Search Results (133)

Mammals display a wide range of coat colors, with the melanocortin 1 receptor gene (MC1R) playing a pivotal role in the genetic regulation of pigmentation. In this study, we investigated MC1R genetic variants in goat populations from four Asian countries to identify genetic factors associated with coat color variation. The complete coding sequence of MC1R was analyzed to detect variants and determine genotypes in goats from Nepal (n = 122), the Philippines (n = 110), Cambodia (n = 30), and Kazakhstan (n = 30). Seven variants were identified, three of which were novel, while four had been previously reported in other goat populations. Among the novel variants, a frameshift mutation (c.147delG) unique to Nepalese goats was predicted to cause substantial disruption of the MC1R protein structure, suggesting its potential role in coat color determination. Additionally, two known missense variants (c.676A > G and c.801C > G) were inferred to affect MC1R function and may contribute to pigmentation variation. Further investigations with larger sample sizes are warranted to clarify the phenotypic effects of these genotypic variants and to better understand the genetic basis of coat color in goats. Full article

The local goat breeds of Chongqing represent the typical goat populations of Southwestern China and play a significant role in global goat research. However, studies on these goats remain limited. Chongqing goats exhibit diverse coat colors, a crucial economic trait essential for individual and breed identification. In this study, we performed genome-wide association analysis (GWAS) of Chongqing goats to identify candidate genes associated with coat color. The results of the GWAS revealed that the ASIP, AHCY, and ITCH genes on chromosome 13 are significantly associated with coat color variation in Chongqing goats. Furthermore, haplotype analysis, gene function annotation, and pathway analysis enrichment further confirmed that a significant region on chromosome 13 is associated with coat color in local Chongqing goats, and that ASIP and AHCY are related to black coat color, whereas ITCH is potentially associated with white coat expression. Additionally, we also identified TPK1 as being associated with coat color in goats, which has hardly been reported. The newly identified genes expand our understanding of the complex genetic architecture underlying pigmentation traits in livestock. Our study identifies the genes related to coat color in local goats, which enriches the genetic resource pool of goats and contributes to a deeper understanding of the genetic mechanisms underlying coat color in these breeds. Full article

Rarámuri Criollo (RC) cattle have been raised by the isolated Tarahumara communities of Chihuahua, Mexico, for nearly 500 years, mostly under natural selection and minimal management. RC cattle were introduced to the United States Department of Agriculture-Agricultural Research Service Jornada Experimental Range (RCJER) in 2005 to begin evaluations of beef production performance and their adaptation to the harsh ecological and climatic conditions of the Northern Chihuahuan Desert. While this research unveiled crucial information on their phenotypic plasticity and adaptation, the genetic diversity and structure of the RCJER population remains poorly understood. This study analyzed the genetic diversity, population structure, ancestral composition, and selection signatures of the RCJER herd using a ~64 K SNP array. The RCJER herd exhibits moderate genetic diversity and low population stratification with no evident clustering, suggesting a shared genetic background among different subfamilies. Admixture analysis revealed the RCJER herd represents a distinctive genetic pool within the Criollo cattle breeds, with significant Iberian ancestry. Selection signatures identified candidate genes and quantitative trait loci (QTL) for traits associated with milk composition, growth, meat and carcass, reproduction, metabolic homeostasis, health, and coat color. The RCJER population represents a distinctive genetic resource adapted to harsh environmental conditions while maintaining productive and reproductive attributes. These findings are crucial to ensuring the long-term genetic conservation of the RCJER and their strategic expansion into locally adapted beef production systems in the USA. Full article

