Identification of runs of homozygosity (ROHs) in Curraleiro Pé-Duro and Pantaneiro cattle breeds.

This study aimed to identify and characterize runs of homozygosis (ROHs), genes involved in production characteristics and adaptation to tropical systems and to estimate the inbreeding coefficient of Curraleiro Pé-Duro (CPD) and Pantaneiro (PANT), two brazilian locally adapted cattle breeds. The results demonstrated that 79.25% and 54.29% of ROH segments were bigger than 8 Mb in CPD and PANT, respectively, indicating recent inbred matings in the studied population. Six homozygosis islands were identified simultaneously in both breeds, where 175 QTLs and 1072 genes previously described as associated with production traits are located. The inbreeding coefficient (FROH) estimated based on ROHs (FROH) showed that inbreeding is low (2 to 4%), which is different from expected for small populations such as locally adapted ones.

Estimating genetic parameters of reproductive, carcass, and meat quality traits in Polled Nellore cattle.

Considering the economic and commercial efficiency of the beef production chain, the yield and quality of the meat produced must also be included in breeding programs. For the Nellore breed, including the polled herd, these aspects have not been much studied. The aim of this study was to estimate genetic parameters for scrotal circumference adjusted to 365 (SC365) and 450 (SC450) days of age, age at first calving (AFC), accumulated productivity (AP), stayability (STAY), longissimus muscle area (LMA), thickness of subcutaneous fat over the 12th-13th ribs (BF), thickness of subcutaneous fat over the rump (RF), and shear force measured by Warner-Bratzler shear force (WBSF) of polled Nellore cattle. Bayesian analyses were performed by adopting a linear animal model, whereas STAY analyses used the linear threshold model. Heritability estimates were 0.31 (SC365), 0.37 (SC450), 0.16 (AFC), 0.25 (AP), 0.16 (STAY), 0.30 (LMA), 0.13 (BF), 0.24 (RF), and 0.15 (WBSF), indicating moderate response to selection. Genetic and residual correlations between SC365 and SC450 were high (0.91 and 0.74, respectively), as well as the genetic correlations of AP with SC365, SC450, AFC, and STAY (0.61, 0.62, - 0.69, and 0.83, respectively). Genetic and residual correlations of WBSF with reproductive and carcass characteristics exhibited high standard deviations, however favorable. Based on the results, it is expected that in the medium term, animals with greater sexual precocity will also have greater accumulated productivity and longer permanence of females in the herd, along with superior carcass traits. However, due to the low heritabilities and small genetic associations with reproductive traits, fat thickness characteristics (BF and RF) will still require direct selection.

Accuracy of genomic predictions in Gyr (Bos indicus) dairy cattle.

Genomic selection may accelerate genetic progress in breeding programs of indicine breeds when compared with traditional selection methods. We present results of genomic predictions in Gyr (Bos indicus) dairy cattle of Brazil for milk yield (MY), fat yield (FY), protein yield (PY), and age at first calving using information from bulls and cows. Four different single nucleotide polymorphism (SNP) chips were studied. Additionally, the effect of the use of imputed data on genomic prediction accuracy was studied. A total of 474 bulls and 1,688 cows were genotyped with the Illumina BovineHD (HD; San Diego, CA) and BovineSNP50 (50K) chip, respectively. Genotypes of cows were imputed to HD using FImpute v2.2. After quality check of data, 496,606 markers remained. The HD markers present on the GeneSeek SGGP-20Ki (15,727; Lincoln, NE), 50K (22,152), and GeneSeek GGP-75Ki (65,018) were subset and used to assess the effect of lower SNP density on accuracy of prediction. Deregressed breeding values were used as pseudophenotypes for model training. Data were split into reference and validation to mimic a forward prediction scheme. The reference population consisted of animals whose birth year was ≤2004 and consisted of either only bulls (TR1) or a combination of bulls and dams (TR2), whereas the validation set consisted of younger bulls (born after 2004). Genomic BLUP was used to estimate genomic breeding values (GEBV) and reliability of GEBV (R2PEV) was based on the prediction error variance approach. Reliability of GEBV ranged from ∼0.46 (FY and PY) to 0.56 (MY) with TR1 and from 0.51 (PY) to 0.65 (MY) with TR2. When averaged across all traits, R2PEV were substantially higher (R2PEV of TR1 = 0.50 and TR2 = 0.57) compared with reliabilities of parent averages (0.35) computed from pedigree data and based on diagonals of the coefficient matrix (prediction error variance approach). Reliability was similar for all the 4 marker panels using either TR1 or TR2, except that imputed HD cow data set led to an inflation of reliability. Reliability of GEBV could be increased by enlarging the limited bull reference population with cow information. A reduced panel of ∼15K markers resulted in reliabilities similar to using HD markers. Reliability of GEBV could be increased by enlarging the limited bull reference population with cow information.

Selection criteria for sexual precocity in Guzerat bulls raised under grazing conditions.

