Comparative analysis of PRNP 12-bp and 23-bp indels in healthy Aberdeen Angus, Aberdeen Angus x Hereford, Holstein Friesian and Uruguayan Creole cattle / Análise comparativa de PRNP 12bp e 23bp indels em bovinos Aberdeen Angus, Aberdeen Angus x Hereford, Holstein Friesian e Crioulo Uruguaio saudáveis

Bovine spongiform encephalopathy (BSE) is a transmissible progressive neurodegenerative disease characterized by the accumulation of a pathological isoform (PrpSC) of the cellular prion protein (PrpC) in the brain of cattle. Two insertion/deletion polymorphisms in the PRNP gene (23bp in the promoter and 12bp in intron 1) have been associated with resistance or susceptibility to the disease. The aim of this study was to analyze the distribution of these polymorphisms in 214 healthy bovines belonging to four different breed groups (Aberdeen Angus, Aberdeen Angus x Hereford, Holstein Friesian and Uruguayan Creole cattle). DNA samples were amplified by end-point PCR. A high frequency of the alleles and haplotype associated with susceptibility to BSE (del12 and del23, and del12-del23, respectively) were found in the Aberdeen Angus, Aberdeen Angus x Hereford and Holstein Friesian animals. At the same time, the Uruguayan Creole cattle presented a higher frequency of the alleles and haplotype associated with resistance to BSE (ins12 and ins23, and ins12-ins23, respectively). These data could indicate a greater genetic resistance of the Uruguayan Creole cattle to BSE compared to other analyzed breeds, reinforcing its value as a zoogenetic resource.

A encefalopatia espongiforme bovina (EEB) é uma doença neurodegenerativa progressiva transmissível dos bovinos, caracterizada pelo acúmulo no cérebro de uma isoforma patológica (PrpSC) da proteína priônica celular (PrpC). Dois polimorfismos de inserção/deleção no gene PRNP (23bp no promotor e 12bp no íntron 1) foram associados à resistência ou suscetibilidade à doença. O objetivo deste trabalho foi analisar a distribuição desses polimorfismos em 214 bovinos sadios, pertencentes a quatro diferentes grupos raciais (Aberdeen Angus, Aberdeen Angus x Hereford, Holstein Friesian e Crioulo Uruguaio). As amostras de DNA foram amplificadas por PCR de tempo final. Uma alta frequência dos alelos e haplótipos associados à suscetibilidade à BSE (del12 e del23 e del12-del23, respectivamente) foram encontrados nos animais Aberdeen Angus, Aberdeen Angus x Hereford e Holstein Friesian, enquanto o gado Crioulo Uruguaio apresentou maior frequência dos alelos e haplótipos associados à resistência à BSE (ins12 e ins23 e ins12-ins23, respectivamente). Esses dados podem indicar uma maior resistência genética do gado Crioulo Uruguaio à BSE em comparação com as outras raças analisadas, reforçando seu valor como recurso zoogenético.

The Search for Cancer Biomarkers: Assessing the Distribution of INDEL Markers in Different Genetic Ancestries.

Cancer is a multifactorial group of diseases, being highly incident and one of the leading causes of death worldwide. In Brazil, there is a great variation in cancer incidence and impact among the different geographic regions, partly due to the genetic heterogeneity of the population in this country, composed mainly by European (EUR), Native American (NAM), African (AFR), and Asian (ASN) ancestries. Among different populations, genetic markers commonly present diverse allelic frequencies, but in admixed populations, such as the Brazilian population, data is still limited, which is an issue that might influence cancer incidence. Therefore, we analyzed the allelic and genotypic distribution of 12 INDEL polymorphisms of interest in populations from the five Brazilian geographic regions and in populations representing EUR, NAM, AFR, and ASN, as well as tissue expression in silico. Genotypes were obtained by multiplex PCR and the statistical analyses were done using R, while data of tissue expression for each marker was extracted from GTEx portal. We highlight that all analyzed markers presented statistical differences in at least one of the population comparisons, and that we found 39 tissues to be differentially expressed depending on the genotype. Here, we point out the differences in genotype distribution and gene expression of potential biomarkers for risk of cancer development and we reinforce the importance of this type of study in populations with different genetic backgrounds.

