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Background The history of African indigenous cattle and their adaptation to environmental and human selection pressure is at the root of their remarkable diversity. Characterization of this diversity is an essential step towards understanding the genomic basis of productivity and adaptation to survival under African farming systems. Results We analyze patterns of African cattle genetic variation by sequencing 48 genomes from five indigenous populations and comparing them to the genomes of 53 commercial taurine breeds. We find the highest genetic diversity among African zebu and sanga cattle. Our search for genomic regions under selection reveals signatures of selection for environmental adaptive traits. In particular, we identify signatures of selection including genes and/or pathways controlling anemia and feeding behavior in the trypanotolerant N’Dama, coat color and horn development in Ankole, and heat tolerance and tick resistance across African cattle especially in zebu breeds. Conclusions Our findings unravel at the genome-wide level, the unique adaptive diversity of African cattle while emphasizing the opportunities for sustainable improvement of livestock productivity on the continent.

Background: No dairy breed or crossbreed has superior overall performance in all environments; therefore, it is necessary to determine which crossbreed is the most suitable for the Mexican tropic and what proportion of European breed is optimum for reproduction. Objective: To assess the effect of the proportion of Bos taurus (Bt) genes on reproductive performance of Holstein×Zebu (HZ) and Brown Swiss×Zebu (BZ) cows, and compare reproductive performance of these genotypes in a dual-purpose production system. Methods: Cows were maintained in a rotational grazing system on African star grass (Cynodon plectostachyus) in Veracruz, Mexico. Cows were milked twice daily. Calves were kept tied to the side of their dams while the cows were milked. Results: The percentage of Bt genes did not affect (p>0.05) fertility traits (age at first calving, days to first service after calving, services per conception, conception rate at first service, days open until conception, gestation length, and calving interval) of BZ cows. In contrast, HZ cows with less than 75% Holstein (H) genes were 0.3 years younger (p<0.05) at first calving and had 39.8 fewer days open (p<0.05) than HZ cows with 75% H genes or more. In addition, the calving interval of HZ cows with less than 75% H genes was 44.8 days shorter (p<0.05) than that of HZ cows with 75% H genes or more. The HZ cows had five fewer days pregnant and were 22.8 kg heavier at calving (p<0.05) than BZ cows. Conclusions: The effect of the percentage of Bt genes on cow fertility depends on the dairy breed used. In general, BZ and HZ cows present similar reproductive performance.

Background Distinct domestication events, adaptation to different climatic zones, and divergent selection in productive traits have shaped the genomic differences between taurine and indicine cattle. In this study, we assessed the impact of artificial selection and environmental adaptation by comparing whole-genome sequences from European taurine and Asian indicine breeds and from African cattle. Next, we studied the impact of divergent selection by exploiting predicted and experimental functional annotation of the bovine genome. Results We identified selective sweeps in beef cattle taurine and indicine populations, including a 430-kb selective sweep on indicine cattle chromosome 5 that is located between 47,670,001 and 48,100,000 bp and spans five genes, i.e. HELB , IRAK3 , ENSBTAG00000026993 , GRIP1 and part of HMGA2 . Regions under selection in indicine cattle display significant enrichment for promoters and coding genes. At the nucleotide level, sites that show a strong divergence in allele frequency between European taurine and Asian indicine are enriched for the same functional categories. We identified nine single nucleotide polymorphisms (SNPs) in coding regions that are fixed for different alleles between subspecies, eight of which were located within the DNA helicase B ( HELB ) gene. By mining information from the 1000 Bull Genomes Project, we found that HELB carries mutations that are specific to indicine cattle but also found in taurine cattle, which are known to have been subject to indicine introgression from breeds, such as N’Dama, Anatolian Red, Marchigiana, Chianina, and Piedmontese. Based on in-house genome sequences, we proved that mutations in HELB segregate independently of the copy number variation HMGA2 -CNV, which is located in the same region. Conclusions Major genomic sequence differences between Bos taurus and Bos indicus are enriched for promoter and coding regions. We identified a 430-kb selective sweep in Asian indicine cattle located on chromosome 5, which carries SNPs that are fixed in indicine populations and located in the coding sequences of the HELB gene. HELB is involved in the response to DNA damage including exposure to ultra-violet light and is associated with reproductive traits and yearling weight in tropical cattle. Thus, HELB likely contributed to the adaptation of tropical cattle to their harsh environment.

