Effect of polymorphisms in the Slc11a1 coding region on resistance to brucellosis by macrophages in vitro and after challenge in two Bos breeds (Blanco Orejinegro and Zebu)

Genomic insights into the population history and adaptive traits of Latin American Criollo cattle

Criollo cattle, the descendants of animals brought by Iberian colonists to the Americas, have been the subject of natural and human-mediated selection in novel tropical agroecological zones for centuries. Consequently, these breeds have evolved distinct characteristics such as resistance to diseases and exceptional heat tolerance. In addition to European taurine (Bos taurus) ancestry, it has been proposed that gene flow from African taurine and Asian indicine (Bos indicus) cattle has shaped the ancestry of Criollo cattle. In this study, we analysed Criollo breeds from Colombia and Venezuela using whole-genome sequencing (WGS) and single-nucleotide polymorphism (SNP) array data to examine population structure and admixture at high resolution. Analysis of genetic structure and ancestry components provided evidence for African taurine and Asian indicine admixture in Criollo cattle. In addition, using WGS data, we detected selection signatures associated with a myriad of adaptive traits, revealing genes linked to thermotolerance, reproduction, fertility, immunity and distinct coat and skin coloration traits. This study underscores the remarkable adaptability of Criollo cattle and highlights the genetic richness and potential of these breeds in the face of climate change, habitat flux and disease challenges. Further research is warranted to leverage these findings for more effective and sustainable cattle breeding programmes.

New insights into the genetic predisposition of brucellosis and its effect on the gut and vaginal microbiota in goats

Goats contribute significantly to the global food security and industry. They constitute a main supplier of meat and milk for large proportions of people in Egypt and worldwide. Brucellosis is a zoonotic infectious disease that causes a significant economic loss in animal production. A case-control genome-wide association analysis (GWAS) was conducted using the infectious status of the animal as a phenotype. The does that showed abortion during the last third period of pregnancy and which were positive to both rose bengal plate and serum tube agglutination tests, were considered as cases. Otherwise, they were considered as controls. All animals were genotyped using the Illumina 65KSNP BeadChip. Additionally, the diversity and composition of vaginal and fecal microbiota in cases and controls were investigated using PCR-amplicone sequencing of the V4 region of 16S rDNA. After applying quality control criteria, 35,818 markers and 66 does were available for the GWAS test. The GWAS revealed a significantly associated SNP (P = 5.01 × 10-7) located on Caprine chromosome 15 at 29 megabases. Four other markers surpassed the proposed threshold (P = 2.5 × 10-5). Additionally, fourteen genomic regions accounted for more than 0.1% of the variance explained by all genome windows. Corresponding markers were located within or in close vicinity to several candidate genes, such as ARRB1, RELT, ATG16L2, IGSF21, UBR4, ULK1, DCN, MAPB1, NAIP, CD26, IFIH1, NDFIP2, DOK4, MAF, IL2RB, USP18, ARID5A, ZAP70, CNTN5, PIK3AP1, DNTT, BLNK, and NHLRC3. These genes play important roles in the regulation of immune responses to the infections through several biological pathways. Similar vaginal bacterial community was observed in both cases and controls while the fecal bacterial composition and diversity differed between the groups (P < 0.05). Faeces from the control does showed a higher relative abundance of the phylum Bacteroidota compared to cases (P < 0.05), while the latter showed more Firmicutes, Spirochaetota, Planctomycetota, and Proteobacteria. On the genus level, the control does exhibited higher abundances of Rikenellaceae RC9 gut group and Christensenellaceae R-7 group (P < 0.05), while the infected does revealed higher Bacteroides, Alistipes, and Prevotellaceae UCG-003 (P < 0.05). This information increases our understanding of the genetics of the susceptibility to Brucella in goats and may be useful in breeding programs and selection schemes that aim at controlling the disease in livestock.