The objectives of the present study were to obtain posterior densities of genetic parameters for scrotal circumference (SC), testicular volume (TV), BW, and age at puberty, to determine their correlations, and to evaluate the inclusion of these traits as selection criteria for sexual precocity in Guzerat bulls. Two-trait analyses were performed including records of SC, TV, and BW at 365, 450, 550, 650, 730, 850, and 970 d of age with age at puberty of 1,783 Guzerat bulls born between 2000 and 2011. The (co)variance components were estimated using Bayesian methods. Posterior means of heritability ranged from 0.45 to 0.60 for SC, from 0.35 to 0.55 for TV, and from 0.39 to 0.60 for BW. Posterior means of heritabilities for age at puberty using the two-trait analysis with SC ranged from 0.46 to 0.55, those with TV ranged from 0.49 to 0.57, and those with BW ranged from 0.49 to 0.62. The genetic correlation between age at puberty and SC ranged from -0.52 to -0.85, those between age at puberty and TV ranged from -0.33 to -0.66, and those between age at puberty and BW ranged from -0.38 to -0.72. In general, the same trend was observed for the phenotypic correlation between age at puberty and SC, TV, and BW. The selection of the top 10% of young males for SC, TV, or BW caused a decrease in age at puberty, with the most favorable expected correlated response in age at puberty at 650 d of age (-119.95 ± 15.1 d per generation), 730 d of age (-82.20 ± 20.9), and 850 d of age (-93.68 ± 21.5), respectively. In conclusion, SC, TV, and BW can be used as selection criteria to improve early sexual development in Guzerat bulls, and SC measured at 650 d of age is the most advantageous indicative selection criterion for improvement of age at puberty in Guzerat young bulls.

Use of nonlinear models for describing scrotal circumference growth in Guzerat bulls raised under grazing conditions.

The objective was to use various nonlinear models to describe scrotal circumference (SC) growth in Guzerat bulls on three farms in the state of Minas Gerais, Brazil. The nonlinear models were: Brody, Logistic, Gompertz, Richards, Von Bertalanffy, and Tanaka, where parameter A is the estimated testis size at maturity, B is the integration constant, k is a maturating index and, for the Richards and Tanaka models, m determines the inflection point. In Tanaka, A is an indefinite size of the testis, and B and k adjust the shape and inclination of the curve. A total of 7410 SC records were obtained every 3 months from 1034 bulls with ages varying between 2 and 69 months (<240 days of age = 159; 241-365 days = 451; 366-550 days = 1443; 551-730 days = 1705; and >731 days = 3652 SC measurements). Goodness of fit was evaluated by coefficients of determination (R(2)), error sum of squares, average prediction error (APE), and mean absolute deviation. The Richards model did not reach the convergence criterion. The R(2) were similar for all models (0.68-0.69). The error sum of squares was lowest for the Tanaka model. All models fit the SC data poorly in the early and late periods. Logistic was the model which best estimated SC in the early phase (based on APE and mean absolute deviation). The Tanaka and Logistic models had the lowest APE between 300 and 1600 days of age. The Logistic model was chosen for analysis of the environmental influence on parameters A and k. Based on absolute growth rate, SC increased from 0.019 cm/d, peaking at 0.025 cm/d between 318 and 435 days of age. Farm, year, and season of birth significantly affected size of adult SC and SC growth rate. An increase in SC adult size (parameter A) was accompanied by decreased SC growth rate (parameter k). In conclusion, SC growth in Guzerat bulls was characterized by an accelerated growth phase, followed by decreased growth; this was best represented by the Logistic model. The inflection point occurred at approximately 376 days of age (mean SC of 17.9 cm). We inferred that early selection of testicular size might result in smaller testes at maturity.

Assessment of swim-up and discontinuous density gradient in sperm sex preselection for bovine embryo production / Avaliação do swim-up e do gradiente descontinuo de densidade na pré-seleção do sexo de espermatozoides na produção de embriões bovinos

The purpose of this work was to associate the modified swim-up method with centrifugation in density gradient for the separation of X-bearing spermatozoa. Sperm viability and integrity were evaluated through the Trypan Blue/Giemsa staining method. Quality control of centrifuged spermatozoa was performed in in vitro produced embryos. The results were validated by the sex ratio of in vitro produced embryos using PCR by Y- specific sequences present in bovine male genomic DNA. After determining genetic sex of in vitro produced embryos, the results showed difference (P<0.05) in deviation of sex ratio when comparing the control group (45.2% females) with the other spermatozoa selection procedures (60.6% females) (P<0.05). The sperm selection methods are capable of selecting X-bearing spermatozoa without compromising the spermatozoa fertility (cleavage and blastocyst rates, 70% and 26%, respectively) and were considered relevant methods to be introduced in bovine in vitro produced embryo programs.

O objetivo do presente trabalho foi associar o método de swim-up modificado à centrifugação em gradiente de densidade para a separação de espermatozoides portadores do cromossomo X. A viabilidade e a integridade espermática foram avaliadas pelo método de coloração Azul de Tripan e Giemsa. O controle de qualidade dos espermatozoides centrifugados foi realizado por meio da produção in vitro de embriões bovinos. Os resultados foram validados pela técnica de PCR para verificar a proporção sexual dos embriões produzidos in vitro, com o uso de sequências Y especificas presente no DNA genômico de machos bovinos. Após determinar o sexo genético dos embriões produzidos in vitro, os resultados não mostraram diferença (P<0,05) no desvio da proporção do sexo quando comparou o grupo controle (45,2% de fêmeas) com os outros processos de seleção de espermatozoides (60,6% de fêmeas) (P<0,05). Os métodos de seleção de espermatozoides são capazes de selecionar espermatozoides portadores do cromossomo X sem comprometer a fertilidade, medida pelas taxas de clivagem e blastocisto de 70% e 26%, respectivamente, e foram considerados métodos de relevância para serem introduzidos nos programas de produção in vitro de embriões bovinos.