Genomic breed composition of pure registered Brazilian Gir.

INTRODUCTION: Gir is a Bos indicus breed originally from India, first imported to Brazil in 1850. High-performance Dairy Gir has been systematically selected in Brazil from its arrival. Since the major phenotypic difference between Gir in India and Brazil is a higher milk production in the former, it is speculated that Brazilian Gir was strategically crossed with Holstein or another Bos taurus to improve milk yield. This study evaluated the purity of Brazilian Gir breed stocks from BASA Farms in Brazil, trying to identify possible admixture events with other cattle breeds based on DNA analysis. MATERIALS AND METHODS: The population included 1061 pure registered individuals genotyped using two commercial platforms with 37 k and 25 k SNPs. Admixture analysis was performed individually to estimate levels of genomic composition derived from six different reference populations, three indicine and three taurine breeds. RESULTS: A Gir ancestry of 99% or higher was found for 94.2% of the population, while the remaining showed levels of non-Gir ancestry up to 6.8%. Only five individuals were identified with possible taurine ancestry, all of them exhibiting levels lower than 2%. The remaining non-Gir ancestry identified was derived from indicine breeds. The levels of admixture observed in the population were from low to non-detectable. No consistent patterns of admixture were observed indicating sustained introgression of taurine lines as means of genetic improvement. CONCLUSION: According to these results, genetic improvement achieved by Brazilian Gir breeders is the result of within-breed selection methods applied intensively over the past five decades, rather than the result from sustained introgression.

Bos taurus haplotypes segregating in Nellore (Bos indicus) cattle.

Brazil is the largest exporter of beef in the world, and most of that beef derives from Nellore cattle. Although considered a zebu breed (Bos indicus), the history of Nellore cattle in Brazil is marked by the importation of bulls from India, the use of a Creole taurine (Bos taurus) maternal lineage to quickly expand the herds and backcrossing to Nellore bulls to recover zebu ancestry. As a consequence, the current Brazilian Nellore population carries an average taurine ancestry of approximately 1%. Although that percentage seems small, some taurine variants deviate substantially from that average, with the better-known cases being the PLAG1-Q haplotype involved with body size variation and the Guarani (PG ) polled variant producing hornless animals. Here, we report taurine haplotypes in 9074 Nellore animals genotyped for 539 657 imputed SNP markers. Apart from PLAG1-Q and PG , our analysis further revealed common taurine haplotypes (>3%) spanning genes related to immunity, growth, reproduction and hair and skin phenotypes. Using data from 22 economically important traits, we showed that many of the major QTL previously reported in the breed are at least partially driven by taurine haplotypes. As B. taurus and B. indicus haplotypes are highly divergent, presenting widely different sets of functional variants, our results provide promising targets for future scrutiny in Nellore cattle.

Heat stress response in slick vs normal-haired Criollo Limonero heifers in a tropical environment.

To assess the effect of hair type on the heat stress response, 20 Criollo Limonero heifers with slick (n = 11) or normal hair (n = 9) were studied. Under a high temperature-humidity index (THI) environment, heat stress response was assessed through physiological variables that included respiration rate (RR), heart rate (HR), ruminal frequency (RMF), rectal temperature (RT), saliva pH (SPH), and lymphocyte count (LC) in the morning (5:00 AM, 27.4 °C, 64% relative humidity, THI = 77) and afternoon (1:00 PM, 34.5 °C, 70% relative humidity, THI = 88). A case-control study using a split plot design was used. Data were analyzed using ANOVA (PROC MIXED SAS 2010) and a statistical model comprising the fixed effects of hair length, sampling hour, interaction of hair length by sampling hour, and the random effect of animal nested within hair type on physiological variables associated with heat stress response. Sampling hour influenced (P < 0.0001) RR, RT, and (P < 0.003) SPH. Hair length influenced RR (P < 0.01) and RT (P < 0.04) and tended to influence LC (P < 0.07). The interaction of sampling hour by hair influenced RR (P < 0.04), RT (P < 0.0002), and both SPH and LC (P < 0.05). During afternoon hours, slick-haired heifers had lower values for RR (81 ± 4.2 vs 102 ± 4.7 bpm; P < 0.01), RT (39.5 ± 0.1 vs 40.3 ± 0.1 C°; P < 0.002), and LC (60 ± 3.2 vs 72.3 ± 3.6; P < 0.09) than normal-haired heifers. In normal-haired heifers, SPH increased during afternoon compared to morning-hours (8.66 ± 0.1 vs 9.11 ± 0.1; P < 0.04). It was concluded that slick-coated heifers exhibited an enhanced capability to cope with heat stress compared to normal-haired heifers likely due to an enhanced capacity for heat dissipation.

