F. F. Cardoso

Predators Suppress Aphis glycines Matsumura Population Growth in Soybean

Abstract The soybean aphid, Aphis glycines Matsumura, is an invasive pest of soybean, first discovered in North America in 2000. We studied the ability of the existing predator community in soybean to suppress A. glycines population growth during June–August 2002, in field studies using predator exclusion and sham cages or no-cage controls. Cages were infested with uniform initial densities of A. glycines adults, and subsequent populations of aphids and predators were monitored. After 2 wk, exclusion and sham cages were switched, with aphid and predator density followed for additional 2 wk. The experiment was repeated a second time, allowing observation of predator community response to both low and high density aphid populations over several time periods and stages of soybean development. Cages had minimal effects on temperature, relative humidity, or soybean growth. In contrast, predator communities and aphid populations were strongly affected by cage treatments. In the first trial, the activity of foliar-foraging predators effectively prevented A. glycines population growth maintaining populations below 10 aphids per plant (adult + nymphs) in sham cages, while populations exceeded 200 aphids per plant in exclusion cages. After cage switch, these high A. glycines populations in the former exclusion cages were rapidly colonized and reduced by nearly an order of magnitude within 2 wk by a combination of generalist and specialist predators. The second trial produced qualitatively similar results, but at much lower aphid densities. The most abundant predators in both trials included: Harmonia axyridis Pallas, Orius insidiosus (Say), and Leucopis spp. These studies demonstrate that existing predator communities comprised of a mixture of indigenous and naturalized species can suppress A. glycines population density in soybean. The impact of existing predator communities should be further investigated as a component of A. glycines management in United States soybean production systems.

Impact of predation on establishment of the soybean aphid, Aphis glycines in soybean, Glycine max

The soybean aphid, Aphis glycines Matsumura is a new invasive pest of soybean in North America. We studied the ability of the existing predator community in soybean to reduce A. glycines establishment in field studies using either predator exclusion, open, or leaky cages that allowed aphid emigration but limited predation. Cages were infested with uniform initial densities of A. glycines adults and subsequent populations of aphids and predators were monitored over 24 h. The most abundant predators in these trials included the carabid beetles Elaphropus anceps (Le Conte), Clavina impressefrons Le Conte, Bembidion quadrimaculatum Say and spiders (Salticidae and Lycosidae). Foliar predators were less abundant and included; Harmonia axyridis Pallas, Coccinella septempunctata (L.), and Orius insidious (Say). Over the 2-year study, we found statistically significant predation on adult A. glycines in one out of six trials at 15 h and two out of six trials at 24 h. There was never significant evidence for predation of nymphs in any trial, however overall survival (adults + nymphs) was significantly reduced in one out of six trials at 15 h and three out of six trials at 24 h. Based on these results we suggest that generalist predators can be a significant but variable factor influencing the establishment of A. glycines populations in soybean. The impact of existing predator communities should be further investigated as a means of managing A.␣glycines populations in North American soybean production systems.

Componentes de (co)variância e parâmetros genéticos de caracteres pós-desmama em bovinos da raça Angus

ABSTRACT - (Co)variance components were determined for post-weaning traits, and covariances with birth weight (BW) and pre-weaning traits, in Angus cattle using an animal model. Records of weaning and yearling weights of 18,921 animals were used and fromthese 4,452 had complete evaluations of visual scores at weaning and post-weaning phases. Records of BW were available for 11,788animals. Heritabilities of post-weaning gain (GP205) and visual scores for conformation (YC), precocity (YP), muscling (YM) and size(YS) were 0.20, 0.19, 0.25, 0.26 and 0.24, respectively. Genetic correlations among all traits considered were positive: between GP205and visual scores the range was from 0.50 to 0.71; for yearling scores among themselves from 0.22 to 0.94; between GP205 and BW was0.14; between GP205 and pre-weaning gain was 0.23 and for the same score at weaning and yearling stages they varied from 0.90 to 0.99.These results indicate that it is possible to select for GP205 without a significant increase in BW and that the selection for GP205 shouldproduce a correlated genetic change on yearling visual scores.Key Words: Angus, beef cattle, genetic correlation, heritability, post-weaning period