Background: According to the One Health concept, the physical proximity between pets and their owners facilitates the interspecies spread of bacteria including those that may harbor numerous antimicrobial resistance genes (ARGs). Methods: A shotgun sequencing metagenomic data-based bacteriome and resistome study of 1830 canine saliva samples was conducted considering the subsets of ARGs with higher public health risk, ESKAPE pathogen relatedness (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species), and survey results on the physical and behavioral characteristics of the participating dogs. Results: A total of 318 ARG types achieved sufficiently high detection rates. These ARGs can affect 31 antibiotic drug classes through various resistance mechanisms. ARGs against tetracyclines, cephalosporins, and, interestingly, peptides appeared in the highest number of samples. Other Critically Important Antimicrobials (CIAs, WHO), such as aminoglycosides, fluoroquinolones, or macrolides, were among the drug classes most frequently affected by ARGs of higher public health risk and ESKAPE pathogen-related ARGs of higher public health risk. Several characteristics, including coat color, sterilization status, size, activity, or aggressiveness, were associated with statistically significant differences in ARG occurrence rates (p < 0.0500). Conclusions: Although the oral microbiome of pet owners is unknown, the One Health and public health implications of the close human–pet bonds and the factors potentially underlying the increase in salivary ARG numbers should be considered, particularly in light of the presence of ARGs affecting critically important drugs for human medicine. Full article

The color of the walnut seed coat is a critical determinant of its market value; however, research into the mechanisms responsible for seed coat color formation is yet to be determined. Using two walnut clones with contrasting pale-yellow and light purple seed coats, we characterized pigmentation, particularly anthocyanin content, using spectrophotometry. We then conducted integrated transcriptomic and metabolomic analyses to identify the molecular mechanisms and pathways underlying their formation. The anthocyanin content in the light purple seed coat clone was significantly greater than that in the clone with a white seed coat. The results of comparative metabolomics indicated that four anthocyanins (delphinidin, cyanidin-3-(caffeoylglucoside), pelargonidin-3-(6″-caffeoylglucoside), and delphinidin-3-O-sophoroside) were significantly more abundant in the light purple seed coat clone. These anthocyanins were the key pigments responsible for the light purple coloration of the walnut seed coat. Furthermore, comparative transcriptomics revealed that structural genes in the anthocyanin biosynthesis pathway (e.g., phenylalanine ammonia-lyase, 4-coumarate-CoA ligase, chalcone isomerase, and bronze-1) were significantly upregulated in the purple seed coat clone. Coexpression network analysis revealed that several transcription factors (e.g., ARF, bHLH, and MYB-related) were significantly correlated with the upregulation of these structural genes and the accumulation of four key anthocyanins. These transcription factors may serve as critical regulators influencing seed coat color formation. In conclusion, these findings establish a strong theoretical foundation for walnut breeding aimed at developing diverse seed coat colors. Full article

Cinnamyl alcohol dehydrogenase (CAD) is essential for lignin precursor synthesis and responses to various abiotic stresses in plants. However, the functions of CAD in Brassica species, especially in Brassica napus, remain poorly characterized. In the present study, we identified a total of 90 CAD genes across the Brassica U-triangle species, including B. rapa, B. nigra, B. oleracea, B. juncea, B. napus, and B. carinata. Comprehensive analyses of phylogenetic relationships, sequence identity, conserved motifs, gene structure, chromosomal distribution, collinearity, and cis-acting elements were performed. Based on phylogenetic analysis, these genes were categorized into four groups, designated as groups I to IV. Most of the CAD genes were implicated in mediating responses to abiotic stresses and phytohormones. Notably, members in group III, containing the bona fide CAD genes, were directly involved in lignin synthesis. Furthermore, the expression profiles of BnaCAD genes exhibited differential responses to drought, osmotic, and ABA treatments. The expression levels of the BnaCAD4a, BnaCAD4b, BnaCAD5b, and BnaCAD5d genes were detected and found to be significantly lower in yellow-seeded B. napus compared to the black-seeded ones. This study provides a comprehensive characterization of CAD genes in Brassica U-triangle species and partially validates their functions in B. napus, thereby contributing to a better understanding of their roles. The insights gained are expected to facilitate the breeding of yellow-seeded B. napus cultivars with enhanced stress tolerance and desirable agronomic traits. Full article