Association of the rs4646994 in ACE gene with susceptibility to tuberculosis in a region of the Brazilian Amazon.

Background: Tuberculosis (TB) is an infectious disease caused by the bacterium Mycobacterium tuberculosis and represents an important global public health issue. Single-nucleotide polymorphisms and INDELs are common genetic variations that can be located in genes associated with immune response and, therefore, they may have direct implications over the phenotype of susceptibility to infections like tuberculosis. This study aimed to investigate the association between the 17 genetic polymorphisms and susceptibility to tuberculosis in a Brazilian population. Methods: This case-control study enrolled 283 individuals with active tuberculosis and 145 health care workers. Four INDELs and 13 single nucleotide polymorphisms and were genotyped using Multiplex PCR method and TaqMan SNP Genotyping Assays. Group comparisons for categorical variables were performed using the chi-squared test, whilst the t-Student test was used to analyze the continuous variables. Multiple logistic regression analyses were performed to estimate the odds ratio (OR) with 95% confidence intervals (CI). Deviation from Hardy-Weinberg equilibrium was assessed using chi-squared tests with Bonferroni correction. The results were analyzed comparing the genotypic distributions adopting the dominant model and the estimated values ​​of p corrected for multiple tests through FDR (False Discovery Rate) test. Results: The HWE test confirmed that the genotypic frequencies for polymorphisms were balanced. The frequency of Del allele was 73 and 75%, in cases and controls respectively. Frequency of Del allele was significantly higher in the control group than TB group. The homozygous Del/Del genotype was present in 51.6% of cases and 58.6% of controls. The rare Ins/Ins genotype was present in only 7.6% of controls and 6% of cases. The ACE Del/Del genotype was significantly higher in the cases than in controls revealing significant protection for TB in the domain model (OR = 0.465; p < 0.005). Conclusions: The Del/Del genotype of the rs4646994 in ACE gene was associated with susceptibility to tuberculosis. The identification of genetic variants responsible for susceptibility to tuberculosis will allow the development of new diagnostic tools for tuberculosis infection. These studies will help improve control and the future eradication of this disease.

Computational Pipeline for Next-Generation Sequencing (NGS) Studies in Genetics of NASH.

High-throughput sequencing (HTS) technologies have contributed to expand current knowledge of the biology of complex diseases, including nonalcoholic fatty liver disease (NAFLD). Genome-wide association studies, whole exome sequencing, and sequencing of entire genes are used to identify variants and/or mutations that predispose to the disease pathogenesis. Here, we present a tutorial that may guide readers to manage high volume of genetics data in the context of Next-Generation Sequencing (NGS) studies.

Association between INDELs in MicroRNAs and Susceptibility to Gastric Cancer in Amazonian Population.

Gastric cancer (GC) is a multifactorial, complex, and aggressive disease with a prevalence of one million new cases and high global mortality. Factors such as genetic, epigenetic, and environmental changes contribute to the onset and progression of the disease. Identification of INDELs in miRNA and its target sites in current studies showed an important role in the development of cancer. In GC, miRNAs act as oncogenes or tumor suppressors, favoring important cancer pathways, such as cell proliferation and migration. This work aims to investigate INDELs in the coding region of miRNAs (hsa-miR-302c, hsa-miR-548AJ-2, hsa-miR-4274, hsa-miR-630, hsa-miR-516B-2, hsa-miR-4463, hsa-miR-3945, hsa-miR-548H_4, hsa-miR-920, has-mir-3171, and hsa-miR-3652) that may be associated with susceptibility and clinical variants of gastric cancer. For this study, 301 patients with GC and 145 individuals from the control group were selected from an admixed population in the Brazilian Amazon. The results showed the hsa-miR-4463, hsa-miR-3945, hsa-miR-548H_4, hsa-miR-920 and hsa-miR-3652 variants were associated with gastric cancer susceptibility. The hsa-miR-4463 was significantly associated with clinical features of GC such as diffuse gastric tumor histological type, "non-cardia" localization region, and early onset. Our findings indicated that INDELs could be potentially functional genetic variants for gastric cancer risk.