The 3D render volume reconstruction CT (3D-RVCT) produced detailed images of the PES region, determining its relationships with the surrounding structures. Despite extensive research in veterinary studies on the PES through gross anatomy and CT, there is a lack of studies on the PES of zebu cattle. The study aimed to analyze the PES of Zebu cattle using gross cross-sectional, radiographic, CT, and morphometric methods, with the use of 3D-RVCT to provide anatomical guidance for surgeons and students. The study was performed on sixteen PES regions to provide hard and soft tissues in CT images. Three are five tarsal bones and two large fused (III and IV) metatarsal bones that were completely fused except for their distal extremities, which were divided distally by the intertrochlear notch. The cortical thickness of the metatarsal bone was equal on both sides. The bony septum divided the medullary cavity between the two fused large metatarsal bones in the proximal distal half only and disappeared in the middle part. The reconstruction showed similar sizes in the right and left limbs, confirming the pes bones. The radiographic and CT images could be used as a normal reference for the interpretation of some clinical diseases in the PES. The 3D CT reconstruction of the pes bones was described by various CT oblique dorsal and plantar views. The study focuses on diagnosing PES disorders using CT imaging, improving medical interventions, improving Zebu cattle health outcomes, and empowering students to contribute to veterinary medicine research and advancements. Highlight The study aimed to analyze the PES region of Zebu cattle using various methods, including 3D-RVCT, to provide anatomical guidance for surgeons and students. The study focused on sixteen PES regions, including three tarsal bones and two large fused metatarsal bones. The cortical thickness of the metatarsal bone was equal on both sides, and the bony septum divided the medullary cavity between the two fused large metatarsal bones in the proximal distal half only. The reconstruction showed similar sizes in the right and left limbs, confirming the pes bones. The radiographic and CT images could be used as a normal reference for interpreting clinical diseases in the PES. The 3D CT reconstruction of the pes bones was described by various CT oblique dorsal and plantar views. The study aims to diagnose PES disorders using CT imaging, improve medical interventions, improve Zebu cattle health outcomes, and empower students to contribute to veterinary medicine research and advancements.

Objetivou-se avaliar a predição de consumo de matéria seca (CMS) pelos sistemas CNCPS 5.0, NRC e BR-CORTE, bem como o consumo de nutrientes por tourinhos zebuínos confinados. Foram utilizados 44 animais em delineamento experimental inteiramente casualizado, sendo: 19 Nelore PO, 7 Nelore LA, 10 Tabapuã PO e 8 Guzerá PO, com peso vivo inicial médio de 394 ± 39; 348 ± 33; 346 ± 28 e 340 ± 30 kg, respectivamente, e idade inicial média de 13 meses. O período experimental foi de 84 dias. O consumo alimentar individual foi obtido com o uso dos indicadores LIPE®, óxido crômico e fibra em detergente ácido indigestível (FDAi). Para comparação do CMS predito pelos sistemas com o observado utilizou-se análise de regressão linear. Os animais Nelore LA apresentaram os menores valores observados para CMS (kg d-1). Ao avaliar o CMS em porcentagem do peso vivo (%PV) e em gramas por quilo de peso vivo metabólico (g kg-1 PM), foi detectada diferença entre os grupos genéticos, sendo que os maiores valores ocorreram para os animais Tabapuã PO e Guzerá PO. Os sistemas NRC, CNCPS 5.0 e o BR-CORTE apresentaram subpredição do CMS. Conclui-se que os sistemas estudados não se mostraram adequados para predizer o consumo de matéria seca em tourinhos zebuínos confinados.The objective of this study was to evaluate the prediction of dry matter intake (DMI) using the CNCPS 5.0, NRC and BR-CUT systems, and of the nutrient intake of confined young Zebu bulls. A completely randomized experimental design of 44 animals as follows was used: 19 Nelore PO, 7 Nelore LA, 10 Tabapua PO e 8 Guzerat PO, with a mean initial live body weight of 394 ± 39, 348 ± 33, 346 ± 28 and 340 ± 30 kg respectively, and a mean initial age of 13 months. The length of the experiment was 84 days. Individual food consumption was calculated with the use of LIPE®, chromium oxide and indigestible acid detergent fiber (iADF) indicators. In order to compare the DMI as predicted by the systems to that observed, linear regression analysis was used. The Nellore LA group showed the lowest observed values for DMI (kg d-1). When assessing DMI as a percentage of live body weight (% BW) and in grams per kilogram of metabolic live weight (g kg-1 MW), a difference between genetic groups was found, with the highest values being observed for the Tabapua PO and Guzerat PO groups. The NRC, CNCPS 5.0 and BR-CUT systems under predicted the DMI. It can be concluded that the systems studied were not adequate for the prediction of the dry matter intake of confined young Zebu bulls.

