Asian water buffalo: domestication, history and genetics

The domestic Asian water buffalo (Bubalus bubalis) is found on all five continents, with a global population of some 202 million. The livelihoods of more people depend on this species than on any other domestic animal. The two distinct types (river and swamp) descended from different wild Asian water buffalo (Bubalus arnee) populations that diverged some 900 kyr BP and then evolved in separate geographical regions. After domestication in the western region of the Indian subcontinent (ca. 6300 years BP), the river buffalo spread west as far as Egypt, the Balkans and Italy. Conversely, after domestication in the China/Indochina border region ca. 3000-7000 years BP, swamp buffaloes dispersed through south-east Asia and China as far as the Yangtze River valley. Molecular and morphological evidence indicates that swamp buffalo populations have strong geographic genetic differentiation and a lack of gene flow, but strong phenotypic uniformity. In contrast, river buffalo populations show a weaker phylogeographic structure, but higher phenotypic diversity (i.e. many breeds). The recent availability of a high-quality reference genome and of a medium-density marker panel for genotyping has triggered a number of genome-wide investigations on diversity, evolutionary history, production traits and functional elements. The growing molecular knowledge combined with breeding programmes should pave the way to improvements in production, environmental adaptation and disease resistance in water buffalo populations worldwide.

Clinical Applications and Factors Involved in Validating Thermal Windows Used in Infrared Thermography in Cattle and River Buffalo to Assess Health and Productivity

Infrared thermography (IRT) is a non-ionizing, non-invasive technique that permits evaluating the comfort levels of animals, a topic of concern due to the growing interest in determining the state of health and welfare of production animals. The operating principle of IRT is detecting the heat irradiated in anatomical regions characterized by a high density of near-surface blood vessels that can regulate temperature gain or loss from/to the environment by modifying blood flow. This is essential for understanding the various vascular thermoregulation mechanisms of different species, such as rodents and ruminants' tails. The usefulness of ocular, nasal, and vulvar thermal windows in the orbital (regio orbitalis), nasal (regio nasalis), and urogenital (regio urogenitalis) regions, respectively, has been demonstrated in cattle. However, recent evidence for the river buffalo has detected discrepancies in the data gathered from distinct thermal regions in these large ruminants, suggesting a limited sensitivity and specificity when used with this species due to various factors: the presence of hair, ambient temperature, and anatomical features, such as skin thickness and variations in blood supplies to different regions. In this review, a literature search was conducted in Scopus, Web of Science, ScienceDirect, and PubMed, using keyword combinations that included "infrared thermography", "water buffalo", "river buffalo" "thermoregulation", "microvascular changes", "lacrimal caruncle", "udder", "mastitis", and "nostril". We discuss recent findings on four thermal windows-the orbital and nasal regions, mammary gland in the udder region (regio uberis), and vulvar in the urogenital region (regio urogenitalis)-to elucidate the factors that modulate and intervene in validating thermal windows and interpreting the information they provide, as it relates to the clinical usefulness of IRT for cattle (Bos) and the river buffalo (Bubalus bubalis).

New Insights on Water Buffalo Genomic Diversity and Post-Domestication Migration Routes From Medium Density SNP Chip Data

The domestic water buffalo is native to the Asian continent but through historical migrations and recent importations, nowadays has a worldwide distribution. The two types of water buffalo, i.e., river and swamp, display distinct morphological and behavioral traits, different karyotypes and also have different purposes and geographical distributions. River buffaloes from Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy, Mozambique, Brazil and Colombia, and swamp buffaloes from China, Thailand, Philippines, Indonesia and Brazil were genotyped with a species-specific medium-density 90K SNP panel. We estimated the levels of molecular diversity and described population structure, which revealed historical relationships between populations and migration events. Three distinct gene pools were identified in pure river as well as in pure swamp buffalo populations. Genomic admixture was seen in the Philippines and in Brazil, resulting from importations of animals for breed improvement. Our results were largely consistent with previous archeological, historical and molecular-based evidence for two independent domestication events for river- and swamp-type buffaloes, which occurred in the Indo-Pakistani region and close to the China/Indochina border, respectively. Based on a geographical analysis of the distribution of diversity, our evidence also indicated that the water buffalo spread out of the domestication centers followed two major divergent migration directions: river buffaloes migrated west from the Indian sub-continent while swamp buffaloes migrated from northern Indochina via an east-south-eastern route. These data suggest that the current distribution of water buffalo diversity has been shaped by the combined effects of multiple migration events occurred at different stages of the post-domestication history of the species.