Natural family-free genomic distance.

BACKGROUND: A classical problem in comparative genomics is to compute the rearrangement distance, that is the minimum number of large-scale rearrangements required to transform a given genome into another given genome. The traditional approaches in this area are family-based, i.e., require the classification of DNA fragments of both genomes into families. Furthermore, the most elementary family-based models, which are able to compute distances in polynomial time, restrict the families to occur at most once in each genome. In contrast, the distance computation in models that allow multifamilies (i.e., families with multiple occurrences) is NP-hard. Very recently, Bohnenkämper et al. (J Comput Biol 28:410-431, 2021) proposed an ILP formulation for computing the genomic distance of genomes with multifamilies, allowing structural rearrangements, represented by the generic double cut and join (DCJ) operation, and content-modifying insertions and deletions of DNA segments. This ILP is very efficient, but must maximize a matching of the genes in each multifamily, in order to prevent the free lunch artifact that would otherwise let empty or almost empty matchings give smaller distances. RESULTS: In this paper, we adopt the alternative family-free setting that, instead of family classification, simply uses the pairwise similarities between DNA fragments of both genomes to compute their rearrangement distance. We adapted the ILP mentioned above and developed a model in which pairwise similarities are used to assign weights to both matched and unmatched genes, so that an optimal solution does not necessarily maximize the matching. Our model then results in a natural family-free genomic distance, that takes into consideration all given genes, without prior classification into families, and has a search space composed of matchings of any size. In spite of its bigger search space, our ILP seems to be boosted by a reduction of the number of co-optimal solutions due to the weights. Indeed, it converged faster than the original one by Bohnenkämper et al. for instances with the same number of multiple connections. We can handle not only bacterial genomes, but also fungi and insects, or sets of chromosomes of mammals and plants. In a comparison study of six fruit fly genomes, we obtained accurate results.

Investigation of INDEL variants in apoptosis: the relevance to gastric cancer.

BACKGROUND: Apoptosis is a type of cell death involved in different pathways inherent to the cell and the evasion from this mechanism has been related to cancer, although this process remains not very well comprehended. Gastric cancer (GC) is one of the most incident and aggressive types of cancer worldwide. In this study, we analyzed the distribution of INDEL variants in GC patients (Case) and individuals from the general population (Control) from the Amazon region, in which GC is remarkably frequent. METHODS: A panel of nine INDEL markers in apoptosis-related genes (BCL2 rs11269260, CASP3 rs4647655, CASP8 rs3834129 and rs59308963, CASP9 rs4645982 and rs61079693, FADD rs4197, FAS rs10562972 and TP53 rs17880560) was developed and genotyped by multiplex PCR in both groups. RESULTS: In our analyses, only marker rs4197 (FADD gene) was associated to GC development as follows: INS/DEL genotype of rs4197 increasing in about 2-fold the chances of developing this type of cancer (P = 0.046; OR = 1.940; 95%CI = 1.011-3.725). CONCLUSION: Our results suggest that rs4197 (FADD gene) might play a role in gastric carcinogenesis in the investigated population. More studies are needed to clarify this relation. Here, we highlight the importance of investigating INDEL variants in genes involved in apoptosis.

Identification of SNPs and InDels associated with berry size in table grapes integrating genetic and transcriptomic approaches.

