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

Uso de modelos no lineales para el ajuste de la curva de crecimiento de bovinos pantaneiros

Los modelos no lineares Brody, Gompertz, Logística y Von Bertalanffy fueron ajustados por el método Gauss-Newton a 1748 registros de peso y edad, desde el nacimiento hasta 27 meses de edad, de bovinos Pantaneiros (92 machos y 78 hembras), nacidos desde 1994 hasta 2000, en el Pantanal de Nhecolândia-MS, Brasil. El objetivo de este trabajo fue estudiar el patrón de crecimiento de animales Pantaneiros en su propio ambiente, así como predecir algunas características de esos modelos para evaluar los desarrollos corporales de machos y hembras. Los registros fueron ajustados para los efectos fijos de año-estación de nacimiento y edad del peso, en términos lineares y cuadráticos, por medio del procedimiento PROC GLM (SAS, 1992). Los registros observados y ajustados formaron los archivos sometidos a análisis usando el procedimiento PROC NLIN (SAS, 1992). Todos los modelos utilizados proporcionaron buena calidad de ajuste a los pesos para ambos sexos, indicando que las hembras alcanzan la madurez en edades más precoces, mientras que los machos, presentan peso adulto más elevado

Uso de modelos no lineales para el ajuste de la curva de crecimiento de bovinos pantaneiros

Los modelos no lineares Brody, Gompertz, Logística y Von Bertalanffy fueron ajustados por el método Gauss-Newton a 1748 registros de peso y edad, desde el nacimiento hasta 27 meses de edad, de bovinos Pantaneiros (92 machos y 78 hembras), nacidos desde 1994 hasta 2000, en el Pantanal de Nhecolândia-MS, Brasil. El objetivo de este trabajo fue estudiar el patrón de crecimiento de animales Pantaneiros en su propio ambiente, así como predecir algunas características de esos modelos para evaluar los desarrollos corporales de machos y hembras. Los registros fueron ajustados para los efectos fijos de año-estación de nacimiento y edad del peso, en términos lineares y cuadráticos, por medio del procedimiento PROC GLM (SAS, 1992). Los registros observados y ajustados formaron los archivos sometidos a análisis usando el procedimiento PROC NLIN (SAS, 1992). Todos los modelos utilizados proporcionaron buena calidad de ajuste a los pesos para ambos sexos, indicando que las hembras alcanzan la madurez en edades más precoces, mientras que los machos, presentan peso adulto más elevado

Uso de los modelos no lineares para el ajuste de la curva de crecimiento de los bovinos pantaneiros

Resumen de la comunicación presentada al III Congreso Ibérico sobre Recursos Genéticos Animale