Marco Antonio Machado

Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping

BackgroundNatural selection has molded evolution across all taxa. At an arguable date of around 330,000 years ago there were already at least two different types of cattle that became ancestors of nearly all modern cattle, the Bos taurus taurus more adapted to temperate climates and the tropically adapted Bos taurus indicus. After domestication, human selection exponentially intensified these differences. To better understand the genetic differences between these subspecies and detect genomic regions potentially under divergent selection, animals from the International Bovine HapMap Experiment were genotyped for over 770,000 SNP across the genome and compared using smoothed FST. The taurine sample was represented by ten breeds and the contrasting zebu cohort by three breeds.ResultsEach cattle group evidenced similar numbers of polymorphic markers well distributed across the genome. Principal components analyses and unsupervised clustering confirmed the well-characterized main division of domestic cattle. The top 1% smoothed FST, potentially associated to positive selection, contained 48 genomic regions across 17 chromosomes. Nearly half of the top FST signals (n = 22) were previously detected using a lower density SNP assay. Amongst the strongest signals were the BTA7:~50 Mb and BTA14:~25 Mb; both regions harboring candidate genes and different patterns of linkage disequilibrium that potentially represent intrinsic differences between cattle types. The bottom 1% of the smoothed FST values, potentially associated to balancing selection, included 24 regions across 13 chromosomes. These regions often overlap with copy number variants, including the highly variable region at BTA23:~24 Mb that harbors a large number of MHC genes. Under these regions, 318 unique Ensembl genes are annotated with a significant overrepresentation of immune related pathways.ConclusionsGenomic regions that are potentially linked to purifying or balancing selection processes in domestic cattle were identified. These regions are of particular interest to understand the natural and human selective pressures to which these subspecies were exposed to and how the genetic background of these populations evolved in response to environmental challenges and human manipulation.

Genetic diversity of four cattle breeds using microsatellite markers

Four cattle breeds (Gyr, Nellore, Guzerat and Holstein) were analyzed by amplification of genomic DNA using microsatellite loci to evaluate the genetic diversity within and among them. DNA samples of 18 animals from each breed were collected to access the genetic content of them. Allele frequencies were calculated and used to generate a Neis genetic distance matrix what was used to build a dendrogram following UPGMA clustering. As expected, Holstein breed was the most distinct from the other breeds: 1.15 in relation to Gyr, 1.12 in relation to Nellore and 0.94 in relation to Guzerat. The closest genetic distance was 0.25 between Guzerat and Nellore. A total of 64 alleles in all four breeds were detected using nine microsatellite primers. Each breed showed 53% of the total number of alleles. The average number of alleles per locus was 7.11 ± 3.21. The most informative locus was BMS1237 with 53% of observed heterozygosity and the least informative locus was BMS3004 with 12% only. The average heterozygosity detected for the nine loci were 35% and the expected value for Hardy-Weinberg equilibrium was 53%. This low heterozygosity suggests a high endogamy level among the animals sampled within each breed.

Genome wide scan for quantitative trait loci affecting tick resistance in cattle (Bos taurus × Bos indicus).

BackgroundIn tropical countries, losses caused by bovine tick Rhipicephalus (Boophilus) microplus infestation have a tremendous economic impact on cattle production systems. Genetic variation between Bos taurus and Bos indicus to tick resistance and molecular biology tools might allow for the identification of molecular markers linked to resistance traits that could be used as an auxiliary tool in selection programs. The objective of this work was to identify QTL associated with tick resistance/susceptibility in a bovine F2 population derived from the Gyr (Bos indicus) × Holstein (Bos taurus) cross.ResultsThrough a whole genome scan with microsatellite markers, we were able to map six genomic regions associated with bovine tick resistance. For most QTL, we have found that depending on the tick evaluation season (dry and rainy) different sets of genes could be involved in the resistance mechanism. We identified dry season specific QTL on BTA 2 and 10, rainy season specific QTL on BTA 5, 11 and 27. We also found a highly significant genome wide QTL for both dry and rainy seasons in the central region of BTA 23.ConclusionsThe experimental F2 population derived from Gyr × Holstein cross successfully allowed the identification of six highly significant QTL associated with tick resistance in cattle. QTL located on BTA 23 might be related with the bovine histocompatibility complex. Further investigation of these QTL will help to isolate candidate genes involved with tick resistance in cattle.