Characterization of innate immune response to Brucella melitensis infection in goats with permissive or restrictive phenotype for Brucella intramacrophagic growth

Caprine brucellosis is a chronic, world-wide distributed disease which causes reproductive failure in goats and Brucella melitensis, its causative agent, bears a great zoonotic potential. There is evidence suggesting that some cattle and pigs have an innate ability to resist Brucella infection, but this has not yet been investigated in goats. In this study, we compared caprine macrophages that exhibit extreme restriction and permissiveness to B. melitensis' intracellular growth in vitro. Monocyte derived macrophages (MDMs) from 110 female goats were cultured and challenged in vitro with B. melitensis 16 M. After initial screening, 18 donor goats were selected based on their macrophages ability to restrict or allow bacterial intracellular growth and some elements of humoral and cellular immunity were studied in depth. MDMs that were able to restrict the pathogen's intracellular growth showed enhanced bacterial internalization, although there were no differences between groups in the production of reactive oxygen and nitrogen intermediates following 48 h treatment with heat-killed B. melitensis. Moreover, there were no differences between groups in the level of antibodies reacting with keyhole limpet hemocyanin (natural antibodies, NAbs) or with Brucella LPS antigens (cross-reacting antibodies, CrAbs), although a strong positive correlation between individual levels of IgM NAbs and IgM CrAbs was detected. Altogether, these results represent an initial step in understanding innate primary host response to B. melitensis, and deciphering which mechanisms may determine a successful outcome of the infection in goats.

Microsatellite markers reveal polymorphisms at the 3′ untranslated region of the SLC11A1 gene in Zhongdian Yellow cattle (Bos taurus)

Solute carrier family 11-member A1 (SLC11A1) gene encodes natural macrophage resistance-associated protein which regulates activity of macrophages against intracellular pathogens. The objective of this study was to study the polymorphism in the microsatellites present at 3′ untranslated region (UTR) of the SLC11A1 gene in 113 Zhongdian Yellow cattle (Bos taurus). Using DNA bi-directional sequencing, we detected seven alleles (GT10–16) for the first microsatellite (MS1), five alleles (GT12–16) for MS2, and four alleles (GT4–7) for MS3. MS3 is studied for the first time and revealed four novel variants (alleles GT4–7). Alleles GT12 (45.1%), GT13 (59.3%), and GT5 (85.4%) were the most frequent alleles at MS1, MS2, and MS3, respectively, Genotypes G12/12, G13/13, and G5/5 had the highest frequency 0.239, 0.540, and 0.743 at MS1, MS2, and MS3, respectively. Haplotypic data revealed that GT12/GT13 was the most frequent haplotype observed followed by GT12/14 haplotype. Three nucleotide variations were observed in MS1 and MS2. Comparative analysis of GT12/GT12 and GT13/GT13 genotype with other bovine genotypes showed significant difference (P > 0.05). Our results suggest that the homozygous genotypes GT12/GT12 and GT13/GT13 in Zhongdian Yellow cattle might be related to disease resistance. The findings reported in this study would be helpful in cattle breeding programs.

Optimization of high molecular weight DNA extraction methods in shrimp for a long-read sequencing platform

Marine organisms are important to global food security as they are the largest source of animal proteins feeding mankind. Genomics-assisted aquaculture can increase yield while preserving the environment to ensure sufficient and sustainable production for global food security. However, only few high-quality genome sequences of marine organisms, especially shellfish, are available to the public partly because of the difficulty in the sequence assembly due to the complex nature of their genomes. A key step for a successful genome sequencing is the preparation of high-quality high molecular weight (HMW) genomic DNA. This study evaluated the effectiveness of five DNA extraction protocols (CTAB, Genomic-tip, Mollusc DNA, TIANamp Marine Animals DNA, and Sbeadex livestock kits) in obtaining shrimp HMW DNA for a long-read sequencing platform. DNA samples were assessed for quality and quantity using a Qubit fluorometer, NanoDrop spectrophotometer and pulsed-field gel electrophoresis. Among the five extraction methods examined without further optimization, the Genomic-tip kit yielded genomic DNA with the highest quality. However, further modifications of these established protocols might yield even better DNA quality and quantity. To further investigate whether the obtained genomic DNA could be used in a long-read sequencing application, DNA samples from the top three extraction methods (CTAB method, Genomic-tip and Mollusc DNA kits) were used for Pacific Biosciences (PacBio) library construction and sequencing. Genomic DNA obtained from Genomic-tip and Mollusc DNA kits allowed successful library construction, while the DNA obtained from the CTAB method did not. Genomic DNA isolated using the Genomic-tip kit yielded a higher number of long reads (N50 of 14.57 Kb) than those obtained from Mollusc DNA kits (N50 of 9.74 Kb). Thus, this study identified an effective extraction method for high-quality HMW genomic DNA of shrimp that can be applied to other marine organisms for a long-read sequencing platform.