BACKGROUND: Berry size is considered as one of the main selection criteria in table grapes breeding programs, due to the consumer preferences. However, berry size is a complex quantitive trait under polygenic control, and its genetic determination of berry weight is not yet fully understood. The aim of this work was to perform marker discovery using a transcriptomic approach, in order to identify and characterize SNP and InDel markers associated with berry size in table grapes. We used an integrative analysis based on RNA-Seq, SNP/InDel search and validation on table grape segregants and varieties with different genetic backgrounds. RESULTS: Thirty SNPs and eight InDels were identified using a transcriptomic approach (RNA-Seq). These markers were selected from SNP/InDel found among segregants from a Ruby x Sultanina population with contrasting phenotypes for berry size. The set of 38 SNP and InDel markers was distributed in eight chromosomes. Genotype-phenotype association analyses were performed using a set of 13 RxS segregants and 41 table grapes varieties with different genetic backgrounds during three seasons. The results showed several degrees of association of these markers with berry size (10.2 to 30.7%) as other berry-related traits such as length and width. The co-localization of SNP and /or InDel markers and previously reported QTLs and candidate genes associated with berry size were analysed. CONCLUSIONS: We identified a set of informative and transferable SNP and InDel markers associated with berry size. Our results suggest the suitability of SNPs and InDels as candidate markers for berry weight in seedless table grape breeding. The identification of genomic regions associated with berry weight in chromosomes 8, 15 and 17 was achieved with supporting evidence derived from a transcriptome experiment focused on SNP/InDel search, as well as from a QTL-linkage mapping approach. New regions possibly associated with berry weight in chromosomes 3, 6, 9 and 14 were identified.

Exome analysis and functional classification of identified variants in racing Quarter Horses.

The main objectives of this study were to identify and functionally classify SNPs and indels by exome sequencing of animals of the racing line of Quarter Horses. Based on the individual genomic estimated breeding values (GEBVs) for maximum speed index (SImax) obtained for 349 animals, two groups of 20 extreme animals were formed. Of these individuals, 20 animals with high GEBVs for SImax and 19 with low GEBVs for SImax had their exons and 5' and 3' UTRs sequenced. Considering SNPs and indels, 105 182 variants were identified in the expressed regions of the Quarter Horse genome. Of these, 72 166 variants were already known and 33 016 are new variants and were deposited in a database. The analysis of the set of gene variants significantly related (Padjusted  < 0.05) to extreme animals in conjunction with the predicted impact of the changes and the physiological role of protein product pointed to two candidate genes potentially related to racing performance: SLC3A1 on ECA15 and CCN6 on ECA10.

Lack of Association between LCT_rs140433552*CA>del Indel Polymorphism and Lactose Intolerance in a Southern Brazilian Population.

BACKGROUND/AIMS: Polymorphisms in the enhancer of the lactase gene (LCT) are strongly associated with lactase persistence, but not always predictive of the phenotype. We investigated a possible association between the regulatory rs140433552*CA>del variant of LCT and lactose intolerance (LI). METHODS: We genotyped 122 individuals for rs140433552 and rs4988235 (-13910*C>T). RESULTS: Associations of rs140433552*CA>del with LI depend on -13910*C>T. Homozygous individuals for the C-CA haplotype, as well as C-CA+/C individuals, seem more likely to manifest LI (OR 3.33 [95% CI 1.32-8.35], p = 0.011, and OR 3.93 [95% CI 1.61-9.61], p = 0.003, respectively), while homozygous individuals for the T-CA haplotype seem more likely to be lactose tolerant (OR 0.04 [95% CI 0.002-0.70], p = 8 × 10-4). CONCLUSIONS: rs140433552*CA>del is not independently associated with LI.

Protein signatures to identify the different genera within the Xanthomonadaceae family.

The Xanthomonadaceae family comprises the genera Xanthomonas and Xylella, which include plant pathogenic species that affect economically important crops. The family also includes the plant growth-promoting bacteria Pseudomonas geniculata and Stenotrophomonas rhizophila, and some other species with biotechnological, medical, and environmental relevance. Previous work identified molecular signatures that helped to understand the evolutionary placement of this family within gamma-proteobacteria. In the present study, we investigated whether insertions identified in highly conserved proteins may also be used as molecular markers for taxonomic classification and identification of members within the Xanthomonadaceae family. Four housekeeping proteins (DNA repair and replication-related and protein translation enzymes) were selected. The insertions allowed discriminating phytopathogenic and plant growth-promoting groups within this family, and also amino acid sequences of these insertions allowed distinguishing different genera and, eventually, species as well as pathovars. Moreover, insertions in the proteins MutS and DNA polymerase III (subunit alpha) are conserved in Xylella fastidiosa, but signatures in DNA ligase NAD-dependent and Valyl tRNA synthetase distinguish particular subspecies within the genus. The genus Stenotrophomonas and Pseudomonas geniculata could be distinguishable based on the insertions in MutS, DNA polymerase III (subunit alpha), and Valyl tRNA synthetase, although insertion in DNA ligase NAD-dependent discriminates these bacteria at the species level. All these insertions differentiate species and pathovars within Xanthomonas. Thus, the insertions presented support evolutionary demarcation within Xanthomonadaceae and provide tools for the fast identification in the field of these bacteria with agricultural, environmental, and economic relevance.

piRNAs in Gastric Cancer: A New Approach Towards Translational Research.

