Asian water buffalo: domestication, history and genetics

Molecular diagnosis and phylogenetic insights of Eimeria species infecting buffaloes (Bubalus bubalis) in Meghalaya's subtropical hilly region, India

Coccidiosis is an intestinal infection caused by Eimeria spp. that results in economic losses owing to morbidity and mortality in young buffalo calves. This study aimed for molecular diagnosis and phylogenetic analysis of Eimeria spp. in buffaloes of Meghalaya's sub-tropical mountainous terrain. Fresh buffaloes' fecal samples were collected from buffalo farms of Umling, Umsning and Bhoirymbong blocks, Ri Bhoi, Meghalaya and screened for Eimeria oocysts using flotation and modified McMaster methods. Fecal sample examination revealed 27.44 % (87/317) infection in buffaloes. Age wise, 64.44 % (29/45), 25.35 % (36/142) and 16.92 % (22/130) infections were recorded in <6 months, 6 months to 1 year and 1-2 year old buffaloes, respectively. Morphological characterization of Eimeria spp. revealed E. bovis (21.83 %), E. bareillyi (18.39 %), E. zuernii (11.49 %), E. ellipsoidalis (3.44 %) and mixed infection (44.82 %). Amplification of ITS-1 gene confirmed Eimeria spp. (410 bp), E. bovis (238 bp) and E. zuernii (344 bp). Phylogenetic analysis of E. bovis Umiam isolate revealed that these were closely related to the E. bovis isolate from South Korea (MH245198.1), and Turkey (KU351711.1) and distantly related to the isolates from Jammu and Kashmir (OQ103422.1) and Uttar Pradesh, Mathura (OK486542.1). E. zuernii isolate from Umiam, Meghalaya was observed to be phylogenetically close to the isolates from South Korea (MH245202.1), Japan (LC171339.1) and Turkey (KU351715.1), whereas phylogenetic divergence was observed between, E. zuernii isolate from Umiam, Meghalaya with isolates of Andhra Pradesh, Tirupati (MN601278.1) and Jammu and Kashmir (OQ103424.1). Therefore, treatment and effective control strategies should be implemented immediately to prevent spread of infection in the buffaloes.

Genome-wide comparative analyses highlight selection signatures underlying saline adaptation in Chilika buffalo

Chilika, a native buffalo breed of the Eastern coast of India, is mainly distributed around the Chilika brackish water lake connected with the Bay of Bengal Sea. This breed possesses a unique ability to delve deep into the salty water of the lake and stay there to feed on local vegetation of saline nature. Adaptation to salinity is a genetic phenomenon; however, the genetic basis underlying salinity tolerance is still limited in animals, specifically in livestock. The present study explores the genetic evolution that unveils the Chilika buffalo's adaptation to the harsh saline habitat, including both water and food systems. For this study, whole genome resequencing data on 18 Chilika buffalo and for comparison 10 Murrah buffalo of normal habitat were generated. For identification of selection sweeps, intrapopulation and interpopulation statistics were used. A total of 709, 309, 468, and 354 genes were detected to possess selection sweeps in Chilika buffalo using the nucleotide diversity (θπ), Tajima's D, nucleotide diversity ratio (θπ-ratio), and FST methods, respectively. Further analysis revealed a total of 23 genes including EXOC6B, VPS8, LYPD1, VPS35, CAMKMT, NCKAP5, COMMD1, myosin light chain kinase 3 (MYLK3), and B3GNT2 were found to be common by all the methods. Furthermore, functional annotation study of identified genes provided pathways such as MAPK signaling, renin secretion, endocytosis, oxytocin signaling pathway, etc. Gene network analysis enlists that hub genes provide insights into their interactions with each other. In conclusion, this study has highlighted the genetic basis underlying the local adaptive function of Chilika buffalo under saline environment.NEW & NOTEWORTHY Indian Chilika buffaloes are being maintained on extensive grazing system and have a unique ability to convert local salty vegetation into valuable human food. However, adaptability to saline habitat of Chilika buffalo has not been explored to date. Here, we identified genes and biological pathways involved, such as MAPK signaling, renin secretion, endocytosis, and oxytocin signaling pathway, underlying adaptability of Chilika buffalo to saline environment. This investigation shed light on the mechanisms underlying the buffalo's resilience in its native surroundings.

Mapping threatened Thai bovids provides opportunities for improved conservation outcomes in Asia

Wild bovids provide important ecosystem functions as seed dispersers and vegetation modifiers. Five wild bovids remain in Thailand: gaur (Bos gaurus), banteng (Bos javanicus), wild water buffalo (Bubalus arnee), mainland serow (Capricornis sumatraensis) and Chinese goral (Naemorhedus griseus). Their populations and habitats have declined substantially and become fragmented by land-use change. We use ecological niche models to quantify how much potential suitable habitat for these species remains within protected areas in Asia and then specifically Thailand. We combined species occurrence data from several sources (e.g. mainly camera traps and direct observation) with environmental variables and species-specific and single, large accessible areas in ensemble models to generate suitability maps, using out-of-sample predictions to validate model performance against new independent data. Gaur, banteng and buffalo models showed reasonable model accuracy throughout the entire distribution (greater than or equal to 62%) and in Thailand (greater than or equal to 80%), whereas serow and goral models performed poorly for the entire distribution and in Thailand, though 5 km movement buffers markedly improved the performance for serow. Large suitable areas were identified in Thailand and India for gaur, Cambodia and Thailand for banteng and India for buffalo. Over 50% of suitable habitat is located outside protected areas, highlighting the need for habitat management and conflict mitigation outside protected areas.

Maternal genetic diversity and phylogenetic analysis of Indian riverine and swamp buffaloes: insights from complete mitochondrial genomes

This study explored the genetic diversity and evolutionary history of riverine and swamp buffaloes in India, utilizing complete mitochondrial genome sequences. Through comprehensive sampling across varied agro-climatic zones, including 91 riverine buffaloes from 12 breeds and 6 non-descript populations, along with 16 swamp buffaloes of the Luit breed, this study employed next-generation sequencing techniques to map the mitogenomic landscape of these subspecies. Sequence alignments were performed with the buffalo mitochondrial reference genome to identify mitochondrial DNA (mtDNA) variations and distinct maternal haplogroups among Indian buffaloes. The results uncovered the existence of 212 variable sites in riverine buffaloes, yielding 67 haplotypes with high haplotype diversity (0.991), and in swamp buffaloes, 194 variable sites resulting in 12 haplotypes, displaying haplotype diversity of 0.950. Phylogenetic analyses elucidated the genetic relationships between Indian buffaloes and the recognized global haplogroups, categorizing Indian swamp buffaloes predominantly into the SA haplogroup. Intriguingly, the haplogroup SB2b was observed for the first time in swamp buffaloes. Conversely, riverine buffaloes conformed to established sub-haplogroups RB1, RB2, and RB3, underscoring the notion of Northwestern India as a pivotal domestication site for riverine buffaloes. The study supports the hypothesis of independent domestication events for riverine and swamp buffaloes, highlighting the critical role of genetic analysis in unraveling the complex evolutionary pathways of domestic animals. This investigation contributes to the global understanding of buffalo mitogenome diversity, offering insights into this important livestock species' domestication and dispersal patterns.

Detection of Polymorphisms in FASN, DGAT1, and PPARGC1A Genes and Their Association with Milk Yield and Composition Traits in River Buffalo of Bangladesh

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.

CSN1S1, CSN3 and LPL: Three Validated Gene Polymorphisms Useful for More Sustainable Dairy Production in the Mediterranean River Buffalo

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.

The behavior and welfare of neglected species: some examples from fish and mammals

Animal welfare is the state of an animal's body and mind and the level to which its requirements are satisfied. Animal welfare is affected by human decisions and actions. Numerous decisions concerning animals are driven by human desires to enhance their own lives, and some of these decisions may be influenced by self-interest or a strong emphasis on economic factors. How to assess the welfare state of animals is a central issue in animal welfare science. Two critical questions can be used to address animal welfare: first, is the animal healthy, and second, does the animal have what it needs? Both of these questions can potentially be answered using the study of animal behavior. The development of behavioral methodologies is crucial for evaluating welfare in contexts where concern for animal welfare is often highest, such as on intensive modern farms and sites where working animals are used. Herein, we discuss animal welfare by focusing on some of its major concepts and explanations. Later, to illustrate key aspects of animal welfare, we chose to examine the information that is available for some 'neglected' livestock species, which are commercially important on a global basis and found in large numbers: buffaloes (Bubalus bubalis), camels (Camelus dromedarius), donkeys (Equus asinus), mules (Equus asinus × Equus caballus), and lumpfish (Cyclopterus lumpus). We chose these species because there are major ongoing concerns about their welfare, and more research is required to help solve the various problems. Overall, there are strong imbalances in terms of the species that are usually studied in terms of animal welfare research, and we call for greater attention to those that have traditionally been neglected.

