Search Results (42)

Background/Objectives: Buffalo populations exhibit distinct genetic variations influenced by domestication history, geographic distribution, and selection pressures. This study investigates the genetic structure and differentiation of 11 buffalo populations, focusing on five loci related to milk protein (CSN1S1 and CSN3) and fat metabolism (LPL, DGAT1 and SCD). The aim is to assess genetic variation between river, swamp, and wild-type buffaloes and identify key loci contributing to population differentiation. Methods: Genetic diversity was analyzed through allele frequency distribution, the Hardy−Weinberg equilibrium testing, and observed (Ho) and expected heterozygosity (He) calculations. Population structure was assessed using principal component analysis (PCA), F_ST statistics, and phylogenetic clustering (k-means and UPGMA tree). The silhouette score (SS) and the Davies−Bouldin index (DBI) were applied to determine optimal population clustering. Results: Significant genetic differentiation was observed between river and swamp buffaloes (p < 0.001). DGAT1 and CSN3 emerged as key markers distinguishing buffalo types. The Italian Mediterranean buffalo exhibited the highest genetic diversity (Ho = 0.464; He = 0.454), while the Indonesian, Chinese, and Vietnamese populations showed low heterozygosity, likely due to selection pressures and geographic isolation. The global F_ST (0.2143; p = 0.001) confirmed moderate differentiation, with closely related populations (e.g., Nepal and Pakistan) exhibiting minimal genetic divergence, while distant populations (e.g., Egypt and Indonesia) showed marked differences, and the Romanian population showed a unique genetic position. Conclusions: These findings contribute to a deeper understanding of buffalo genetic diversity and provide a valuable basis for exploiting the potential of this species in the light of future breeding and conservation strategies specific for each buffalo type. Full article

Tailings generated by mining account for the largest world-wide waste from industrial activities. As an element, copper is relatively uncommon, with low concentrations in sediments and waters, yet is very elevated around mining operations. On the Keweenaw Peninsula of Michigan, USA, jutting out into Lake Superior, 140 mines extracted native copper from the Portage Lake Volcanic Series, part of an intercontinental rift system. Between 1901 and 1932, two mills at Gay (Mohawk, Wolverine) sluiced 22.7 million metric tonnes (MMT) of copper-rich tailings (stamp sands) into Grand (Big) Traverse Bay. About 10 MMT formed a beach that has migrated 7 km from the original Gay pile to the Traverse River Seawall. Another 11 MMT are moving underwater along the coastal shelf, threatening Buffalo Reef, an important lake trout and whitefish breeding ground. Here we use remote sensing techniques to document geospatial environmental impacts and initial phases of remediation. Aerial photos, multiple ALS (crewed aeroplane) LiDAR/MSS surveys, and recent UAS (uncrewed aircraft system) overflights aid comprehensive mapping efforts. Because natural beach quartz and basalt stamp sands are silicates of similar size and density, percentage stamp sand determinations utilise microscopic procedures. Studies show that stamp sand beaches contrast greatly with natural sand beaches in physical, chemical, and biological characteristics. Dispersed stamp sand particles retain copper, and release toxic levels of dissolved concentrations. Moreover, copper leaching is elevated by exposure to high DOC and low pH waters, characteristic of riparian environments. Lab and field toxicity experiments, plus benthic sampling, all confirm serious impacts of tailings on aquatic organisms, supporting stamp sand removal. Not only should mining companies end coastal discharges, we advocate that they should adopt the UNEP “Global Tailings Management Standard for the Mining Industry”. Full article