BACKGROUND: Gastric cancer is currently the third leading cause of cancer-related deaths worldwide, usually diagnosed at late stages. The development of new biomarkers to improve its prevention and patient management is critical for disease control. piRNAs are small regulatory RNAs important for gene silencing mechanisms, mainly associated with the silencing of transposable elements. piRNA pathways may also be involved in gene regulation and the deregulation of piRNAs may be an important factor in carcinogenic processes. Thus, several studies suggest piRNAs as potential cancer biomarkers. Translational studies suggest that piRNAs may regulate key genes and pathways associated with gastric cancer progression, though there is no functional annotation in piRNA databases. The impacts of genetic variants in piRNA genes and their influence in gastric cancer development remains elusive, highlighting the gap in piRNA regulatory mechanisms knowledge. Here, we discuss the current state of understanding of piRNA-mediated regulation and piRNA functions and suggest that genetic alterations in piRNA genes may affect their functionality, thus, it may be associated with gastric carcinogenesis. CONCLUSIONS: In the era of precision medicine, investigations about genetic and epigenetic mechanisms are essential to further comprehend gastric carcinogenesis and the role of piRNAs as potential biomarkers for translational research.

Molecular characterization of Cry1F resistance in fall armyworm, Spodoptera frugiperda from Brazil.

Fall armyworm, Spodoptera frugiperda (J.E. Smith) is a major lepidopteran pest of maize in Brazil and its control particularly relies on the use of genetically engineered crops expressing Bacillus thuringiensis (Bt) toxins such as Cry1F. However, control failures compromising the efficacy of this technology have been reported in many regions in Brazil, but the mechanism of Cry1F resistance in Brazilian fall armyworm populations remained elusive. Here we investigated the molecular mechanism of Cry1F resistance in two field-collected strains of S. frugiperda from Brazil exhibiting high levels of Cry1F resistance. We first rigorously evaluated several candidate reference genes for normalization of gene expression data across strains, larval instars and gut tissues, and identified ribosomal proteins L10, L17 and RPS3A to be most suitable. We then investigated the expression pattern of ten potential Bt toxin receptors/enzymes in both neonates and 2nd instar gut tissue of Cry1F resistant fall armyworm strains compared to a susceptible strain. Next we sequenced the ATP-dependent Binding Cassette subfamily C2 gene (ABCC2) and identified three mutated sites present in ABCC2 of both Cry1F resistant strains: two of them, a GY deletion (positions 788-789) and a P799 K/R amino acid substitution, located in a conserved region of ABCC2 extracellular loop 4 (EC4) and another amino acid substitution, G1088D, but in a less conserved region. We further characterized the role of the novel mutations present in EC4 by functionally expressing both wild type and mutated ABCC2 transporters in insect cell lines, and confirmed a critical role of both sites for Cry1F binding by cell viability assays. Finally, we assessed the frequency of the mutant alleles by pooled population sequencing and pyrosequencing in 40 fall armyworm populations collected from maize fields in different regions in Brazil. We found that the GY deletion being present at high frequency. However we also observed many rare alleles which disrupt residues between sites 783-799, and their diversity and abundance in field collected populations lends further support to the importance of the EC4 domain for Cry1F toxicity.

