Accounting for population structure in selective cow genotyping strategies

The objective of the present study was to investigate the impact of considering population structure in cow genotyping strategies over the accuracy and bias of genomic predictions. A small dairy cattle population was simulated to address these objectives. Based on four main traditional designs (random, top‐yield, extreme‐yield and top‐accuracy cows), different numbers (1,000; 2,000 and 5,000) of cows were sampled and included in the reference population. Traditional designs were replicated considering or not population structure and compared among and with a reference population containing only bulls. The inclusion of cows increased accuracy in all scenarios compared with using only bulls. Scenarios accounting for population structure when choosing cows to the reference population slightly outperformed their traditional versions by yielding higher accuracy and lower bias in genomic predictions. Building a cow‐based reference population from groups of related individuals considering the frequency of individuals from those same groups in the validation population yielded promising results with applications on selection for expensive‐ or difficult‐to‐measure traits. Methods here presented may be easily implemented in both new or already established breeding programs, as they improved prediction and reduced bias in genomic evaluations while demanding no additional costs.     

Pedigree analysis and inbreeding depression on growth traits in Brazilian Marchigiana and Bonsmara breeds

The study of population structure by pedigree analysis is useful to identify important circumstances that affect the genetic history of populations. The intensive use of a small number of superior individuals may reduce the genetic diversity of populations. This situation is very common for the beef cattle breeds. Therefore, the objectives of the present study were to analyze the pedigree and possible inbreeding depression on traits of economic interest in the Marchigiana and Bonsmara breeds and to test the inclusion of the individual inbreeding coefficient (F(i)) or individual increases in inbreeding coefficient (ΔF(i)) in the genetic evaluation model for the quantification of inbreeding depression. The complete pedigree file of the Marchigiana breed included 29,411 animals born between 1950 and 2003. For the Bonsmara breed, the pedigree file included 18,695 animals born between 1988 and 2006. Only animals with at least 2 equivalent generations of known pedigree were kept in the analyses of inbreeding effect on birth weight, weaning weight measured at about 205 d, and BW at 14 mo in the Marchigiana breed, and on birth weight, weaning weight, and scrotal circumference measured at 12 mo in the Bonsmara breed. The degree of pedigree knowledge was greater for Marchigiana than for Bonsmara animals. The average generation interval was 7.02 and 3.19 for the Marchigiana and Bonsmara breed, respectively. The average inbreeding coefficient was 1.33% for Marchigiana and 0.26% for Bonsmara. The number of ancestors explaining 50% of the gene pool and effective population size computed via individual increase in coancestry were 13 and 97.79 for Marchigiana and 41 and 54.57 for Bonsmara, respectively. These estimates indicate reduction in genetic variability in both breeds. Inbreeding depression was observed for most of the growth traits. The model including ΔF(i) can be considered more adequate to quantify inbreeding depression. The inclusion of F(i) or ΔF(i) in the genetic evaluation model may not result in better fit to the data. A genetic evaluation with simultaneous estimation of inbreeding depression can be performed in Marchigiana and Bonsmara breeds, providing additional information to producers and breeders.     

沧州市滨海盐碱区耕层土壤盐分特征

为了解沧州市滨海盐碱区耕层土壤的盐渍化特征,采集三个时期沧州不同地区耕层土壤（0~20 cm）样品,结合样品实验分析,探究土壤盐分特征。结果表明：①沧州滨海盐碱区耕层土壤离子类型多样,检测的八大离子中氯离子、钠离子、硫酸根、碳酸根+碳酸氢根离子为主要盐分离子,土壤类型为硫酸盐-氯化物型。②相关分析表明,耕层土样中总含盐量与氯离子和钠离子均存在显著或极显著相关关系,沧州市滨海盐碱地耕层土壤的总含盐量一定程上取决于土壤中氯化钠的含量;氯化钠、氯化镁和氯化钙为氯化物的主要组成部分;主要硫酸盐类为硫酸钠、硫酸镁和硫酸钙。③方差分析表明,三个不同采样时期和不同地区均对沧州市滨海区盐碱地的盐渍化的影响存在显著或极显著差异。④主成分分析表明,钠离子、氯离子、镁离子、钙离子和硫酸根与第1主成分相关性较高;钾离子和碳酸根+碳酸氢根与第2主成分相关性较高;第3主成分主要反映硅酸盐类对土壤离子成分的影响。由于钠离子、氯离子、钙离子和硫酸根在土壤中含量相对较高,是表征沧州滨海盐碱区土壤盐渍化的主要特征因子。     

