Pleiotropic effects on Sarcopenia subphenotypes point to potential molecular markers for the disease.

Sarcopenia is a progressive age-related muscle disease characterized by low muscle strength, quantity and quality, and low physical performance. The clinical overlap between these subphenotypes (reduction in muscle strength, quantity and quality, and physical performance) was evidenced, but the genetic overlap is still poorly investigated. Herein, we investigated whether there is a genetic overlap amongst sarcopenia subphenotypes in the search for more effective molecular markers for this disease. For that, a Bioinformatics approach was used to identify and characterize pleiotropic effects at the genome, loci and gene levels using Genome-wide association study results. As a result, a high genetic correlation was identified between gait speed and muscle strength (rG=0.5358, p=3.39 × 10-8). Using a Pleiotropy-informed conditional and conjunctional false discovery rate method we identified two pleiotropic loci for muscle strength and gait speed, one of them was nearby the gene PHACTR1. Moreover, 11 pleiotropic loci and 25 genes were identified for muscle mass and muscle strength. Lastly, using a gene-based GWAS approach three candidate genes were identified in the overlap of the three Sarcopenia subphenotypes: FTO, RPS10 and CALCR. The current study provides evidence of genetic overlap and pleiotropy among sarcopenia subphenotypes and highlights novel candidate genes and molecular markers associated with the risk of sarcopenia.

Genomic approachesidentifySTT4 as a new component in glucose-induced activation of yeast plasma membrane H+-ATPase.

Many studies have focused on identifying the signaling pathway by which addition of glucose triggers post-translational activation of the plasma membrane H+-ATPase in yeast. They have revealed that calcium signaling is involved in the regulatory pathway, supported for instance by the phenotype of mutants inARG82 that encodes an inositol kinase that phosphorylates inositol triphosphate (IP3). Strong glucose-induced calcium signaling, and high glucose-induced plasma membrane H+-ATPase activation have been observed in a specific yeast strain with the PJ genetic background. In this study, we have applied pooled-segregant whole genome sequencing, QTL analysis and a new bioinformatics methodology for determining SNP frequencies to identify the cause of this discrepancy and possibly new components of the signaling pathway. This has led to the identification of an STT4 allele with 6 missense mutations as a major causative allele, further supported by the observation that deletion of STT4 in the inferior parent caused a similar increase in glucose-induced plasma membrane H+-ATPase activation. However, the effect on calcium signaling was different indicating the presence of additional relevant genetic differences between the superior and reference strains. Our results suggest that phosphatidylinositol-4-phosphate might play a role in the glucose-induced activation of plasma membrane H+-ATPase by controlling intracellular calcium release through the modulation of the activity of phospholipase C.

De novo assembly of the complete mitochondrial genome of Mycetophylax simplex Emery, 1888 through organelle targeting revels no substantial expansion of gene spacers, but rather some slightly shorter genes.

Mitochondria play a key role in cell biology and have their own genome, residing in a highly oxidative environment that induces faster changes than the nuclear genome. Because of this, mitochondrial markers have been exploited to reconstruct phylogenetic and phylogeographic relationships in studies of adaptation and molecular evolution. In this study, we determined the complete mitogenome of the fungus-farming ant Mycetophylax simplex (Hymenoptera, Formicidae) and conducted a comparative analysis among 29 myrmicine ant mitogenomes. Mycetophylax simplex is an endemic ant that inhabits sand dunes along the southern Atlantic coast. Specifically, the species occur in the ecosystem known as "restinga", within the Atlantic Forest biome. Due to habitat degradation, land use and decline of restinga habitats, the species is considered locally extinct in extremely urban beaches and is listed as vulnerable on the Brazilian Red List (ICMBio). We employed a mitochondrion-targeting approach to obtain the complete mitogenome through high-throughput DNA sequencing technology. This method allowed us to determine the mitogenome with high performance, coverage and low cost. The circular mitogenome has a length of 16,367 base pairs enclosing 37 genes (13 protein-coding genes, 22 tRNAs and 2 rRNAs) along with one control region (CR). All the protein-coding genes begin with a typical ATN codon and end with the canonical stop codons. All tRNAs formed the fully paired acceptor stems and fold into the typical cloverleaf-shaped secondary structures. The gene order is consistent with the shared Myrmicinae structure, and the A + T content of the majority strand is 81.51%. Long intergenic spacers were not found but some gene are slightly shorter. The phylogenetic relationships based on concatenated nucleotide and amino acid sequences of the 13 protein-coding genes, using Maximum Likelihood and Bayesian Inference methods, indicated that mitogenome sequences were useful in resolving higher-level relationship within Formicidae.

