Single Nucleotide Variants And Indels Identified From Whole-genome Re-sequencing Of Guzerat, Gyr, Girolando And Holstein Cattle Breeds

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Whole-genome re-sequencing, alignment and annotation analyses were undertaken for 12 sires representing four important cattle breeds in Brazil: Guzerat (multi-purpose), Gyr, Girolando and Holstein (dairy production). A total of approximately 4.3 billion reads from an Illumina HiSeq 2000 sequencer generated for each animal 10.7 to 16.4-fold genome coverage. A total of 27,441,279 single nucleotide variations (SNVs) and 3,828,041 insertions/deletions (InDels) were detected in the samples, of which 2,557,670 SNVs and 883,219 InDels were novel. The submission of these genetic variants to the dbSNP database significantly increased the number of known variants, particularly for the indicine genome. The concordance rate between genotypes obtained using the Bovine HD BeadChip array and the same variants identified by sequencing was about 99.05%. The annotation of variants identified numerous non-synonymous SNVs and frameshift InDels which could affect phenotypic variation. Functional enrichment analysis was performed and revealed that variants in the olfactory transduction pathway was over represented in all four cattle breeds, while the ECM-receptor interaction pathway was over represented in Girolando and Guzerat breeds, the ABC transporters pathway was over represented only in Holstein breed, and the metabolic pathways was over represented only in Gyr breed. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Gyr, Girolando, Guzerat and Holstein breeding programs. © 2017 Stafuzza et al.This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.123Conselho Nacional de Desenvolvimento Científico e TecnológicoCAPES, Coordenação de Aperfeiçoamento de Pessoal de Nível SuperiorFAPEMIG, Fundação de Amparo à Pesquisa do Estado de Minas GeraisConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES

Study On The Introgression Of Beef Breeds In Canchim Cattle Using Single Nucleotide Polymorphism Markers

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)The aim of this study was to evaluate the level of introgression of breeds in the Canchim (CA: 62.5% Charolais-37.5% Zebu) and MA genetic group (MA: 65.6% Charolais-34.4% Zebu) cattle using genomic information on Charolais (CH), Nelore (NE), and Indubrasil (IB) breeds. The number of animals used was 395 (CA and MA), 763 (NE), 338 (CH), and 37 (IB). The Bovine 50SNP BeadChip from Illumina panel was used to estimate the levels of introgression of breeds considering the Maximum likelihood, Bayesian, and Single Regression method. After genotype quality control, 32,308 SNPs were considered in the analysis. Furthermore, three thresholds to prune out SNPs in linkage disequilibrium higher than 0.10, 0.05, and 0.01 were considered, resulting in 15,286, 7,652, and 1,582 SNPs, respectively. For k = 2, the proportion of taurine and indicine varied from the expected proportion based on pedigree for all methods studied. For k = 3, the Regression method was able to differentiate the animals in three main clusters assigned to each purebred breed, showing more reasonable according to its biological viewpoint. Analyzing the data considering k = 2 seems to be more appropriate for Canchim-MA animals due to its biological interpretation. The usage of 32,308 SNPs in the analyses resulted in similar findings between the estimated and expected breed proportions. Using the Regression approach, a contribution of Indubrasil was observed in Canchim-MA when k = 3 was considered. Genetic parameter estimation could account for this breed composition information as a source of variation in order to improve the accuracy of genetic models. Our findings may help assemble appropriate reference populations for genomic prediction for Canchim-MA in order to improve prediction accuracy. Using the information on the level of introgression in each individual could also be useful in breeding or crossing design to improve individual heterosis in crossbred cattle. © 2017 Buzanskas et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.12202663/09-0, CAPES, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior449564/2014-2, CNPq, Conselho Nacional de Desenvolvimento Científico e TecnológicoCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

A Survey of mid and large bodied mammals in Núcleo Caraguatatuba, Serra do Mar State Park, Brazil

