Nutrient supplementation of beef female calves at pre-weaning enhances the commitment of fibro-adipogenic progenitor cells to preadipocytes.

We aimed to evaluate the impact of nutrient supplementation of beef female calves at pre-weaning on adipogenic determination. Thirty-four female calves were assigned to two experimental treatments: Control (CON, n = 17), where animals were supplemented only with mineral mixture; Supplemented (SUP, n = 17), where animals received energy-protein supplement containing minerals (5 g/kg of BW per day) of their body weight. Animals were supplemented from 100 to 250 days of age, and muscle samples were biopsied at the end of the supplementation period. Regarding the performance variables, there were no differences between treatments for initial body weight (P = 0.75). The final body weight (P = 0.07), average daily gain (P = 0.07), rib eye area (P = 0.03), and rib fat thickness (P = 0.08) were greater in SUP female calves compared with CON treatment. The number of fibro-adipogenic progenitor cells (P = 0.69) did not differ between treatments, while a greater number of intramuscular pre-adipocytes were observed in SUP than CON female calves (P = 0.01). The expression of miRNA-4429 (P = 0.20) did not differ between treatments, while the expression of miRNA-129-5p (P = 0.09) and miRNA-129-2-3p (P = 0.05) was greater in CON than SUP female calves. Our results suggest that nutrient supplementation at early postnatal stages of development enhances the commitment of fibro-adipogenic progenitor cells into the adipogenic lineages allowing to an increase in intramuscular fat deposition potential of the animals later in life.

Genome-wide association study and annotating candidate gene networks affecting age at first calving in Nellore cattle.

We performed a genome-wide mapping for the age at first calving (AFC) with the goal of annotating candidate genes that regulate fertility in Nellore cattle. Phenotypic data from 762 cows and 777k SNP genotypes from 2,992 bulls and cows were used. Single nucleotide polymorphism (SNP) effects based on the single-step GBLUP methodology were blocked into adjacent windows of 1 Megabase (Mb) to explain the genetic variance. SNP windows explaining more than 0.40% of the AFC genetic variance were identified on chromosomes 2, 8, 9, 14, 16 and 17. From these windows, we identified 123 coding protein genes that were used to build gene networks. From the association study and derived gene networks, putative candidate genes (e.g., PAPPA, PREP, FER1L6, TPR, NMNAT1, ACAD10, PCMTD1, CRH, OPKR1, NPBWR1 and NCOA2) and transcription factors (TF) (STAT1, STAT3, RELA, E2F1 and EGR1) were strongly associated with female fertility (e.g., negative regulation of luteinizing hormone secretion, folliculogenesis and establishment of uterine receptivity). Evidence suggests that AFC inheritance is complex and controlled by multiple loci across the genome. As several windows explaining higher proportion of the genetic variance were identified on chromosome 14, further studies investigating the interaction across haplotypes to better understand the molecular architecture behind AFC in Nellore cattle should be undertaken.

Multiple-trait genomewide mapping and gene network analysis for scrotal circumference growth curves in Brahman cattle.

Fertility traits are economically important in cattle breeding programs. Scrotal circumference (SC) measures are repeatable, easily obtained, highly heritable, and positively correlated with female fertility traits and sperm quality traits in males. A useful approach to summarize SC measures over time is using nonlinear models, which summarize specific measures of SC in a few parameters with biological interpretation. This approach facilitates the selection of bulls with larger SC and maturity index (K), that is, early maturing animals. Because SC is a sex-limited trait, identifying the underlying genomics of growth curve parameters will allow selection across both males and females. We reported the first multitrait genomewide association study (GWAS) of estimated growth curve parameters for SC data in Brahman cattle. Five widely used nonlinear models were tested to fit a total of 3,612 SC records, measured at 6, 12, 18, and 24 mo of age. The von Bertalanffy model, individually fitted for each animal, best fit this SC data. Parameter estimates SC at maturity (A) and K as well as SC at all ages were jointly analyzed in a GWAS to identify 1-Mb regions most strongly associated with each trait. Heritabilities were 0.25 for K and 0.32 for A and ranged from 0.51 to 0.72 for SC at 6 (SC6), 12 (SC12), 18 (SC18), and 24 mo of age (SC24). An overlapping window on chromosome 14 explaining around 0.8% of genetic variance for K, SC12, SC18, and SC24 was observed. The major positional candidate genes within 1 Mb upstream and downstream of this overlapping window were , , , and . Windows of 1 Mb explaining more than 0.4% of each trait on chromosomes 1, 3, 6, 7, 14, 17, 18, 24, 25, and 26 were identified. Pathways and net-work analyses were indicated through transcription factors playing a role on fertility traits: , , , , , , and . Further validation studies on larger populations or other breeds are required to validate these findings and to improve our understanding of the biology and complex genetic architecture of traits associated with scrotal growth and male fertility in cattle.