Progressive strength training can reverse sarcopenia stage in middle-aged and older adults regardless of their genetic profile.

The aim of this study was to verify the association of the ACTN3-R577X polymorphism with sarcopenia stage, according to the Revised European Consensus on the Definition and Diagnosis of Sarcopenia, in middle-aged and older adults, pre- and post- ST. In the 12-week longitudinal study, 71 middle-aged and older adults were evaluated; the participants were assigned to either control or intervention group. The intervention group underwent progressive ST three times a week. All participants underwent blood collection, DNA extraction, genotyping of the ACTN3-R577X polymorphism, anthropometric evaluations, and diagnostic tests for sarcopenia. The last two tests were repeated after 12 weeks. No association of the ACTN3-R577X polymorphism with sarcopenia stage was observed before and after 12 weeks. However, the intervention group remained non-sarcopenic (n = 25, p <0.05) or achieved changes in sarcopenia stage (from sarcopenic to non-sarcopenic) (n = 13, p <0.05). Our study demonstrates that progressive ST performed regularly can reverse or prevent sarcopenia regardless of genotype for the ACTN3-R577X polymorphism.

Effect of 12 weeks of strength training on the static balance of the elderly / Efeito de 12 semanas de treinamento de força sobre o equilíbrio estático de idosos

Abstract Aging has a direct impact on balance due to changes in sensory and motor response, sarcopenia, reduced muscle strength and range of motion that occur in the elderly. In this context, strength training (ST) programs are seen as a valuable strategy to minimize the deleterious effect of aging on strength production and balance in this population. The purpose of the study was to evaluate the effect of 12 weeks of progressive intensity ST on static balance variables in the elderly. The study included 23 elderly with an average age of 65±8.61 years, of both sexes, who performed a twelve-week strength training program, with a frequency of three times a week and with progressive intensity (60 - 85% of 1-RM). Balance was assessed before and after the intervention period, through stabilometric assessment on a force plate. After the intervention, there was a reduction in the anteroposterior amplitude (p=0.01), in the anteroposterior velocity (p=0.01) and in the total displaced area (p=0.04). It is concluded that the strength training can be used as a key tool to minimize the deleterious effect of aging on the maintenance of static balance.

Resumo O envelhecimento tem impacto direto no equilíbrio devido a alterações da resposta sensorial e motora, sarcopenia e redução da força muscular e da amplitude de movimento que ocorre nos idosos. Nesse contexto, programas de treinamento de força (TF) são vistos como valiosa estratégia para minimizar o efeito deletério do envelhecimento na produção de força e no equilíbrio dessa população. O objetivo do estudo foi avaliar o efeito de 12 semanas de TF com intensidade progressiva sobre as variáveis de equilíbrio estático em idosos. Participaram do estudo 23 idosos com idade média de 65±8,61 anos, de ambos os sexos, que realizaram um programa de TF de doze semanas, com frequência de três vezes por semana e com intensidade progressiva (60 - 85% de 1-RM). O equilíbrio foi avaliado antes e após o período de intervenção, por meio de avaliação estabilométrica em plataforma de força. Após a intervenção houve redução na amplitude anteroposterior (p=0,01), na velocidade anteroposterior (p=0,01) e na área total deslocada (p= 0,04). Conclui-se que o treinamento de força pode ser utilizado como ferramenta chave para minimizar o efeito deletério do envelhecimento na manutenção do equilíbrio estático.

Selected cachaça yeast strains share a genomic profile related to traits relevant to industrial fermentation processes.

