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

Accuracy of genomic prediction of dry matter intake in Dutch Holsteins using sequence variants from meta-analyses

We evaluated the accuracy of biology informed genomic prediction for dry matter intake in 2,162 Dutch Holstein cows. Sequence variants were selected from meta-analyses including GWAS summary statistics for QTL and metabolomic QTL in several dairy and crossbred beef populations. Selected variants were prioritized in GBLUP models in a five-fold cross-validation. The accuracies were compared to genomic prediction based on routine 50k genotype data. The average accuracy for the 50k scenario was 0.683. Adding selected sequence variants in the GBLUP model did not improve the accuracies for dry matter intake. Next steps will include testing Bayesian variable selection methods to prioritize variants in genomic prediction for dry matter intake

Association of CSSM066 and ILSTS011 microsatellite markers and thyroglobulin gene SNP with backfat in Canchim cattle

Canchim, a synthetic breed of cattle derived from the Charolais and Zebu group has been used in the beef-cattle industry in Brazil as an alternative for intensifying production. One of the main concerns with this breed is its poor fat deposition and consequently, there is an effort to increase the performance for this trait. The thyroglobulin gene is located in a QTL region for fat deposition, and reports describe the influence of a polymorphism in the 5´ leader sequence of that gene on marbling and subcutaneous fat thickness. This study analyzed the association of this polymorphism in the thyroglobulin gene, as well as of two flanking microsatellite markers, CSSM066 and ILSTS011, with backfat thickness in 987 Canchim beef cattle. The CSSM066 and ILSTS011 microsatellite markers have a effect on fat thickness in the studied populations. However, this trait did not have association with the polymorphism of the thyroglobulin gene, which suggests that other genes of bovine chromosome 14 may be responsible for the variation in this trait

Meta-análise de parâmetros genéticos relacionados ao consumo alimentar residual e a suas características componentes em bovinos

O objetivo deste trabalho foi estimar, por meio de meta-análise, a herdabilidade (h²) e as correlações genética (r g) e fenotípica (r f) do consumo alimentar residual (CAR), e das suas características componentes, em bovinos de 19 raças ou grupamentos genéticos. Foram utilizados 22 trabalhos científicos publicados entre 1963 e 2011, de oito países, o que totalizou 52.637 bovinos com idades que variaram de 28 dias até a idade de abate. As estimativas de CAR, consumo de matéria seca (CMS), ganho médio diário (GMD) e peso metabólico (PV0, 75) foram ponderadas pelo inverso da variância amostral. A variação da h² de cada característica entre os estudos foi analisada por quadrados mínimos ponderados. Os efeitos de sexo, país e raça foram significativos para h² de CAR e explicaram 67% da variação entre os estudos. Para CMS, os efeitos de país e raça foram significativos e explicaram 96% da variação. As estimativas combinadas de h² foram: 0, 255±0, 008, 0, 278±0, 012, 0, 321±0, 015 e 0, 397±0, 032 para CAR, CMS, GMD e PV0, 75, respectivamente. As estimativas combinadas de correlação genética e fenotípica foram baixas entre CAR e GMD e entre CAR e PV0, 75 (de -0, 021±0, 034 a 0, 025±0, 035), e de média magnitude entre CAR e CMS (0, 636±0, 035 a 0, 698±0, 041) e entre CMS, GMD e PV0, 75 (0, 441±0, 062 a 0, 688±0, 032). O CAR apresenta estimativa de herdabilidade menor que a de suas características componentes

A Genome Scan to Detect Quantitative Trait Loci for Economically Important Traits in Holstein Cattle Using Two Methods and a Dense Single Nucleotide Polymorphism Map

Genome scans for detection of bovine quantitative trait loci (QTL) were performed via variance component linkage analysis and linkage disequilibrium single-locus regression (LDRM). Four hundred eighty-four Holstein sires, of which 427 were from 10 grandsire families, were genotyped for 9,919 single nucleotide polymorphisms (SNP) using the Affymetrix MegAllele GeneChip Bovine Mapping 10K SNP array. A hybrid of the granddaughter and selective genotyping designs was applied. Four thousand eight hundred fifty-six of the 9,919 SNP were located to chromosomes in base-pairs and formed the basis for the analyses. The mean polymorphism information content of the SNP was 0.25. The SNP centimorgan position was interpolated from their base-pair position using a microsatellite framework map. Estimated breeding values were used as observations, and the following traits were analyzed: 305-d lactation milk, fat, and protein yield; somatic cell score; herd life; interval of calving to first service; and age at first service. The variance component linkage analysis detected 102 potential QTL, whereas LDRM analysis found 144 significant SNP associations after accounting for a 5% false discovery rate. Twenty potential QTL and 49 significant SNP associations were in close proximity to QTL cited in the literature. Both methods found significant regions on Bos taurus autosome (BTA) 3, 5, and 16 for milk yield; BTA 14 and 19 for fat yield; BTA 1, 3, 16, and 28 for protein yield; BTA 2 and 13 for calving to first service; and BTA 14 for age at first service. Both approaches were effective in detecting potential QTL with a dense SNP map. The LDRM was well suited for a first genome scan due to its approximately 8 times lower computational demands. Further fine mapping should be applied on the chromosomal regions of interest found in this study