Transcriptome profiling reveals SLC5A5 regulates chicken ovarian follicle granulosa cell proliferation, apoptosis, and steroid hormone synthesis

The egg-laying performance of hens holds significant economic importance within the poultry industry. Broody inheritance of the parent stock of chickens can result in poor options for the improvement of egg production, and is a phenomenon influenced by multiple genetic factors. However, few studies have been conducted to delineate the molecular mechanism of ovarian regression in brooding chickens. Here, we explored the pivotal genes responsible for the regulation of ovarian follicles in laying hens, using RNA-sequencing analysis on the small ovarian follicles from broody and laying chickens. Sequencing data analysis revealed the differential expression of 200 genes, with a predominant enrichment in biological processes related to cell activation and metabolism. Among these genes, we focused on solute carrier family 5 member 5 (SLC5A5), which exhibited markedly higher RNA expression levels in follicles from laying compared with broody chickens. Subsequent cellular function studies with knockdown of SLC5A5 in chicken ovarian follicle granulosa cells (GCs) led to the down-regulation of genes associated with cell proliferation and steroid hormone synthesis, and concurrent promotion of gene expression linked to apoptosis. These findings indicated that SLC5A5 deficiency led to the inhibition of proliferation, steroid hormone synthesis and secretion, and promotion of apoptosis in chicken GCs. Our study demonstrated a pivotal role for SLC5A5 in the development and function of chicken GCs, shedding light on its potential significance in the broader context of chicken ovarian follicle development, and providing a prospective target to improve the egg-laying performance of chickens via molecular marker-assisted breeding technology.

Seroprevalence of Toxoplasma gondii in water buffaloes and cats in Guangxi, China

Toxoplasma gondii is a pathogen that poses a serious threat to human health and causes significant economic losses to the global livestock industry. The prevalence of toxoplasmosis infection has been reported to be high in humans and animals around the world, but the occurrence of the disease has not yet been reported in water buffaloes in Guangxi Zhuang Autonomous Region, southern China. To understand the overall seroprevalence of T. gondii infection in Guangxi, a total of 1041 water buffalo and 114 cat serum samples were examined using an indirect enzyme-linked immunosorbent assay (I-ELISA). Of the 1041 water buffaloes analyzed, an overall seroprevalence of 52.9% (551/1041) was obtained, with year, season, and city location being significant factors affecting the rate of T. gondii infection in water buffaloes (P < 0.001). The results also revealed a high seroprevalence of 57% (65/114) in cats. Given that buffalo milk and meat products are vital food sources, these findings suggest that toxoplasmosis in water buffaloes may be a public health threat. This study provides the first T. gondii seroprevalence data in Guangxi, which could contribute to the prevention and control of toxoplasmosis in the region.

Detection of genome-wide copy number variation in Murrah buffaloes

Riverine Buffaloes, especially the Murrah breed because of their adaptability to harsh climatic conditions, is farmed in many countries to convert low-quality feed into valuable dairy products and meat. Here, we investigated the copy number variations (CNVs) in 296 Murrah buffalo using the Axiom® Buffalo Genotyping Array 90K (Affymetrix, Santa Clara, CA, USA). The CNVs were detected on the autosomes, using the Copy Number Analysis Module (CNAM) using the univariate analysis. 7937 CNVs were detected in 279 Buffaloes, the average length of the CNVs was 119,048.87 bp that ranged between 7800 and 4,561,030 bp. These CNVs were accounting for 10.33% of the buffalo genome, which was comparable to cattle, sheep, and goat CNV analyses. Further, CNVs were merged and 1541 CNVRs were detected using the Bedtools-mergeBed command. 485 genes were annotated within 196 CNVRs that were identified in at least 10 animals of Murrah population. Out of these, 40 CNVRs contained 59 different genes that were associated with 69 different traits. Overall, the study identified a significant number of CNVs and CNVRs in the Murrah breed of buffalo, with a wide range of lengths and frequencies across the autosomes. The identified CNVRs contained genes associated with important traits related to production and reproduction, making them potentially important targets for future breeding and genetic improvement efforts.

Neospora caninum seroprevalence in water buffaloes in Guangxi, China

Neospora caninum is an important obligate intracellular apicomplexan parasite that causes spontaneous abortions in cattle and leads to huge economic losses to the farming industry. Although a high prevalence of N. caninum infection has been reported in Asia, data on the prevalence of water buffaloes in China remain unclear. To understand the seroprevalence of N. caninum infection in water buffaloes and its definitive host dogs in China, a total of 987 water buffalo sera from Guangxi Province were tested using an indirect enzyme-linked immunosorbent assay. We obtained an overall seroprevalence of 50.9% (502/987) for water buffalo samples. And the positive rate was higher in border cities (56.8%, 425/748) than in central cities (32.3%, 77/239). We further tested 240 serum samples from dogs in Guangxi and found an overall prevalence of 57.9% (139/240). The high prevalence of N. caninum infection in both dogs and water buffaloes was first reported in southern China, and these data will surely contribute to the prevention and control of the disease.

Signatures of selection in riverine buffalo populations revealed by genome-wide SNP data

The detection of selection signatures assists in understanding domestication, evolution, and the identification of genomic regions related to adaptation and production traits in buffaloes. The emergence of high-throughput technologies like Next Generation Sequencing and SNP genotyping had expanded our ability to detect these signatures of selection. In this study, we sought to identify signatures of selection in five buffalo populations (Brazilian Murrah, Bulgarian Murrah, Indian Murrah, Nili-Ravi, and Kundi) using Axiom Buffalo 90 K Genotyping Array data. Using seven different methodologies (Tajima's D, CLR, ROH, iHS, FST, FLK and hapFLK), we identified selection signatures in 374 genomic regions, spanning a total of 381 genes and 350 quantitative trait loci (QTLs). Among these, several candidate genes were associated with QTLs for milk production, reproduction, growth and carcass traits. The genes and QTLs reported in this study provide insight into selection signals shaping the genome of buffalo breeds. Our findings can aid in further genomic association studies, genomic prediction, and the implementation of breeding programmes in Indian buffaloes.

Biodiversity of Indonesian indigenous buffalo: First review of the status, challenges, and development opportunities

In Indonesia, the buffalo is important for small and marginal farmers' livelihood and economic development as a source of food, working animal, and tourist attraction. Therefore, an in-depth study is needed to examine challenges and opportunities for buffalo development in Indonesia. In Indonesia, the buffalo is divided into two types: swamp buffalo and river buffalo. The buffalo population in Indonesia has declined significantly. A decrease of approximately 39.35% was recorded from 2022 to 2017. The decline occurred due to low reproduction rate and suboptimal rearing management systems. There are three buffalo-rearing systems: Intensive, semi-intensive, and extensive. The productivity of buffalo is diverse and closely related to the characteristics of the regional agroecosystem, consistent with existing natural resources and rearing management systems. The diversity of buffalo productivity provides a good opportunity to improve productivity. Improvement of buffalo genetics is urgently needed, by improving mating management, etc., especially to reduce potential inbreeding. In recent years, genetic and molecular research on Indonesian buffalo has made progress, including use of molecular markers, such as microsatellites and single-nucleotide polymorphisms, to evaluate genetic diversity within and among buffalo populations across Indonesia. In addition, studies are being conducted on the relationship of genotype mutations that contribute to appearance and phenotypic performance (heat stress, reproduction, behavior, coat color, and production attributes) in buffaloes. Identification of genetic diversity in local buffaloes can be improved using various genetic and genomic techniques. These findings will form a basis for the targeted conservation of local buffaloes in Indonesia. This study aimed to collect information on the genetic resources of the local buffalo, particularly its status and production system and provide recommendations for developing buffalo production in Indonesia.

