Draft genome of the river water buffalo

Research Progress and Applications of Bovine Genome in the Tribe Bovini

Various bovine species have been domesticated and bred for thousands of years, and they provide adequate animal-derived products, including meat, milk, and leather, to meet human requirements. Despite the review studies on economic traits in cattle, the genetic basis of traits has only been partially explained by phenotype and pedigree breeding methods, due to the complexity of genomic regulation during animal development and growth. With the advent of next-generation sequencing technology, genomics projects, such as the 1000 Bull Genomes Project, Functional Annotation of Animal Genomes project, and Bovine Pangenome Consortium, have advanced bovine genomic research. These large-scale genomics projects gave us a comprehensive concept, technology, and public resources. In this review, we summarize the genomics research progress of the main bovine species during the past decade, including cattle (Bos taurus), yak (Bos grunniens), water buffalo (Bubalus bubalis), zebu (Bos indicus), and gayal (Bos frontalis). We mainly discuss the development of genome sequencing and functional annotation, focusing on how genomic analysis reveals genetic variation and its impact on phenotypes in several bovine species.

Evolutionary analysis of buffalo sterol regulatory element-binding factor (SREBF) family genes and their affection on milk traits

The sterol regulatory element-binding factor (SREBF) genes are a vital group of proteins binding to the sterol regulatory element 1 (SRE-1) regulating the synthesis of fatty acid. Two potential candidate genes (SREBF1 and SREBF2) have been identified as affecting milk traits. This study aims to identify the SREBF family of genes and find candidate markers or SREBF genes influencing lactation production in buffalo. A genome-wide study was performed and identified seven SREBF genes randomly distributed on 7 chromosomes and 24 protein isoforms in buffalos. The SREBF family of genes were also characterized in cattle, goat, sheep and horse, and using these all-protein sequences, a phylogenetic tree was built. The SREBF family genes were homologous between each other in the five livestock. Eight single nucleotide polymorphisms (SNPs) within or near the SREBF genes in the buffalo genome were identified and at least one milk production trait was associated with three of the SNP. The expression of SREBF genes at different lactation stages in buffalo and cattle from published data were compared and the SREBF genes retained a high expression throughout lactation with the trend being the same for buffalo and cattle. These results provide valuable information for clarifying the evolutionary relationship of the SREBF family genes and determining the role of SREBF genes in the regulation of milk production in buffalo.

Identification of core genes affecting IMF deposition in bovine

Intramuscular fat (IMF) content is an important economic factor in beef production. However, knowledge on the key factors controlling bovine IMF is limited. In this study, using weighted gene co-expression network analysis (WGCNA), nine modules were identified and the number of transcripts in these modules ranged from 36 to 3191. Two modules were found to be significantly associated with fat deposition and three genes (TCAP, MYH7, and TNNC1) were further identified by Protein-protein interaction (PPI), which may be the hub genes regulating bovine IMF deposition. In addition, considering the genetic variation, the PCK1 gene was found by functional enrichment analysis of overlapping genes, which was previously reported to be involved in IMF deposition. We noted that the core promoter region of buffalo PCK1 binds to transcription factors involved in lipid metabolism while cattle PCK1 binds transcription factors involved in muscle development. The results suggest that PCK1 participated in IMF deposition of buffalo and cattle in different ways. In summary, gene expression networks and new candidate genes associated with IMF deposition identified in this study. This would lay the foundation for further research into the molecular regulatory mechanisms underlying bovine IMF deposition.