Tick-borne diseases (TBDs) are a major hindrance to livestock production in pastoral communities of Africa. Although information on tick-borne infections is necessary for setting up control measures, this information is limited in the pastoral communities of Tanzania. Therefore, this study aimed to provide an overview of the tick-borne infections in the indigenous cattle of Tanzania. A total of 250 blood samples were collected from the indigenous zebu cattle in the Tanga region, Tanzania. Then, we conducted a molecular survey using the polymerase chain reaction (PCR) and gene sequencing to detect and identify the selected tick-borne pathogens. The PCR was conducted using assays, based on Theileria spp. (18S rRNA), Theileria parva (p104), Theileria mutans and T. taurotragi (V4 region of the 18S rRNA), Babesia bigemina (RAP-1a), B. bovis (SBP-2), Anaplasma marginale (heat shock protein groEL) and Ehrlichia ruminantium (pCS20). The PCR screening revealed an overall infection rate of (120/250, 48%) for T. mutans, (64/250, 25.6%) for T. parva, (52/250, 20.8%) for T. taurotragi, (33/250, 13.2%) for B. bigemina and (81/250, 32.4%) for A. marginale. Co-infections of up to four pathogens were revealed in 44.8% of the cattle samples. A sequence analysis indicated that T. parva p104 and A. marginale groEL genes were conserved among the sampled animals with sequence identity values of 98.92–100% and 99.88–100%, respectively. Moreover, the B. bigemina RAP-1a gene and the V4 region of the 18S rRNA of T. mutans genes were diverse among the sampled cattle, indicating the sequence identity values of 99.27–100% and 22.45–60.77%, respectively. The phylogenetic analyses revealed that the T. parva (p104) and A. marginale (groEL) gene sequences of this study were clustered in the same clade. In contrast, the B. bigemina (RAP-1a) and the T. mutans V4 region of the 18S rRNA gene sequences appeared in the different clades. This study provides important basement data for understanding the epidemiology of tick-borne diseases and will serve as a scientific basis for planning future control strategies in the study area.

Asparagopsis taxiformis has potent antimethanogenic activity as a feed supplement at 2 % of organic matter in in vitro bioassays. This study identified the main bioactive natural products and their effects on fermentation using rumen fluid from Bos indicus steers. Polar through to non-polar extracts (water, methanol, dichloromethane and hexane) were tested. The dichloromethane extract was most active, reducing methane production by 79 %. Bromoform was the most abundant natural product in the biomass of Asparagopsis (1723 μg g −1 dry weight [DW] biomass), followed by dibromochloromethane (15.8 μg g −1 DW), bromochloroacetic acid (9.8 μg g −1 DW) and dibromoacetic acid (0.9 μg g −1 DW). Bromoform and dibromochloromethane had the highest activity with concentrations ≥1 μM inhibiting methane production. However, only bromoform was present in sufficient quantities in the biomass at 2 % organic matter to elicit this effect. Importantly, the degradability of organic matter and volatile fatty acids were not affected at effective concentrations.