Chromosome Abnormalities and Fertility in Domestic Bovids: A Review

Simple Summary

In domestic bovids, numerical autosome abnormalities have been rarely reported, as they present abnormal animal phenotypes quickly eliminated by breeders. However, numerical abnormalities involving sex chromosomes and structural (balanced) chromosome anomalies have been more frequently detected because they are most often not phenotypically visible to breeders. For this reason, these chromosome abnormalities, without a cytogenetic control, escape animal selection, with subsequent deleterious effects on fertility, especially in female carriers.

Abstract

After discovering the Robertsonian translocation rob(1;29) in Swedish red cattle and demonstrating its harmful effect on fertility, the cytogenetics applied to domestic animals have been widely expanded in many laboratories in order to find relationships between chromosome abnormalities and their phenotypic effects on animal production. Numerical abnormalities involving autosomes have been rarely reported, as they present abnormal animal phenotypes quickly eliminated by breeders. In contrast, numerical sex chromosome abnormalities and structural chromosome anomalies have been more frequently detected in domestic bovids because they are often not phenotypically visible to breeders. For this reason, these chromosome abnormalities, without a cytogenetic control, escape selection, with subsequent harmful effects on fertility, especially in female carriers. Chromosome abnormalities can also be easily spread through the offspring, especially when using artificial insemination. The advent of chromosome banding and FISH-mapping techniques with specific molecular markers (or chromosome-painting probes) has led to the development of powerful tools for cytogeneticists in their daily work. With these tools, they can identify the chromosomes involved in abnormalities, even when the banding pattern resolution is low (as has been the case in many published papers, especially in the past). Indeed, clinical cytogenetics remains an essential step in the genetic improvement of livestock.

The single nucleotide polymorphism g.133A>C in the stearoyl CoA desaturase gene (SCD) promoter affects gene expression and quali-quantitative properties of river buffalo milk

The stearoyl-CoA desaturase (SCD) gene has been investigated in depth in ruminants because of its effect on milk fat composition. In river buffalo, the single nucleotide polymorphism (SNP) g.133A>C in the gene promoter has been associated with milk quality and yield. However, the biological reason for such effects remains unexplored. In this study, we combined mRNA profile analysis, an electromobility shift assay, and quantitative PCR to elucidate the role of this SNP on gene transcription and its effects on milk fat traits. A preliminary genotyping of g.133A>C was carried out on a group of 303 river buffaloes to choose individuals for the downstream applications. Analysis of allele frequencies showed an increase in the minor allele C (0.25) compared with previous findings (0.16). Six animals (2 for each genotype) were chosen for cloning and 216 positive cDNA recombinant clones for SCD (72 per genotype) were analyzed by PCR. All clones showed the same length on agarose gel; therefore, random clones were chosen for sequencing. No qualitative differences were found and all gene transcripts assembled correctly. An electrophoretic mobility shift assay was performed to evaluate the binding of the transcription factor Sp1 to DNA sequences including g.133A>C. Genotype CC showed a higher binding (mean ± standard error of the mean) than genotype AA in 2 different conditions [Enzo buffer (EB), Enzo Life Science Inc., Farmingdale, NY: 201.77 ± 4.06 vs. 141.65 ± 3.77 band intensity values and Poletto buffer (PB): 95.90 ± 1.15 vs. 67.30 ± 2.14 band intensity values]. The subsequent quantitative PCR confirmed the upregulation of the CC genotype compared with the AA and AC genotypes. The association study with milk fat traits revealed a favorable effect of allele C. The heterozygous genotype had the highest values for monounsaturated fatty acids, oleic acid (C18:1 cis-9), polyunsaturated fatty acids, and odd- and branched-chain fatty acids, and the lowest values for saturated fatty acids and atherogenic and thrombogenic indices; the heterozygous genotype differed significantly from the AA genotype. The AC genotype has previously been associated with higher milk yield. Therefore, the g.133A>C SNP is a marker with dual effects and is an interesting candidate for assisted selection programs in river buffalo. These data clarified the biological role of the SNP g.133A>C in the SCD promoter and how it affects gene function, providing important knowledge on the genetic background of lipid metabolism, including the future possibility of selecting alleles with quantitatively or qualitatively favorable effects.