The seed-coat color and seed size have an impact on both the evolutionary fitness and the grain yield of crops. Soybean is a major oil crop, and the seed-coat color and seed size exhibit natural diversity among the different soybean varieties. Here, we found an R2R3-MYB transcription factor of GmMYB62, which shows a significant increase in expression as the seed-coat color changes from yellow to black in different soybean varieties. The GmMYB62 was specifically highly expressed in reproductive organs, especially in floral organs in soybeans. The GmMYB62 encodes a nuclear protein that contains two MYB domains. In the phylogenetic analysis, the GmMYB62 was relatively conserved after the divergence of the monocots and dicots, and it also grouped with transcriptional repressors of MYBs in anthocyanin synthesis. The GmMYB62 was overexpressed in Arabidopsis and the seeds displayed a pale-brown coat in GmMYB62 overexpression lines, in contrast to the dark-brown seed coat observed in wild-type of Col-0. The anthocyanin content in the GmMYB62 overexpression lines was dramatically reduced when compared to Col-0. Additionally, the seeds in overexpression lines showed shorter lengths, larger widths, and lower thousand-seed weights than those in Col-0. Furthermore, the genes related to anthocyanin synthesis and seed size regulation were investigated, and expression of eight genes that involved in anthocyanin synthesis pathway, like chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), and anthocyanidin synthase (ANS) were severely inhibited in the GmMYB62 overexpression lines when compared to Col-0. In addition, the ARGOS-LIKE (ARL), B-Type Cyclin 1 (CYCB1), and enhancer of DA1-1 (EOD3), which govern cell expansion and proliferation, were highly expressed in GmMYB62 overexpression lines when compared to Col-0. Overall, this study sheds new light on the control of seed-coat color and seed size by GmMYB62 and provides potentially valuable targets for improving crop seed quality. Full article

The conservation and utilization of livestock genetic resources is essential for the maintenance of biodiversity and breed innovation. Whole genome sequencing (WGS) was performed on 90 samples from Chinese Yangtze River Delta White goats (YRD), sourced from two populations of Chongming island white goats and Haimen white goats, aiming to dissect their genomic characteristics. In addition, 262 WGS data from nine other breeds of goats were downloaded from the NCBI database. These WGS data obtained were used to identify and analyze genetic variation with the goat reference genome, and the genetic structure of goat populations was analyzed. Through selective sweep analysis, the selection-signature genes and their polymorphic features were identified. It was found that the most significant genomic selection region in YRD goats was in the region of 62.9–64.6 Mb on chromosome 13, which contained genes related to the coat color and muscle growth of the goats. Nucleotide diversity of MYH7B, a gene related to the development of the goat’s skeletal muscle, within the Yangtze River Delta white goat population was significantly lower than in other domestic and foreign goat breeds, suggesting that the gene was subject to selection. In addition, the IGF2BP2 gene, reported to be associated with litter size in goats, showed clear selection-signature characteristics in the Boer goats compared to the YRD goats. Full article

Background/Objectives: Research on cashmere goat coat color is crucial for optimizing cashmere goat breeds and increasing their economic value. To identify key genes associated with the formation of cashmere goat coat color and to provide molecular markers for breeding purposes, three healthy, 3-year-old does with similar weights and distinct coat colors—white, black, and light brown—were selected. Methods: Skin samples were collected for transcriptome sequencing, and bioinformatics methods were applied to screen for differentially expressed genes (DEGs) in the skin of cashmere goats with varying coat colors. Real-time fluorescence quantitative PCR (qRT-PCR) and immunofluorescence were subsequently conducted to examine the expression patterns of these DEGs. Results: The results showed that a total of 1153 DEGs were identified across the three groups of cashmere goats. According to GO and KEGG analyses, these DEGs were involved in key biological processes and structures, such as the melanin biosynthetic process (GO:0042438), melanosome membrane (GO:0033162), and melanin biosynthesis from tyrosine (GO:0006583). Employing Cytoscape, a gene interaction network was plotted, highlighting a compact network of DEGs associated with coat color formation. Critical genes identified included TYRP1, TYR, DCT, ASIP, PMEL, LOC102180584, MLANA, TSPAN10, TRPM1, CLDN16, AHCY, LOC106503350, and LOC102175263. qRT-PCR and fluorescence immunohistochemistry further determined that TYRP1, TYR, DCT, and PMEL expression levels were high in black goats (BGs), while ASIP and AHCY expression levels were high in white goats (WGs). The expression levels of these six genes in light brown goats (RGs) were intermediate between those in BGs and WGs. Conclusions: TYRP1, TYR, DCT, and PMEL were believed to play pivotal roles in the formation of black coat color, while ASIP and AHCY regulated the formation of white coat color in cashmere goats. Full article