Background/Objectives: Sterol regulatory element-binding transcription factor 2 (SREBF2) is a key transcription factor involved in regulating cholesterol homeostasis. However, its role in buffalo mammary gland lipid metabolism remains unclear. Methods: To address this, we isolated and characterized the SREBF2 gene from buffalo mammary glands and performed an in-depth analysis of its molecular characteristics, tissue-specific expression, and functional roles in buffalo mammary epithelial cells (BuMECs). Additionally, we investigated the single nucleotide polymorphisms (SNPs) of SREBF2 in both river and swamp buffalo. Results: The coding sequence (CDS) of buffalo SREBF2 is 3327 bp long and encodes a protein of 1108 amino acid residues. Bioinformatics analysis revealed that the molecular characteristics of buffalo SREBF2 were highly similar across Bovidae species, with collinearity being observed among them. An expression profile analysis revealed that SREBF2 is expressed in all 11 tested tissues of buffalo, with its expression level in the mammary gland being higher during lactation than in the dry period. The knockdown of SREBF2 in BuMECs during lactation led to a significant reduction in the expression of genes involved in triglyceride (TAG) and cholesterol synthesis, including PI3K, AKT, mTOR, SREBF1, PPARG, INSIG1, ACACA, SCD, DGAT1, LPL, CD36, HMGCR, and SQLE. This knockdown led to a 23.53% and 94.56% reduction in TAG and cholesterol levels in BuMECs, respectively. In addition, a total of 22 SNPs were identified in both buffalo types, of which four non-synonymous substitutions (c.301G>C, c.304A>T, c.1240G>A, and c.2944G>A) were found exclusively in the SREBF2 CDS of swamp buffalo, and the assessment revealed that these substitutions had no impact on SREBF2 function. Conclusions: These findings emphasize the critical role of SREBF2 in regulating both triglyceride and cholesterol biosynthesis, providing valuable insights into its functions in buffalo mammary glands. Full article

Understanding the state of the swamp buffalo population in Calayan Island is important to strengthen the conservation and management program in the country. This study aimed to provide insights into the morphology, population structure, and health profile of the swamp buffaloes on the island. In total, 35 fresh blood samples were analyzed using 27 polymorphic microsatellite markers to determine the population structure analysis. Data were gathered for the morphological features of Calayan swamp buffaloes and served as the baseline information for the descriptive traits. Furthermore, samples were tested for surra and brucellosis using PCR and serological tests, respectively. The results showed that Calayan swamp buffaloes were morphologically bigger, except for body length, compared with other populations. A genotype analysis using microsatellite markers showed remarkable discriminatory power to distinguish distinct populations within the tested population, and could discriminate subspecies of swamp and river types plus crossbreds. The study also reports the first incidence of surra and brucellosis on the island. Overall, the new insights provided on the newly detected Philippine carabao lineage in Calayan Island would be highly recommended for the ex situ conservation and animal health control strategy. The conservation strategy would encompass collecting, cryopreserving, and storing viable germplasms from local swamp buffalo on Calayan Island. 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

This study aimed to identify SNPs in the intron, exon, and UTR regions of the FASN, DGAT1, and PPARGC1A genes and to investigate their possible association with milk yield and composition traits in the riverine buffalo of Bangladesh. A total of 150 DNA samples from riverine buffalo were used for PCR amplification with five pairs of primers, followed by association studies using a generalized linear model in R. SNP genotyping was performed by direct sequencing of the respective amplicon. Traits analyzed included DMY, fat%, protein%, and SNF%. This study identified 8 SNPs in FASN (g.7163G>A and g.7271C>T), DGAT1 (g.7809C>T and g.8525C>T) and PPARGC1A (g.387642C>T, g.387758A>G, g.409354A>G, and g.409452G>A). Genotypic and allelic frequencies differed significantly for each SNP genotype and did not follow the Hardy–Weinberg principle (p < 0.01 or p < 0.001) in most cases. The g.7163G>A and g.7271C>T SNP genotypes of the FASN gene were significantly associated with milk fat%, with the latter also significantly associated with SNF%. The g.8525C>T polymorphism of the DGAT1 gene significantly affected protein% (p < 0.01). Additionally, PPARGC1A gene polymorphisms showed significant associations: g.387642C>T with fat% (p < 0.05); g.387758A>G and g.409354A>G with protein% (p < 0.001) and SNF% (p < 0.01); and g.409452G>A with DMY (p < 0.001), fat% (p < 0.05), and protein% (p < 0.01). Reconstructed haplotypes of the PPARGC1A gene were significantly associated (p < 0.01) with all traits except SNF%. These findings suggest that polymorphisms in these three candidate genes have the potential as molecular markers for improving milk yield and composition traits in the riverine buffalo of Bangladesh. Full article