The Challenge of Global Warming in Water Buffalo Farming: Physiological and Behavioral Aspects and Strategies to Face Heat Stress

Water buffaloes have morphological and behavioral characteristics for efficient thermoregulation. However, their health, welfare, and productive performance can be affected by GW. The objective of this review was to analyze the adverse effects of GW on the productive behavior and health of water buffaloes. The physiological, morphological, and behavioral characteristics of the species were discussed to understand the impact of climate change and extreme meteorological events on buffaloes' thermoregulation. In addition, management strategies in buffalo farms, as well as the use of infrared thermography as a method to recognize heat stress in water buffaloes, were addressed. We concluded that heat stress causes a change in energy mobilization to restore animal homeostasis. Preventing hyperthermia limits the physiological, endocrine, and behavioral changes so that they return to thermoneutrality. The use of fans, sprinklers, foggers, and natural sources of water are appropriate additions to current buffalo facilities, and infrared thermography could be used to monitor the thermal states of water buffaloes.

Large mammals and trees in eastern monsoonal China: anthropogenic losses since the Late Pleistocene and restoration prospects in the Anthropocene

Massive human-induced declines of large-sized animals and trees (megabiota) from the Late Pleistocene to the Anthropocene have resulted in downsized ecosystems across the globe, in which components and functions have been greatly simplified. In response, active restoration projects of extant large-sized species or functional substitutes are needed at large scales to promote ecological processes that are important for ecosystem self-regulation and biodiversity maintenance. Despite the desired global scope of such projects, they have received little attention in East Asia. Here, we synthesise the biogeographical and ecological knowledge of megabiota in ancient and modern China, with relevant data mostly located in eastern monsoonal China (EMC), aiming to assess its potential for restoring functionally intact ecosystems modulated by megabiota. We found that during the Late Pleistocene, 12 mammalian megafaunal (carnivores ≥15 kg and herbivores ≥500 kg) species disappeared from EMC: one carnivore Crocuta ultima (East Asian spotted hyena) and 11 herbivores including six megaherbivores (≥1000 kg). The relative importance of climate change and humans in driving these losses remains debated, despite accumulating evidence in favour of the latter. Later massive depletion of megafauna and large-sized (45-500 kg) herbivores has been closely associated with agricultural expansion and societal development, especially during the late Holocene. While forests rich in large timber trees (33 taxa in written records) were common in the region 2000-3000 years ago, millennial-long logging has resulted in considerable range contractions and at least 39 threatened species. The wide distribution of C. ultima, which likely favoured open or semi-open habitats (like extant spotted hyenas), suggests the existence of mosaic open and closed vegetation in the Late Pleistocene across EMC, in line with a few pollen-based vegetation reconstructions and potentially, or at least partially, reflecting herbivory by herbivorous megafauna. The widespread loss of megaherbivores may have strongly compromised seed dispersal for both megafruit (fleshy fruits with widths ≥40 mm) and non-megafruit plant species in EMC, especially in terms of extra-long-distance (>10 km) dispersal, which is critical for plant species that rely on effective biotic agents to track rapid climate change. The former occurrence of large mammals and trees have translated into rich material and non-material heritages passed down across generations. Several reintroduction projects have been implemented or are under consideration, with the case of Elaphurus davidianus a notable success in recovering wild populations in the middle reaches of the Yangtze River, although trophic interactions with native carnivorous megafauna have not yet been restored. Lessons of dealing with human-wildlife conflicts are key to public support for maintaining landscapes shared with megafauna and large herbivores in the human-dominated Anthropocene. Meanwhile, potential human-wildlife conflicts, e.g. public health risks, need to be scientifically informed and effectively reduced. The Chinese government's strong commitment to improved policies of ecological protection and restoration (e.g. ecological redlines and national parks) provides a solid foundation for a scaling-up contribution to the global scope needed for solving the crisis of biotic downsizing and ecosystem degradation.

Exploring the Milk Microbiota of Healthy and Mastitic Nili Ravi Buffalo Using 16S rRNA Gene Base Metagenomic Analysis

The Nili Ravi, a buffalo breed from Pakistan, significantly contributes to the dairy industry. Mastitis is one of the major challenges affecting milk production in this breed. The objective of the current study was to identify the bacterial communities and diversity in healthy and mastitic milk of this breed. Milk samples (n = 14) were collected from Nili Ravi buffaloes with different udder health statuses, i.e., healthy (5), subclinical mastitis (4), and clinical mastitis (5). The DNAs were extracted, subjected to partial amplification of 16S rDNA (V3 and V4 regions), and sequenced using the Illumina platform. The results revealed variations in the bacterial communities in the milk of animals with different udder health statuses. Proteobacteria was the predominant phylum in the healthy group, while clinical and subclinical mastitis milk had a higher abundance of Firmicutes. Dominant bacterial genera in the healthy group were Streptococcus (11.60%), Herbaspirillum (7.65%), and Staphylococcus (4.70%), whereas the clinical mastitis group was dominated by Streptococcus (33.96%), Staphylococcus (7.87%), and Corynebacterium (2.68%), and the subclinical mastitis group was dominated by Bacillus (15.70%), Corynebacterium (6.70%), and Staphylococcus (6.58%). Assignment of operational taxonomic units at the species level resulted in most species being assigned to uncultured or unknown bacteria or remaining unassigned. Alpha diversity indices indicated lower microbial diversity in the clinical mastitis group, while beta diversity indices showed a scattered pattern of sample clustering in PCA plots among different groups. It is concluded that bacterial diversity in the milk of Nili Ravi buffaloes suffering from clinical mastitis is lower compared to healthy and subclinical mastitis cases. It is concluded that the variations in the microbiota of healthy and mastitic milk may be further investigated and exploited as signature microbes associated with the udder health status of Nili Ravi buffalo.

A Multi-Tissue Gene Expression Atlas of Water Buffalo (Bubalus bubalis) Reveals Transcriptome Conservation between Buffalo and Cattle

We generated 73 transcriptomic data of water buffalo, which were integrated with publicly available data in this species, yielding a large dataset of 355 samples representing 20 major tissue categories. We established a multi-tissue gene expression atlas of water buffalo. Furthermore, by comparing them with 4866 cattle transcriptomic data from the cattle genotype-tissue expression atlas (CattleGTEx), we found that the transcriptomes of the two species exhibited conservation in their overall gene expression patterns, tissue-specific gene expression and house-keeping gene expression. We further identified conserved and divergent expression genes between the two species, with the largest number of differentially expressed genes found in the skin, which may be related to structural and functional differences in the skin of the two species. This work provides a source of functional annotation of the buffalo genome and lays the foundations for future genetic and evolutionary studies in water buffalo.

Global prevalence and species diversity of tick-borne pathogens in buffaloes worldwide: a systematic review and meta-analysis

BACKGROUND

Buffaloes are important contributors to the livestock economy in many countries, particularly in Asia, and tick-borne pathogens (TBPs) commonly infect buffaloes, giving rise to serious pathologies other than their zoonotic potential.

METHODS

The present investigation focuses on the prevalence of TBPs infecting buffaloes worldwide. All published global data on TBPs in buffaloes were collected from different databases (e.g., PubMed, Scopus, ScienceDirect, and Google Scholar) and subjected to various meta-analyses using OpenMeta[Analyst] software, and all analyses were conducted based on a 95% confidence interval.

RESULTS

Over 100 articles discussing the prevalence and species diversity of TBPs in buffaloes were retrieved. Most of these reports focused on water buffaloes (Bubalus bubalis), whereas a few reports on TBPs in African buffaloes (Syncerus caffer) had been published. The pooled global prevalence of the apicomplexan parasites Babesia and Theileria, as well as the bacterial pathogens Anaplasma, Coxiella burnetii, Borrelia, Bartonella, and Ehrlichia in addition to Crimean-Congo hemorrhagic fever virus, were all evaluated based on the detection methods and 95% confidence intervals. Interestingly, no Rickettsia spp. were detected in buffaloes with scarce data. TBPs of buffaloes displayed a fairly high species diversity, which underlines the high infection risk to other animals, especially cattle. Babesia bovis, B. bigemina, B. orientalis, B. occultans and B. naoakii, Theileria annulata, T. orientalis complex (orientalis/sergenti/buffeli), T. parva, T. mutans, T. sinensis, T. velifera, T. lestoquardi-like, T. taurotragi, T. sp. (buffalo) and T. ovis, and Anaplasma marginale, A. centrale, A. platys, A. platys-like and "Candidatus Anaplasma boleense" were all were identified from naturally infected buffaloes.