Current Knowledge on River Buffalo Meat: A Critical Analysis

Simple Summary

Buffaloes are reared for different purposes, primarily for milk and dairy products. Meat is often a secondary product and mainly derives from old animals at the end of their productive or working life. However, in recent years buffalo meat has gained increased popularity due to its nutritional properties. Therefore, a huge economic potential might arise from the development of the meat sector in buffalo breeding. This review provides an overview of the recent advances in the knowledge on river buffalo meat, with a special focus on quality traits, and offers insights for future research aimed at improving the meat sector in this species.

Abstract

The estimated world population of water buffalo counts around 204 million head, mostly reared for milk production. However, buffaloes also largely contribute to the meat sector, with around 4.3 million tonnes produced in 2019, mainly derived from old animals at the end of their productive or working life and only to a small extent from young animals. Therefore, buffalo meat production has been generally considered unsatisfactory for both quantity and quality. In fact, the dressing percentage is generally lower than 50% and the meat is considered of poor quality mainly due to its dark colour and reduced tenderness. However, in recent years, the healthy properties highlighted by some studies have led to a renewed interest in buffalo meat, with a parallel increase in research. Therefore, this review aims at providing an updated picture on carcass and meat quality traits in river buffalo, with special attention to the intrinsic and extrinsic factors contributing to their variability. The research done so far has demonstrated that river buffaloes can efficiently contribute to the quanti-qualitative production of meat, provided that the meat supply chain is specifically organised for this purpose. The analysis of the available data also showed that further research is needed on the factors affecting meat production in order to gain greater knowledge essential for planning more targeted interventions.

Congenital Malformations in River Buffalo (Bubalus bubalis)

Simple Summary

Congenital malformations (due to genetic causes) represent a hidden danger for animal production, above all when genetic selection is undertaken for production improvements. These malformations are responsible for economic losses either because they reduce the productivity of the farm, or because their spread in the population would decrease the total productivity of that species/breed. River buffalo is a species of increasing interest all over the world for its production abilities, as proved by the buffalo genome project and the genetic selection plans that are currently performed in different countries. The aim of this review is to provide a general view of different models of congenital malformations in buffalo and their world distribution. This would be useful either for those who performed buffalo genetic selection or for researchers in genetic diseases, which would be an advantage to their studies with respect to the knowledge of gene mutations and interactions in this species.

Abstract

The world buffalo population is about 168 million, and it is still growing, in India, China, Brazil, and Italy. In these countries, buffalo genetic breeding programs have been performed for many decades. The occurrence of congenital malformations has caused a slowing of the genetic progress and economic loss for the breeders, due to the death of animals, or damage to their reproductive ability or failing of milk production. Moreover, they cause animal welfare reduction because they can imply foetal dystocia and because the affected animals have a reduced fitness with little chances of survival. This review depicts, in the river buffalo (Bubalus bubalis) world population, the present status of the congenital malformations, due to genetic causes, to identify their frequency and distribution in order to develop genetic breeding plans able to improve the productive and reproductive performance, and avoid the spreading of detrimental gene variants. Congenital malformations most frequently reported in literature or signaled by breeders to the Department of Veterinary Medicine and Animal Production of the University Federico II (Naples, Italy) in river buffalo are: musculoskeletal defects (transverse hemimelia, arthrogryposis, umbilical hernia) and disorders of sexual development. In conclusion this review put in evidence that river buffalo have a great variety of malformations due to genetic causes, and TH and omphalocele are the most frequent and that several cases are still not reported, leading to an underestimation of the real weight of genetic diseases in this species.