The search for DNA polymorphisms useful for the genetic improvement of dairy farm animals has spanned more than 40 years, yielding relevant findings in cattle for milk traits, where the best combination of alleles for dairy processing has been found in casein genes and in DGAT1. Nowadays, similar results have not yet been reached in river buffaloes, despite the availability of advanced genomic technologies and accurate phenotype records. The aim of the present study was to investigate and validate the effect of four single nucleotide polymorphisms (SNP) in the CSN1S1, CSN3, SCD and LPL genes on seven milk traits in a larger buffalo population. These SNPs have previously been reported to be associated with, or affect, dairy traits in smaller populations often belonging to one farm. A total of 800 buffaloes were genotyped. The following traits were individually recorded, monthly, throughout each whole lactation period from 2010 to 2021: daily milk yield (dMY, kg), protein yield (dPY, kg) and fat yield (dFY, kg), fat and protein contents (dFP, % and dPP, %), somatic cell count (SCC, 10³ cell/mL) and urea (mg/dL). A total of 15,742 individual milk test day records (2496 lactations) were available for 680 buffalo cows, with 3.6 ± 1.7 parities (from 1 to 13) and an average of 6.1 ± 1.2 test day records per lactation. Three out four SNPs in the CSN1S1, CSN3 and LPL genes were associated with at least one of analyzed traits. In particular, the CSN1S1 (AJ005430:c.578C>T) gave favorable associations with all yield traits (dMY, p = 0.022; dPY, p = 0.014; dFY, p = 0.029) and somatic cell score (SCS, p = 0.032). The CSN3 (HQ677596: c.536C>T) was positively associated with SCS (p = 0.005) and milk urea (p = 0.04). Favorable effects on daily milk yield (dMY, p = 0.028), fat (dFP, p = 0.027) and protein (dPP, p = 0.050) percentages were observed for the LPL. Conversely, the SCD did not show any association with milk traits. This is the first example of a confirmation study carried out in the Mediterranean river buffalo for genes of economic interest in the dairy field, and it represents a very important indication for the preselection of young bulls destined for breeding programs aimed at more sustainable dairy production. Full article

Household buffalo dairy farming is gaining popularity nowadays in Bangladesh because of the outstanding food value of buffalo milk as well as the lower production cost of buffalo compared to cattle. An initiative has recently been taken for the genetic improvement of indigenous dairy buffaloes. The present study was carried out to determine the influence of some environmental factors like age, parity, season of calving, calving interval, dry period on the lactation yield, and lactation curve of indigenous dairy buffaloes of Bangladesh. A total of 384 indigenous dairy buffaloes from the 3rd and 4th parity of seven herds under two different agroecological zones covering four seasons were selected and ear tagged for individual buffalo milk recording. A milk yield of 300 days (MY300d) was calculated following the International Committee for Animal Recording (ICAR) and the data were evaluated using the generalized linear model (GLM). In production traits, the mean of calculated lactation period (CLP), calculated lactation yield (CLY), and milk yield of 300 days (MY300d) of the overall population were 267.28 days, 749.36 kg, and 766.92 kg, respectively, whereas calving interval (CI) and dry period (DP) as reproductive traits were 453.06 days and 185.78 days, respectively. The season of calving, age of buffalo cows, population or herd, agroecological zone, calving interval, and dry period had significant effects on production traits (p < 0.05 to p < 0.001). The season of calving, level of milk production of 300 days, population, and agroecological zone significantly affected the reproduction traits (p < 0.01 to p < 0.001). Parity was found to be non-significant for both types of traits. The average peak yield of test day (TD) milk production was highest at TD4 (4.47 kg, 98th day of lactation). The average MY300d of milk production was the highest in the Lalpur buffalo population (1076.13 kg) and the lowest in the buffalo population of Bhola (592.44 kg). The correlations between milk production traits (CLP, CLY, and MY-300d) and reproduction traits (CI and DP) were highly significant (p < 0.01 to p < 0.001). Positive and high correlation was found within milk traits and reproduction traits, but correlation was negative between milk traits and reproduction traits. Therefore, these non-genetic factors should be considered in the future for any genetic improvement program for indigenous dairy buffaloes in Bangladesh. Full article

