@article{carvalho_sanglard_nascimento_moriel_sommer_merrill_poore_duarte_serao_2020, title={miRNAs explain the variation in muscle and blood transcriptomes of beef calves born from dams with or without energy restriction during late gestation}, volume={98}, ISSN={["1525-3163"]}, DOI={10.1093/jas/skaa054.292}, abstractNote={Abstract
               Maternal energy restriction during late gestation affects the expression of genes related to energy metabolism in muscle and immune response in blood. MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression post-transcriptionally. The aim of this study was to identify potentials miRNA involved in the expression of differentially expressed genes (DEG) in muscle and blood following exposure to maternal gestational energy restriction. Forty days before the expected calving date, cows were assigned to one of two diets: 100% (CTRL) or 70% (REST) of the daily energy requirement. For RNA-seq analysis, muscle samples were collected from 12 heifers and 12 steers, and blood samples were collected from 12 steers. miRNAs were identified from the RNA-seq data based on the bovine genome annotation, with 38 and 10 miRNAs identified in blood and muscle, respectively. The expression of the miRNAs and the previously identified 160 and 450 DEGs in muscle and blood, respectively, was pre-adjusted for fixed effects before final analyses. A stepwise selection (P-value < 0.05) was used to identify miRNAs (dependent variables) explaining variation in DEGs, for each DEG at a time, and analyses performed separately for blood and muscle. The R2 of selected models ranged from 0.88 to 0.99 in muscle and 0.92 to 0.99 in blood. Of the most selected miRNA in muscle, MiR-133a and MiR-1 are known to be related to muscle hypertrophy, and MiR-143 and bta-let-7i promote adipocyte differentiation. Of the most selected miRNA in blood, MiR-21 regulates immune system by different pathways. Using RNA-seq data, we identified miRNAs explaining a large amount of the variation of DEGs, with the identification of important miRNAs related to muscle development and immune system.}, journal={JOURNAL OF ANIMAL SCIENCE}, author={Carvalho, Elisa B. and Sanglard, Leticia P. and Nascimento, Moyses and Moriel, Philipe and Sommer, Jeffrey and Merrill, Melissa and Poore, Matthew and Duarte, Marcio and Serao, Nick}, year={2020}, month={Nov}, pages={165–165} }
 @article{sanglard_nascimento_moriel_sommer_ashwell_poore_duarte_serão_2018, title={Impact of energy restriction during late gestation on the muscle and blood transcriptome of beef calves after preconditioning}, volume={19}, ISSN={1471-2164}, url={http://dx.doi.org/10.1186/s12864-018-5089-8}, DOI={10.1186/s12864-018-5089-8}, abstractNote={Maternal nutrition has been highlighted as one of the main factors affecting intra-uterine environment. The increase in nutritional requirements by beef cows during late gestation can cause nutritional deficiency in the fetus and impact the fetal regulation of genes associated with myogenesis and immune response.Forty days before the expected calving date, cows were assigned to one of two diets: 100% (control) or 70% (restricted group) of the daily energy requirement. Muscle samples were collected from 12 heifers and 12 steers, and blood samples were collected from 12 steers. The objective of this work was to identify and to assess the biological relevance of differentially expressed genes (DEG) in the skeletal muscle and blood of beef calves born from cows that experienced [or not] a 30% energy restriction during the last 40 days of gestation.A total of 160, 164, and 346 DEG (q-value< 0.05) were identified in the skeletal muscle for the effects of diet, sex, and diet-by-sex interaction, respectively. For blood, 452, 1392, and 155 DEG were identified for the effects of diet, time, and diet-by-time interaction, respectively. For skeletal muscle, results based on diet identified genes involved in muscle metabolism. In muscle, from the 10 most DEG down-regulated in the energy-restricted group (REST), we identified 5 genes associated with muscle metabolism and development: SLCO3A1, ATP6V0D1, SLC2A1, GPC4, and RASD2. In blood, among the 10 most DEG, we found genes related to response to stress up-regulated in the REST after weaning, such as SOD3 and INO80D, and to immune response down-regulated in the REST after vaccination, such as OASL, KLRF1, and LOC104968634.In conclusion, maternal energy restriction during late gestation may limit the expression of genes in the muscle and increase expression in the blood of calves. In addition, enrichment analysis showed that a short-term maternal energy restriction during pregnancy affects the expression of genes related to energy metabolism and muscle contraction, and immunity and stress response in the blood. Therefore, alterations in the intra-uterine environment can modify prenatal development with lasting consequences to adult life.}, number={1}, journal={BMC Genomics}, publisher={Springer Science and Business Media LLC}, author={Sanglard, Leticia P and Nascimento, Moysés and Moriel, Philipe and Sommer, Jeffrey and Ashwell, Melissa and Poore, Matthew H and Duarte, Márcio de S and Serão, Nick V L}, year={2018}, month={Sep} }
 @article{nascimento_campana nascimento_silva_barili_vale_carneiro_cruz_souza carneiro_lopes serao_2018, title={Quantile regression for genome-wide association study of flowering time-related traits in common bean}, volume={13}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0190303}, abstractNote={Flowering is an important agronomic trait. Quantile regression (QR) can be used to fit models for all portions of a probability distribution. In Genome-wide association studies (GWAS), QR can estimate SNP (Single Nucleotide Polymorphism) effects on each quantile of interest. The objectives of this study were to estimate genetic parameters and to use QR to identify genomic regions for phenological traits (Days to first flower—DFF; Days for flowering—DTF; Days to end of flowering—DEF) in common bean. A total of 80 genotypes of common beans, with 3 replicates were raised at 4 locations and seasons. Plants were genotyped for 384 SNPs. Traditional single-SNP and 9 QR models, ranging from equally spaced quantiles (τ) 0.1 to 0.9, were used to associate SNPs to phenotype. Heritabilities were moderate high, ranging from 0.32 to 0.58. Genetic and phenotypic correlations were all high, averaging 0.66 and 0.98, respectively. Traditional single-SNP GWAS model was not able to find any SNP-trait association. On the other hand, when using QR methodology considering one extreme quantile (τ = 0.1) we found, respectively 1 and 7, significant SNPs associated for DFF and DTF. Significant SNPs were found on Pv01, Pv02, Pv03, Pv07, Pv10 and Pv11 chromosomes. We investigated potential candidate genes in the region around these significant SNPs. Three genes involved in the flowering pathways were identified, including Phvul.001G214500, Phvul.007G229300 and Phvul.010G142900.1 on Pv01, Pv07 and Pv10, respectively. These results indicate that GWAS-based QR was able to enhance the understanding on genetic architecture of phenological traits (DFF and DTF) in common bean.}, number={1}, journal={PLOS ONE}, author={Nascimento, Moyses and Campana Nascimento, Ana Carolina and Silva, Fabyano and Barili, Leiri Daiane and Vale, Naine Martins and Carneiro, Jose Eustaquio and Cruz, Cosme Damiao and Souza Carneiro, Pedro Crescencio and Lopes Serao, Nick Vergara}, year={2018}, month={Jan} }