On the Search for Markers of Tick Resistance in Bovines

Genetic differences in susceptibility to ticks (Rhipicephalus (Boophilus) microplus) are considerable in bovines. Here, mapping, association and gene expression approaches were employed to further advance our understanding of the molecular basis of tick resistance. A B. taurus x B. indicus F2 population was developed by Embrapa and 382 individuals were measured for parasitic load. Scanning of all chromosomes is in progress. Quantitative trait loci (QTL) for tick load were mapped to chromosomes 4, 5, 7, 10, 14, 18 and 23 out of the 20 chromosomes scanned and were dependent on the season in which the phenotype was scored. In the candidate gene approach, females from the genetic groups Nelore (NE--184), Canchim x Nelore (CN--153), Aberdeen Angus x Nelore (AN--123) and Simmental x Nelore (SN--120) were evaluated under natural infestation. Microsatellite markers close to the genes for interleukin 2 (IL2), interleukin 4 (IL4) and interferon gamma (IFNG) were analysed. Tick counts were associated with the marker for interleukin 4 (P < 0.05) in three genetic groups. Differences in cytokine mRNA levels of naive versus infested Nelore calves as well as between resistant versus susceptible cows from NE, CN and AN genetic groups were also investigated. Comparison of cytokines from infested and naïve animals showed downregulation of IL2. When resistant cows were compared to susceptible animals, IL8 was downregulated. These results reinforce the multiloci nature of tick resistance and the need to consider QTL and environment interactions.

Association of the bovine major histocompatibility complex (BoLA) BoLA-DRB3 gene with fat and protein production and somatic cell score in Brazilian Gyr dairy cattle (Bos indicus)

The effect of the bovine major histocompatibility complex (BoLA) locus on animal health may be due to a direct action of its alleles on immune functions, whereas its indirect effect on production traits might be explained by the better general health conditions of more productive animals. In the present study, the BoLA-DRB3 gene was investigated in 1058 cows belonging to seven Brazilian Gyr Dairy herds (Bos indicus, Zebu cattle). A total of 37 alleles were identified, 15 of them described for the first time in a Zebu breed. A highly significant association (p < 0.02) was observed between allele *54 and a decrease (-26.1 kg) in milk protein yield and there was a significant association (p < 0.05) between this allele and lower (-26.07 kg) milk fat yield. There was also a significant association (p < 0.05) between allele *6 and decreased (-12.47 kg) milk protein and allele *7 and increased (12.72 kg) milk protein. There were also indications of association (p < 0.10) between somatic cell score (SCS) and alleles *3 (SCS increased by 0.54 units) and *31 (SCS increased by 0.46 units). The highly significant association of allele *54 with lower protein yield suggests the possible use of this allele in marker-assisted selection programs.

Effect of oxygen tension and serum during IVM on developmental competence of bovine oocytes.

With an aim to improve the in vitro production of bovine embryos, the present study investigated the effect of serum and oxygen tension during IVM on oocyte developmental competence. Four experimental groups were evaluated: G1, 10% oestrus cow serum (OCS) with 20% O(2); G2, 0.1% polyvinyl alcohol (PVA) with 20% O(2); G3, 10% OCS with 5% O(2); and G4, 0.1% PVA with 5% O(2). The proportion of MII oocytes, blastocyst rates and total cell number were not affected (P > 0.05) when the OCS was replaced with PVA under 5% O(2), whereas a higher (P < 0.05) blastocyst rate and total cell number were found with OCS compared with PVA under 20% O(2). The apoptosis index was lower in blastocysts from oocytes matured with PVA under 5% O(2) (G4) compared with other groups (G1, G2 and G3), but no differences (P > 0.05) were found in maturation and blastocyst rates. Significant differences were found in the amount of specific transcripts in oocytes matured under different conditions. In conclusion maturation with PVA and 5% O(2) provides an efficient in vitro culture condition for the maturation of bovine oocytes.

Species-level identification of staphylococci isolated from bovine mastitis in Brazil using partial 16S rRNA sequencing

Staphylococci isolated from bovine milk and not classified as Staphylococcus aureus represent a heterogeneous group of microorganisms that are frequently associated with bovine mastitis. The identification of these microorganisms is important, although it is difficult and relatively costly. Genotypic methods add precision in the identification of Staphylococcus species. In the present study, partial 16S rRNA sequencing was used for the species identification of coagulase-positive and coagulase-negative staphylococci isolated from bovine mastitis. Two hundred and two (95%) of the 213 isolates were successfully identified at the species level. The assigning of an isolate to a particular species was based on ≥99% identity with 16S rRNA sequences deposited in GenBank. The identified isolates belonged to 13 different Staphylococcus species; Staphylococcus chromogenes, S. aureus and Staphylococcus epidermidis were the most frequently identified species. Eight isolates could not be assigned to a single species, as the obtained sequences showed 99% or 100% similarity to sequences from two or three different Staphylococcus species. The relatedness of these isolates with the other isolates and reference strains was visualized using a cladogram. In conclusion, 16S rRNA sequencing was an objective and accurate method for the proper identification of Staphylococcus species isolated from bovine mastitis. Additional target genes could be used in non-conclusive cases for the species-level identification of these microorganisms.