Taming transposable elements in livestock and poultry: a review of their roles and applications

Livestock and poultry play a significant role in human nutrition by converting agricultural by-products into high-quality proteins. To meet the growing demand for safe animal protein, genetic improvement of livestock must be done sustainably while minimizing negative environmental impacts. Transposable elements (TE) are important components of livestock and poultry genomes, contributing to their genetic diversity, chromatin states, gene regulatory networks, and complex traits of economic value. However, compared to other species, research on TE in livestock and poultry is still in its early stages. In this review, we analyze 72 studies published in the past 20 years, summarize the TE composition in livestock and poultry genomes, and focus on their potential roles in functional genomics. We also discuss bioinformatic tools and strategies for integrating multi-omics data with TE, and explore future directions, feasibility, and challenges of TE research in livestock and poultry. In addition, we suggest strategies to apply TE in basic biological research and animal breeding. Our goal is to provide a new perspective on the importance of TE in livestock and poultry genomes.

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.

Evaluation of the application opportunities of precision livestock farming (PLF) for water buffalo (Bubalus bubalis) breeding: SWOT analysis

The use of technology in agriculture is increasing daily with the development of technology in all areas. With the help of PLF (precision livestock farming) technologies and efficient use of inputs, economic, environmentally friendly, and better-quality products are obtained. Significantly its use in dairy cattle is increasing daily, contributing to sustainable milk production in both economic and ecological terms. As the demand increased in the world for water buffalo meat, milk, and dairy products, different breeding systems have been applied for more and higher-quality production purposes. This way the number of water buffalo farms breeding in intensive conditions is increasing. It is necessary to investigate the possibilities of using PLF technologies, which are still widespread in dairy cattle, in water buffalo breeding, and to benefit from the advanced technology in this regard. This study aims to discuss the applicability of PLF technologies by surveying buffalo breeders. With the data obtained from the survey results made with the water buffalo breeders, the strengths, opportunities, threats, and effects of the weaknesses were discussed with the SWOT analysis.

Draft genome of the lowland anoa (Bubalus depressicornis) and comparison with buffalo genome assemblies (Bovidae, Bubalina)

Genomic data for wild species of the genus Bubalus (Asian buffaloes) are still lacking while several whole genomes are currently available for domestic water buffaloes. To address this, we sequenced the genome of a wild endangered dwarf buffalo, the lowland anoa (Bubalus depressicornis), produced a draft genome assembly and made comparison to published buffalo genomes. The lowland anoa genome assembly was 2.56 Gbp long and contained 103,135 contigs, the longest contig being 337.39 kbp long. N50 and L50 values were 38.73 and 19.83 kbp, respectively, mean coverage was 44× and GC content was 41.74%. Two strategies were adopted to evaluate genome completeness: (1) determination of genomic features with de novo and homology-based predictions using annotations of chromosome-level genome assembly of the river buffalo and (2) employment of benchmarking against universal single-copy orthologs (BUSCO). Homology-based predictions identified 94.51% complete and 3.65% partial genomic features. De novo gene predictions identified 32,393 genes, representing 97.14% of the reference’s annotated genes, whilst BUSCO search against the mammalian orthologs database identified 71.1% complete, 11.7% fragmented, and 17.2% missing orthologs, indicating a good level of completeness for downstream analyses. Repeat analyses indicated that the lowland anoa genome contains 42.12% of repetitive regions. The genome assembly of the lowland anoa is expected to contribute to comparative genome analyses among bovid species.

Effect of replacing soybean meal by a blend of ground corn and urea-ammonium sulphate on milk production and composition, digestibility and N balance of dairy Murrah buffaloes

