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The present study aimed to investigate whether different lines of a composite breed (5/8 Charolais × 3/8 Zebu), formed at different times, and genetically improved, would result in differences in animal performance, enteric methane emissions, and carcass traits. Forty-six Canchim steers (15 months, 280 ± 33 kg liveweight) from three different lines were used: old, new, and their cross. These three breed lines were considered the treatments (arranged in four randomized blocks based on initial liveweight) and were evaluated under grazing and feedlot conditions in relation to the performance and emission of enteric methane. During the grazing period, the new line was found to be superior to the old only in relation to the average daily liveweight gain (0.692 vs. 0.547 kg/day), and with no differences in relation to the cross line (0.692 vs. 0.620). In the feedlot finishing phase, only the average daily liveweight gain was significantly higher in the new line compared to the cross and old line (1.44 vs. 1.32 and 1.23 kg/day). The new and cross lines demonstrated higher dry matter intake when compared to the old line (10.25 and 10.42 vs. 9.11 kg/day), with the crossline animals demonstrating the best feed conversion. The new line showed higher enteric methane emissions compared to the old line (178 vs. 156 g/day). The line had an effect on the carcass dressing of the animals, with greater fat thickness in carcasses from the new and cross lines than the old line (4.4 and 3.8 vs. 3.2 mm). Canchim cattle selected for improved productive performance characteristics does not guarantee animals with lower methane emissions under grazing conditions; while in feedlots, can lead to increased daily feed consumption, and hence, to higher emissions of methane.

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BACKGROUND: 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)). RESULTS: 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. CONCLUSION: 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.

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We adapted a method that allows the identification of X chromosome copy number by quantitative real-time polymerase chain reaction (PCR) in a short amount of time. It may be used for sex and aneuploidy involving X chromosome large population screening tests.

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