Nós aplicamos técnicas de amostragem complementares para obter uma lista de espécies de mamíferos de médio e grande porte no Núcleo Caraguatatuba, Parque Estadual da Serra do Mar, Brasil. As amostragens de campo realizaram-se nos meses de Maio e Setembro de 2011. Utilizou-se, censo ao longo de transectos (212,4 km), armadilhas fotográficas (223,2 armadilhas-dias) e armadilhas de pegadas (478 armadilhas-dias). Foram obtidos registros de 18 espécies, pertencentes a 14 famílias e oito ordens. Nós registramos a presença de sete espécies consideradas ameaçadas no Estado de São Paulo, incluindo primatas (Brachyteles arachnoides), Artiodactyla (Mazama americana e Tayassu pecari), Carnivora (Leopardus pardalis, Leopardus tigrinus e Puma concolor) e Perissodactyla (Tapirus terrestris). Com base em numa extrapolação da riqueza de espécies (First order jackknife) nós prevemos que existem entre 19 e 32 espécies de mamíferos de médio e grande porte no Núcleo. Nosso Mammal Priority Index classificou o Núcleo Caraguatatuba como uma área de importância média para a conservação de mamíferos de médio e grande porte na Mata Atlântica. Combinado com o número e a diversidade de espécies registradas, nossos resultados demonstram que este Núcleo é uma área importante para a conservação de mamíferos no Estado.We applied complementary survey techniques to obtain a baseline species list of mid and large bodied mammals in Núcleo Caraguatatuba, Serra do Mar State park, Brazil. Between May and September 2011 we surveyed the community of mid and large bodied mammals using diurnal line transect census (212.4 km), camera-traps (223.2 camera-trap days) and track-stations (478 track-station days). A total of 18 species were recorded from 14 families in eight orders. We recorded the presence of seven species considered threatened in the State of São Paulo, including Primates (Brachyteles arachnoides), Artiodactyla (Mazama cf. americana and Tayassu pecari), Carnivora (Leopardus pardalis, Leopardus tigrinus and Puma concolor) and Perissodactyla (Tapirus terrestris). Based on extrapolated (First order jackknife) species richness estimates we predict that there are between 19 and 32 species of mid and large bodied mammals in the Núcleo. Our revised Mammal Priority Index ranked Núcleo Caraguatatuba as being of medium overall importance for the conservation of mid and large bodied mammals in the Atlantic Forest. Combined with the number and diversity of species recorded, our results demonstrate that this Núcleo is an important area for mammal conservation

Análise genética de características reprodutivas na raça brahman

Aiming to establish selection criteria for the Brahman cattle in Brazil, the objective of this paper was to estimate genetic and environmental parameters for birth weight (BW), gestation length (GL) and scrotal circumference at 365 (SC365), 455 (SC455) and 550 (SC 550) days of age, and relative efficiency of indirect versus direct selection for these traits. Data were obtained from 15 851 animals belonging to 16 herds in six states, enrolled in a genetic breeding program. (Co)variance and heritability coefficients and genetic and environ- mental correlations between traits were estimated by restricted maximum likelihood (REML) under a multi trait animal model. The model included as fixed effects the contemporary group and the age of cow at calving as a covariate (linear and quadratic), and as random the direct genetic, the permanent environmental and residual effects. For BW and GL it was also considered the maternal genetic effect as random. Estimates of direct heritabilities were 0.36, 0.29, 0.55, 0.43 and 0.40 for BW, GL, SC365, SC455 and SC550, respectively. Genetic correlations between BW and GL, GL and SC365, GL and SC455, GL and SC550, SC365 and SC455, SC365 and SC550 and SC455 and SC550, were respectively 0.06, 0.13, 0.20, 0.13, 0.96, 0.98 and 0.99. The heritabilities estimates for all traits indicated these show enough additive genetic variability to respond favorably to selection. For sexual precocity, the best option would be SC365, due to the high value of heritability and to indirect selection at this age being more efficient than direct selection for PE455.Para fins de estabelecer critérios de seleção para a raça Brahman, no Brasil, este estudo objetivou estimar parâmetros genéticos e ambien- tal para peso ao nascer (PN), período de gestação (PG) e perímetro escrotal aos 365 (PE365), 455 (PE455) e 550 (PE550) dias de idade e eficiências relativas de seleção indireta versus a direta para essas características. Os dados referem-se a 15 851 animais de 16 rebanhos de seis estados, participantes de um programa de melhoramento genético. Componentes de (co)variância e coefi- cientes de herdabilidade e de correlações genéticas e ambientais entre características foram estimados pelo método da máxima verossimilhança restrita, sob modelo animal multi-característica. No modelo, foram incluídos como efeitos fixos, grupo de contemporâneos e idade da vaca ao parto como covariável (efeitos linear e quadrático) e, como efeitos aleatórios, genético aditivo direto, ambiente permanente da vaca e resíduo. Para PN e PG considerou-se ainda o efeito aleatório genético materno. As herdabilidades estimadas para PN, PG, PE365, PE455 e PE550 foram, respectivamen- te, 0,36; 0,29; 0,55; 0,43 e 0,40. As correlações genéticas entre PN e PG, PG e PE365, PG e PE455, PG e PE550, PE365 e PE455, PE365 e PE550 e PE455 e PE550 foram, respectivamente, 0,06; 0,13; 0,20; 0,13; 0,96; 0,98 e 0,99. Todas as características apresentaram variabilidade genética aditiva suficiente para responder favoravelmente à seleção. No que tange a precocidade sexual, a melhor opção seria PE365, devido à alta herdabilidade estimada, além de que a seleção indireta a esta idade seria mais eficiente que a direta para PE455