The increasing drought frequency poses a significant threat to global and regional river systems and ecosystem functioning, especially in the complex topographical Buffalo River catchment area of the Eastern Cape Province, South Africa. This study explored the impact of drought on riparian vegetation dynamics using the Normalize Difference Vegetation Index (NDVI), Transformed Difference Vegetation Index (TDVI) and Modified Normalized Difference Water Index (MNDWI) from satellite-derived Landsat data from 1990 to 2020. The least-squares linear regression and Pearson’s correlation coefficient were used to evaluate the long-term drought in riparian vegetation cover and the role of precipitation and streamflow. The correlation results revealed a moderate positive correlation (r = 0.77) between precipitation and streamflow with a significant p-value of 0.04 suggesting consequences on riparian vegetation health. Concurrent with the precipitation, the vegetation trends showed that precipitation increased insignificantly with less of an influence while the reverse was the case with the streamflow in the long term. The results show that the NDVI and TDVI were significant indices for detecting water-stressed vegetation in river catchment dynamics. Much of these changes were reflected for MNDWI in dry areas with a higher accuracy (87.47%) and dense vegetation in the upper catchment areas. The standardized precipitation index (SPI) revealed the inter-annual and inter-seasonal variations in drought-stressed years between 1991–1996, 2000–2004, 2009–2010, 2015, and 2018–2019, while 2020 exhibited slight sensitivity to drought. The findings of this study underscore the need for heightened efforts on catchment-scale drought awareness for policy development, programs, and practices towards ecosystem-based adaptation. Full article

Historically, 23 freshwater mussel species have been documented from the Buffalo National River (BNR), a 246 km, free-flowing river in northern Arkansas. The potential threats to BNR include land use/land cover changes, eutrophication, recreation, physical habitat changes, and various climate change-related effects. Twelve quantitative mussel bed sites were established and then sampled using a stratified random sampling protocol to evaluate the long-term changes between 2006 and 2020–2021 in population and assemblage characteristics. We compared (1) overall mussel bed persistence, sampling confidence levels and study-wide relative abundances, and compared species’ size and size-frequency distributions; (2) 10 overall site assemblage variables using paired t-tests; (3) site-level mean density, richness, and diversity indices using pair-wise Mann–Whitney U statistics; and (4) assemblage composition using Non-Metric Multidimensional Scaling. The major findings included the following: (1) sampling efforts based on a targeted 80% confidence level appears relatively robust, (2) BNR mussel assemblage composition and structure were relatively stable (however, small mussel bed persistence is a concern), (3) 7 of 23 sites were outliers based on freshwater mussel composition and habitat characteristics, and (4) assemblage composition changed with three species declining (Actinonaias ligamentina, Lasmigona costata, and Ptychobranchus occidentalis) and four species increasing (Cambarunio hesperus, Cyclonaias tuberculata, Eurynia dilatata, and Venustaconcha pleasii) between monitoring events. Full article

The ATP-binding cassette subfamily G member 2 (ABCG2) serves crucial roles in secreting riboflavin and biotin vitamins into the milk of cattle, mice, and humans, as well as in the transportation of xenotoxic and cytostatic drugs across the plasma membrane. However, the specific role of the ABCG2 gene in water buffaloes (Bubalus bubalis), especially its effect on milk fat synthesis in buffalo mammary epithelial cells (BuMECs), remains inadequately understood. In this study, the full-length CDS of the buffalo ABCG2 gene was isolated and identified from the mammary gland in buffaloes. A bioinformatics analysis showed a high degree of similarity in the transcriptional region, motifs, and conservative domains of the buffalo ABCG2 with those observed in other Bovidae species. The functional role of buffalo ABCG2 was associated with the transportation of solutes across lipid bilayers within cell membranes. Among the 11 buffalo tissues detected, the expression levels of ABCG2 were the highest in the liver and brain, followed by the mammary gland, adipose tissue, heart, and kidney. Notably, its expression in the mammary gland was significantly higher during peak lactation than during non-lactation. The ABCG2 gene was identified with five SNPs in river buffaloes, while it was monomorphic in swamp buffaloes. Functional experiments revealed that ABCG2 increased the triglyceride (TAG) content by affecting the expression of liposynthesis-related genes in BuMECs. The results of this study underscore the pivotal role of the ABCG2 gene in influencing the milk fat synthesis in BuMECs. Full article

The prevalence of Schistosoma mekongi in humans in the Lao People’s Democratic Republic (Lao PDR) has been relatively well monitored and has decreased due to effective interventions such as preventative chemotherapy with mass drug administration of praziquantel and community awareness programs. However, the prevalence among potential domestic reservoir animals remains broadly unclear, except for a few villages in the endemic area. Therefore, we conducted S. mekongi surveys for the domestic animals that had contact with Mekong River water. We conducted a cross-sectional study of the domestic animals in the seven sentinel villages in the Khong and Mounlapamok Districts of Champasak Province in southern Lao PDR in 2018 by random sampling with a statistically reliable sample size. Stool samples of the five predominant domestic animal species, cattle (n = 160), pig (n = 154), buffalo (n = 149), dog (n = 143), and goat (n = 85), were collected and examined using parasitological FECT method and the LAMP technique. The microscopic analysis did not detect any eggs of S. mekongi in the stool samples of any animal species. However, S. mekongi DNA was detected by the LAMP test in dog stool samples (0.7%; 1/143). On the other hand, the prevalence of other helminths was quite high and heterogeneous among animal species and sentinel sites by the microscopic analysis. These findings suggested that an intervention for S. mekongi infection should focus solely on human populations. However, periodic surveillance for S. mekongi infection among dogs should be conducted to monitor a possible resurgence of S. mekongi infection in the domestic animal population. Full article