The isolation and selection of yeast strains to improve the quality of the cachaça-Brazilian Spirit-have been studied in our research group. Our strategy considers Saccharomyces cerevisiae as the predominant species involved in sugarcane juice fermentation and the presence of different stressors (osmolarity, temperature, ethanol content, and competition with other microorganisms). It also considers producing balanced concentrations of volatile compounds (higher alcohols and acetate and/or ethyl esters), flocculation capacity, and ethanol production. Since the genetic bases behind these traits of interest are not fully established, the whole genome sequencing of 11 different Saccharomyces cerevisiae strains isolated and selected from different places was analyzed to identify the presence of a specific genetic variation common to cachaça yeast strains. We have identified 20,128 single-nucleotide variants shared by all genomes. Of these shared variants, 37 were new variants (being six missenses), and 4,451 were identified as missenses. We performed a detailed functional annotation (using enrichment analysis, protein-protein interaction network analysis, and database and in-depth literature searches) of these new and missense variants. Many genes carrying these variations were involved in the phenotypes of flocculation, tolerance to fermentative stresses, and production of volatile compounds and ethanol. These results demonstrate the existence of a genetic profile shared by the 11 strains under study that could be associated with the applied selective strategy. Thus, this study points out genes and variants that may be used as molecular markers for selecting strains well suited to the fermentation process, including genetic improvement by genome editing, ultimately producing high-quality beverages and adding value.IMPORTANCEThis work demonstrates the existence of new genetic markers related to different phenotypes used to select yeast strains and mutations in genes directly involved in producing flavoring compounds and ethanol, and others related to flocculation and stress resistance.

12 weeks of resistance training with progressive intensity improves the diagnostic parameters of sarcopenia in individuals of advanced age.

OBJECTIVE: The objective of this study was to evaluate the effects of 12 weeks of resistance training (RT) with progressive intensity on factors associated with sarcopenia in older individuals. METHODS: A cross-sectional study was conducted with 74 participants (64.27 ± 7.06-y-old) who were divided into a control group (n = 37) and an intervention group (n = 37). The intervention group underwent 12 weeks of RT three times a week, with an initial training of 60% and final training of 85% of one-repetition maximum (1RM). Both groups were evaluated before and after the 12-week training period to assess improvements in strength and physical performance. RESULTS: The intervention group showed an increase in physical performance, as evidenced by a reduction in the time to perform the Timed Up and Go (TUG) test (p < 0.01) and the Five Times Sit to Stand Test (p < 0.01). Furthermore, the RT proved to be efficient for increasing hand grip and overall muscular strength, as confirmed through the 1RM test. However, the muscle mass index (MMI) and walking speed did not show any significant alterations in both groups. CONCLUSIONS: In conclusion, 12 weeks of RT with progressive intensity has a positive effect on the diagnostic parameters of sarcopenia, leading to improvements in physical performance and muscular strength while maintaining the MMI.

Genetic diversity and relatedness in captive collared peccaries Dicotyles tajacu (Linnaeus, 1758) (Cetartiodactyla: Tayassuidae) estimated by microsatellite genotyping using high-throughput sequencing: Implications for their conservation and reintroduction.

The global population of Dicotyles tajacu (Linnaeus, 1758) (Cetartiodactyla: Tayassuidae), commonly known as the collared peccary and distributed in the Neotropics, is currently in decline due to anthropogenic pressures. In this study, five microsatellite loci were used to genetically characterize a group of 20 captive-born collared peccaries intended for reintroduction. This study aimed to evaluate the genetic diversity and relatedness of captive individuals using microsatellite markers. The genetic data generated were used to evaluate the viability of the reintroduction and to propose measures for the management and conservation of this species. In this study, we found relatively high genetic diversity indices, indicating that the group was genetically diverse. Inbreeding coefficients with negative values were observed, indicating an excess of alleles in heterozygosis and an absence of inbreeding. One locus showed deviation from Hardy-Weinberg equilibrium, which may have been caused by the mixing of individuals from different origins. Relatedness analysis indicated that some individuals were highly related, with coefficients indicating they may be first-degree relatives. Our findings indicate that the studied group has enough genetic diversity to be released into nature, but the high individual relatedness found would require the adoption of strategies after the release of animals in the wild to ensure their persistence.