Pain at the Slaughterhouse in Ruminants with a Focus on the Neurobiology of Sensitisation

Simple Summary

We pose based on a fundamental science examination that events that occur around the time of slaughter have the potential to intensify the pain response, through a process called sensitisation, or an exaggerated response to painful stimuli. Health conditions which result in inflammation, injuries arising from transport and handling and exaggerated fear responses may all be present at the slaughterhouse. Whilst there is limited evidence of a direct effect of these on the processes of sensitisation in animals at slaughter, by analogy with the human neurobiology literature the connection seems plausible. In this review we outline the biology of such a response, and the rationale for suggestion of a possible linkage between events at slaughter and a heightened animal pain response.

Abstract

We pose, based on a neurobiological examination, that events that occur around the time of slaughter have the potential to intensify the pain response, through the processes of sensitisation and enhanced transmission. Sensitisation, or an enhanced response to painful stimuli, is a well-discussed phenomenon in the human medical literature, which can arise from previous injury to an area, inflammatory reactions, or previous overstimulation of the stress axes. A number of events that occur prior to arrival at, or in the slaughterhouse, may lead to presence of these factors. This includes previous on-farm pathology, injuries arising from transport and handling and lack of habituation to humans. Whilst there is limited evidence of a direct effect of these on the processes of sensitisation in animals at slaughter, by analogy with the human neurobiology literature the connection seems plausible. In this review a neurobiological approach is taken to discuss this hypothesis in the light of basic science, and extrapolations from existing literature on the slaughter of ruminants. To confirm the postulated link between events at slaughter, and processes of hypersensitisation, further dedicated study is required.

Transcript analysis at DGAT1 reveals different mRNA profiles in river buffaloes with extreme phenotypes for milk fat

Buffalo DGAT1 (diacylglycerol O-acyltransferase 1) was mainly investigated for the characterization of the gene itself and for the identification of the K232A polymorphism, similar to what has been accomplished in cattle, although no information has been reported so far at the mRNA level. The importance of DGAT1 for lipid metabolism led us to investigate the transcript profiles of lactating buffaloes characterized as high (9.13 ± 0.23) and low (7.94 ± 0.29) for milk fat percentage, and to explore the genetic diversity at the RNA and DNA level. A total of 336 positive clones for the DGAT1 cDNA were analyzed by PCR and chosen for sequencing according to the differences in length. The clone assembling revealed a very complex mRNA pattern with a total of 21 transcripts differently represented in the 2 groups of animals. Apart from the correct transcript (17 exons long), the skipping of exon 12 is the most significant in terms of distribution of clones with 11.6% difference between the 2 groups, whereas a totally different mRNA profile was found in approximately 12% of clones. The sequencing of genomic DNA allowed the identification of 10 polymorphic sites at the intron level, which clarify, at least partially, the genetic events behind the production of complex mRNA. Genetic diversity was found also at the exon level. The single nucleotide polymorphism c.1053C>T represents the first example of polymorphism in a coding region for the DGAT1 in the Italian Mediterranean breed. To establish whether this polymorphism is present in other buffalo breeds, a quick method based on PCR-RFLP was set up for allelic discrimination in the Italian Mediterranean and the Romanian Murrah (200 animals in total). The alleles were equally represented in the overall population, whereas the analysis of the 2 breeds showed different frequencies, likely indicating diverse genetic structure of the 2 breeds. The T allele might be considered as the ancestral condition of the DGAT1 gene, being present in the great part of the sequenced species. These data add knowledge at the transcript and genetic levels for the buffalo DGAT1 and open the opportunity for further investigation of other genes involved in milk fat metabolism for the river buffalo, including the future possibility of selecting alleles with quantitative or qualitative favorable effects (or both).