Toll-like receptors (TLRs) are transmembrane proteins important for directing immune responses. Their primary role is to recognize pathogens based on single-nucleotide polymorphism (SNP) characteristics. TLR2 is categorized as a pattern recognition receptor (PRR) that is important for the recognition of pathogens. Nucleotide variation in the coding region determines the conformation of the TLR protein, affecting its protein domain efficiency. This study aimed to identify SNPs in the coding region of TLR2 to enhance available genetic tools for improving health and production in swamp buffalo. A total of 50 buffaloes were randomly sampled from the northeastern part of Thailand for genomic DNA extraction and sequencing. Nucleotide sequences were aligned and compared with cattle and river buffalo based on the database. The results showed, there were 29 SNP locations in swamp buffalo and 14 different locations in both cattle and buffaloes. Haplotype analysis revealed that 27 haplotypes occurred. Swamp buffalo were identified from 13 SNPs based on biallelic analysis, which found eight synonymous and five nonsynonymous SNPs. Nucleotide diversity (π) was 0.16, indicating genetic diversity. Genetic diversity (haplotype diversity; HD) was high at 0.99 ± 0.04. This indicates a high probability that the two sample haplotypes are different. The π and HD values are important indicators of the genetic diversity of the swamp buffalo population. In summary, the Thai swamp buffalo population detected a polymorphism of the coding region of the TRL2 gene. Therefore, further, in-depth study of the relationship between these genes in the immune system and disease resistance should be recommended. Full article

The water bodies of the Saskatchewan Prairies suffer multiple stressors, and demand for water is expected to increase. Water quality models can help evaluate water management strategies and risks such as climate change. This study assesses the impact of interbasin water transfers on the water quality of a strategic, eutrophic prairie reservoir that receives poor-quality watershed run-off. A one-dimensional WASP model was used to estimate nutrient transformations in the transfers along a 97 km river channel. The WASP model was then loosely coupled to a two-dimensional CE-QUAL-W2 model of the downstream receiving reservoir. Output from the WASP model was manually transformed into boundary conditions for the CE-QUAL-W2 reservoir model. This method improves on an earlier attempt to estimate nutrient transformations in the transfers using linear regression. Results from the loosely coupled models suggest Buffalo Pound Lake would respond well to the interbasin transfers. The number of threshold exceedances decreased for all modeled water quality variables. Nutrient concentrations were most influenced in the open water season following spring freshet. Any additional reduction of threshold exceedances during winter was minimal in comparison. These results are interesting from a management perspective as increased transfers under winter operations risk ice damage to the river channel. Full article

Fat deposition is a significant economic trait in livestock animals. Adipose tissues (ATs) developed in subcutaneous and visceral depots are considered waste whereas those within muscle are highly valued. In river buffaloes, lipogenesis is highly active in subcutaneous (especially in the sternum subcutaneous) and visceral depots but not in muscle tissue. Revealing the features and functions of ATs in different depots is significant for the regulation of their development. Here, we characterize the cell size, composition, and function of six AT depots in river buffaloes. Our data support that the subcutaneous AT depots have a larger cell size than visceral AT depots, and the subcutaneous AT depots, especially the sternum subcutaneous AT, are mainly associated with the extracellular matrix whereas the visceral AT depots are mainly associated with immunity. We found that sternum subcutaneous AT is significantly different from ATs in other depots, due to the high unsaturated fatty acid content and the significant association with metabolic protection. The perirenal AT is more active in FA oxidation for energy supply. In addition, the expression of HOX paralogs supports the variable origins of ATs in different depots, indicating that the development of ATs in different depots is mediated by their progenitor cells. The present study enhances our understanding of the cellular and molecular features, metabolism, and origin of AT depots in buffaloes, which is significant for the regulation of fat deposition and provides new insights into the features of AT depots in multiple discrete locations. Full article