Development of tetra-primer ARMS-PCR protocol to genotype the prolactin receptor SNP 39136666 and assessment of this SNP in Brazilian locally adapted cattle breeds / [Desenvolvimento de protocolo de tetra-primer ARMS- PCR para genotipagem do SNP 39136666 do receptor da prolactina e avaliação desse SNP em raças bovinas brasileiras localmente adaptadas]

As raças taurinas de origem ibérica Limonero e Carora (Bos primigenius taurus) possuem o fenótipo de pelo curto, liso e com baixa densidade folicular, o que confere a esses animais maior tolerância térmica e melhor produtividade em regiões quentes. Diferentes mutações associadas a esse fenótipo foram descritas no gene do receptor de prolactina PRLR, localizado no cromossomo bovino BTA20. Uma mutação recentemente encontrada é a substituição do nucleotídeo C por T, SNP 39136666 (p. R497*), no exon 11, que gera um códon de parada e, consequentemente, uma menor isoforma desse receptor. Neste trabalho, desenvolveu-se um protocolo rápido e de baixo custo para detecção desse SNP, utilizando-se a técnica de tetra-primer ARMS-PCR. Assim, foi possível detectar essa mutação nas raças brasileiras de origem ibérica localmente adaptadas: Caracu, Crioulo Lageano, Mocho Nacional e Pantaneiro. O alelo T foi mais frequente na raça Caracu (80%), enquanto o alelo C foi mais frequente na raça Crioulo Lageano (84%). Essa simples metodologia pode ser usada para genotipar esse SNP e ajudar na aplicação dessas informações moleculares em programas de melhoramento focados na tolerância térmica em bovinos taurinos e seus mestiços.(AU)

A genome-wide scan for selection signatures in Nellore cattle.

Brazilian Nellore cattle (Bos indicus) have been selected for growth traits for over more than four decades. In recent years, reproductive and meat quality traits have become more important because of increasing consumption, exports and consumer demand. The identification of genome regions altered by artificial selection can potentially permit a better understanding of the biology of specific phenotypes that are useful for the development of tools designed to increase selection efficiency. Therefore, the aims of this study were to detect evidence of recent selection signatures in Nellore cattle using extended haplotype homozygosity methodology and BovineHD marker genotypes (>777,000 single nucleotide polymorphisms) as well as to identify corresponding genes underlying these signals. Thirty-one significant regions (P < 0.0001) of possible recent selection signatures were detected, and 19 of these overlapped quantitative trait loci related to reproductive traits, growth, feed efficiency, meat quality, fatty acid profiles and immunity. In addition, 545 genes were identified in regions harboring selection signatures. Within this group, 58 genes were associated with growth, muscle and adipose tissue metabolism, reproductive traits or the immune system. Using relative extended haplotype homozygosity to analyze high-density single nucleotide polymorphism marker data allowed for the identification of regions potentially under artificial selection pressure in the Nellore genome, which might be used to better understand autozygosity and the effects of selection on the Nellore genome.

Identification and characterization of microRNAs expressed in chicken skeletal muscle.

MicroRNAs (miRNAs, miRs) encompass a class of small non-coding RNAs that often negatively regulate gene expression. miRNAs play an essential role in skeletal muscle, determining the proper development and maintenance of this tissue. In comparison to other organs and tissues, the full set of muscle miRNAs and its expression patterns are still poorly understood. In this report, a chicken skeletal muscle miRNA library was constructed, and the expression of selected miRNAs was further characterized during muscle development in chicken lines with distinct muscling phenotypes. Clone library sequence analysis revealed 40 small RNAs with similarities to previously described chicken miRNAs, seven miRNAs that were never identified before in chicken, and some sequence clusters representing other possible novel miRNAs. Temporal expression profiles of three miRNAs associated with cell proliferation and differentiation (miR-125b, miR-221, and miR-206) in two chicken lines (broiler and layer) revealed the differential steady-state levels of these miRs during skeletal muscle growth and suggests that miR-206 is involved in the muscling phenotype that is observed in growth-selected chicken lines.

Whole-genome analysis for backfat thickness in a tropically adapted, composite cattle breed from Brazil.