This study evaluated the effect of replacing soybean meal by a blend of ground corn and urea-ammonium sulphate (GCU-S) in the diet of lactating buffaloes on milk production and composition, digestibility, N balance and blood metabolites. Twelve multiparous dairy Murrah buffaloes (Bubalus bubalis), at 100 ± 4 d in milk and yielding 10 ± 2.5 kg/d, were randomly distributed in a triple 4 × 4 Latin square, with four different inclusions of GCU-S at U-S levels: 0 (control), 8.0, 16.4 and 24.1 g/kg dry matter (DM) total. Replacing soybean meal with GC-US had a significant depressing effect on absolute DM intake, which was still numerically evident but no longer significant when expressed on a body weight-related basis. Intakes of crude protein (CP) and N as well as N-urinary excretion were also significantly depressed. Digestibility of dry matter was improved and, as a proportion of DMI, intake of total digestible nutrients increased significantly. Perhaps as a result, feed efficiency (kg DMI required per kg 6% fat-corrected milk) was significantly improved. Efficiency of protein use for milk production was significantly improved, but not when expressed as milk protein output. N transfer into milk, as a proportion of total N intake, also increased significantly. However, GC-US inclusion had no significant effect on milk production or milk composition, nor did it affect serum metabolites, digestibilities (apart from dry matter) or N measures of balance apart from those mentioned above. Inclusion of this blend of ground corn with urea and ammonium suplate can be recommended for dairy buffalo because, although it decreases DMI and N-excretion, it improves DM digestibility and feeding efficiency whilst maintaining milk production and composition.

A draft genome of Drung cattle reveals clues to its chromosomal fusion and environmental adaptation

Drung cattle (Bos frontalis) have 58 chromosomes, differing from the Bos taurus 2n = 60 karyotype. To date, its origin and evolution history have not been proven conclusively, and the mechanisms of chromosome fusion and environmental adaptation have not been clearly elucidated. Here, we assembled a high integrity and good contiguity genome of Drung cattle with 13.7-fold contig N50 and 4.1-fold scaffold N50 improvements over the recently published Indian mithun assembly, respectively. Speciation time estimation and phylogenetic analysis showed that Drung cattle diverged from Bos taurus into an independent evolutionary clade. Sequence evidence of centromere regions provides clues to the breakpoints in BTA2 and BTA28 centromere satellites. We furthermore integrated a circulation and contraction-related biological process involving 43 evolutionary genes that participated in pathways associated with the evolution of the cardiovascular system. These findings may have important implications for understanding the molecular mechanisms of chromosome fusion, alpine valleys adaptability and cardiovascular function.

Evolutionary and Association Analysis of Buffalo FABP Family Genes Reveal Their Potential Role in Milk Performance

The fatty acid-binding protein (FABP) family gene encode a group of proteins that affect long-chain fatty acid (LCFAs) trafficking and play a crucial function in the regulation of milk fat synthesis. Nevertheless, little is known regarding the identification of members, theevolutionary background, and functional characteristics of FABP genes in buffalo. In this study, in silico analysis was performed to identify the members of FABPs in buffalo. The results revealed that a total of 17 FABP genes were identified. Based on their phylogenetic relationships, these sequences clustered into five groups with similar motif patterns and gene structures. According to positive selection analyses, all duplicated gene pairs containing FABPs in buffalo had Ka/Ks (nonsynonymous/synonymous) ratios that were less than 1, suggesting that they were under purifying selection. Association analysis showed that one SNP in LOC102401361 was found significantly associated with buffalo milk yield. The expression levels of several FABPs in buffalo mammary epithelial cells were regulated by palmitic and stearic acid treatment. The findings of this study provide valuable information for further research on the role of FABPs in regulating buffalo milk synthesis.

Genomic Identification, Evolution, and Expression Analysis of Bromodomain Genes Family in Buffalo

Bromodomain (BRD) is an evolutionarily conserved protein-protein interaction module that is critical in gene regulation, cellular homeostasis, and epigenetics. This study aimed to conduct an identification, evolution, and expression analysis of the BRD gene family in the swamp buffalo (Bubalus bubalis). A total of 101 BRD protein sequences deduced from 22 BRD genes were found in the buffalo genome. The BRD proteins were classified into six groups based on phylogenetic relationships, conserved motifs, and conserved domains. The BRD genes were irregularly distributed in 13 chromosomes. Collinearity analysis revealed 20 BRD gene pairs that had remarkable homologous relationships between the buffalo and cattle, although no tandem or segmental duplication event was found in the buffalo BRD genes. Comparative transcriptomics using a 10x sequencing platform analysis showed that 22 BRD genes were identified in the Sertoli cells (SCs) at different developmental stages of buffalo. Further, the mRNA expression levels of bromodomain and the extraterminal (BET) family in SCs at the pubertal stage were higher than that at the prepubertal stage of buffalo. However, the SMARCA2, PHIP, BRD9, and TAF1 genes exhibited the opposite trend. The maturation process of SCs may be regulated by the BRD family members expressed differentially in SCs at different developmental stages of buffalo. In summary, our findings provide an understanding of the evolutionary, structural, and functional properties of the buffalo BRD family members, and further characterize the function of the BRD family in the maturation of SCs. It also provides a theoretical basis for further understanding in the future of the mechanism of SCs regulating spermatogenesis.