CONCLUSIONS

Several important aspects were highlighted for the status of TBPs, which have serious economic implications for the buffalo as well as cattle industries, particularly in Asian and African countries, which should aid in the development and implementation of prevention and control methods for veterinary care practitioners, and animal owners.

The prevalence and risk factors of subclinical mastitis in water buffalo (Bubalis bubalis) in Bangladesh

Subclinical mastitis (SCM) in water buffalo is responsible for reduced milk yield and quality. This cross-sectional study was carried out to a) estimate the prevalence of SCM, b) identify risk factors associated with SCM, and c) identify farm-level risk factors associated with bulk milk somatic cell count (BMSCC). The buffalo farms included in this study represented five rearing systems: free-range, semi-free-range, household, semi-intensive, and intensive, providing a total of 3491 functional quarters of 880 lactating buffalo on 248 farms. The California mastitis test score was used to identify SCM. Bulk milk samples (n = 242) were used for farm-level BMSCC. Quarter and buffalo-level risk factors for SCM were measured using questionnaires and observations. The overall SCM prevalence was high at 27.9% at the quarter-level (25th and 75th percentiles: 8.3% and 41.7%) and 51.5% at buffalo-level (25th and 75th percentiles: 33.3% and 66.7%). The geometric mean BMSCC was 217,000 cells/mL of milk (ranging from 36,000-1,213,000 cells/mL), which is low on average, but some farms could improve substantially. The buffalo rearing system, udder location (left versus right), teat shape, udder asymmetry, number of milkers, and having a quarantine facility were associated with buffalo udder health. Our findings suggest that mainly using free-range rearing systems may help decrease the prevalence of SCM primarily by employing buffalo breeding and better farm biosecurity, and udder health control strategies can be designed based on our findings.

Dairy Buffalo Behavior: Calving, Imprinting and Allosuckling

Maternal behavior, in water buffalo and other ruminants, is a set of patterns of a determined species, including calving, imprinting, and suckling. This behavior is mainly triggered by hormone concentration changes and their interactions with their respective receptors in the brain, particularly oxytocin. These chemical signals also influence mother-young bonding, a critical process for neonatal survival that develops during the first postpartum hours. Currently, dairy buffalo behavior during parturition has rarely been studied. For this reason, this review aims to analyze the existing scientific evidence regarding maternal behavior in water buffalo during calving. It will address the mechanisms of imprinting, maternal care, and allosuckling strategies that may influence the survival and health of calves.

Trajectory of livestock genomics in South Asia: A comprehensive review

Livestock plays a central role in sustaining human livelihood in South Asia. There are numerous and distinct livestock species in South Asian countries. Several of them have experienced genetic development in recent years due to the application of genomic technologies and effective breeding programs. This review discusses genomic studies on cattle, buffalo, sheep, goat, pig, horse, camel, yak, mithun, and poultry. The frontiers covered in this review are genetic diversity, admixture studies, selection signature research, QTL discovery, genome-wide association studies (GWAS), and genomic selection. The review concludes with recommendations for South Asian livestock systems to increasingly leverage genomic technologies, based on the lessons learned from the numerous case studies. This paper aims to present a comprehensive analysis of the dichotomy in the South Asian livestock sector and argues that a realistic approach to genomics in livestock can ensure long-term genetic advancements.

An Age Effect of Rumen Microbiome in Dairy Buffaloes Revealed by Metagenomics

Age is an important factor in shaping the gut microbiome. However, the age effect on the rumen microbial community for dairy buffaloes remains less explored. Using metagenomics, we examined the microbial composition and functions of rumen microbiota in dairy Murrah buffaloes of different ages: Y (1 year old), M (3−5 years old), E (6−8 years old), and O (>9 years old). We found that Bacteroidetes and Firmicutes were the predominant phyla, with Prevotella accounting for the highest abundance at the genus level. The proportion of Bacteroides and Methanobrevibacter significantly increased with age, while the abundance of genus Lactobacillus significantly decreased with age (LDA > 3, p < 0.05). Most differed COG and KEGG pathways were enriched in Y with carbohydrate metabolism, while older buffaloes enriched more functions of protein metabolism and the processing of replication and repair (LDA > 2, p < 0.05). Additionally, the functional contribution analysis revealed that the genera Prevotella and Lactobacillus of Y with more functions of CAZymes encoded genes of glycoside hydrolases and carbohydrate esterases for their roles of capable of metabolizing starch and sucrose-associated oligosaccharide enzyme, hemicellulase, and cellulase activities than the other three groups (LDA > 2, p < 0.05), thus affecting the 1-year-old dairy buffalo rumen carbohydrate metabolism. This study provides comprehensive dairy buffalo rumen metagenome data and assists in manipulating the rumen microbiome for improved dairy buffalo production.

Effect of Prepartum Dietary Energy Level on Production and Reproduction in Nili Ravi Buffaloes

The objective of this study was to evaluate the effect of prepartum dietary energy level on postpartum production and reproduction in Nili Ravi buffaloes (n = 21). The buffaloes were offered low energy (LE: 1.31 Mcal/kg DM NEL (net energy for lactation)), medium energy (ME: 1.42 Mcal/kg DM NEL) or high energy (HE: 1.54 Mcal/kg DM NEL) diet for 63 days prepartum, and received the same lactation diet (LD: 1.22 Mcal/kg DM NEL) during 14 weeks postpartum. The effects of dietary energy level and week were analyzed with Proc GLIMMIX model. Dry matter intake (DMI) was lower in buffaloes fed the LE diet compared with buffaloes fed the ME or HE diet. Calf birth weight (CBW) was higher in buffaloes fed the HE diet compared with buffaloes fed the ME or LE diet. Milk production was similar in buffaloes fed the HE, ME or LE diet within 14 weeks postpartum and throughout the lactation. Milk fat was higher in buffaloes fed the LE diet compared with buffaloes fed the ME or HE diet. Milk protein and lactose yields was high in buffaloes fed the HE diet compared with buffaloes fed the ME or LE diet. Body condition score was high in HE and was affected by diet × week interactions during pre and postpartum period. The concentrations of β-hydroxybutyrate (BHBA) and triglycerides in serum was lowest in buffaloes fed the HE diet compared with the buffaloes fed the ME or LE diet. The buffaloes fed the HE diet had early uterine involution (UI), first estrus, short dry days, and calving interval (CI) compared with buffaloes fed the ME or LE diet. None of buffaloes fed the LE diet exhibited estrus during the first 14 weeks postpartum compared with buffaloes fed the ME or HE diet. In conclusion, prepartum feeding of high energy diet can be helpful in improving the postpartum productive and reproductive performance in Nili Ravi buffaloes.

Genome-wide SNP analysis reveals the selection signatures of two indigenous buffalo breeds in Sichuan

Sichuan Province spawned abundant of indigenous buffalo varieties, which probably harbor valuable gene resources beneficial to the genetic improvement of buffalo. However, limited genetic information was publicly available. To better understand their selection signatures between different populations, we performed a restriction site-associated DNA sequencing (RADseq) to explore genome-wide SNPs among two indigenous breeds of Sichuan buffaloes. As a result, a total of 2,110,077 high-quality SNPs were finally obtained. Population genetic analysis indicated a obviously genetic differentiation between two breeds. The detection of selective genes showed that 995 and 910 protein-coding genes underwent positive selection in Yibin buffalo (GYBS) and Dechang buffalo (XCS). Further functional analysis revealed distinctly discrepant selection in two breeds. Candidate genes that positively selected from Yibin buffaloes have mainly occurred in functions closely related to meat quality, complex living environment adaption capability, and disease resistance. While they were significantly enriched in cell proliferation and cell components in Dechang buffalo, indicating the selection pressure primarily derived from the requirement of organism growth and development speed during breed formation. Our dataset constitutes a promising reservoir of genome-wide SNP markers of Sichuan buffaloes and provides potentially traits selected in different local populations. Such comprehensive genetic resources offer an unprecedented opportunity for genetic association analysis of economically important traits and precision breeding programs in buffaloes.