Endothelin Receptor Type B (EDNRB) is expressed in a variety of cells during embryonic stage, including melanocyte precursors cells. Our previous studies found that 11 bp deletion of EDNRB caused the two-end black (TEB) coat color in Chinese pigs. In this study, we aimed to explore the mutant EDNRB on the formation of TEB coat color in Chinese pigs. We constructed recombinant plasmid for wild and mutant EDNRB and EDN1, respectively, and transfected the recombinant plasmid into mouse B16 melanoma cells in groups. Real-time fluorescent quantitative PCR (RT-qPCR) was performed to detect expression of genes that participate in melanin pathway, including PLCγ, Raf, MITF. Comparing to the wild-type EDNRB cells, expression of the three genes in the cell line expressing mutant EDNRB cells was significantly reduced. We measured the melanin content produced by transfected recombinant granulocytes of wild and mutant EDNRB and found that the amount of melanin in mutant EDNRB cells was significantly lower than that of the wild. Wound-healing assay confirmed that the migration and mobility rate of mutant EDNRB cells were significantly lower than the wild. Co-immunoprecipitation further confirmed that mutant EDNRB could not interact with the EDN1 protein. In conclusion, this study revealed that the 11 bp deletion of EDNRB reduced the melanin production, which may be caused by inhibiting the expression of PLCγ, Raf, and MITF. The mutant EDNRB reduced melanocyte migration and could not interact with the EDN1 protein. We explored the effect of mutant EDNRB in Chinese pigs with TEB coat color, and the results provided a reference for exploring molecular mechanism of mutant EDNRB on the formation of TEB coat color pigs. Full article

Background: 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. Methods: In this study, four lines of seed coats with different colors (medium yellow 14, black, green, and brown) were selected from the F_2:5 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. Results: 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. Conclusions: 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. Full article

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. Full article

Background/Objectives: The Mongolian horse, one of the oldest and most genetically diverse breeds, exhibits a wide variety of coat colors and patterns, including both wild-type and unique features. A notable characteristic of dun Mongolian horses is the presence of Bider markings—symmetrical, black-mottled patterns observed on the shoulder blades. These markings are also seen in Przewalski’s horses. The dun coat color, a common wild-type phenotype in domestic horses, is characterized by pigment dilution with distinct dark areas and is regulated by mutations in the TBX3 gene. This study aimed to investigate the role of TBX3 in the development of Bider markings in dun Mongolian horses. Methods: Skin tissue samples were collected from three key anatomical regions of dun Mongolian horses with Bider markings: the croup, dorsal midline, and shoulder. Histological staining was conducted to examine the skin and hair follicle structure and pigment distribution. RT-qPCR was used to measure TBX3 mRNA expression, while immunoblotting and immunohistochemistry were employed to analyze TBX3 protein levels and localization. Results: Hematoxylin and eosin staining revealed the skin and hair follicle structures, including the epidermis, hair shaft, and hair bulb across different stages of the hair growth cycle. Differences in pigmentation were observed across the sampling sites. The croup and the light-colored area of the shoulder showed asymmetrical pigmentation, while the dorsal midline and dark-colored area of the shoulder displayed symmetrical pigmentation. TBX3 mRNA expression levels were significantly higher in the croup compared to the shoulder and dorsal midline; however, corresponding TBX3 protein expression did not show significant differences. Immunohistochemical analysis localized TBX3 protein predominantly in the hair bulb and epidermis. Conclusions: This study demonstrates region-specific differences in TBX3 expression that correlate with pigmentation patterns in dun Mongolian Bider horses. These findings provide valuable insights into the molecular mechanisms underlying Bider markings, offering a deeper understanding of the genetic regulation of coat color and primitive markings in equines. Full article