Genome Wide Prediction, Mapping and Development of Genomic Resources of Mastitis Associated Genes in Water Buffalo

Water buffalo (Bubalus bubalis) are an important animal resource that contributes milk, meat, leather, dairy products, and power for plowing and transport. However, mastitis, a bacterial disease affecting milk production and reproduction efficiency, is most prevalent in populations having intensive selection for higher milk yield, especially where the inbreeding level is also high. Climate change and poor hygiene management practices further complicate the issue. The management of this disease faces major challenges, like antibiotic resistance, maximum residue level, horizontal gene transfer, and limited success in resistance breeding. Bovine mastitis genome wide association studies have had limited success due to breed differences, sample sizes, and minor allele frequency, lowering the power to detect the diseases associated with SNPs. In this work, we focused on the application of targeted gene panels (TGPs) in screening for candidate gene association analysis, and how this approach overcomes the limitation of genome wide association studies. This work will facilitate the targeted sequencing of buffalo genomic regions with high depth coverage required to mine the extremely rare variants potentially associated with buffalo mastitis. Although the whole genome assembly of water buffalo is available, neither mastitis genes are predicted nor TGP in the form of web-genomic resources are available for future variant mining and association studies. Out of the 129 mastitis associated genes of cattle, 101 were completely mapped on the buffalo genome to make TGP. This further helped in identifying rare variants in water buffalo. Eighty-five genes were validated in the buffalo gene expression atlas, with the RNA-Seq data of 50 tissues. The functions of 97 genes were predicted, revealing 225 pathways. The mastitis proteins were used for protein-protein interaction network analysis to obtain additional cross-talking proteins. A total of 1,306 SNPs and 152 indels were identified from 101 genes. Water Buffalo-MSTdb was developed with 3-tier architecture to retrieve mastitis associated genes having genomic coordinates with chromosomal details for TGP sequencing for mining of minor alleles for further association studies. Lastly, a web-genomic resource was made available to mine variants of targeted gene panels in buffalo for mastitis resistance breeding in an endeavor to ensure improved productivity and the reproductive efficiency of water buffalo.

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.

Genetic Features of Reproductive Traits in Bovine and Buffalo: Lessons From Bovine to Buffalo

Bovine and buffalo are important livestock species that have contributed to human lives for more than 1000 years. Improving fertility is very important to reduce the cost of production. In the current review, we classified reproductive traits into three categories: ovulation, breeding, and calving related traits. We systematically summarized the heritability estimates, molecular markers, and genomic selection (GS) for reproductive traits of bovine and buffalo. This review aimed to compile the heritability and genome-wide association studies (GWASs) related to reproductive traits in both bovine and buffalos and tried to highlight the possible disciplines which should benefit buffalo breeding. The estimates of heritability of reproductive traits ranged were from 0 to 0.57 and there were wide differences between the populations. For some specific traits, such as age of puberty (AOP) and calving difficulty (CD), the majority beef population presents relatively higher heritability than dairy cattle. Compared to bovine, genetic studies for buffalo reproductive traits are limited for age at first calving and calving interval traits. Several quantitative trait loci (QTLs), candidate genes, and SNPs associated with bovine reproductive traits were screened and identified by candidate gene methods and/or GWASs. The IGF1 and LEP pathways in addition to non-coding RNAs are highlighted due to their crucial relevance with reproductive traits. The distribution of QTLs related to various traits showed a great differences. Few GWAS have been performed so far on buffalo age at first calving, calving interval, and days open traits. In addition, we summarized the GS studies on bovine and buffalo reproductive traits and compared the accuracy between different reports. Taken together, GWAS and candidate gene approaches can help to understand the molecular genetic mechanisms of complex traits. Recently, GS has been used extensively and can be performed on multiple traits to improve the accuracy of prediction even for traits with low heritability, and can be combined with multi-omics for further analysis.