Caracterización de la variabilidad genética de cepas de campo de Brucella canis aisladas en Antioquia / Characterization of the genetic variability of field strains of Brucella canis isolated in Antioquia

Brucella canis, un patógeno intracelular facultativo, es responsable de la brucelosis canina, una enfermedad zoonótica que afecta a los caninos y al hombre. En los primeros causa abortos y fallas reproductivas; en el ser humano genera síntomas inespecíficos. En el año 2005 se demostró la presencia de B. canis en Antioquia (Colombia). Las cepas halladas se identificaron como tipo 2. La secuenciación del genoma completo de una cepa de campo denominada Brucella canis str. Oliveri mostró indels específicos de especie; a partir de estos se buscó conocer características genómicas de las cepas de B. canis aisladas y establecer relaciones filogenéticas, así como el tiempo de divergencia de la cepa Oliveri. Se realizó PCR convencional y secuenciación de 30 cepas de campo, se identificaron 5 indels reconocidos en B. canis str. Oliveri, se empleó ADN de Brucella suis, Brucella melitensis y cepas vacunales de Brucella abortus como controles. Se determinó que las cepas de campo estudiadas comparten 4 de los 5 indels de la cepa Oliveri, lo que indica la presencia de más de una cepa de B. canis circulando en la región. El análisis filogenético se realizó con 24 cepas de Brucella mediante secuencias concatenadas de genes marcadores de especie. Se probó la hipótesis del reloj molecular y adicionalmente se realizó test de tasas relativas de Tajima. De esta manera se demostró que la cepa Oliveri, al igual que las otras cepas de B. canis analizadas, divergen de B. suis. Se rechazó la hipótesis del reloj molecular entre las especies de Brucella y se demostró una tasa de evolución y una distancia genética similar entre las cepas de B. canis.

Brucella canis is a facultative intracellular pathogen responsible for canine brucellosis, a zoonotic disease that affects canines, causing abortions and reproductive failure; and the production of non-specific symptoms in humans. In 2005 the presence of B. canis in Antioquia was demonstrated and the strains were identified as type 2. The sequencing of the genome of a field strain denoted Brucella canis str. Oliveri, showed species-specific indel events, which led us to investigate the genomic characteristics of the B. canis strain isolated and to establish the phylogenetic relationships and the divergence time of B. canis str. Oliveri. Conventional PCR sequencing was performed in 30 field strains identifying 5 indel events recognized in B. canis str. Oliveri. ADN from Brucella suis, Brucella melitensis and vaccine strains from Brucella abortus were used as control, and it was determined that all of the studied field strains shared 4 out of the 5 indels of the sequenced Oliveri strain, indicating the presence of more than one strain circulating in the region. Phylogenetic analysis was performed with 24 strains of Brucella using concatenated sequences of genetic markers for species differentiation. The molecular clock hypothesis and Tajima's relative rate test were tested, showing that the Oliveri strain, similarly to other canis species, diverged from B. suis. The molecular clock hypothesis between Brucella species was rejected and an evolution rate and a similar genetic distance between the B. canis were demonstrated.

Better horizontal transmission of a US non-InDel strain compared with a French InDel strain of porcine epidemic diarrhoea virus.

From the severe porcine epidemic diarrhoea (PED) epidemics that struck in 2013 in the United States of America and other countries of North and South America, two types of porcine epidemic diarrhoea virus (PEDV) were isolated, namely the InDel and the non-InDel strains. They are differentiated by insertions/deletions in the S1 nucleotide sequence of the S gene, and differences in virulence were observed from the clinical cases. In 2014, a PED outbreak occurred in a pig farm in France, from which an InDel strain was isolated. This study aimed at comparing, under experimental conditions, the pathogenicity and the direct and indirect transmissions between a non-InDel strain isolated from a PED-affected piglet in 2014 in the USA and the French InDel strain. All infected pigs showed clinical signs with the non-InDel strain although only the inoculated and direct contact pigs showed clinical signs in the InDel strain group. Although viral RNA was detected in air samples with both strains, the indirect contact pigs remained free from infection with the InDel strain in contrast to the non-InDel group in which airborne transmission occurred in the indirect contact pigs. All infected pigs shed virus in faeces regardless of PEDV strain with 9 of 30 pigs showing intermittent faecal shedding. The transmission rate by direct contact was found to be 2.17-fold higher than the non-InDel strain compared with the InDel. In conclusion, the InDel strain was less pathogenic than the non-InDel strain in our experimental conditions. The transmission route differed between the two strains. Direct contact was the main transmission route for the InDel strain, although the non-InDel strain was transmitted through direct contact and indirectly through the air.

