodes a seven-bladed β-propeller WDR protein, while Z encodes a R2R3 MYB protein. Deletions and SNPs in T and Z mutants, respectively, altered the 3D structure of these proteins. Modeling of the Z MYB/P bHLH/T WDR MBW complex identified interfacing sequence domains and motifs in all three genes that are conserved in dicots. One Z MYB motif is a possible beta-molecular recognition feature (β-MoRF) that only appears in a structured state when Z MYB is modeled as a component of a MBW complex. Complexes containing mutant T and Z proteins changed the interaction of members of the complex in ways that would alter their role in regulating the expression of genes in the flavonoid pathway.

Agouti-Signaling Protein and Melanocortin-1-Receptor Mutations Associated with Coat Color Phenotypes in Fallow Deer (Dama dama).

Four dominant coat color phenotypes are found in fallow deer (Dama dama). Brown is the most common. Black, menil, and white occur with varying frequencies. In order to gain insights into the molecular genetic background of these phenotypes, 998 fallow animals (772 brown, 62 black, 126 menil, and 38 white) were examined for mutations in the ASIP, MC1R, TYR, and SLC45A2 genes. In ASIP, two mutations (ASIP-M-E2, located at the boundary from exon 2 to intron 2; and ASIP-M-E3, an InDel of five nucleotides) were found, leading to black fallow deer being either homozygous or heterozygous in combination. There were also two mutations found in MC1R. Whereby the mutation MC1R-M1 (leucine to proline, L48P) homozygous leads to a white coat, while the mutation MC1R-M2 (glycine to aspartic acid, G236D) homozygous is associated with the menil phenotype. When both mutations occur together in a heterozygous character state, it results in a menil coat. Since the mutations in the two genes are only present alternatively, 36 genotypes can be identified that form color clusters to which all animals can be assigned. No mutations were found in the TYR and SLC45A2 genes. Our investigations demonstrate that the four dominant coat colors in fallow deer can be explained by ASIP and MC1R mutations only.

Genome-Wide Identification of B-Box Family Genes and Their Potential Roles in Seed Development under Shading Conditions in Rapeseed.

B-box (BBX) proteins, a subfamily of zinc-finger transcription factors, are involved in various environmental signaling pathways. In this study, we conducted a comprehensive analysis of BBX family members in Brassica crops. The 482 BBX proteins were divided into five groups based on gene structure, conserved domains, and phylogenetic analysis. An analysis of nonsynonymous substitutions and (Ka)/synonymous substitutions (Ks) revealed that most BBX genes have undergone purifying selection during evolution. An analysis of transcriptome data from rapeseed (Brassica napus) organs suggested that BnaBBX3d might be involved in the development of floral tissue-specific RNA-seq expression. We identified numerous light-responsive elements in the promoter regions of BnaBBX genes, which were suggestive of participation in light signaling pathways. Transcriptomic analysis under shade treatment revealed 77 BnaBBX genes with significant changes in expression before and after shading treatment. Of these, BnaBBX22e showed distinct expression patterns in yellow- vs. black-seeded materials in response to shading. UPLC-HESI-MS/MS analysis revealed that shading influences the accumulation of 54 metabolites, with light response BnaBBX22f expression correlating with the accumulation of the flavonoid metabolites M46 and M51. Additionally, BnaBBX22e and BnaBBX22f interact with BnaA10.HY5. These results suggest that BnaBBXs might function in light-induced pigment accumulation. Overall, our findings elucidate the characteristics of BBX proteins in six Brassica species and reveal a possible connection between light and seed coat color, laying the foundation for further exploring the roles of BnaBBX genes in seed development.

Genetic diversity and signatures of selection in Icelandic horses and Exmoor ponies

BackgroundThe Icelandic horse and Exmoor pony are ancient, native breeds, adapted to harsh environmental conditions and they have both undergone severe historic bottlenecks. However, in modern days, the selection pressures on these breeds differ substantially. The aim of this study was to assess genetic diversity in both breeds through expected (HE) and observed heterozygosity (HO) and effective population size (Ne). Furthermore, we aimed to identify runs of homozygosity (ROH) to estimate and compare genomic inbreeding and signatures of selection in the breeds.ResultsHO was estimated at 0.34 and 0.33 in the Icelandic horse and Exmoor pony, respectively, aligning closely with HE of 0.34 for both breeds. Based on genomic data, the Ne for the last generation was calculated to be 125 individuals for Icelandic horses and 42 for Exmoor ponies. Genomic inbreeding coefficient (FROH) ranged from 0.08 to 0.20 for the Icelandic horse and 0.12 to 0.27 for the Exmoor pony, with the majority of inbreeding attributed to short ROHs in both breeds. Several ROH islands associated with performance were identified in the Icelandic horse, featuring target genes such as DMRT3, DOCK8, EDNRB, SLAIN1, and NEURL1. Shared ROH islands between both breeds were linked to metabolic processes (FOXO1), body size, and the immune system (CYRIB), while private ROH islands in Exmoor ponies were associated with coat colours (ASIP, TBX3, OCA2), immune system (LYG1, LYG2), and fertility (TEX14, SPO11, ADAM20).ConclusionsEvaluations of genetic diversity and inbreeding reveal insights into the evolutionary trajectories of both breeds, highlighting the consequences of population bottlenecks. While the genetic diversity in the Icelandic horse is acceptable, a critically low genetic diversity was estimated for the Exmoor pony, which requires further validation. Identified signatures of selection highlight the differences in the use of the two breeds as well as their adaptive trait similarities. The results provide insight into genomic regions under selection pressure in a gaited performance horse breed and various adaptive traits in small-sized native horse breeds. This understanding contributes to preserving genetic diversity and population health in these equine populations.