Factor analysis applied to genome prediction for high-dimensional phenotypes in pigs.

The aim of the present study was to propose and evaluate the use of factor analysis (FA) in obtaining latent variables (factors) that represent a set of pig traits simultaneously, for use in genome-wide selection (GWS) studies. We used crosses between outbred F2 populations of Brazilian Piau X commercial pigs. Data were obtained on 345 F2 pigs, genotyped for 237 SNPs, with 41 traits. FA allowed us to obtain four biologically interpretable factors: "weight", "fat", "loin", and "performance". These factors were used as dependent variables in multiple regression models of genomic selection (Bayes A, Bayes B, RR-BLUP, and Bayesian LASSO). The use of FA is presented as an interesting alternative to select individuals for multiple variables simultaneously in GWS studies; accuracy measurements of the factors were similar to those obtained when the original traits were considered individually. The similarities between the top 10% of individuals selected by the factor, and those selected by the individual traits, were also satisfactory. Moreover, the estimated markers effects for the traits were similar to those found for the relevant factor.

After genome-wide association studies: Gene networks elucidating candidate genes divergences for number of teats across two pig populations.

Number of teats (NT) is an important trait affecting both piglet's welfare and the production level of pig farms. Biologically, embryonic mammary gland development requires the coordination of many signaling pathways necessary for the proper development of teats. Several QTL for NT have been identified; however, further analysis is still lacking. Therefore, gene networks derived from genomewide association study (GWAS) results can be used to examine shared pathways and functions of putative candidate genes. Besides, such analyses may also be helpful to understand the genetic diversity between populations for the same trait or traits. In this study, we identified significant SNP for Landrace-based (line C) and Large White-based (line D) dam lines. Besides, gene-transcription factor (TF) networks were constructed aiming to obtain the most likely candidate genes for NT in each line followed by a comparative analysis between both lines to access similarities or dissimilarities at the marker and gene level. We identified 24 and 19 significant SNP (Bayes factor ≥ 100) for lines C and D, respectively. Only 1 significant SNP overlapped both lines. Network analysis illustrated gene interactions consistent with known mammal's breast biology and captured known TF. We observed different sets of putative candidate genes for NT in each line evaluated that may have common effects on the phenotype. Based on these results, we demonstrated the importance of post-GWAS analyses increasing the biological understanding of relevant genes for a complex trait. Moreover, we believe that this genomic diversity across lines should be taken into account, considering breed-specific reference populations for genomic selection.

Review: Animal model and the current understanding of molecule dynamics of adipogenesis.

Among several potential animal models that can be used for adipogenic studies, Wagyu cattle is the one that presents unique molecular mechanisms underlying the deposit of substantial amounts of intramuscular fat. As such, this review is focused on current knowledge of such mechanisms related to adipose tissue deposition using Wagyu cattle as model. So abundant is the lipid accumulation in the skeletal muscles of these animals that in many cases, the muscle cross-sectional area appears more white (adipose tissue) than red (muscle fibers). This enhanced marbling accumulation is morphologically similar to that seen in numerous skeletal muscle dysfunctions, disease states and myopathies; this might indicate cross-similar mechanisms between such dysfunctions and fat deposition in Wagyu breed. Animal models can be used not only for a better understanding of fat deposition in livestock, but also as models to an increased comprehension on molecular mechanisms behind human conditions. This revision underlies some of the complex molecular processes of fat deposition in animals.

Bayesian GWAS and network analysis revealed new candidate genes for number of teats in pigs.