Parâmetros genéticos de características de carcaça e de crescimento de bovinos da raça nelore

The objectives of this study were to estimate genetic parameters involving yearling weight (Ps), carcass weight (Pc), hip height (Ag) and the scores of conformation (C), precocity (P) and musculature (M) and carcass yield (Rd) and finishing score (Ac) in Nellore cattle in order to define criteria for selection in this breed. The data of the 20 732 animals were obtained from Agrope- cuária Jacarezinho, SP. Data were analyzed by restricted maximum likelihood using animal model multi-trait analysis, which included fixed effects of contemporary groups (animals born at the same month and slaughtered on the same day) and the covariate age at slaughter (linear) for carcass traits, and contemporary groups (animals of the same farm, age, sex and management group at weaning and yearling) and yearling age (linear) for growth and as random, the additive effects and residual effects. Estimates ranged from 0.13 (Ac and Rd) to 0.36 (Ag) for heritability and from -0.59 ± 0.62 (Rd with Ac) to 0.71 ± 0.17 (Pc with C) for genetic correlations. Selection for Pc, C, P, M, Ag or Ps may be efficient because their heritability estimates are of magnitude moderate. Selection for Ps and C can favor heavier Pc, considering their positive and high genetic correlation.Objetivou-se estimar parâmetros genéticos envolvendo o peso ao sobreano (Ps) e de carcaça (Pc), altura de garupa (Ag) e os escores de conformação (C), precocidade (P), musculatura (M), rendimento (Rd) e acabamento (Ac), em bovinos Nelore, com o intuito de definir critérios de seleção nesta raça. Os dados de 20 732 animais foram oriundos da Agropecuária Jacarezinho, SP. Análises foram realizadas pelo método da máxima verossimilhança restrita, em modelo animal multicaracterística, que incluiu os efeitos fixos de grupo de contemporâneos (animais nascidos no mesmo mês e mesmo dia de abate) e a covariável idade de abate para as características de carcaça, e grupo de contemporâneos (animais de mesma fazenda, ano e mês de nascimento, sexo, grupo de manejo à desmama e ao sobreano) e a covariável idade ao sobreano (linear) para as de crescimento e como aleatório, para ambas características, o efeito aditivo e o residual. As estimativas de herdabilidade variaram de 0,13 (Ac e Rd) a 0,36 (Ag) e as estimativas de correlação genética variaram de -0,59 ± 0,62 (entre Rd e Ac) a 0,71 ± 0,17 (entre Pc e C). As características Pc, C, P, M, Ag e Ps podem responder à seleção por apresentarem estimativas de herdabilidade de média magnitude. A seleção baseada em Ps em C deve promover resposta correlacionada para maiores Pc nos animais, uma vez que as correlações genéticas foram positivas e altas