Karyotype analysis, DNA content and molecular screening in Lippia alba (Verbenaceae)

Cytogenetic analyses, of pollen viability, nuclear DNA content and RAPD markers were employed to study three chemotypes of Lippia alba (Mill.) (Verbenaceae) in order to understand the genetic variation among them. Different ploidy levels and mixoploid individuals were observed. This work comprises the first report of different chromosome numbers (cytotypes) in L. alba. The chromosome numbers of La2-carvone and La3-linalool chemotypes suggested that they are polyploids. Flow cytometric analysis showed an increase of nuclear DNA content that was not directly proportional to ploidy level variation. A cluster analysis based on RAPD markers revealed that La3-linalool shares genetic markers with La1-citral and La2-carvone. The analysis showed that the majority of genetic variation of La3-linalool could be a consequence of ixoploidy. ur data indicates that sexual reproduction aong those three chemotypes is unlikely and suggests the beginning of reproductive isolation. The results demonstrated that chromosome analysis, nuclear DNA content estimation and RAPD markers constitute excellent tools for detecting genetic variation among L. alba chemotypes.

Novel thalidomide analogues from diamines inhibit pro-inflammatory cytokine production and CD80 expression while enhancing IL-10.

Thalidomide is used to treat a variety of diseases including erythema nodosum leprosum, an inflammatory complication of leprosy. However, this drug has severe teratogenic activity and novel thalidomide analogues might be used to treat diseases without this severe side effect. A series of diamine compounds containing two hydrolyzed phthalimide units were chosen as analogues of thalidomide and evaluated regarding their capacity to regulate the production of molecules involved in inflammatory responses. TNF-α, IL-12 and IL-10 production, and the expression of CD80 and CD86 were investigated in LPS plus IFN-γ-stimulated J774A.1 cells by ELISA and flow cytometry, respectively. The expression of TNF-α and IL-10 mRNA was analyzed by real time RT-PCR. TNF-α, IL-6, IFN-γ, CXCL9 and CXCL10 production by human peripheral blood mononuclear cells (PBMC) were evaluated by flow cytometry. Compounds 3, 6 and 9 greatly inhibited TNF-α and IL-12 production while enhancing IL-10. In addition, CD80 expression was inhibited, but not CD86. The compounds inhibited TNF-α production by PBMC more than thalidomide and also had an inhibitory effect on the production of IL-6, IFN-γ, CXCL9 and CXCL10. Levels of mRNA for TNF-α were reduced after treatment with the compounds, suggesting post- transcriptional effects. The compounds had no effect on cell viability. Our results indicate that the novel diamine compounds 3, 6 and 9 inhibit critical pro-inflammatory cytokines and stimulate IL-10, which make them attractive candidate drugs for the treatment of certain inflammatory conditions and cancer.

Tumour necrosis factor receptors and apoptosis of alveolar macrophages during early infection with attenuated and virulent Mycobacterium bovis.

Apoptosis of macrophages has been reported as an effective host strategy to control the growth of intracellular pathogens, including pathogenic mycobacteria. Tumour necrosis factor‐α (TNF‐α) plays an important role in the modulation of apoptosis of infected macrophages. It exerts its biological activities via two distinct cell surface receptors, TNFR1 and TNFR2, whose extracellular domain can be released by proteolysis forming soluble TNF receptors (sTNFR1 and sTNFR2). The signalling through TNFR1 initiates the majority of the biological functions of TNF‐α, leading to either cell death or survival whereas TNFR2 mediates primarily survival signals. Here, the expression of TNF‐α receptors and the apoptosis of alveolar macrophages were investigated during the early phase of infection with attenuated and virulent mycobacteria in mice. A significant increase of apoptosis and high expression of TNFR1 were observed in alveolar macrophages at 3 and 7 days after infection with attenuated Mycobacterium bovis but only on day 7 in infection with the virulent M. bovis. Low surface expression of TNFR1 and increased levels of sTNFR1 on day 3 after infection by the virulent strain were associated with reduced rates of apoptotic macrophages. In addition, a significant reduction in apoptosis of alveolar macrophages was observed in TNFR1−/− mice at day 3 after bacillus Calmette–Guérin infection. These results suggest a potential role for TNFR1 in mycobacteria‐induced alveolar macrophage apoptosis in vivo. In this scenario, shedding of TNFR1 seems to contribute to the modulation of macrophage apoptosis in a strain‐dependent manner.