Genome to Phenome: Improving Animal Health, Production, and Well-Being - A New USDA Blueprint for Animal Genome Research 2018-2027

In 2008, a consortium led by the Agricultural Research Service (ARS) and the National Institute for Food and Agriculture (NIFA) published the "Blueprint for USDA Efforts in Agricultural Animal Genomics 2008-2017," which served as a guiding document for research and funding in animal genomics. In the decade that followed, many of the goals set forth in the blueprint were accomplished. However, several other goals require further research. In addition, new topics not covered in the original blueprint, which are the result of emerging technologies, require exploration. To develop a new, updated blueprint, ARS and NIFA, along with scientists in the animal genomics field, convened a workshop titled "Genome to Phenome: A USDA Blueprint for Improving Animal Production" in November 2017, and these discussions were used to develop new goals for the next decade. Like the previous blueprint, these goals are grouped into the broad categories "Science to Practice," "Discovery Science," and "Infrastructure." New goals for characterizing the microbiome, enhancing the use of gene editing and other biotechnologies, and preserving genetic diversity are included in the new blueprint, along with updated goals within many genome research topics described in the previous blueprint. The updated blueprint that follows describes the vision, current state of the art, the research needed to advance the field, expected deliverables, and partnerships needed for each animal genomics research topic. Accomplishment of the goals described in the blueprint will significantly increase the ability to meet the demands for animal products by an increasing world population within the next decade.

Tick burden in Bos taurus cattle and its relationship with heat stress in three agroecological zones in the tropics of Colombia

BACKGROUND

Ticks have a negative effect on dairy and beef cattle production systems around the world, with the concomitant risk they represent for the transmission of some important infectious diseases. Colombian cattle breeds are distributed across different agroecological regions and are exposed to different environmental challenges. In humid and warmer climates such as those from the tropics, tick burden and heat stress are important factors that can compromise livestock performance. The aim of this study was to characterize tick burden in four Colombian cattle breeds and evaluate the relationship between heat stress and tick burden in Bos taurus cattle under tropical conditions. Tick counting was conducted in 1332 cattle from Romosinuano (ROMO), Costeño con Cuernos (CCC), San Martinero (SM) and Blanco Orejinegro (BON) breeds, located in the Caribbean, Orinoquia and Andean regions. Vital signs and environmental variables were taken to calculate an adaptability index (AI) and a temperature humidity index (THI). An AI < 2 indicates maximum adaptability while an AI ≥ 2 indicates a state of lower adaptability. In beef cattle, productivity starts to be affected by heat stress when environmental conditions allow an estimation of a THI > 75.

RESULTS

Results showed a differing distribution of ticks on the body of individuals that varied according to the agroecological region. There was a significant effect of breed, sex, family, age and live weight on cattle tick burden. The lowest tick burden was observed in the ROMO breed (12.8 ± 2.6), while the highest tick burden was observed in CCC (31.8 ± 2.3), which were located in the same agroecological region. SM and ROMO animals with an AI > 2 had a higher tick burden than their counterparts that had an AI < 2.

CONCLUSIONS

Cattle breed, sex, age and live weight affect the tick burden in Bos taurus Colombian cattle breeds. The tick burden is higher in cattle with lower adaptability to heat stress. Moreover, it decreases as heat stress levels increase in a tropical environment. The interaction between tick burden and environmental heat stress can be affected by characteristics of the agroecological region itself, the breed and the genetic resistance of the individual tick, as well as the thermal adaptability of cattle.