Ancestry analysis in rural Brazilian populations of African descent.

Rural communities comprise around 20% of Caribbean and South American populations, but are under-represented in autosomal marker databases. That deficiency is problematic for forensic genetics, as it relies on accurate descriptions of genetic variation and population structure. Brazilian populations were shaped by an intense, complex and heterogeneous process of admixture encompassing mainly Amerindians, Sub-Saharan Africans and Europeans. Quilombos are Brazilian populations with significant African descent that have remained genetically isolated to some extent from surrounding populations. In the reported study, we analyzed three rural Quilombo populations: Kalunga; Riacho de Sacutiaba e Sacutiaba; and Mocambo, along with a dataset from the HGDP-CEPH panel. Aiming to contribute to representative genetic databases of forensic interest, we analyse the three rural Quilombos populations and investigate how their genetic makeup relates to their history by analyzing an established forensic test, comprising 46 ancestry-informative (AIM) Indels. The panel was chosen for its high power in differentiating the main contributing populations of Brazil. Parental populations were selected from HGDP-CEPH data available at the forInDel allele frequency browser based on historic patterns applicable to the study populations and the amount of variability observed within and between continents. Our results show the main admixture components in the Quilombos are African and European. Those estimates are in accordance with previous analyses for both uniparental and autosomal markers. PCA, structure analysis and ancestry estimates indicate a correlation between the extent of isolation and the degree of admixture in the Quilombos: Kalunga is the most isolated population and accordingly has a higher African admixture component (67.3%). Sacutiaba is the smallest and most impacted by migration, with the highest European component (46.8%). Mocambo neighbors a Native American population and therefore has the highest Amerindian contribution (12.2%). Our results are consistent with the history and demography of Quilombos. The heterogeneity observed in these populations stresses the genetic diversity that Latin American and Caribbean rural populations can have and reiterates the need to describe them in greater detail.

Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines.

BACKGROUND: Meat and egg-type chickens have been selected for several generations for different traits. Artificial and natural selection for different phenotypes can change frequency of genetic variants, leaving particular genomic footprints throghtout the genome. Thus, the aims of this study were to sequence 28 chickens from two Brazilian lines (meat and white egg-type) and use this information to characterize genome-wide genetic variations, identify putative regions under selection using Fst method, and find putative pathways under selection. RESULTS: A total of 13.93 million SNPs and 1.36 million INDELs were identified, with more variants detected from the broiler (meat-type) line. Although most were located in non-coding regions, we identified 7255 intolerant non-synonymous SNPs, 512 stopgain/loss SNPs, 1381 frameshift and 1094 non-frameshift INDELs that may alter protein functions. Genes harboring intolerant non-synonymous SNPs affected metabolic pathways related mainly to reproduction and endocrine systems in the white-egg layer line, and lipid metabolism and metabolic diseases in the broiler line. Fst analysis in sliding windows, using SNPs and INDELs separately, identified over 300 putative regions of selection overlapping with more than 250 genes. For the first time in chicken, INDEL variants were considered for selection signature analysis, showing high level of correlation in results between SNP and INDEL data. The putative regions of selection signatures revealed interesting candidate genes and pathways related to important phenotypic traits in chicken, such as lipid metabolism, growth, reproduction, and cardiac development. CONCLUSIONS: In this study, Fst method was applied to identify high confidence putative regions under selection, providing novel insights into selection footprints that can help elucidate the functional mechanisms underlying different phenotypic traits relevant to meat and egg-type chicken lines. In addition, we generated a large catalog of line-specific and common genetic variants from a Brazilian broiler and a white egg layer line that can be used for genomic studies involving association analysis with phenotypes of economic interest to the poultry industry.

[Characterization of the genetic variability of field strains of Brucella canis isolated in Antioquia]. / Caracterización de la variabilidad genética de cepas de campo de Brucella canis aisladas en Antioquia.