Extensive research has shown that miRNAs play a crucial role in regulating biological processes within organisms. This study analyzed miRNAs differentially expressed and potentially associated with immune function and tissue-specific expression in Yunnan Zebu and Holstein cattle. To achieve this, 20 liver and spleen tissue samples from the two cattle breeds were collected for high-throughput miRNA sequencing, with the liver tissue as a reference. The findings revealed that bta-miR-122 and bta-miR-143 are the most abundantly expressed known miRNAs in the liver and spleen tissues of Yunnan Zebu and Holstein cattle, respectively. Additionally, AC_000181.1_27195 and AC_000168.1_14386 emerged as the most highly expressed novel miRNAs in these tissues, exhibiting significant homology with human hsa-miR-3591-3p and hsa-miR-126-3p, respectively. Six differentially expressed miRNAs were selected for validation using stem-loop RT-qPCR, and the results were largely consistent with the high-throughput sequencing data. Functional enrichment analysis of the target genes of these known miRNAs revealed their association with critical metabolic and immune-related pathways in cattle, such as the insulin pathway, mTOR signaling, IFN-γ pathway, and signaling mechanisms mediated by IL5 and IL3. These results enriched the miRNA database for liver and spleen tissues of Yunnan Zebu and Holstein cattle.

Background The Boran ( Bos indicus ), indigenous Zebu cattle breed from sub-Saharan Africa, is remarkably well adapted to harsh tropical environments. Due to financial constraints and low-quality forage, African livestock are rarely fed at 100% maintenance energy requirements (MER) and the effect of sub-optimal restricted feeding on the rumen microbiome of African Zebu cattle remains largely unexplored. We collected 24 rumen fluid samples from six Boran cattle fed at sub-optimal and optimal MER levels and characterised their rumen microbial composition by performing shotgun metagenomics and de novo assembly of metagenome-assembled genomes (MAGs). These MAGs were used as reference database to investigate the effect of diet restriction on the composition and functional potential of the rumen microbiome of African cattle. Results We report 1200 newly discovered MAGs from the rumen of Boran cattle. A total of 850 were dereplicated, and their uniqueness confirmed with pairwise comparisons (based on Mash distances) between African MAGs and other publicly available genomes from the rumen. A genome-centric investigation into sub-optimal diets highlighted a statistically significant effect on rumen microbial abundance profiles and a previously unobserved relationship between whole microbiome shifts in functional potential and taxon-level associations in metabolic pathways. Conclusions This study is the first to identify 1200 high-quality African rumen-specific MAGs and provides further insight into the rumen function in harsh environments with food scarcity. The genomic information from the rumen microbiome of an indigenous African cattle breed sheds light on the microbiome contribution to rumen functionality and constitutes a vital resource in addressing food security in developing countries.

Longer-lived cows tend to be more profitable and the stayability trait is a selection criterion correlated to longevity. An alternative to the traditional approach to evaluate stayability is its definition based on consecutive calvings, whose main advantage is the more accurate evaluation of young bulls. However, no study using this alternative approach has been conducted for Zebu breeds. Therefore, the objective of this study was to compare linear random regression models to fit stayability to consecutive calvings of Guzerá, Nelore and Tabapuã cows and to estimate genetic parameters for this trait in the respective breeds. Data up to the eighth calving were used. The models included the fixed effects of age at first calving and year-season of birth of the cow and the random effects of contemporary group, additive genetic, permanent environmental and residual. Random regressions were modeled by orthogonal Legendre polynomials of order 1 to 4 (2 to 5 coefficients) for contemporary group, additive genetic and permanent environmental effects. Using Deviance Information Criterion as the selection criterion, the model with 4 regression coefficients for each effect was the most adequate for the Nelore and Tabapuã breeds and the model with 5 coefficients is recommended for the Guzerá breed. For Guzerá, heritabilities ranged from 0.05 to 0.08, showing a quadratic trend with a peak between the fourth and sixth calving. For the Nelore and Tabapuã breeds, the estimates ranged from 0.03 to 0.07 and from 0.03 to 0.08, respectively, and increased with increasing calving number. The additive genetic correlations exhibited a similar trend among breeds and were higher for stayability between closer calvings. Even between more distant calvings (second v. eighth), stayability showed a moderate to high genetic correlation, which was 0.77, 0.57 and 0.79 for the Guzerá, Nelore and Tabapuã breeds, respectively. For Guzerá, when the models with 4 or 5 regression coefficients were compared, the rank correlations between predicted breeding values for the intercept were always higher than 0.99, indicating the possibility of practical application of the least parameterized model. In conclusion, the model with 4 random regression coefficients is recommended for the genetic evaluation of stayability to consecutive calvings in Zebu cattle.