Association between human brucellosis and adverse pregnancy outcome: a cross-sectional population-based study

To investigate the association between the incidence of human brucellosis (HB) and adverse pregnancy outcomes (APOs), a population-based, cross-sectional aggregate data study was conducted in Israel between 2010 and 2014. HB-endemic localities were matched by ethnicity, population size and socioeconomic status to localities with a low incidence of HB. We compared APO rates in high-incidence vs low-incidence localities. The primary outcome was intrauterine fetal demise (IUFD). Secondary outcomes were premature birth (less than 37 weeks), early or threatened labour and poor fetal growth. APOs are expressed as events per 1,000 live or dead births. Eleven high-incidence localities, all Arab villages or cities, were matched to 11 low-incidence localities. Localities were well-matched with regard to the matching criteria, fertility indices, health insurance access and education, but were imbalanced geographically. All defined APOs occurred significantly more frequently in the high-incidence localities. The associations translated to an absolute increase of 3.6 cases of IUFD (95% CI 1.6-5.3), 11.7 preterm births (4.8-18.3), 6.6 cases of early or threatened labour (2.2-10.9) and 7 cases of poor fetal growth (3-10.8), per 10,000 live or dead births. Owing to a geographic imbalance between high- and low-incidence localities, we conducted an analysis restricted to Southern localities of Arab Bedouins showing a significant association between yearly HB incidence and IUFD incidence, odds ratio 1.05 (1.03-1.06). HB incidence is epidemiologically linked to serious pregnancy complications. Early detection of infection through active surveillance during pregnancy followed by appropriate treatment should be evaluated as additional public heath strategy in endemic settings.

Quantification and comparison of TLR2 activity in monocyte-derived macrophages of zebu and crossbred cattle

The present study was conducted to quantify and compare TLR2 (toll-like receptor 2) activity in monocyte-derived macrophages of zebu (Tharparkar) and crossbred (Holstein-Friesian × Jersey × Brown Swiss × Hariana) cattle. The cells were either induced with Pam3CSK4 or kept as control. The TLR2 activity was quantified in terms of IκB-α inhibitory subunit (NFKBIA) messenger RNA (mRNA) copies using real-time, one-step reverse transcription-polymerase chain reaction (RT-PCR). Toll-like receptor 2 activity of induced cells was in the range of 1060421 ± 477937 (n=3) to 3514715 ± 290222 (n=3) copies for Tharparkar cattle (n=7) and in the range of 1365532 ± 47243 (n=3) to 3016510 ± 172340 (n=3) copies for the crossbred cattle (n=7). For uninduced cells, this activity was within the range of 117 ± 51 (n=3) to 293 ± 103 (n=3) copies for the Thraparkar cattle (n=7), and in the range of 182 ± 122 (n=3) to 296 ± 88 (n=3) copies for the crossbred cattle (n=7). The TLR2 activity of induced cells in both groups was found to be significantly higher than that of the respective uninduced cells (P<0.0001). Furthermore, upon comparison, TLR2 activities of induced and uninduced cells of the Tharparkar were not found to be significantly different from those of the crossbred cattle (P=0.8154 and P=0.6670). In the present study, we have quantified and compared, for the first time, TLR2 activity in terms of NFKBIA mRNA copies in monocyte-derived macrophages of Tharparkar and crossbred cattle and found that both have equivalent TLR2 activity.

