Genome-wide association study for backfat thickness in Canchim beef cattle using Random Forest approach

Background: Meat quality involves many traits, such as marbling, tenderness, juiciness, and backfat thickness, all of which require attention from livestock producers. Backfat thickness improvement by means of traditional selection techniques in Canchim beef cattle has been challenging due to its low heritability, and it is measured late in an animal's life. Therefore, the implementation of new methodologies for identification of single nucleotide polymorphisms (SNPs) linked to backfat thickness are an important strategy for genetic improvement of carcass and meat quality.Results: The set of SNPs identified by the random forest approach explained as much as 50% of the deregressed estimated breeding value (dEBV) variance associated with backfat thickness, and a small set of 5 SNPs were able to explain 34% of the dEBV for backfat thickness. Several quantitative trait loci (QTL) for fat-related traits were found in the surrounding areas of the SNPs, as well as many genes with roles in lipid metabolism.Conclusions: These results provided a better understanding of the backfat deposition and regulation pathways, and can be considered a starting point for future implementation of a genomic selection program for backfat thickness in Canchim beef cattle. © 2013 Mokry et al.; licensee BioMed Central Ltd

Study on the introgression of beef breeds in Canchim cattle using single nucleotide polymorphism markers

<div><p>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 Bovine50SNP 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.</p></div

Strategies for genotype imputation in composite beef cattle

Genotype imputation has been used to increase genomic information, allow more animals in genome-wide analyses, and reduce genotyping costs. In Brazilian beef cattle production, many animals are resulting from crossbreeding and such an event may alter linkage disequilibrium patterns. Thus, the challenge is to obtain accurately imputed genotypes in crossbred animals. The objective of this study was to evaluate the best fitting and most accurate imputation strategy on the MA genetic group (the progeny of a Charolais sire mated with crossbred Canchim X Zebu cows) and Canchim cattle. The data set contained 400 animals (born between 1999 and 2005) genotyped with the Illumina BovineHD panel. Imputation accuracy of genotypes from the Illumina-Bovine3K (3K), Illumina-BovineLD (6K), GeneSeek-Genomic-Profiler (GGP) BeefLD (GGP9K), GGP-IndicusLD (GGP20Ki), Illumina-BovineSNP50 (50K), GGP-IndicusHD (GGP75Ki), and GGP-BeefHD (GGP80K) to Illumina-BovineHD (HD) SNP panels were investigated. Seven scenarios for reference and target populations were tested; the animals were grouped according with birth year (S1), genetic groups (S2 and S3), genetic groups and birth year (S4 and S5), gender (S6), and gender and birth year (S7). Analyses were performed using FImpute and BEAGLE software and computation run-time was recorded. Genotype imputation accuracy was measured by concordance rate (CR) and allelic R square (R(2)). The highest imputation accuracy scenario consisted of a reference population with males and females and a target population with young females. Among the SNP panels in the tested scenarios, from the 50K, GGP75Ki and GGP80K were the most adequate to impute to HD in Canchim cattle. FImpute reduced computation run-time to impute genotypes from 20 to 100 times when compared to BEAGLE. The genotyping panels possessing at least 50 thousands markers are suitable for genotype imputation to HD with acceptable accuracy. The FImpute algorithm demonstrated a higher efficiency of imputed markers, especially in lower density panels. These considerations may assist to increase genotypic information, reduce genotyping costs, and aid in genomic selection evaluations in crossbred animals

Crossing schemes to obtain animals from the Canchim breed (CA) and other genetic groups through crossings between Charolais (CH) and Zebu (ZB) animals.

<p>Crossing schemes to obtain animals from the Canchim breed (CA) and other genetic groups through crossings between Charolais (CH) and Zebu (ZB) animals.</p

Genome-wide estimates of effective population size from 1 to 200 generations in the past based on estimates of linkage disequilibrium.

<p>Genome-wide estimates of effective population size from 1 to 200 generations in the past based on estimates of linkage disequilibrium.</p

Breed composition per animal considering the number of populations of two (k = 2).

<p>Analyses were carried out using ADMIXTURE (A) and STRUCTURE (B) software and Single Regression method (C) and considered 32,308 (1), 15,286 (2), 7,652 (3), and 1,582 (4) SNPs. Orange and blue represents the <i>Bos primigenius indicus</i> (cluster 1) and <i>Bos primigenius taurus</i> (cluster 2) proportions, respectively. The breeds analyzed were Canchim and MA genetic group together as one breed (CAN), Nelore (NE), Charolais (CH), and Indubrasil (IB).</p

Plot of the first 2 principal components (PC) obtained for the studied breeds.

<p>Canchim (C1, C2, C3, and CA), MA genetic group (MA), Charolais (CH), Nelore (NE), and Indubrasil (IB) using 32,308 SNP (A), 15,286 SNP (B), 7,652 SNP (C), and 1,582 SNP (D).</p

Mean, standard deviation (SD), and median of the expected and observed heterozygosities in the full genotype data (30K) and in the pruned data according to linkage disequilibrium (15K, 7K, and 1K).

<p>Mean, standard deviation (SD), and median of the expected and observed heterozygosities in the full genotype data (30K) and in the pruned data according to linkage disequilibrium (15K, 7K, and 1K).</p

Comparison between the levels of introgression of breeds present in Canchim-MA animals based on pedigree and prediction methods (ADMIXTURE, STRUCTURE, and Regression).

<p>The second cluster of each prediction method was used as a reference for the <i>Bos primigenius taurus</i> (Charolais) contribution. The highlighted values in bold were considered highly similar.</p