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 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

Genetic evaluation of heat tolerance in Holsteins using test-day production records and NASA POWER weather data

ABSTRACT: Heat stress is a prominent issue in livestock production, even for intensively housed dairy herds in Canada. Production records and meteorological data can be combined to assess heat tolerance in dairy cattle. The overall aim of this study was to evaluate the possibility of genetic evaluation for heat tolerance in Canadian dairy cattle. The 2 specific objectives were (1) to estimate the genetic parameters for milk, fat, and protein yield for Holsteins while accounting for high environmental heat loads, and (2) to determine if a genotype-by-environment interaction causes reranking of top-ranked sires between environments with low and high heat loads. A repeatability test-day model with a heat stress function was used to evaluate the genetic merit for milk, fat, and protein yield under heat stress and at thermal comfort for first parity in 5 regions in Canada. The heat stress function for each trait was defined using a specific temperature-humidity index (THI) threshold. The purpose of this function was to quantify the level of heat stress that was experienced by the dairy cattle. The estimated genetic correlation between the general additive genetic effect and the additive effect on the slope of the change in the trait phenotype for milk, fat, and protein yield ranged from −0.16 to −0.30, −0.20 to −0.44, and −0.28 to −0.42, respectively. These negative correlations imply that there is an antagonistic relationship between sensitivity to heat stress and level of production. The heritabilities for milk, fat, and protein yield at 15 units above the THI threshold ranged from 0.15 to 0.27, 0.11 to 0.15, and 0.11 to 0.15, respectively. Finally, the rank correlations between the breeding values from a repeatability model with no heat stress effect and the breeding values accounting for heat stress for the 100 top-ranked bulls indicated possible interaction between milk production traits and THI, resulting in substantial reranking of the top-ranked sires in Canada, especially for milk yield. This is the first study to implement weather data from the NASA POWER database in a genetic evaluation of heat tolerance in dairy cattle. The NASA POWER database is a novel alternative meteorological resource that is potentially more reliable and consistent and with broader coverage than weather station data increasing the number of animals that could be included in a heat stress evaluation