The genetic improvement of reproductive traits such as the number of teats is essential to the success of the pig industry. As opposite to most SNP association studies that consider continuous phenotypes under Gaussian assumptions, this trait is characterized as a discrete variable, which could potentially follow other distributions, such as the Poisson. Therefore, in order to access the complexity of a counting random regression considering all SNPs simultaneously as covariate under a GWAS modeling, the Bayesian inference tools become necessary. Currently, another point that deserves to be highlighted in GWAS is the genetic dissection of complex phenotypes through candidate genes network derived from significant SNPs. We present a full Bayesian treatment of SNP association analysis for number of teats assuming alternatively Gaussian and Poisson distributions for this trait. Under this framework, significant SNP effects were identified by hypothesis tests using 95% highest posterior density intervals. These SNPs were used to construct associated candidate genes network aiming to explain the genetic mechanism behind this reproductive trait. The Bayesian model comparisons based on deviance posterior distribution indicated the superiority of Gaussian model. In general, our results suggest the presence of 19 significant SNPs, which mapped 13 genes. Besides, we predicted gene interactions through networks that are consistent with the mammals known breast biology (e.g., development of prolactin receptor signaling, and cell proliferation), captured known regulation binding sites, and provided candidate genes for that trait (e.g., TINAGL1 and ICK).

A rare case of necrotic thymoma.

The Authors report the case of a patient who underwent resection of a huge anterior mediastinal mass, revealing to be a necrotic thymoma. The patient had been previously submitted to surgical biopsies of the mass yielding non-diagnostic results due to extensive necrosis. A sternotomy was then performed to resect the mediastinal mass originating from the thymus, en-bloc with the mediastinal fat and the apparently infiltrated lung. Histopathology showed a possible cyst/thymoma in massive necrosis, not further definable; revision by a specialized experienced pathologist (J. Rosai) confirmed total mass necrosis and no lung infiltration, thus orientating diagnosis towards a necrotic thymoma and excluding a lymphoblastic lymphoma, with similar histopathological features but more frequent in children or characterized by neoplastic infiltration of surrounding lung. Total body computed tomography (CT) scan and fluorodeoxyglucose positron emission tomography (18F-FDG-PET)/CT, show neither local recurrence, nor distant metastases two years after surgery. In case of anterior mediastinal mass with difficult histopathological diagnosis due to massive necrosis, the hypothesis of a necrotic thymoma should be considered. After radical removal prognosis is generally favourable and no adjuvant treatment is required.

Identification and validation of differentially expressed genes from pig skeletal muscle.

Pig is an important animal for meat production; this is generally associated with characteristics determined prenatally during myogenesis. Expressed sequence tags (EST) can provide direct information on the transcriptome and indirect information on the relation between the genome and phenotype, giving information about differentially expressed genes (DEG). In this work, the identification and annotation of DEG from EST libraries of three pig breeds (Duroc, Large White and Local Breed Piau) were performed followed by real-time PCR analyses during pre- and postnatal stages (21, 40, 70 and 90 days of pregnancy and 107, 121 and 171 days postnatal) from commercial breed animals for analysis of genes expression levels. Therefore, 34 genes differentially expressed were identified, of which 21 grouped in a network related with muscle development. From this, the expression profile of 13 genes was measured, to confirm their relationship with myogenesis like ANKRD2, MYBPC1, NEB and MYL2. These genes showed a prenatal high expression in this study. Besides, novels candidates for muscle development (TP53 and DCTN1) were listed. These findings can contribute to better explaining gene function mechanism and are helpful in uncovering the pathways that mediate pre- and postnatal skeletal muscle development in vertebrates.

Detecção de locos de características quantitativas nos cromossomos 1, 2, 3, 12, 14, 15 e X de suínos: características de desempenho / Detection of quantitative trait loci on chromosomes 1, 2, 3, 12, 14, 15, X in pigs: performance characteristics

Mapeou-se quantitative trait loci (QTL) associados a características de desempenho nos cromossomos 1, 2, 3, 12, 14, 15 e X de suínos pertencentes a uma população F2, formada a partir do cruzamento entre dois machos da raça naturalizada brasileira Piau e 18 fêmeas comerciais (Landrace x Large White x Pietrain). O mapa genético de ligação da população foi construído após a genotipagem dos animais para 35 marcadores microssatélites. As estimativas do conteúdo de informação polimórfica indicaram que os marcadores microssatélites foram adequados para as análises de QTL. Os dados foram analisados pelo mapeamento por intervalo usando-se o programa GridQTL. Encontraram-se seis QTL, sendo que o QTL genômico para idade ao abate atingiu a significância de 5% de probabilidade. As informações dos QTL detectados neste estudo são úteis para identificar genes que podem ser usados em conjunto com os métodos convencionais de seleção, aumentar a acurácia deles e prover uma compreensão dos fenótipos produtivos de suínos.