Sero-epidemiological survey and risk factors associated with bovine brucellosis among slaughtered cattle in Nigeria

Bovine brucellosis is endemic in Nigeria; however, limited data exist on nationwide studies and risk factors associated with the disease. Using a cross-sectional sero-epidemiological survey, we determined the prevalence of and risk factors for brucellosis in slaughtered cattle in three geographical regions of Nigeria. Serum samples from randomly selected unvaccinated cattle slaughtered over a period of 3 years (between December 2010 and September 2013) from northern, southern and south-western Nigeria were tested for antibodies to Brucella abortus using the Rose Bengal test. Data associated with risk factors of brucellosis were analysed by Stata Version 12. In all, 8105 cattle were screened. An overall seroprevalence of 3.9% (315/8105) was recorded by the Rose Bengal test, with 3.8%, 3.4% and 4.0% from the northern, southern and south-western regions, respectively. Bivariate analysis showed that cattle screened in northern Nigeria were less likely to be seropositive for antibodies to Brucella spp. than those from south-western Nigeria (odds ratio = 0.94; 95% confidence interval: 0.73–1.22). However, logistic regression analysis revealed that breed ( p = 0.04) and sex ( p £ 0.0001) of cattle were statistically significant for seropositivity to Brucella spp. The study found that brucellosis was endemic at a low prevalence among slaughtered cattle in Nigeria, with sex and breed of cattle being significant risk factors. Considering the public health implications of brucellosis, we advocate coordinated surveillance for the disease among diverse cattle populations in Nigeria, as is carried out in most developed countries.

Molecular comparison of Slc11a1 and Slc11a2 genes of swamp- and riverine-type water buffaloes

Solute-linked carrier 11a and 11a2 (Slc) have been associated with disease resistance and/or susceptibility across animal species. These genes have an important mechanism in the regulation against intracellular infection. This study analysed the genetic characteristic of Slc 11a and 11a2 in swamp-type and riverine-type water buffaloes to understand their immunological distinction. Characterization of Slc11a1 and Slc11a2 genes from swamp- and riverine-type water buffaloes was carried out by molecular cloning, sequencing and phylogenetic analysis. The cloned cDNA of Slc11a1 and Slc11a2 contained an open reading frame of 1647 and 1723 nucleotides, encoding 549 and 574 amino acids, respectively. Nucleotide sequence homology of both Slc11a1 and Slc11a2 had 99% in swamp and riverine type, which gives almost identical polypeptide. However, Slc11a1 and Slc11a2 have substitutions of 5 and 1 amino acid residues, correspondingly. These substitutions suggest as a potential gene markers for resistance and/or susceptibility to intracellular infection. Furthermore, phylogenetic analysis confirmed the degree of relationship between the bubaline species and justifies the distinctness of each breed by the bootstrap value generated.

Influence of endogamy and mitochondrial DNA on immunological parameters in cattle

BACKGROUND

Endogamy increases the risk of manifestation of deleterious recessive genes. Mitochondrial DNA allows the separation of American Zebu (Bos indicus and Bos taurus) and evaluate the effect of mitochondrial DNA on productive traits of cattle. However, the effect of endogamy and mitochondrial DNA (mtDNA) on the immune system remains unclear. The aim of this study was to evaluate the association between endogamy, mtDNA and immune parameters.

RESULTS

A total of 86 cattle (43 cows and 43 calves) were used in this study. Age, endogamy, milk yield, and origin of mtDNA were measured and their influence on immunological parameters was evaluated. Older cows had increased CD4+ T cells, decreased CD21+ and γδhigh T cells as well as increased CD4+/CD8+ and T/B ratio. Multiple regression analysis indicated that endogamy in calves was associated with increased CD8+ T and CD21+ B lymphocytes, and decreased γδhigh T cells in peripheral blood. Cows with medium and lower endogamy had a lower percentage of B lymphocytes and γδlow T cells and cows with lower endogamy had higher levels of γδ T cells and γδhigh T cells, as well as the CD4+/CD48+ cell ratio. Calves with higher endogamy had higher levels of CD8+ T lymphocytes, whereas calves with lower endogamy had lower levels of γδlow T cells.

CONCLUSIONS

These results demonstrated for the first time that endogamy influences the immune system of cattle.