Phenotypic variation in milk fatty acid composition and its association with stearoyl-CoA desaturase 1 (SCD1) gene polymorphisms in Gir cows.

Individual variation in milk fatty acid (FA) composition has been partially attributed to stearoyl-CoA desaturase 1 (SCD1) gene polymorphisms in taurine breeds, but much less is known for Zebu breeds. This study investigated the phenotypic variation in milk FA composition, and the influence of SCD1 variants on this trait and on milk fat desaturase indices (DI) in Gir cows. The functional impact of SCD1 variants was predicted using bioinformatics tools. Milk and blood samples were collected from 312 cows distributed in 10 herds from five states of Brazil. SCD1 variants were identified through target sequencing, and milk FA composition was determined by gas chromatography. Phenotypic variation in milk FA composition fell within the range reported for taurine breeds, with SCD18 index showing the lowest variation among the DI. Fourteen SCD1 variants were identified, six of which not previously described. Regarding the A293V polymorphism, all cows were homozygous for the C allele (coding for alanine), whereas all genotypes were detected for the second SNP affecting the 293 codon (G > A), with compelling evidence for functional effects. Significant associations (based on raw p-values) were found between this SNP and C12:0, cis-9, trans-11 CLA and short-chain FA, and between another SNP (rs523411937) and C15:0 and odd-chain linear FA. A new SNP on Chr26:21277069 was associated with trans-11 C18:1, cis-9, trans-11 CLA, C18:3 n-3 and n-3 FA. These findings indicate that SCD1 polymorphisms also contributes to the phenotypic variation in milk FA composition of Gir cows, with potential use in their breeding programmes.

Influence of Alpha-Actinin-3 R577X Polymorphism on Muscle Damage and the Inflammatory Response after an Acute Strength Training Session.

The objective of this study was to verify the influence of the ACTN3 R577X polymorphism on muscle damage and the inflammatory response after an acute strength training (ST) session. Twenty-seven healthy male individuals (age: 25 ± 4.3 years) participated in the study, including 18 RR/RX and 9 XX individuals. The participants were divided into two groups (RR/RX and XX groups) and subjected to an acute ST session, which consisted of a series of leg press, leg extension machine, and seated leg curl machine. The volunteers were instructed to perform the greatest volume of work until concentric muscle failure. Each volunteer's performance was analyzed as the load and total volume of training, and the blood concentrations of C-C motif chemokine ligand 2 (CCL2), interleukin-8 (IL-8), creatine kinase (CK), lactate dehydrogenase (LDH), myoglobin, testosterone, and cortisol were measured before the ST session and 30 min and 24 h postsession. The ACTN3 R577X polymorphism effect was observed, with increased concentrations of CCL2 (p < 0.01), IL-8 (p < 0.01), and LDH (p < 0.001) in XX individuals. There was an increase in the concentration of CK in the RR/RX group compared to XX at 24 h after training (p > 0.01). The testosterone/cortisol ratio increased more markedly in the XX group (p < 0.001). Regarding performance, the RR/RX group presented higher load and total volume values in the training exercises when compared to the XX group (p < 0.05). However, the XX group presented higher values of delayed onset muscle soreness (DOMS) than the RR/RX group (p < 0.05). The influence of ACTN3 R577X polymorphism on muscle damage and the inflammatory response was observed after an acute ST session, indicating that the RR/RX genotype shows more muscle damage and a catabolic profile due to a better performance in this activity, while the XX genotype shows more DOMS.

Polymorphism of the angiotensin converting enzyme gene (ACE-I/D) differentiates the aerobic and speed performance of football players.