The accomplishment of the present study had the objective of mapping Quantitative Trait Loci (QTL) related to performance traits in a F2 pig population developed by mating two Brazilian Piau breed sires with 18 dams from a commercial line (Landrace × Large White × Pietrain). The linkage map for this population was constructed after genotyping the animals for 35 microsatellite markers. Estimates of polymorphic information content indicated that the microsatellite markers were appropriate for QTL analyses. The genotypes were analyzed by interval mapping using the GridQTL program. A total of six QTL were found, of which the QTL for slaughter age (days) was significant at the 5% genome-wise level. The information of the significant QTL detected in this study is useful for future fine-mapping studies for the identification of genes. Such information can be used together with traditional methods in breeding programs or even for a better understanding of the phenotypes of swine production.

Mapeamento de QTL nos cromossomos 1, 2, 3, 12, 14, 15 e X em suínos: características de carcaça e qualidade de carne / Mapping of QTL on chromosomes 1, 2, 3, 12, 14, 15 and X in pigs: characteristics carcass and quality of meat

A realização do presente estudo teve como objetivo mapear Quantitative Trait Loci (QTL) de carcaça e qualidade de carne em uma população F2 de suínos desenvolvida pelo cruzamento de dois reprodutores da raça brasileira Piau com 18 fêmeas comerciais (Landrace x Large White x Pietrain). O mapa de ligação para essa população foi construído após a genotipagem de 684 animais para 35 marcadores microssatélites. Os dados foram analisados pelo mapeamento por intervalo usando-se sexo, lote e genótipo halotano como efeitos fixos e peso de carcaça ao abate, peso da carcaça direita e idade ao abate como covariáveis. Um total de 18 QTLs foi encontrado; os QTLs para maior espessura de toucinho na região da copa, na linha dorsolombar, e a perda por cozimento foram significativos em nível de 5% genômico. A característica espessura de toucinho foi essencialmente associada aos alelos da raça Piau, conhecido como porco tipo banha. As informações dos QTLs significativos encontrados servem para futuros estudos de mapeamento fino para identificação de genes a serem usados em conjunto com os métodos tradicionais de seleção, para melhorar a eficiência dos programas de melhoramento, assim como prover informação acerca da fisiologia envolvida no desenvolvimento das características quantitativas dos suínos.

The accomplishment of the present study had as objective to map Quantitative Trait Loci (QTL) associated to carcass and quality traits in a F2 pig population developed by mating two Brazilian Piau breed sires with 18 dams from a commercial line (Landrace × Large White × Pietrain). The linkage map for this population was constructed after genotyping the 684 animals for 35 microsatellite markers. Data were analyzed by interval mapping using sex, batch and halothane genotype as fixed effects and carcass weight at slaughter, direct carcass weight and slaugher age as covariables. A total of 18 QTL were identified, the QTL for higher backfat thickness on the shoulder region and cooking loss was significant at 5% genome-wise level. The backfat thickness trait was mainly associated with the Piau breed allele, known as a fat pig. The information of the significant QTL detected in this study is useful for future fine-mapping studies for identification of genes and might be used together with traditional selection methods to improve the efficiency of breeding programs, moreover, this information can also provide new insights to the understanding of the physiology of the quantatiative traits in pigs.

Transcript profiling of expressed sequence tags from semimembranosus muscle of commercial and naturalized pig breeds.