Genetic analysis of the 3' untranslated region of the bovine SLC11A1 gene reveals novel polymorphisms

Polymorphisms in microsatellites at the 3' untranslated region (3'UTR) of the SLC11A1 (solute carrier family 11 member A1) gene have been associated with natural resistance to Brucella abortus and Mycobacterium bovis infection in livestock species. Here, we carried out an individual genetic analysis of the two microsatellites present at the 3'UTR SLC11A1 gene in 254 Bos taurus purebred, 125 B. indicus purebred and 54 B. taurus × B. indicus crossbred cattle. The genotyping by capillary electrophoresis showed the presence of four alleles (157, 159, 161 and 163) for the first microsatellite (MS1) and six alleles (175, 177, 179, 181, 183 and 185) for the second microsatellite (MS2). The alleles 159 and 175 were the most frequent in all breeds analyzed. B. taurus showed the most homogeneous haplotype and genotype for both microsatellites, whereas B. indicus showed the most heterogeneous haplotype and genotype. Two novel variants (alleles 161 and 163) within the MS1 are reported as well as novel variants in MS2 in Holstein breed. The knowledge of the polymorphisms distribution in both microsatellites at the 3'UTR of the SLC11A1 gene in cattle breeds is useful for future experimental design to evaluate the association between reported genotypes and natural resistance to pathogens infection.

A large seroprevalence survey of brucellosis in cattle herds under diverse production systems in northern Nigeria

BACKGROUND

This study was carried out to investigate the status of brucellosis in cattle under various management systems in Adamawa, Kaduna and Kano states, northern Nigeria. Using multi-stage sampling, serum samples of 4,745 cattle from 271 herds were tested using the Rose-Bengal plate-agglutination test (RBPT) and positives were confirmed using a competitive enzyme-linked immunosorbent assay (c-ELISA).

RESULTS

Prevalence estimates were calculated by adjusting for sampling weights and where possible for test sensitivity and specificity. Thirty-seven percent of all animals were RBPT positive, and after confirmation with c-ELISA the overall animal-level prevalence, adjusted for sampling weights, was 26.3% (95% CI, 22.1%-31.0%). Of the herds sampled, 210 (77.5%; 95% CI, 68.6%-84.5%) had at least one animal positive to both tests; this did not differ significantly between states (P = 0.538). Mean within-herd seroprevalence in positive herds was 30.2% (95% CI, 25.3%-35.1%) and ranged from 3.1% to 85.7%. Overall animal-level seroprevalences of 29.2% (95% CI, 22.5%-36.9%) n = 1,827, 23.3% (95% CI, 18.9%-28.3%) n = 1,870 and 26.7% (95% CI, 18.8%-36.7%) n = 1,048 were observed in Adamawa, Kaduna and Kano states, respectively (P = 0.496). A significantly higher seroprevalence was found in males (38.2%; 95% CI, 31.7%-45.2%) than in females (24.7%; 95% CI, 20.4%-29.5%) (P < 0.001) and in non-pregnant females (27.8%; 95% CI, 22.9%-33.5%) than in pregnant females (17.2%; 95% CI, 13.6%-21.5%) (P < 0.001). Seroprevalence increased with increasing age (P < 0.001), from 13.5% (95% CI, 8.9%-19.9%) in cattle <4 years to 35.0% (95% CI, 28.5%-42.3%) in cattle >7 years. Seroprevalence also varied between management systems (P < 0.001): pastoral systems 45.1% (95% CI, 38.6%-51.9%), zero-grazing systems 23.8% (95% CI, 6.8%-59.2%), agro-pastoral systems 22.0% (95% CI, 17.3%-27.8%), and commercial farms 15.9% (95% CI, 9.5%-25.5%). Seroprevalence did not differ significantly between breeds or lactation status.

CONCLUSION

This is the first large study to assess the prevalence of bovine brucellosis over a wide geographic area of northern Nigeria, in a variety of management systems and using accurate tests. The seroprevalence of brucellosis was high, and higher than results of previous studies in northern Nigeria. The pastoral management systems of the traditional Fulanis may be encouraging the dissemination of the disease. Public enlightenment of the farmers about the disease, vaccination and appropriate national control measures are recommended.