Whole-Genome-Based Web Genomic Resource for Water Buffalo (Bubalus bubalis)

Water buffalo (Bubalus bubalis), belonging to the Bovidae family, is an economically important animal as it is the major source of milk, meat, and drought in numerous countries. It is mainly distributed in tropical and subtropical regions with a global population of approximately 202 million. The advent of low cost and rapid sequencing technologies has opened a new vista for global buffalo researchers. In this study, we utilized the genomic data of five commercially important buffalo breeds, distributed globally, namely, Mediterranean, Egyptian, Bangladesh, Jaffrarabadi, and Murrah. Since there is no whole-genome sequence analysis of these five distinct buffalo breeds, which represent a highly diverse ecosystem, we made an attempt for the same. We report the first comprehensive, holistic, and user-friendly web genomic resource of buffalo (BuffGR) accessible at http://backlin.cabgrid.res.in/buffgr/, that catalogues 6028881 SNPs and 613403 InDels extracted from a set of 31 buffalo tissues. We found a total of 7727122 SNPs and 634124 InDels distributed in four breeds of buffalo (Murrah, Bangladesh, Jaffarabadi, and Egyptian) with reference to the Mediterranean breed. It also houses 4504691 SSR markers from all the breeds along with 1458 unique circRNAs, 37712 lncRNAs, and 938 miRNAs. This comprehensive web resource can be widely used by buffalo researchers across the globe for use of markers in marker trait association, genetic diversity among the different breeds of buffalo, use of ncRNAs as regulatory molecules, post-transcriptional regulations, and role in various diseases/stresses. These SNPs and InDelscan also be used as biomarkers to address adulteration and traceability. This resource can also be useful in buffalo improvement programs and disease/breed management.

Genetic structure and phylogeography of Echinococcus granulosus sensu stricto genotypes G1 and G3 in Pakistan and other regions of the world based on nad5 gene

Pakistan is a neglected endemic focus for Echinococcus granulosus sensu lato, a zoonotic parasite species complex with the ability to infect wide spectrum of hosts. Wide gaps exist in literature for etiological agents of cystic echinococcosis (CE) in Pakistan due to a very low number of studies on identifying the exact genotypes involved in epidemiological manifestation of this disease. Focusing on transmission patterns and epidemiological dynamics, this study aimed at investigating infective genotypes among the cattle population of south Punjab, Pakistan, employing a mitochondrial marker nad5 (680 bp). Nucleotide sequences retrieved from 28 hydatid cyst isolates displayed considerable intraspecific variation revealing the existence of G3 and G1 strains of Echinococcus granulosus sensu stricto. The G3 genotype emerged as the predominant cause (78.57%) of hydatidosis in cattle. Apart from this, to understand phylogeographical relations, homologous nucleotide sequences of the partial nad5 gene from six major regions of the world were employed in the population genetics analysis to have an insight into genetic variability and demographics of G3 genotype in particular. Diversification of G3 and its haplotypes in Pakistan (n = 11) and other regions of the world (India, Iran, Turkey, Italy and France) was demonstrated. It was further demonstrated that the South Asian population (Pakistan and India) was highly differentiated from the other regions. It could, therefore, be speculated that G3 is diverging and expanding its population with South Asia as the main focal point.

Identification and Functional Verification Reveals that miR-195 Inhibiting THRSP to Affect Fat Deposition in Xinyang Buffalo

The buffalo population is extensive in China, but its meat quality is relatively inferior. Therefore, improving meat quality should be one of the breeding goals. microRNAs (miRNAs) play an essential regulatory role in the post-transcriptional expression of genes. Some studies have reported their function regulating genes related to fat deposition and adipocyte differentiation in cattle, but there is limited reports in buffalo. We performed small RNA transcriptome sequencing of Xinyang buffalo adipose tissue between calves and adults in this study. As a result, 282 mature miRNAs were significantly differentially expressed, and co-expression analysis showed that 454 miRNAs were significantly associated with developmental stages. Target gene identification, GO (gene ontology) annotation, and KEGG analysis of miRNAs showed that miR-195, miR-192, and miR-24-3p could target key genes for lipogenesis and thus regulate adipose deposition and differentiation. Among them, miR-195 was significantly upregulated in adipose tissue and induced adipocytes of adult buffaloes, and its overexpression significantly inhibited lipid accumulation in primary adipocytes. Dual-luciferase reporter gene analysis showed that miR-195 reduced the expression of thyroid hormone response protein (THRSP) by targeting its 3′ untranslated terminal region, suggesting that miR-195 may inhibit lipid accumulation in adipocytes by regulating THRSP. The results confirmed the reliability of predictive screening of miRNAs and provided theoretical support for buffalo fattening.

Signatures of selection reveal candidate genes involved in production traits in Chinese crossbred buffaloes

Identification of selection signature is important for a better understanding of genetic mechanisms that affect phenotypic differentiation in livestock. However, the genome-wide selection responses have not been investigated for the production traits of Chinese crossbred buffaloes. In this study, an SNP data set of 133 buffaloes (Chinese crossbred buffalo, n = 45; Chinese local swamp buffalo, n = 88) was collected from the Dryad Digital Repository database (https://datadryad.org/stash/). Population genetics analysis showed that these buffaloes were divided into the following 2 groups: crossbred buffalo and swamp buffalo. The crossbred group had higher genetic diversity than the swamp group. Using 3 complementary statistical methods (integrated haplotype score, cross population extended haplotype homozygosity, and composite likelihood ratio), a total of 31 candidate selection regions were identified in the Chinese crossbred population. Here, within these candidate regions, 25 genes were under the putative selection. Among them, several candidate genes were reported to be associated with production traits. In addition, we identified 13 selection regions that overlapped with bovine QTLs that were mainly involved in milk production and composition traits. These results can provide useful insights regarding the selection response for production traits of Chinese crossbred buffalo, as identified candidate genes influence production performance.

Current status and unique attributes of Indian Chilika buffalo for adaptation to brackish water ecology

Chilika buffalo is native to the Eastern coast of India and well adapted to the largest coastal brackish water lagoon of Asia, Chilika Lake. We present here a report on the Chilika buffalo breed emphasizing the conservational urgency based on unique biochemical and molecular evidence related to liver and kidney functions while comparing it with tropically adapted other water buffalo breeds (Bubalus bubalis) of India. It is found that the Chilika buffalo breed has a better ability to withstand a long dehydration period as evident from its better glomerular filtration and higher expression of the ion transport channel. Mitochondrial D-loop sequencing results have shown these buffaloes being closer to swamp-type buffaloes of Bangladesh and northeast India and represent a unique "hybrid zone" on the eastern coast of India. Conservation of such uniquely adapted germplasm is crucial owing to the current global trend, where the introduction of exotic breeds has negatively impact "sui-generis" germplasm and they require higher managerial resource consumption for maintaining higher productivity. Further, the introduction of unconventional fisheries activities has proved detrimental to the lagoon ecosystem, potentially causing more threat to the buffalo's population.

Comparative Signatures of Selection Analyses Identify Loci Under Positive Selection in the Murrah Buffalo of India

India is home to a large and diverse buffalo population. The Murrah breed of North India is known for its milk production, and it has been used in breeding programs in several countries. Selection signature analysis yield valuable information about how the natural and artificial selective pressures have shaped the genomic landscape of modern-day livestock species. Genotype information was generated on six buffalo breeds of India, namely, Murrah, Bhadawari, Mehsana, Pandharpuri, Surti, and Toda using ddRAD sequencing protocol. Initially, the genotypes were used to carry out population diversity and structure analysis among the six breeds, followed by pair-wise comparisons of Murrah with the other five breeds through XP-EHH and F _ST methodologies to identify regions under selection in Murrah. Admixture results showed significant levels of Murrah inheritance in all the breeds except Pandharpuri. The selection signature analysis revealed six regions in Murrah, which were identified in more than one pair-wise comparison through both XP-EHH and F _ST analyses. The significant regions overlapped with QTLs for milk production, immunity, and body development traits. Genes present in these regions included SLC37A1, PDE9A, PPBP, CXCL6, RASSF6, AFM, AFP, ALB, ANKRD17, CNTNAP2, GPC5, MYLK3, and GPT2. These genes emerged as candidates for future polymorphism studies of adaptability and performance traits in buffaloes. The results also suggested ddRAD sequencing as a useful cost-effective alternative for whole-genome sequencing to carry out diversity analysis and discover selection signatures in Indian buffalo breeds.