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.

Historical Introgression from Wild Relatives Enhanced Climatic Adaptation and Resistance to Pneumonia in Sheep

How animals, particularly livestock, adapt to various climates and environments over short evolutionary time is of fundamental biological interest. Further, understanding the genetic mechanisms of adaptation in indigenous livestock populations is important for designing appropriate breeding programs to cope with the impacts of changing climate. Here, we conducted a comprehensive genomic analysis of diversity, interspecies introgression, and climate-mediated selective signatures in a global sample of sheep and their wild relatives. By examining 600K and 50K genome-wide single nucleotide polymorphism data from 3,447 samples representing 111 domestic sheep populations and 403 samples from all their seven wild relatives (argali, Asiatic mouflon, European mouflon, urial, snow sheep, bighorn, and thinhorn sheep), coupled with 88 whole-genome sequences, we detected clear signals of common introgression from wild relatives into sympatric domestic populations, thereby increasing their genomic diversities. The introgressions provided beneficial genetic variants in native populations, which were significantly associated with local climatic adaptation. We observed common introgression signals of alleles in olfactory-related genes (e.g., ADCY3 and TRPV1) and the PADI gene family including in particular PADI2, which is associated with antibacterial innate immunity. Further analyses of whole-genome sequences showed that the introgressed alleles in a specific region of PADI2 (chr2: 248,302,667-248,306,614) correlate with resistance to pneumonia. We conclude that wild introgression enhanced climatic adaptation and resistance to pneumonia in sheep. This has enabled them to adapt to varying climatic and environmental conditions after domestication.

Genomic Identification, Evolution and Sequence Analysis of the Heat-Shock Protein Gene Family in Buffalo

Heat-shock proteins (HSP) are conserved chaperones crucial for protein degradation, maturation, and refolding. These adenosine triphosphate dependent chaperones were classified based on their molecular mass that ranges between 10-100 kDA, including; HSP10, HSP40, HSP70, HSP90, HSPB1, HSPD, and HSPH1 family. HSPs are essential for cellular responses and imperative for protein homeostasis and survival under stress conditions. This study performed a computational analysis of the HSP protein family to better understand these proteins at the molecular level. Physiochemical properties, multiple sequence alignment, and phylogenetic analysis were performed for 64 HSP genes in the Bubalus bubalis genome. Four genes were identified as belonging to the HSP90 family, 10 to HSP70, 39 to HSP40, 8 to HSPB, one for each HSPD, HSPH1, and HSP10, respectively. The aliphatic index was higher for HSP90 and HSP70 as compared to the HSP40 family, indicating their greater thermostability. Grand Average of hydropathicity Index values indicated the hydrophilic nature of HSP90, HSP70, and HSP40. Multiple sequence alignment indicated the presence of highly conserved consensus sequences that are plausibly significant for the preservation of structural integrity of proteins. In addition, this study has expanded our current knowledge concerning the genetic diversity and phylogenetic relatedness of HSPs of buffalo with other mammalian species. The phylogenetic tree revealed that buffalo is more closely related to Capra hircus and distantly associated with Danio rerio. Our findings provide an understanding of HSPs in buffalo at the molecular level for the first time. This study highlights functionally important HSPs and indicates the need for further investigations to better understand the role and mechanism of HSPs.