BACKGROUND: The aim of this study was to evaluate the distribution of ACE-I/D polymorphisms on Brazilian football players performance in aerobic capacity, strength and speed tests. METHODS: The participants in this study were 212 Brazilian first division male football players genotyped in DD, ID or II. Genotyping of DNA from leucocytes was performed using polymerase chain reaction and restriction fragment length polymorphism methods. We evaluated speed using a 30-meter sprint test with speed measured at 10 meters (V10), 20 meters (V20), and 30 meters (V30); muscular strength using counter-movement-jump and squat jump tests; and aerobic endurance using the Yo-Yo endurance test. The athletes were ranked in ascending order according to their performance in each test and divided into quartiles: first quartile (0-25%, weak), second (25-50%, normal), third (50-75%, good), and fourth (75-100%, excellent); these were clustered according to genotype frequency. RESULTS: We identified significant differences in the V20 test values and in the aerobic capacity test. Higher frequencies of the ACE-DD genotype were observed in the excellent performance group in the V20. In the aerobic capacity test, higher frequencies of the ACE-II genotype were observed in excellent and good performance groups. CONCLUSIONS: Players with higher performance in anaerobic and aerobic tests are ACE-DD and ACE-II genotypes, respectively.

Identification and in silico characterization of structural and functional impacts of genetic variants in milk protein genes in the Zebu breeds Guzerat and Gyr.

Whole genome sequencing of bovine breeds has allowed identification of genetic variants in milk protein genes. However, functional repercussion of such variants at a molecular level has seldom been investigated. Here, the results of a multistep Bioinformatic analysis for functional characterization of recently identified genetic variants in Brazilian Gyr and Guzerat breeds is described, including predicted effects on the following: (i) evolutionary conserved nucleotide positions/regions; (ii) protein function, stability, and interactions; (iii) splicing, branching, and miRNA binding sites; (iv) promoters and transcription factor binding sites; and (v) collocation with QTL. Seventy-one genetic variants were identified in the caseins (CSN1S1, CSN2, CSN1S2, and CSN3), LALBA, LGB, and LTF genes. Eleven potentially regulatory variants and two missense mutations were identified. LALBA Ile60Val was predicted to affect protein stability and flexibility, by reducing the number the disulfide bonds established. LTF Thr546Asn is predicted to generate steric clashes, which could mildly affect iron coordination. In addition, LALBA Ile60Val and LTF Thr546Asn affect exonic splicing enhancers and silencers. Consequently, both mutations have the potential of affecting immune response at individual level, not only in the mammary gland. Although laborious, this multistep procedure for classifying variants allowed the identification of potentially functional variants for milk protein genes.

Putative Causal Variant on Vlgr1 for the Epileptic Phenotype in the Model Wistar Audiogenic Rat.

Wistar Audiogenic Rat is an epilepsy model whose animals are predisposed to develop seizures induced by acoustic stimulation. This model was developed by selective reproduction and presents a consistent genetic profile due to the several generations of inbreeding. In this study, we performed an analysis of WAR RNA-Seq data, aiming identified at genetic variants that may be involved in the epileptic phenotype. Seventeen thousand eighty-five predicted variants were identified as unique to the WAR model, of which 15,915 variants are SNPs and 1,170 INDELs. We filter the predicted variants by pre-established criteria and selected five for validation by Sanger sequencing. The genetic variant c.14198T>C in the Vlgr1 gene was confirmed in the WAR model. Vlgr1 encodes an adhesion receptor that is involved in the myelination process, in the development of stereocilia of the inner ear, and was already associated with the audiogenic seizures presented by the mice Frings. The transcriptional quantification of Vlgr1 revealed the downregulation this gene in the corpus quadrigeminum of WAR, and the protein modeling predicted that the mutated residue alters the structure of a domain of the VLGR1 receptor. We believe that Vlgr1 gene may be related to the predisposition of WAR to seizures and suggest the mutation Vlgr1/Q4695R as putative causal variant, and the first molecular marker of the WAR strain.

Genetic Diversity and Population Genetic Structure of a Guzerá (Bos indicus) Meta-Population.