In general, genetic differences across different breeds of pig lead to variation in mature body size and slaughter age. The Commercial breeds Duroc and Large White and the local Brazilian breed Piau are ostensibly distinct in terms of growth and muscularity, commercial breeds are much leaner while local breeds grow much slower and are fat type pigs. However, the genetic factors that underlie such distinctions remain unclear. We used expressed sequence tags (ESTs) to characterize and compare transcript profiles in the semimembranosus muscle of these pig breeds. Our aim was to identify differences in breed-related gene expression that might influence growth performance and meat quality. We constructed three non-normalized cDNA libraries from semimembranosus muscle, using two samples from each one, of these three breeds; 6902 high-quality ESTs were obtained. Cluster analysis was performed and these sequences were clustered into 3670 unique sequences; 24.7% of the sequences were categorized as contigs and 75.3% of the sequences were singletons. Based on homology searches against the SwissProt protein database, we were able to assign a putative protein identity to only 1050 unique sequences. Among these, 58.5% were full-length protein sequences and 17.2% were pig-specific sequences. Muscle structural and cytoskeletal proteins, such as actin, and myosin, were the most abundant transcripts (16.7%) followed by those related to mitochondrial function (12.9%), and ribosomal proteins (12.4%). Furthermore, ESTs generated in this study provide a rich source for identification of novel genes and for the comparative analysis of gene expression patterns in divergent pig breeds.

Candidate gene expression and intramuscular fat content in pigs.

Seventy-two pigs of three genetic groups (Brazilian indigenous breed Piau, Commercial line and Crossbred) of both sexes were slaughtered at four live weights (30, 60, 90 and 120 kg). Intramuscular fat (IMF) content in Longissimus dorsi muscle of each animal was extracted and correlated with candidate gene mRNA expression (ATN1, EEF1A2, FABP3, LDLR, MGP, OBSCN, PDHB, TRDN and RYR1). Within slaughter weight of 120 kg, Piau and Crossbred pigs showed higher IMF content (p < 0.05) than commercial animals, with 2.48, 2.08 and 1.00% respectively. Barrows presented higher values of IMF (p < 0.05) than gilts (1.54 and 1.30% respectively). Gene expression of EEF1A2, FABP3, LDLR, OBSCN, PDHB, TRDN and RYR1 were correlated with IMF (p < 0.05) using the whole dataset. For Piau data only, expression of FABP3, LDLR, MGP, OBSCN, PDHB, TRDN and RYR1 showed correlation with IMF (p < 0.05). Genes that have important roles in lipid transportation inside the cell (FABP3) and tissues (LDLR) showed correlation with IMF of, respectively, 0.68 and 0.63 using the whole data set, and 0.90 and 0.91 using data from Piau animals. The highly positive correlation of the LDLR and FAPB3 expression with IMF content may confirm that these genes are important for fat deposition in the porcine L. dorsi muscle.

Health outcomes of women exposed to household alcohol abuse: a Family Practice Training Site Research Network (FPTSRN) study.

BACKGROUND: There is a paucity of knowledge about the effects of exposure to alcohol abuse in the household on women who do not abuse alcohol. The purpose of this study was to determine whether women who did not abuse alcohol demonstrated any health-related adverse effects because they lived with family members who did abuse alcohol. METHODS: This study was a historical prospective survey of female patients at five primary care practices. Survey instruments included the CAGE questionnaire, a five-item screening test for exposure to alcoholism, and the Medical Outcomes Study 36-item Short Form Health Survey (MOS SF-36). Patient records were examined for specific diagnoses. RESULTS: A total of 267 patients completed the questionnaires and had complete medical records available for analysis. Forty-two (15.7%) potential alcohol abusers were excluded from the sample leaving a working total of 225; 70 (31.1%) were potentially exposed to alcoholism in the household. Women exposed to alcohol abuse in the home did not experience an increased risk for the medical diagnoses studied, but they did demonstrate decreased health-related quality of life as measured by the MOS-SF-36 for the following scales: role physical (P = .025), role emotional (P = .038), social functioning (P = .001), bodily pain (P = .016), and mental health (P = .040). CONCLUSIONS: Women exposed to alcohol abuse in the household are more likely to perceive themselves as less healthy. Although they may not have received a clinical diagnosis of depression, they are more likely to feel depressed. The extent to which subjects' health-related quality of life is influenced by exposure to alcohol abuse suggests that the medical diagnosis may be insensitive as a description of health status in this population.