The Chinese Tan sheep is a unique breed of sheep that is typical throughout China, mainly used for fur and meat production. They are widely distributed in northwestern China and are famous for their lambskin and shiny white curly wool. In this study, the phenotypic traits of wool length, birth weight, and head coat color were evaluated in 256 Chinese Tan sheep breeds. Whole genome sequencing generated 23.67 million high-quality SNPs for genome-wide association studies (GWAS). We identified 208 significant SNPs associated with birth wool length, implicating RAD50, MACROD2, SAMD5, SASH1, and SPTLC3 as potential candidate genes for this trait. For birth weight, 1056 significant SNPs, with 76.89% of them located on chromosome 2, were identified by GWAS, and XPA, INVS, LOC121818504, GABBR2, LOC101114941, and LOC106990096 were identified as potential candidate genes for birth weight. The GWAS for head coat color identified 1424 significant SNPs across three chromosomes, with 99.65% on chromosome 14, and SPIRE2, TCF25, and MC1R as candidate genes were found to be possibly involved in the development of the black-headed coat color in sheep. Furthermore, we selected head coat color as a representative trait and performed an independent test of our GWAS findings through multiplex PCR SNP genotyping. The findings validated five mutation sites in chromosome 14 (14,251,947 T>A, 14,252,090 G>A, 14,252,158 C>T, 14,252,329 T>G, and 14,252,464 C>T) within the exon1 of the MC1R gene (517 bp), as identified by GWAS in an additional 102 Tan sheep individuals, and revealed that black-headed sheep predominantly exhibited heterozygous genotypes, possibly contributing to their color change. Our results provide a valuable foundation for further study of these three economically important traits, and enhance our understanding of genetic structure and variation in Chinese Tan sheep. Full article

(1) Background: Buffaloes are crucial livestock species for food and service in tropical and subtropical regions. Buffalo genetics, particularly in indigenous Chinese breeds such as the Xiangxi white buffalo (XWB), remains an intriguing area of study due to its unique traits and regional significance. (2) Methods: This investigation utilized the whole-genome sequences of twenty XWBs (newly sequenced), along with eighty published whole-genome sequences of other buffalo breeds (including Guizhou white buffalo, river buffalo, and Chinese buffalo in the Yangtze River). Using whole-genome sequencing analysis technology, the population structure, genomic diversity, and selection signatures of XWB were determined. (3) Results: This study revealed that the XWB, being phylogenetically positioned in the middle and lower reaches of the Yangtze River, exhibited substantial genomic diversity. Employing four selection sweep detection methods (CLR, iHS, π-ratio, and F_ST), several genes were positively identified for adaptive traits in the XWB, including coat color phenotypes (ASIP, KIT), the nervous system (GRIK2), reproduction (KCNIP4), growth and development (IFNAR1, BMP6, HDAC9, MGAT4C, and SLC30A9), the body (LINGO2, LYN, and FLI1), immunity (IRAK3 and MZB1), and lactation (TP63, LPIN1, SAE1). (4) Conclusions: In conclusion, this study enhances our understanding of the genetic distinctiveness and adaptive traits of XWB, highlighting selection signatures crucial for future breeding and conservation and ensuring sustainable use of this vital livestock resource. Full article