Circulating Metabolic Hormones During the Peripubertal Period and Their Association with Testicular Development in Bulls

The objective of the present study was to characterize changes in serum metabolic hormones concentrations from 20 weeks before to 20 weeks post-puberty in bulls and to investigate the associations of metabolic hormones concentrations with testicular development. Leptin concentrations increased from 16 weeks before puberty to 8 weeks post-puberty and insulin concentrations increased from puberty to 8 weeks post-puberty. Growth hormone concentrations decreased after 4 weeks post-puberty, whereas IGF-I concentrations increased from 8 weeks before puberty to 8 weeks post-puberty. During this period, testicular growth was accelerated and testosterone secretion increased substantially, without any significant changes in gonadotropin secretion. Monthly circulating concentrations of leptin, IGF-I and insulin accounted for 63% of the variation in scrotal circumference and 59% of the variation in paired testes volume. In conclusion, the secretion of metabolic hormones was not associated with changes in gonadotropins concentrations. Furthermore, the associations of leptin, IGF-I and insulin concentrations with testes size indicated that these hormones might be involved in a gonadotropin-independent mechanism regulating the testicular development in peripubertal bulls.     

Inclusion of weaning management group as a random effect in the genetic evaluation of postweaning traits in Nellore cattle

The objective of this study was to evaluate the impact of including weaning management group (WMG) as an uncorrelated random effect in the genetic evaluation of postweaning traits. Data from 186,507 Nellore animals' sons to 1,734 sires and 75,016 cows were analyzed. Three single-trait models were studied. These models included the contemporary group (CG) as a fixed effect and age of animal at measurement and age of dam at calving as covariates, in addition to the direct additive breeding value as random effect. The CGs for postweaning traits varied between models which included or not WMG as part of the concatenation of fixed effects. In the model in which WMG was not part of the CG, the trait was included as an uncorrelated random effect. The results suggest that although no significant effects were observed on genetic parameter estimates or animal ranking, the inclusion of WMG as an uncorrelated random effect increased the number of observations per CG and contributed to maintaining animals in the analysis that would be discarded because they were in a CG with a small number of observations. This model could therefore be recommended for the genetic evaluation of this Nellore population.     

Testicular traits as selection criteria for young Nellore bulls

The objective of this study was to evaluate the possible use of biometric testicular traits as selection criteria for young Nellore bulls using Bayesian inference to estimate heritability coefficients and genetic correlations. Multitrait analysis was performed including 17,211 records of scrotal circumference obtained during andrological assessment (SCAND) and 15,313 records of testicular volume and shape. In addition, 50,809 records of scrotal circumference at 18 mo (SC18), used as an anchor trait, were analyzed. The (co)variance components and breeding values were estimated by Gibbs sampling using the Gibbs2F90 program under an animal model that included contemporary groups as fixed effects, age of the animal as a linear covariate, and direct additive genetic effects as random effects. Heritabilities of 0.42, 0.43, 0.31, 0.20, 0.04, 0.16, 0.15, and 0.10 were obtained for SC18, SCAND, testicular volume, testicular shape, minor defects, major defects, total defects, and satisfactory andrological evaluation, respectively. The genetic correlations between SC18 and the other traits were 0.84 (SCAND), 0.75 (testicular shape), 0.44 (testicular volume), -0.23 (minor defects), -0.16 (major defects), -0.24 (total defects), and 0.56 (satisfactory andrological evaluation). Genetic correlations of 0.94 and 0.52 were obtained between SCAND and testicular volume and shape, respectively, and of 0.52 between testicular volume and testicular shape. In addition to favorable genetic parameter estimates, SC18 was found to be the most advantageous testicular trait due to its easy measurement before andrological assessment of the animals, even though the utilization of biometric testicular traits as selection criteria was also found to be possible. In conclusion, SC18 and biometric testicular traits can be adopted as a selection criterion to improve the fertility of young Nellore bulls.