The Cytogenetics of the Water Buffalo: A Review

The water buffalo (Bubalus bubalis), also known as the Asian buffalo, is an essential domestic bovid. Indeed, although its world population (~209 million heads) is approximately one-ninth that of cattle, the management of this species involves a larger human population than that involved with raising cattle. Compared with cattle, water buffalo have been understudied for many years, but interest in this species has been increasing, especially considering that the world population of these bovids grows every year-particularly that of the river buffalo. There are two genera of buffalo worldwide: the Syncerus (from the African continent), and the Bubalus (from the southwest Asian continent, Mediterranean area, southern America, and Australia). All species belonging to these two genera have specific chromosome numbers and shapes. Because of such features, the study of chromosomes is a fascinating biological basis for differentiating various species (and hybrids) of buffaloes and characterizing their karyotypes in evolutionary, clinical, and molecular studies. In this review, we report an update on essential cytogenetic studies in which various buffalo species were described from evolutionary, clinical, and molecular perspectives-particularly considering the river buffalo (Bubalus bubalis 2n = 50). In addition, we show new data on swamp buffalo chromosomes.

The Impact of Feed Supplementations on Asian Buffaloes: A Review

Simple Summary

Apart from feeding with forages, dietary supplementation with concentrate and rumen bypass fat is one of the feeding strategies to enhance nutrient availability and improve buffalo performance and productivity. This review paper thoroughly discussed the utilization of concentrate and bypass fat as dietary supplementation in buffalo feeding, and discussed the effects on performance, fermentation characteristics and general health of buffaloes to give better insight about the potential and challenges of dietary supplementation in buffalo diet. Based on the literature studies, it can be summarized that supplementation of concentrate and bypass fat in buffaloes may overcome the nutritional problems and improve the growth performance, health status, rumen environment and carcass traits.

Abstract

With the increase in the global buffalo herd, the use of supplementation in the ruminant feeding has become an important area for many researchers who are looking for an isocaloric and isonitrogenous diet to improve production parameters. In order to improve the performance of the Asian water buffalo, the optimal balance of all nutrients, including energy and protein, are important as macronutrients. Dietary supplementation is one of the alternatives to enhance the essential nutrient content in the buffalo diet and to improve the rumen metabolism of the animal. Researchers have found that supplementation of concentrate and rumen bypass fat could change growth performance and carcass traits without causing any adverse effects on the buffalo growth. Some studies showed that dry matter intake, body condition score and some blood parameters and hormones related to growth responded positively to concentrate and rumen bypass fat supplementation. In addition, changes of feeding management by adding the supplement to the ruminant basal diet helped to increase the profit of the local farmers due to the increased performance and productivity of the animals. Nevertheless, the effects of dietary supplementation on the performance of ruminants are inconsistent. Thus, its long-term effects on the health and productivity of buffaloes still need to be further investigated.

Large-scale genomic analysis reveals the genetic cost of chicken domestication

BACKGROUND

Species domestication is generally characterized by the exploitation of high-impact mutations through processes that involve complex shifting demographics of domesticated species. These include not only inbreeding and artificial selection that may lead to the emergence of evolutionary bottlenecks, but also post-divergence gene flow and introgression. Although domestication potentially affects the occurrence of both desired and undesired mutations, the way wild relatives of domesticated species evolve and how expensive the genetic cost underlying domestication is remain poorly understood. Here, we investigated the demographic history and genetic load of chicken domestication.

RESULTS

We analyzed a dataset comprising over 800 whole genomes from both indigenous chickens and wild jungle fowls. We show that despite having a higher genetic diversity than their wild counterparts (average π, 0.00326 vs. 0.00316), the red jungle fowls, the present-day domestic chickens experienced a dramatic population size decline during their early domestication. Our analyses suggest that the concomitant bottleneck induced 2.95% more deleterious mutations across chicken genomes compared with red jungle fowls, supporting the "cost of domestication" hypothesis. Particularly, we find that 62.4% of deleterious SNPs in domestic chickens are maintained in heterozygous states and masked as recessive alleles, challenging the power of modern breeding programs to effectively eliminate these genetic loads. Finally, we suggest that positive selection decreases the incidence but increases the frequency of deleterious SNPs in domestic chicken genomes.

CONCLUSION

This study reveals a new landscape of demographic history and genomic changes associated with chicken domestication and provides insight into the evolutionary genomic profiles of domesticated animals managed under modern human selection.

Circular Rep-Encoding Single-Stranded DNA Sequences in Milk from Water Buffaloes (Bubalus arnee f. bubalis)

Isolation and characterization of circular replicase-encoding single-stranded (ss) DNA from animal, plant and environmental samples are rapidly evolving in virology. We detected 21 circular DNA elements, including one genomoviral sequence, in individual milk samples from domesticated Asian water buffaloes (Bubalus arnee f. bubalis). Most of the obtained genomes are related to Sphinx 1.76 and Sphinx 2.36 sequences and share a high degree of similarity to recently published circular DNAs—named BMMF (bovine meat and milk factors)—that have been isolated from commercial milk, as well as from bovine serum. Characteristic features such as rep genes, tandem repeats and inverted repeats were detected. These BMMF have recently been found to be present in taurine-type dairy cattle breeds descending from the aurochs (Bos primigenius). Importantly, the occurrence of BMMF has been linked to the higher incidence of colorectal and breast cancer in North America and Western Europe compared with Asia. This is the first report of circular ssDNA detected in milk from the domesticated form of the wild Asian water buffalo (B. arnee) belonging to the subfamily Bovinae. This novelty should be taken into account in view of the above-mentioned cancer hypothesis.

Water buffalo production in the Brazilian Amazon Basin: a review

The Brazilian Amazon has witnessed, in the last decades, an increase in the water buffalo (Bubalus bubalis) inventory, with interesting productivity results. As the Brazilian Amazon contains the main water buffalo population in the Americas, the aim of this work is to review its most relevant production systems and some peculiarities about meat and milk production in this territory. The opening section describes the Amazon Basin, the most common water buffalo breeds, a brief history of the local livestock farming beginning in 1644. Also, it presents how water buffaloes gradually replaced bovine herds, especially where the latter had a lower productive performance. The use of extensive or more intensified models is pointed out and the ecosystems in which buffaloes are raised are detailed since native or cultivated pastures can be used in floodplains or drylands. Buffalo raising is favored in the Amazon due to the climate, soil, genetic variability of forages, animal adaptability, and physical space. Thus, it is clear that buffaloes have a high potential for meat and milk production and are an alternative in the use of altered areas of the Amazon; and, in the recent past, the low profitability of buffalo farming in traditional production systems in the Amazon was the reason which made this activity economically unattractive. Most recent technologies as outdoor confinements and silvopastoral systems are pointed out as more suitable regarding land-use policies, and buffalo farming for meat and milk production fits perfectly in this context, with productivity and beneficial socioeconomic.

Empirical Evaluation and Prediction of Protein Requirements for Maintenance and Growth of 18-24 Months Old Thai Swamp Buffaloes

Simple Summary

Thai swamp buffalo is a domesticated swamp buffalo (Bubalus bubalis) which has a functional significance for the livestock production system and for the economic benefit of Thailand. For instance, meat supply derived from Thai swamp buffalo is a secondary consideration in recently years. Therefore, there is mounting interest concerning the regulation of the nutrient requirements of Thai swamp buffalo to optimize their production. However, no systematic report is available on the nutrient requirements of the growing Thai swamp buffalo. This study investigates and predicts protein requirement systems that can provide an abundant energy intake and can be included in the 18–24 months old Thai swamp buffalo’s diet, as well as supply the recommended amount of net nitrogen or crude protein requirement to optimize their growth and maintenance. Protein requirement, nutrient utilization, and microorganism profile are included to corroborate the influences mentioned.