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.

Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication

More people globally depend on the water buffalo than any other domesticated species, and as the most closely related domesticated species to cattle they can provide important insights into the shared evolutionary basis of domestication. Here, we sequence the genomes of 79 water buffalo across seven breeds and compare patterns of between breed selective sweeps with those seen for 294 cattle genomes representing 13 global breeds. The genomic regions under selection between cattle breeds significantly overlap regions linked to stature in human genetic studies, with a disproportionate number of these loci also shown to be under selection between water buffalo breeds. Investigation of potential functional variants in the water buffalo genome identifies a rare example of convergent domestication down to the same mutation having independently occurred and been selected for across domesticated species. Cross-species comparisons of recent selective sweeps can consequently help identify and refine important loci linked to domestication.

The comparative genomics of domesticated lineages can yield insights into the signatures of artificial selection. This study sequences 79 water buffalo genomes from 7 breeds and reveals examples of convergent domestication at the genetic level between water buffalo and cattle.

Sequencing and assembly of the Egyptian buffalo genome

Water buffalo (Bubalus bubalis) is an important source of meat and milk in countries with relatively warm weather. Compared to the cattle genome, a little has been done to reveal its genome structure and genomic traits. This is due to the complications stemming from the large genome size, the complexity of the genome, and the high repetitive content. In this paper, we introduce a high-quality draft assembly of the Egyptian water buffalo genome. The Egyptian breed is used as a dual purpose animal (milk/meat). It is distinguished by its adaptability to the local environment, quality of feed changes, as well as its high resistance to diseases. The genome assembly of the Egyptian water buffalo has been achieved using a reference-based assembly workflow. Our workflow significantly reduced the computational complexity of the assembly process, and improved the assembly quality by integrating different public resources. We also compared our assembly to the currently available draft assemblies of water buffalo breeds. A total of 21,128 genes were identified in the produced assembly. A list of milk virgin-related genes; milk pregnancy-related genes; milk lactation-related genes; milk involution-related genes; and milk mastitis-related genes were identified in the assembly. Our results will significantly contribute to a better understanding of the genetics of the Egyptian water buffalo which will eventually support the ongoing breeding efforts and facilitate the future discovery of genes responsible for complex processes of dairy, meat production and disease resistance among other significant traits.

Genomic Identification, Evolution, and Expression Analysis of Collagen Genes Family in Water Buffalo during Lactation

Collagens, as extracellular matrix proteins, support cells for structural integrity and contribute to support mammary basic structure and development. This study aims to perform the genomic identification, evolution, and expression analyses of the collagen gene family in water buffalo (Bubalus bubalis) during lactation. A total of 128 buffalo collagen protein sequences were deduced from the 45 collagen genes identified in silico from buffalo genome, which classified into six groups based on their phylogenetic relationships, conserved motifs, and gene structure analyses. The identified collagen sequences were unequally distributed on 16 chromosomes. The tandem duplicated genes were found within three chromosomes, while only one segmental event occurred between Chr3 and Chr8. Collinearity analysis revealed that a total of 36 collagen gene pairs were orthologous between buffalo and cattle genomes despite having different chromosome numbers. Comparative transcription analyses revealed that a total of 23 orthologous collagen genes were detected in the milk samples at different lactation periods between the two species. Notably, the duplicated gene pair of COL4A1-COL4A2 during lactation had a higher mRNA expression level than that of cattle, while a higher expression level of COL6A1-COL6A2 pair was found in cattle compared with that of buffalo. The present study provides useful information for investigating the potential functions of the collagen family in buffalo during lactation and helps in the functional characterization of collagen genes in additional research.