Prevalence of bovine trypanosomosis and tsetse fly density in Loka Abaya and Derara districts in Sidama Regional State, Ethiopia.

Animal trypanosomosis is a significant livestock disease with economic and social repercussions, reducing the supply of animal products and restricting the utilization of animals for traction and transportation. In Ethiopia, it is prevalent and poses a major hindrance to the advancement of animal production. This repeated cross-sectional study was aimed at assessing seasonal variation in bovine trypanosomosis prevalence and tsetse fly density and identifying the potential risk factors in the Loka Abaya and Derara districts of the Sidama National Regional State. Blood samples were collected from 964 cattle, 484 samples during the dry season, and 480 during the wet season. The buffy coat method was employed to analyze these samples. Furthermore, 78 standard NGU traps were set up at various locations in the two districts during both seasons for entomological investigation. The overall apparent prevalence of trypanosomosis was 9% (95% CI 7.3-11.0), without a significant difference (p > 0.05) between the dry season (7.4%) and wet season (10.6%). The apparent prevalence was significantly higher in Loka Abaya (11.8%) than in Derara (6.3%) district (OR = 2.04; p = 0.003) and in cattle with black coat color (29%) than in mixed color (6.8%) (OR = 5.3; p < 0.001). The majority of infections were caused by Trypanosoma congolense (70%), followed by T. vivax (29%), and mixed infections (1%) with the two species. The average packed cell volume (PCV) was significantly (p < 0.0001) lower in infected animals (20.7 ± 4%) compared to uninfected ones (25.5 ± 5.4%), in cattle examined during the dry season (24.1 ± 6%) versus the wet season (26.1 ± 4.7%), in cattle sampled from the Loka Abaya district (24.2 ± 5.5%) versus Derara district (26 ± 5.3%), and in cattle with poor body condition (23.6 ± 5.7%) compared to those with good body condition (26.5 ± 5.3%). A total of 5282 flies were captured during the study, with 4437 (84%) being tsetse flies (Glossina pallidipes), 439 (8.3%) Tabanids, 190 (3.6%) Stomoxys spp., and 216 (4.1%) Musca spp. The apparent density (AD) of G. pallidipes was 28.4 flies/trap/day, showing no statistically significant difference between wet (32.1) and dry (24.6) seasons (p > 0.05). The AD of G. pallidipes was significantly (p < 0.001) higher in the Loka Abaya district (57.3) than in the Derara district (0.9). The study highlights a moderate trypanosomosis apparent prevalence and high AD of G. pallidipes, showing significant variation between the study districts but no seasonal difference. The observed apparent prevalence of trypanosomosis and tsetse fly density notably affects animal health and productivity. As a result, strategies for vector control like insecticide-treated targets, trypanocidal medications for infected animals, and community-based initiatives such as education and participation in control programs are recommended.

Production system analysis and breeding practices of indigenous goats in North Wollo zone, Amhara region, Ethiopia

ABSTRACT This study describes the goat production system and breeding practices in selected districts of North Wollo zone, Ethiopia. Data were collected from 180 respondents through a semi-structured questionnaire and group discussions. Descriptive and GLM procedures were employed for data analysis. A mixed crop-livestock production system was the main production system in the area. The mean number of goats per household is 9.66 and they are mainly kept for cash income and meat consumption. The flock structure of indigenous goats consisted of a large number of female goats. Natural pasture and crop residue were the major feed resources in the dry and wet seasons, with an overall mean of 37.53% and 54.26%, respectively. Feed shortage, diseases, and drought were the major constraints for goat production. Most goat owners (97.1%) practiced an uncontrolled mating system. Most farmers (88.93%) reported selecting breeding goats to be a parent for the next generation. Body conformation and coat colour were the preferred traits for the selection of goats. The current level of goat management and breeding methods would not significantly enhance goats’ productivity and profitability. Therefore, designing management and genetic improvement programmes would be vital to improving the productivity of indigenous goats.

Whole-genome analyses reveal selective signals in four Xinjiang cattle breeds

Xinjiang is home to three indigenous cattle breeds (Xinjiang Mongolian, Altay white-headed, and Kazakh cattle) and one crossbreed (Xinjiang Brown cattle), each possessing distinct and remarkable characteristics. In this study, we conducted comprehensive genome analyses of these four breeds in comparison with eight representative cattle breeds from around the world. Despite being predominantly Bos taurus, the proportion of Bos indicus ancestry in these indigenous breeds decreases with increasing latitude. This mixed genomic composition contributes to higher nucleotide diversity, lower linkage disequilibrium, and larger effective population sizes. Notably, Xinjiang Brown cattle exhibited higher LD at short distances, faster LD decay, and the largest effective population size, indicative of hybrid characteristics. Furthermore, we identified selective signals for lipids dynamics and coat colour in Altay white-headed cattle, immune resistance to local pathogens in Kazakh cattle, hydro-electrolyte balance and immune response in Xinjiang Mongolian cattle, and rapid growth and large body size in Xinjiang Brown cattle, as well as substance metabolism in three indigenous cattle. Our findings not only deepen the understanding of breed origins and diversity but also provide a foundation for exploring the genetic mechanisms underlying breed characteristics and facilitating further breed improvement.