Dual-Purpose Water Buffalo Production Systems in Tropical Latin America: Bases for a Sustainable Model

Simple Summary

Buffaloes in the Latin American tropics have gained relevance in recent years thanks to the rusticity and productivity of this species and the potential of these ecosystems. Through a specialized literature review, the options were explored to promote efficient, profitable and sustainable dual-purpose production systems, which implied taking into consideration the characteristics of a fragile environment such as the tropics but with abundant forage resources. Buffaloes have distinctive characteristics with respect to cattle, such as a high fat milk content, ability to produce healthy and heavy calves from dairy cows and their need for thermoregulation, which implies the availability of water ponds and shade in grazing areas. Therefore, we propose the basis for designing intensive rotational grazing models and, under certain silvopastoral conditions, taking advantage of the gregarious behavior of buffaloes. These models require integral forms of management, including the organization and participation of producers in commercial channels, in order to value meat, milk and dairy products, given that their nutritional qualities allow them to be sold as differentiated products. There have been successful experiences in the region with this dual-purpose model, which, with the necessary adaptations, can be strengthened with buffaloes.

Abstract

Tropical regions of Latin America have been incorporated into development in recent decades, with extensive cattle ranching as one of the main economic activities but without adequate planning, drastically degrading the ecosystem. In recent years, buffalo production has been incorporated into the region, with possibilities for development in profitable and sustainable models. To study this option in depth, a broad bibliographic review was carried out focusing on the ecological characteristics of tropical zones and the physiological and productive characteristics of buffaloes. We also investigated the structure and functioning of dual-purpose systems that have worked in cattle and that can be optimized with this alternative animal species. The possibility of taking sustainable advantage of abundant forage resources in the region was detected through intensive grazing models, as well as agrosilvopastoral systems, due to the gregarious qualities of buffaloes and responding to their thermoregulation needs. In this way, the productive and regenerative capacities of the dual-purpose system could be increased, as well as the quality of meat and milk, which could be marketed as differentiated products, taking advantage of their outstanding nutritional qualities. Integral management of the dual-purpose system is proposed, retaking the bases of the original model of family characters, diversified and with low investments and risks, which with specific innovations can be an effective development option for producers 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.

Molecular Cytogenetics in Domestic Bovids: A Review

The discovery of the Robertsonian translocation (rob) involving cattle chromosomes 1 and 29 and the demonstration of its deleterious effects on fertility focused the interest of many scientific groups on using chromosome banding techniques to reveal chromosome abnormalities and verify their effects on fertility in domestic animals. At the same time, comparative banding studies among various species of domestic or wild animals were found useful for delineating chromosome evolution among species. The advent of molecular cytogenetics, particularly the use of fluorescence in situ hybridization (FISH), has allowed a deeper investigation of the chromosomes of domestic animals through: (a) the physical mapping of specific DNA sequences on chromosome regions; (b) the use of specific chromosome markers for the identification of the chromosomes or chromosome regions involved in chromosome abnormalities, especially when poor banding patterns are produced; (c) better anchoring of radiation hybrid and genetic maps to specific chromosome regions; (d) better comparisons of related and unrelated species by comparative FISH mapping and/or Zoo-FISH techniques; (e) the study of meiotic segregation, especially by sperm-FISH, in some chromosome abnormalities; (f) better demonstration of conserved or lost DNA sequences in chromosome abnormalities; (g) the use of informatic and genomic reconstructions, in addition to CGH arrays, to predict conserved or lost chromosome regions in related species; and (h) the study of some chromosome abnormalities and genomic stability using PCR applications. This review summarizes the most important applications of molecular cytogenetics in domestic bovids, with an emphasis on FISH mapping applications.