The domesticated buffalo - An emerging model for experimental and therapeutic use of extraembryonic tissues

Large animals play important roles as model animals for biomedical sciences and translational research. The water buffalo (Bubalus bubalis) is an economically important, multipurpose livestock species. Important assisted reproduction techniques, such as in vitro fertilization, cryo-conservation of sperm and embryos, embryo transfer, somatic cell nuclear transfer, genetic engineering, and genome editing have been successfully applied to buffaloes. Recently, detailed whole genome data and transcriptome maps have been generated. In addition, rapid progress has been made in stem cell biology of the buffalo. Apart from embryonic stem cells, bubaline extra-embryonic stem cells have gained particular interest. The multipotency of non-embryonic stem cells has been revealed, and their utility in basic and applied research is currently investigated. In particular, success achieved in bubaline extra-embryonic stem cells may have important roles in experimental biology and therapeutic regenerative medicine. Progress in other farm animals in assisted reproduction techniques, stem cell biology and genetic engineering, which could be of importance for buffalo, will also be briefly summarized.

Genome-wide identification of Diacylglycerol Acyltransferases (DGAT) family genes influencing Milk production in Buffalo

Background

The diacylglycerol acyltransferases (DGAT) are a vital group of enzymes in catalyzing triacylglycerol biosynthesis. DGAT genes like DGAT1 and DGAT2, have been identified as two functional candidate genes affecting milk production traits, especially for fat content in milk. Buffalo milk is famous for its excellent quality, which is rich in fat and protein content. Therefore, this study aimed to characterize DGAT family genes in buffalo and to find candidate markers or DGAT genes influencing lactation performance.

Results

We performed a genome-wide study and identified eight DGAT genes in buffalo. All the DGAT genes classified into two distinct clades (DGAT1 and DGAT2 subfamily) based on their phylogenetic relationships and structural features. Chromosome localization displayed eight buffalo DGAT genes distributed on five chromosomes. Collinearity analysis revealed that the DGAT family genes were extensive homologous between buffalo and cattle. Afterward, we discovered genetic variants loci within the genomic regions that DGAT genes located in buffalo. Seven haplotype blocks were constructed and were associated with buffalo milk production traits. Single marker association analyses revealed four most significant single nucleotide polymorphisms (SNPs) mainly affecting milk protein percentage or milk fat yield in buffalo. Genes functional analysis indicated that these DGAT family genes could influence lactation performance in the mammal through regulating lipid metabolism.

Conclusion

In the present study, we performed a comprehensive analysis for the DGAT family genes in buffalo, which including identification, structural characterization, phylogenetic classification, chromosomal distribution, collinearity analysis, association analysis, and functional analysis. These findings provide useful information for an in-depth study to determine the role of DGAT family gens play in the regulation of milk production and milk quality improvement in buffalo.

Understanding divergent domestication traits from the whole-genome sequencing of swamp- and river-buffalo populations

Domesticated buffaloes have been integral to rice-paddy agro-ecosystems for millennia, yet relatively little is known about the buffalo genomics. Here, we sequenced and assembled reference genomes for both swamp and river buffaloes and we re-sequenced 230 individuals (132 swamp buffaloes and 98 river buffaloes) sampled from across Asia and Europe. Beyond the many actionable insights that our study revealed about the domestication, basic physiology and breeding of buffalo, we made the striking discovery that the divergent domestication traits between swamp and river buffaloes can be explained with recent selections of genes on social behavior, digestion metabolism, strengths and milk production.

Genomic insights into ruminant evolution: from past to future prospects

Ruminants (Ruminantia) are among the most successful herbivorous mammals, exhibiting wide-ranging morphological and ecological characteristics (such as headgear and multichambered stomach) and including various key livestock species (e.g., cattle, buffalo, yak, sheep, and goat). Understanding their evolution is of great significance not only in scientific research but also in applications potential for human society. The rapid growth of genomic resources provides unprecedented opportunities to dissect the evolutionary histories and molecular mechanisms underlying the distinct characteristics of ruminants. Here we summarize our current understanding of the genetic, morphological, and ecological diversity of ruminants and provide prospects for future studies.