Abstract

In some geographical areas and in certain breeding situations, the interpretation of increased gain in the bovine is difficult to investigate. Due to their inherent genetic variations, their energy and protein needs vary as a function of inherent genetic differences, making these requirements difficult to accurately assess in bull species, e.g., Thai swamp buffalo. The study aimed at investigating and predicting protein requirement systems, by the provision of an abundant energy intake of 2.2 Mcal/kg DM for the maintenance and growth of Thai swamp buffaloes using a comparative prolonged feeding trial for 90 days. Sixteen bull Thai swamp buffaloes at the initial (Age: 18–24 months; BW: 233 ± 25.0 kg) were assigned into four treatment groups, four buffaloes each, fed 5.4, 6.6, 8.5, and 10.5% DM crude protein (CP). CP intake, BW, and physiological fluid were determined. The net CP requirements for maintenance and growth of Thai swamp buffaloes were 5.41 g CP/kg W^0.75 and 0.46 g CP/g average daily gain (ADG), respectively. Our results indicated that CP requirement increases when the BW increases. An increased dietary CP resulted in increased amounts of blood urine nitrogen (N), N absorption, total volatile fatty acid, urinary purine derivative, and the microbial N. Notably, the net CP requirement for growth of Thai swamp buffalo was higher than it reported in NRC, but the maintenance was lower.

The genome of the lowland anoa (Bubalus depressicornis) illuminates the origin of river and swamp buffalo

Two types of domestic water buffalo are currently recognized: the river buffalo from the Indian subcontinent and Mediterranean countries and the swamp buffalo from China and Southeast Asia. To test the hypothesis of two separate species of water buffalo, we sequenced the genome of the lowland anoa, Bubalus depressicornis, which is a dwarf wild buffalo endemic to Sulawesi, and two genomes of swamp buffalo, and made comparisons with 12 additional genomes. Three genomic data sets were constructed to infer phylogenetic relationships: the mitochondrial genome (15,468 bp; maternal transmission), two concatenated Y-chromosomal genes, AMELY and DDX3Y (20,036 bp; paternal transmission), and a selection of 30 nuclear genes representing all cattle chromosomes (364,887 bp; biparental transmission). The comparisons between our 30 nuclear gene sequences obtained by read mapping and those directly extracted from Bos taurus and Bubalus bubalis genome assemblies show that the mapping approach revealed higher levels of heterozygosity at both nucleotide sites and indels (insertions and deletions) (0.09-0.15%), as well as several sequence errors (0.07%). Our phylogenetic and molecular dating analyses provide strong evidence that the lowland anoa, river buffalo, and swamp buffalo are three distinct taxa which separated rapidly from each other during the Pleistocene epoch. We therefore conclude that two species of domestic water buffalo should be distinguished: Bubalus bubalis for the river buffalo and Bubalus kerabau for the swamp buffalo. The new classification can have deep implications for understanding the evolution and selection of domesticated forms and for the conservation and management of wild buffalo populations in South and Southeast Asia.

Comparative Growth and Economic Performances between Indigenous Swamp and Murrah Crossbred Buffaloes in Malaysia

Simple Summary

A buffalo breeding farm was selected to study the growth performance of Swamp and Murrah crossbred buffaloes. The farm was practicing extensive grazing system without supplementation since 2010 to 2011. In early 2012, the farm had implemented a new intervention to improve the growth performance via improving the feed and the feeding management. Farm records between 2010 to 2015 were analyzed for growth performance and partial budget analysis. So far, there is no comparative study done between Swamp and Murrah crossbred buffaloes in Malaysia. Therefore, in the present study, we aimed to study the differences in the biological and economical performances between Swamp and crossbred buffaloes in Malaysia. With a new intervention, a significant improvement was reported of the number of calves born, average birth weight, and reduced percentage of calf mortality rate, calving interval, and weaning age. Crossbred buffalo showed dominance in biological performance in terms of higher pre- and post-weaning daily weight gain and taking a shorter period to achieve market and breeding weight compared to Swamp buffaloes. Thus, reared Murrah crossbred buffaloes with new intervention management would give a farmer a higher profit return. However, with reared Swamp, the farmer potentially conserves the local indigenous breed of Swamp buffalo.

Abstract

This study was conducted to compare the growth and economic performances between Swamp and Murrah crossbred buffaloes. The records of 108 Swamp and 276 Murrah crossbred buffaloes born between January 2010 and December 2015 were used in this study. The farm was practicing an extensive grazing system without supplementation from January 2010 to December 2011 (pre-intervention) and a new implementation of supplement in the feeding regime from January 2012 to December 2015 (post-intervention). The birth, weaning, and body weight at three monthly intervals, number of calves born, and mortality rate of calves at different years and during pre- and post-intervention were analyzed using a general linear model procedure. The interventions in 2012 had a positive effect on increasing the number of calves born for both breeds, average birth weight, economic performance, and reduce mortality calf rate. As a result, the birth weight of Murrah crossbred buffaloes was higher (36.63 ± 0.50 kg) than Swamp buffaloes (34.69 ± 0.40 kg) (p < 0.05). The average pre-weaning daily weight gain for Swamp and Murrah crossbred buffaloes was 0.73 and 0.98 kg/day (p < 0.05), while the average post-weaning daily weight gain was 0.39 and 0.44 kg/day, respectively (p < 0.05). The Swamp and Murrah crossbred buffaloes achieved the targeted market weight of 250 kg at 18 and 15 months old, respectively, while the targeted breeding weight of 385 kg was achieved at 30 and 26 months old, respectively. In this farm, on average a total of 64 calves were born yearly, with the ratio number of born calves per number of mated dams recorded higher in Murrah crossbred buffaloes as compared to Swamp buffalo (0.64 vs. 0.37) (p < 0.05). Furthermore, the average number of calves born in the post-intervention period (January 2012–December 2015) was significantly higher than in the pre-intervention period (January 2010–December 2011), respectively (Swamp: 23 vs. 8 and Murrah crossbred: 53 vs. 31, respectively) (p < 0.05). Partial budget method was used to estimate the net gain or loss between the two breeds. The average annual revenue was 2304.14 MYR (566.13 USD) for Swamp buffaloes and 4531.50 MYR (1113.39 USD) for Murrah crossbred buffaloes. The average annual cost saving was 340.02 MYR (83.54 USD) for Swamp and 215.75 MYR (53.01 USD) for Murrah crossbred buffaloes. On the other hand, annual added cost was 84.95 MYR (20.87 USD) for Swamp and 96.76 MYR (23.77 USD) for Murrah crossbred buffaloes. Therefore, the annual net benefit was 2559.21 MYR (628.80 USD) for Swamp and 4650.49 MYR (1142.63 USD) for Murrah crossbred buffaloes. As a conclusion, this study had shown that the higher average daily weight gain contributes to better cost savings, as shown by the crossbred buffaloes.

Whole-Genome Sequencing and Characterization of Buffalo Genetic Resources: Recent Advances and Future Challenges

The buffalo was domesticated around 3000-6000 years ago and has substantial economic significance as a meat, dairy, and draught animal. The buffalo has remained underutilized in terms of the development of a well-annotated and assembled reference genome de novo. It is mandatory to explore the genetic architecture of a species to understand the biology that helps to manage its genetic variability, which is ultimately used for selective breeding and genomic selection. Morphological and molecular data have revealed that the swamp buffalo population has strong geographical genomic diversity with low gene flow but strong phenotypic consistency, while the river buffalo population has higher phenotypic diversity with a weak phylogeographic structure. The availability of recent high-quality reference genome and genotyping marker panels has invigorated many genome-based studies on evolutionary history, genetic diversity, functional elements, and performance traits. The increasing molecular knowledge syndicate with selective breeding should pave the way for genetic improvement in the climatic resilience, disease resistance, and production performance of water buffalo populations globally.

Opportunities and Challenges for Improving the Productivity of Swamp Buffaloes in Southeastern Asia

The swamp buffalo is a domesticated animal commonly found in Southeast Asia. It is a highly valued agricultural animal for smallholders, but the production of this species has unfortunately declined in recent decades due to rising farm mechanization. While swamp buffalo still plays a role in farmland cultivation, this species' purposes has shifted from draft power to meat, milk, and hide production. The current status of swamp buffaloes in Southeast Asia is still understudied compared to its counterparts such as the riverine buffaloes and cattle. This review discusses the background of swamp buffalo, with an emphasis on recent work on this species in Southeast Asia, and associated genetics and genomics work such as cytogenetic studies, phylogeny, domestication and migration, genetic sequences and resources. Recent challenges to realize the potential of this species in the agriculture industry are also discussed. Limited genetic resource for swamp buffalo has called for more genomics work to be done on this species including decoding its genome. As the economy progresses and farm mechanization increases, research and development for swamp buffaloes are focused on enhancing its productivity through understanding the genetics of agriculturally important traits. The use of genomic markers is a powerful tool to efficiently utilize the potential of this animal for food security and animal conservation. Understanding its genetics and retaining and maximizing its adaptability to harsher environments are a strategic move for food security in poorer nations in Southeast Asia in the face of climate change.