The Brazilian Guzerá population originated from a few founders introduced from India. These animals adapted well to the harsh environments in Brazil, were selected for beef, milk, or dual-purpose (beef and milk), and were extensively used to produce crossbred animals. Here, the impact of these historical events with regard to the population structure and genetic diversity in a Guzerá meta-population was evaluated. DNA samples of 744 animals (one dairy, nine dual-purpose, and five beef herds) were genotyped for 21 microsatellite loci. Ho, He, PIC, Fis, Fit, and Fst estimates were obtained considering either farms or lineages as subpopulations. Mean Ho (0.73) and PIC (0.75) suggest that genetic diversity was efficiently conserved. Fit, Fis and Fst values (95% CI) pointed to a low fixation index, and large genetic diversity: Fit (Farms = 0.021-0.100; lineages = 0.021-0.100), Fis (Farms = -0.007-0.076; lineages = -0.014-0.070), and Fst (Farms = 0.0237-0.032; lineages = 0.029-0.038). The dual-purpose herds/selection lines are the most uniform subpopulation, while the beef one preserved larger amounts of genetic diversity among herds. In addition, the dairy herd showed to be genetically distant from other herds. Taken together, these results suggest that this Guzerá meta-population has high genetic diversity, a low degree of population subdivision, and a low inbreeding level.

Genetic evaluation of migratory fish: Implications for conservation and stocking programs.

Fish stocking programs have been implemented to mitigate the blockage of original riverbeds by the construction of hydropower dams, which affects the natural migration of fish populations. However, this method raises concerns regarding the genetic rescue of the original populations of migratory fish species. We investigated the spatial distribution of genetic properties, such as genetic diversity, population structure, and gene flow (migration), of the Neotropical migratory fish Prochilodus costatus in the Três Marias dam in the São Francisco River basin, Brazil, and examined the possible effects of fish stocking programs on P. costatus populations in this region. In total, 1,017 specimens were sampled from 12 natural sites and a fish stocking program, and genotyped for high-throughput sequencing at 8 microsatellite loci. The populations presented low genetic variability, with evidence of inbreeding and the presence of only four genetic pools; three pools were observed throughout the study region, and the fourth was exclusive to one area in the Paraopeba River. Additionally, we identified high unidirectional gene flow between regions, and a preferred migratory route between the Pará River and the upper portion of the São Francisco River. The fish stocking program succeeded in transposing the genetic pools from downstream to upstream of the Três Marias dam, but, regrettably, promoted genetic homogenization in the upper São Francisco River basin. Moreover, the data show the fragility of this species at the genetic level. This monitoring strategy could be a model for the development of conservation and management measures for migratory fish populations that are consumed by humans.

Draft genome sequence of Wickerhamomyces anomalus LBCM1105, isolated from cachaça fermentation.

Wickerhamomyces anomalus LBCM1105 is a yeast isolated from cachaça distillery fermentation vats, notable for exceptional glycerol consumption ability. We report its draft genome with 20.5x in-depth coverage and around 90% extension and completeness. It harbors the sequences of proteins involved in glycerol transport and metabolism.

Alpha-Actinin-3 R577X Polymorphism Influences Muscle Damage and Hormonal Responses After a Soccer Game.

Coelho, DB, Pimenta, EM, Rosse, IC, Veneroso, C, Pussieldi, GDA, Becker, LK, De Oliveira, EC, Carvalho, MRS, and Silami-Garcia, E. Alpha-actinin-3 R577X polymorphism influences muscle damage and hormonal responses after a soccer game. J Strength Cond Res 33(10): 2655-2664, 2019-The purpose of this study was to evaluate indicators of muscle damage and hormonal responses after soccer matches and its relation to alpha-actinin-3 (ACTN3) gene expression (XX vs. RR/RX), considering that the R allele produces alpha-actinin-3 and provides greater muscle strength and power. Thirty players (10 XX and 20 RR/RX) younger than 16 years were evaluated in this study. Blood samples were collected immediately before, after, 2, and 4 hours after the games to assess muscle damage (creatine kinase [CK] and alpha-actin) and hormonal responses (interleukin-6 [IL-6], cortisol, and testosterone). Postgame CK was higher as compared to the pregame values in both groups and it was also higher in the RR/RX (p < 0.05) than in the XX. The concentrations of alpha-actin and IL-6 were similar for both groups and did not change over time. Testosterone was increased after the game only in the RR/RX group (p < 0.05). Cortisol concentrations in group RR/RX were higher immediately after the game than before the game, and 2 and 4 hours after the game the concentration decreased (p < 0.05). The RR and RX individuals presented higher markers of muscle microtrauma and hormonal stress, probably because they performed more speed and power actions during the game, which is a self-regulated activity. From the different responses presented by RR/RX and XX genotypes, we conclude that the genotypic profile should be taken into account when planning training workloads and recovery of athletes.