Comparative analyses of copy number variations between swamp buffaloes and river buffaloes

As an important source of genomic variation, copy number variation (CNV) contributes to environmental adaptation in worldwide buffaloes. Despite this importance, CNV divergence between swamp buffaloes and river buffaloes has not been studied previously. Here, we report 21 152 CNV regions (CNVRs) in 141 buffaloes of 20 breeds detected through multiple CNV calling strategies. Only 248 CNVRs were shared between river buffalo and swamp buffalo, reflecting great variation of CNVRs between the two subspecies. Population structure analysis based on CNVs successfully separated the two buffalo subspecies. We further assessed CNV divergence by calculating F_ST for genome-wide CNVs. Totally, we identified 110 significantly divergent CNV segments and 44 putatively selected genes between river buffaloes and swamp buffaloes. In particular, LALBA, a key gene controlling milk production in cattle, presented a highly differentiated CNV in the promoter region, which makes it a strong functional candidate gene for differences between swamp buffaloes and river buffaloes in traits related to milk production. Our study provides useful information of CNVs in buffaloes, which may help explain the genetic differences between the two subspecies.

Comparative Fluorescence In Situ Hybridization (FISH) Mapping of Twenty-Three Endogenous Jaagsiekte Sheep Retrovirus (enJSRVs) in Sheep (Ovis aries) and River Buffalo (Bubalus bubalis) Chromosomes

Endogenous retroviruses (ERVs) are the remnants of ancient infections of host germline cells, thus representing key tools to study host and viral evolution. Homologous ERV sequences often map at the same genomic locus of different species, indicating that retroviral integration occurred in the genomes of the common ancestors of those species. The genome of domestic sheep (Ovis aries) harbors at least twenty-seven copies of ERVs related to the exogenous and pathogenic Jaagsiekte sheep retrovirus (JSRVs), thus referred to as enJSRVs. Some of these loci are unequally distributed between breeds and individuals of the host species due to polymorphic insertions, thereby representing invaluable tools to trace the evolutionary dynamics of virus populations within their hosts. In this study, we extend the cytogenetic physical maps of sheep and river buffalo by performing fluorescent in situ hybridization (FISH) mapping of twenty-three genetically characterized enJSRVs. Additionally, we report the first comparative FISH mapping of enJSRVs in domestic sheep (2n = 54) and river buffalo (Bubalus bubalis, 2n = 50). Finally, we demonstrate that enJSRV loci are conserved in the homologous chromosomes and chromosome bands of both species. Altogether, our results support the hypothesis that enJSRVs were present in the genomes of both species before they differentiated within the Bovidae family.

Birth weight and stillbirth genetic parameter estimation in a river buffalo simulated population

Stillbirth (SB) is a threshold character that has been detected as the most important factor affecting the future reproductive life of an animal. In buffaloes, stillbirth accounts for approximately 42% of all reproductive disorders being considered as the main reproductive disorder in buffalo calves. The present study aimed to estimate the heritability values and to determine the genetic and phenotypic correlation between stillbirth rate and birth weight (BW) using a Bayesian approach via Gibbs sampling method in a river buffalo population. A stochastic simulation was used to create a population in which random mating was used for 15 discrete generations. A bivariate animal model including maternal effects was used. Maternal effects were significant (p < .05) for both BW and SB. The results showed that when the SB rate increased from 1% to 50%, the estimated direct heritability of SB increased. Yet, by increasing the SB rate from 50% to 99%, a decrease of the SB estimated direct heritability was observed. The genetic correlation between BW and SB was decreased by increasing the level of occurrence of SB in the population from 1% to 99%. The root mean square error (RMSE) of heritability was increased from 40% to 70% level of occurrence of SB. Based on findings, it can be concluded that to reduce stillbirth rate in the population, it is possible to use genetic improvement program and birth weight could be one of the main components of a selection goal.