Brucella canis is a facultative intracellular pathogen responsible for canine brucellosis, a zoonotic disease that affects canines, causing abortions and reproductive failure; and the production of non-specific symptoms in humans. In 2005 the presence of B. canis in Antioquia was demonstrated and the strains were identified as type 2. The sequencing of the genome of a field strain denoted Brucella canis str. Oliveri, showed species-specific indel events, which led us to investigate the genomic characteristics of the B. canis strain isolated and to establish the phylogenetic relationships and the divergence time of B. canis str. Oliveri. Conventional PCR sequencing was performed in 30 field strains identifying 5 indel events recognized in B. canis str. Oliveri. ADN from Brucella suis, Brucella melitensis and vaccine strains from Brucella abortus were used as control, and it was determined that all of the studied field strains shared 4 out of the 5 indels of the sequenced Oliveri strain, indicating the presence of more than one strain circulating in the region. Phylogenetic analysis was performed with 24 strains of Brucella using concatenated sequences of genetic markers for species differentiation. The molecular clock hypothesis and Tajima's relative rate test were tested, showing that the Oliveri strain, similarly to other canis species, diverged from B. suis. The molecular clock hypothesis between Brucella species was rejected and an evolution rate and a similar genetic distance between the B. canis were demonstrated.

African ancestry is associated with facial melasma in women: a cross-sectional study.

BACKGROUND: Melasma is a chronic acquired focal hypermelanosis affecting photoexposed areas, especially for women during fertile age. Several factors contribute to its development: sun exposure, sex steroids, medicines, and family history. Melanic pigmentation pathway discloses several SNPs in different populations. Here, we evaluated the association between genetic ancestry and facial melasma. METHODS: A cross-sectional study involving women with melasma and an age-matched control group from outpatients at FMB-Unesp, Botucatu-SP, Brazil was performed. DNA was extracted from oral mucosa swabs and ancestry determined by studying 61 INDELs. The genetic ancestry components were adjusted by other known risk factors by multiple logistic regression. RESULTS: We evaluated 119 women with facial melasma and 119 controls. Mean age was 39 ± 9 years. Mean age at beginning of disease was 27 ± 8 years. Pregnancy (40%), sun exposure (37%), and hormonal oral contraception (22%) were the most frequently reported melasma triggers. All subjects presented admixed ancestry, African and European genetic contributions were significantly different between cases and controls (respectively 10% vs 6%; 77% vs 82%; p < 0.05). African ancestry (OR = 1.04; 95% CI 1.01 to 1.07), first generation family history (OR = 3.04; 95% CI 1.56 to 5.94), low education level (OR = 4.04; 95% CI 1.56 to 5.94), and use of antidepressants by individuals with affected family members (OR = 6.15; 95% CI 1.13 to 33.37) were associated with melasma, independently of other known risk factors. CONCLUSIONS: Facial melasma was independently associated with African ancestry in a highly admixed population.

Potential forensic use of a 33 X-InDel panel in the Argentinean population.

Polymorphic genetic markers located on the X chromosome might become a complement in particular forensic identification when the biological kinship are deficient. We analyzed forensic statistical parameters of 33 X-chromosome InDel polymorphisms in a sample of 320 individuals from Argentina. The X-chromosome InDel polymorphism (X-InDel) panel was amplified in a single multiplex PCR reaction. Hardy-Weinberg Equilibrium was determined in the female cohort, whereas the male cohort was used to calculate linkage disequilibrium (LD) tested by an extension of Fisher's exact test, D', and Chi-square values. Regarding LD, 15 markers were organized and grouped into six blocks containing two or three linked loci each, namely block I (MID356-MID357), block II (MID448804-MID3703-MID218), block III (MID3705-MID3706-MID304737), block IV (MID197147-MID3754), block V (MID3664-MID284601-MID103547), and block VI (MID3763-MID3728). The haplotype diversity was higher than 0.99 in all cases. Blocks III and VI showed the highest match probability in the studied population, whereas block II showed the lowest. The accumulated power of discrimination was 99.9999991 % in women and 99.9992925 % in men. The mean exclusion chance in trios and duos were 99.9891736 and 99.6099391 %, respectively. Since 15 markers are associated as haplotypic blocks, for a conservative treatment of the data, statistical evaluation should consider their haplotypic frequencies and the remaining 18 markers can be evaluated as independent loci.