Genomic Analysis Revealed a Convergent Evolution of LINE-1 in Coat Color: A Case Study in Water Buffaloes (Bubalus bubalis)

Visible pigmentation phenotypes can be used to explore the regulation of gene expression and the evolution of coat color patterns in animals. Here, we performed whole-genome and RNA sequencing and applied genome-wide association study, comparative population genomics and biological experiments to show that the 2,809-bp-long LINE-1 insertion in the ASIP (agouti signaling protein) gene is the causative mutation for the white coat phenotype in swamp buffalo (Bubalus bubalis). This LINE-1 insertion (3' truncated and containing only 5' UTR) functions as a strong proximal promoter that leads to a 10-fold increase in the transcription of ASIP in white buffalo skin. The 165 bp of 5' UTR transcribed from the LINE-1 is spliced into the first coding exon of ASIP, resulting in a chimeric transcript. The increased expression of ASIP prevents melanocyte maturation, leading to the absence of pigment in white buffalo skin and hairs. Phylogenetic analyses indicate that the white buffalo-specific ASIP allele originated from a recent genetic transposition event in swamp buffalo. Interestingly, as a similar LINE-1 insertion has been identified in the cattle ASIP gene, we discuss the convergent mechanism of coat color evolution in the Bovini tribe.

The distribution of runs of homozygosity in the genome of river and swamp buffaloes reveals a history of adaptation, migration and crossbred events

Background

Water buffalo is one of the most important livestock species in the world. Two types of water buffalo exist: river buffalo (Bubalus bubalis bubalis) and swamp buffalo (Bubalus bubalis carabanensis). The buffalo genome has been recently sequenced, and thus a new 90 K single nucleotide polymorphism (SNP) bead chip has been developed. In this study, we investigated the genomic population structure and the level of inbreeding of 185 river and 153 swamp buffaloes using runs of homozygosity (ROH). Analyses were carried out jointly and separately for the two buffalo types.

Results

The SNP bead chip detected in swamp about one-third of the SNPs identified in the river type. In total, 18,116 ROH were detected in the combined data set (17,784 SNPs), and 16,251 of these were unique. ROH were present in both buffalo types mostly detected (~ 59%) in swamp buffalo. The number of ROH per animal was larger and genomic inbreeding was higher in swamp than river buffalo. In the separated datasets (46,891 and 17,690 SNPs for river and swamp type, respectively), 19,760 and 10,581 ROH were found in river and swamp, respectively. The genes that map to the ROH islands are associated with the adaptation to the environment, fitness traits and reproduction.

Conclusions

Analysis of ROH features in the genome of the two water buffalo types allowed their genomic characterization and highlighted differences between buffalo types and between breeds. A large ROH island on chromosome 2 was shared between river and swamp buffaloes and contained genes that are involved in environmental adaptation and reproduction.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-021-00616-3.

Haplotype diversity in the mitochondrial genome of the Egyptian river buffalo (Bubalus bubalis)

Here, we sequenced the complete mitochondrial genome of 29 Egyptian river buffaloes collected in two breeding stations of Egypt. The genome is 16,357-16,359 base pairs in length and contains the 37 genes found in a typical mammalian genome. The overall base composition is A: 33.1%, C: 26.6%, G: 13.9%, and T: 26.4%. Our analyses confirm that the mitochondrial genomes of swamp and river buffaloes are divergent (mean nucleotide distance = 2.3%), and show that Indian river buffalo haplotypes cluster into three haplogroups, named RB1, RB2, and RB3 (mean distance = 0.25-0.26%) and that the 24 Egyptian buffalo haplotypes fall into RB1 (with the Bangladeshi, Chinese and Italian buffalo haplotypes) and RB2.

Inclusion of Probiotics into Fermented Buffalo (Bubalus bubalis) Milk: An Overview of Challenges and Opportunities

Buffalo-milk-based dairy products provide various health benefits to humans since buffalo milk serves as a rich source of protein, fat, lactose, calcium, iron, phosphorus, vitamin A and natural antioxidants. Dairy products such as Meekiri, Dadih, Dadi and Lassie, which are derived from Artisanal fermentation of buffalo milk, have been consumed for many years. Probiotic potentials of indigenous microflora in fermented buffalo milk have been well documented. Incorporation of certain probiotics into the buffalo-milk-based dairy products conferred vital health benefits to the consumers, although is not a common practice. However, several challenges are associated with incorporating probiotics into buffalo-milk-based dairy products. The viability of probiotic bacteria can be reduced due to processing and environmental stress during storage. Further, incompatibility of probiotics with traditional starter cultures and high acidity of fermented dairy products may lead to poor viability of probiotics. The weak acidifying performance of probiotics may affect the organoleptic quality of fermented dairy products. Besides these challenges, several innovative technologies such as the use of microencapsulated probiotics, ultrasonication, the inclusion of prebiotics, use of appropriate packaging and optimal storage conditions have been reported, promising stability and viability of probiotics in buffalo-milk-based fermented dairy products.

Bubalus bubalis: A Short Story

The domestic buffalo (Bubalus bubalis), also known as water buffalo or Asian buffalo to prevent confusion with the American bison (Bison bison), wrongly named buffalo in North America, comprises two subspecies: the river buffalo (B. bubalis bubalis) and the swamp buffalo (B. bubalis kerebau). The swamp buffalo has a consistent phenotype and is considered as one type, even if many breeds are recognized within it; conversely, the river buffalo subspecies has many breeds. We found limited information available regarding the worldwide distribution of buffaloes. The best estimate is that 208,098,759 buffalo head are distributed in 77 countries in five continents. In this review, we presented the basic aspects of the water buffalo and unraveled the buffalo path followed from the origin of the species to its current global distribution. We reviewed several data sources to provide a better estimate of the world buffalo count and distribution.

Whole-Genome Resequencing Reveals Adaptation Prior to the Divergence of Buffalo Subspecies

The application of high-throughput genotyping or sequencing data helps us to understand the genomic response to natural and artificial selection. In this study, we scanned the genomes of five indigenous buffalo populations belong to three recognized breeds, adapted to different geographical and agro-ecological zones in Iran, to unravel the extent of genomic diversity and to localize genomic regions and genes underwent past selection. A total of 46 river buffalo whole genomes, from West and East Azerbaijan, Gilan, Mazandaran, and Khuzestan provinces, were resequenced. Our sequencing data reached to a coverage above 99% of the river buffalo reference genome and an average read depth around 9.2× per sample. We identified 20.55 million SNPs, including 63,097 missense, 707 stop-gain, and 159 stop-loss mutations that might have functional consequences. Genomic diversity analyses showed modest structuring among Iranian buffalo populations following frequent gene flow or admixture in the recent past. Evidence of positive selection was investigated using both differentiation (Fst) and fixation (Pi) metrics. Analysis of fixation revealed three genomic regions in all three breeds with aberrant polymorphism contents on BBU2, 20, and 21. Fixation signal on BBU2 overlapped with the OCA2-HERC2 genes, suggestive of adaptation to UV exposure through pigmentation mechanism. Further validation using resequencing data from other five bovine species as well as the Axiom Buffalo Genotyping Array 90K data of river and swamp buffaloes indicated that these fixation signals persisted across river and swamp buffaloes and extended to taurine cattle, implying an ancient evolutionary event occurred before the speciation of buffalo and taurine cattle. These results contributed to our understanding of major genetic switches that took place during the evolution of modern buffaloes.

Evolution and domestication of the Bovini species

Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10 000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species - taurine cattle, zebu and yak - and their genetic interactions. The global dispersion of taurine and zebu cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation of the mitochondrial and Y-chromosomal DNA. The high diversity of European breeds has been shaped through isolation-by-distance, different production objectives, breed formation and the expansion of popular breeds. The overlapping and broad ranges of taurine and zebu cattle led to hybridization with each other and with other bovine species. For instance, Chinese gayal carries zebu mitochondrial DNA; several Indonesian zebu descend from zebu bull × banteng cow crossings; Tibetan cattle and yak have exchanged gene variants; and about 5% of the American bison contain taurine mtDNA. Analysis at the genomic level indicates that introgression may have played a role in environmental adaptation.