Backfat thickness affects the preservation of the beef carcass after slaughter and confers organoleptic characteristics assessed by the consumer. One of the breeding goals for Canchim, a tropically adapted breed, is to comprehensively increase fat thickness. Our goals were to identify genomic regions associated with backfat in Canchim populations and validate the association of single nucleotide polymorphisms (SNPs) overlapping previously identified QTL regions known to affect fat deposition. Fifteen animals with lower and 15 animals with higher residues for backfat, according to a linear model using the SAS GLM procedure, were selected from a population of 1171 animals and genotyped using the BovineSNP50 BeadChip. Initial analysis revealed more than 100 SNPs that discriminated the tails of phenotypic distribution. One extended region of association included the centromeric region of chromosome (Chr) 14. Because this region overlapped with QTL from previous reports, we developed SNP assays to interrogate two linkage disequilibrium blocks, one in the centromeric region and another in the middle region of Chr 14 to confirm the association. The analysis validated the presence of specific haplotypes affecting fat thickness.

Discovery, profiling and identification of polymorphic mRNA target sites in cattle

Our laboratory is interested in post-translational modifications of histone proteins, with studies ranging from identification of novel modifications to functional characterization of these marks. Ultimately, we seek to provide a greater understanding of how histone modifications work together to form a ‘histone code. This code is thought to regulate the recruitment of effector proteins that regulate the diverse functions associated with DNA, including gene transcription and DNA repair. Our recent studies show that RNA polymerase II recruits a variety of chromatinmodifying enzymes that contribute to the disruption, reassembly and maintenance of chromatin structure during the transcription elongation process. One enzyme we have focused on is Set2, which associates with the transcribing polymerase and methylates nucleosomal H3 on lysine 36. H3K36 methylation results in the recruitment of a histone deacetylase complex which functions to prevent inappropriate transcription initiation from occurring within the transcribed regions of genes. I will discuss our recent progress toward understanding how Set2 contributes to the organization and function of chromatin. In addition, I will highlight our progress on a proteomics project that is providing new insights into how “readers” of the histone code bind their cognate modifications using high-density histone peptide arrays.(AU)

Discovery, profiling and identification of polymorphic mRNA target sites in cattle

Our laboratory is interested in post-translational modifications of histone proteins, with studies ranging from identification of novel modifications to functional characterization of these marks. Ultimately, we seek to provide a greater understanding of how histone modifications work together to form a ‘histone code’. This code is thought to regulate the recruitment of effector proteins that regulate the diverse functions associated with DNA, including gene transcription and DNA repair. Our recent studies show that RNA polymerase II recruits a variety of chromatinmodifying enzymes that contribute to the disruption, reassembly and maintenance of chromatin structure during the transcription elongation process. One enzyme we have focused on is Set2, which associates with the transcribing polymerase and methylates nucleosomal H3 on lysine 36. H3K36 methylation results in the recruitment of a histone deacetylase complex which functions to prevent inappropriate transcription initiation from occurring within the transcribed regions of genes. I will discuss our recent progress toward understanding how Set2 contributes to the organization and function of chromatin. In addition, I will highlight our progress on a proteomics project that is providing new insights into how “readers” of the histone code bind their cognate modifications using high-density histone peptide arrays.

Mapping of quantitative trait loci controlling tick [Riphicephalus (Boophilus) microplus] resistance on bovine chromosomes 5, 7 and 14.

Differences in domestication and selection processes have contributed to considerable phenotypic and genotypic differences between Bos taurus and Bos indicus cattle breeds. Of particular interest in tropical and subtropical production environments are those genetic differences between subspecies that underlie the phenotypic extremes in tolerance and susceptibility to parasite infection. In general, B. taurus cattle are more susceptible to ectoparasites than B. indicus cattle in tropical environments, and much of this difference is under genetic control. To identify genomic regions involved in tick resistance, we developed a B. taurus x B. indicus F(2) experimental population to map quantitative trait loci (QTL) for resistance to the Riphicephalus (Boophilus) microplus tick. About 300 individuals were measured for parasite load in two seasons (rainy and dry) and genotyped for 23 microsatellite markers covering chromosomes 5, 7 and 14. We mapped a suggestive chromosome-wide QTL for tick load in the rainy season (P < 0.05) on chromosome 5. For the dry season, suggestive (P < 0.10) chromosome-wide QTL were mapped on chromosomes 7 and 14. The additive effect of the QTL on chromosome 14 corresponds to 3.18% of the total observed phenotypic variance. Our QTL-mapping study has identified different genomic regions controlling tick resistance; these QTL were dependent upon the season in which the ticks were counted, suggesting that the QTL in question may depend on environmental factors.