Evidence for a Role of ACTN3 R577X Polymorphism in Football Player's Career Progression.

The aim was to investigate a possible role of the ACTN3 R577X polymorphism in a Brazilian football player's career progression. 2 questions were formulated: 1. Does ACTN3 polymorphism affect the probability of an individual being a professional football player? 2. Does this polymorphism affect the progression of the athlete throughout his career? The study included 353 players from first division Brazilian football clubs in the following categories: under-14 (U-14), U-15, U-17, U-20, and professional (PRO). The control group (CON) was composed of 100 healthy non-athletes. The chi-squared test was used to assess differences between the allele and genotype frequencies. Comparing football categories, the XX genotype was less frequent among professional players than in the U-20 (p<0.05) or the U-15 category (p<0.05). The RX genotype also presented more frequently in the PRO category than the U-14 category (p<0.05). Moreover, a trend towards a higher frequency of the RX genotype and a lower frequency of the XX genotype was observed in the professional category compared to U-20. These results suggest that the genotype in the ACTN3 polymorphism affects the probability of a football player progressing throughout his career and becoming professional, meaning that playing football selects against the ACTN3 XX genotype.

High-Throughput Sequencing Strategy for Microsatellite Genotyping Using Neotropical Fish as a Model.

Genetic diversity and population studies are essential for conservation and wildlife management programs. However, monitoring requires the analysis of multiple loci from many samples. These processes can be laborious and expensive. The choice of microsatellites and PCR calibration for genotyping are particularly daunting. Here we optimized a low-cost genotyping method using multiple microsatellite loci for simultaneous genotyping of up to 384 samples using next-generation sequencing (NGS). We designed primers with adapters to the combinatorial barcoding amplicon library and sequenced samples by MiSeq. Next, we adapted a bioinformatics pipeline for genotyping microsatellites based on read-length and sequence content. Using primer pairs for eight microsatellite loci from the fish Prochilodus costatus, we amplified, sequenced, and analyzed the DNA of 96, 288, or 384 individuals for allele detection. The most cost-effective methodology was a pseudo-multiplex reaction using a low-throughput kit of 1 M reads (Nano) for 384 DNA samples. We observed an average of 325 reads per individual per locus when genotyping eight loci. Assuming a minimum requirement of 10 reads per loci, two to four times more loci could be tested in each run, depending on the quality of the PCR reaction of each locus. In conclusion, we present a novel method for microsatellite genotyping using Illumina combinatorial barcoding that dispenses exhaustive PCR calibrations, since non-specific amplicons can be eliminated by bioinformatics analyses. This methodology rapidly provides genotyping data and is therefore a promising development for large-scale conservation-genetics studies.

Reducing cryptic relatedness in genomic data sets via a central node exclusion algorithm.

Cryptic relatedness is a confounding factor in genetic diversity and genetic association studies. Development of strategies to reduce cryptic relatedness in a sample is a crucial step for downstream genetic analyses. This study uses a node selection algorithm, based on network degrees of centrality, to evaluate its applicability and impact on evaluation of genetic diversity and population stratification. 1,036 Guzerá (Bos indicus) females were genotyped using Illumina Bovine SNP50 v2 BeadChip. Four strategies were compared. The first and second strategies consist on a iterative exclusion of most related individuals based on PLINK kinship coefficient (φij) and VanRaden's φij, respectively. The third and fourth strategies were based on a node selection algorithm. The fourth strategy, Network G matrix, preserved the larger number of individuals with a better diversity and representation from the initial sample. Determining the most probable number of populations was directly affected by the kinship metric. Network G matrix was the better strategy for reducing relatedness due to producing a larger sample, with more distant individuals, a more similar distribution when compared with the full data set in the MDS plots and keeping a better representation of the population structure. Resampling strategies using VanRaden's φij as a relationship metric was better to infer the relationships among individuals. Moreover, the resampling strategies directly impact the genomic inflation values in genomewide association studies. The use of the node selection algorithm also implies better selection of the most central individuals to be removed, providing a more representative sample.