Linear reaction norm models for genetic merit prediction of Angus cattle under genotype by environment interaction

The objectives of this work were to assess alternative linear reaction norm (RN) models for genetic evaluation of Angus cattle in Brazil. That is, we investigated the interaction between genotypes and continuous descriptors of the environmental variation to examine evidence of genotype by environment interaction (G×E) in post-weaning BW gain (PWG) and to compare the environmental sensitivity of national and imported Angus sires. Data were collected by the Brazilian Angus Improvement Program from 1974 to 2005 and consisted of 63,098 records and a pedigree file with 95,896 animals. Six models were implemented using Bayesian inference and compared using the Deviance Information Criterion (DIC). The simplest model was M(1), a traditional animal model, which showed the largest DIC and hence the poorest fit when compared with the 4 alternative RN specifications accounting for G×E. In M(2), a 2-step procedure was implemented using the contemporary group posterior means of M(1) as the environmental gradient, ranging from -92.6 to +265.5 kg. Moreover, the benefits of jointly estimating all parameters in a 1-step approach were demonstrated by M(3). Additionally, we extended M(3) to allow for residual heteroskedasticity using an exponential function (M(4)) and the best fitting (smallest DIC) environmental classification model (M(5)) specification. Finally, M(6) added just heteroskedastic residual variance to M(1). Heritabilities were less at harsh environments and increased with the improvement of production conditions for all RN models. Rank correlations among genetic merit predictions obtained by M(1) and by the best fitting RN models M(3) (homoskedastic) and M(5) (heteroskedastic) at different environmental levels ranged from 0.79 and 0.81, suggesting biological importance of G×E in Brazilian Angus PWG. These results suggest that selection progress could be optimized by adopting environment-specific genetic merit predictions. The PWG environmental sensitivity of imported North American origin bulls (0.046 ± 0.009) was significantly larger (P < 0.05) than that of local sires (0.012 ± 0.013). Moreover, PWG of progeny of imported sires exceeded that of native sires in medium and superior production levels. On the other hand, Angus cattle locally selected in Brazil tended to be more robust to environmental changes and hence be more suitable when production environments for potential progeny is uncertain.

Genotype × environment interaction for long-yearling weight in Canchim cattle quantified by reaction norm analysis.

The objective of this study was to investigate the presence of genotype × environment interactions (G×E) for long-yearling weight in Canchim cattle (5/8 Charolais + 3/8 zebu) in Brazil using reaction norms (RN). The hierarchical RN model included the fixed effect of age of the animal (linear coefficient) and random effects of contemporary groups and additive animal genetic intercept and slope of the RN and contemporary group effects as random effects. Contemporary groups as the most elemental representation of management conditions in beef cattle were chosen to represent the environmental covariate of the RN. The deviance information criteria demonstrated that a homoskedastic residual RN model provided a better data fit compared with a heteroskedastic counterpart and with a traditional animal model, which had the worst fit. The environmental gradient for long-yearling weight based on contemporary group effects ranged from -105 to 150 kg. The additive direct variance and heritability estimates increased with increasing environmental gradient from 74.33 ± 22.32 to 1,922.59 ± 258.99 kg(2) and from 0.08 ± 0.02 to 0.68 ± 0.03, respectively. The high genetic correlation (0.90 ± 0.03) between the intercept and the slope of the RN shows that animals with the greatest breeding values best responded to environmental improvement, characterizing scale effect as the source of G×E for long-yearling weight. The phenotypic plasticity demonstrated by the slope of the RN of the animal indicates the possibility to change genotype expression along the environmental gradient through selection. The results demonstrate the importance of accounting for G×E in the genetic evaluation of this population.

Genome-wide linkage analysis of global gene expression in loin muscle tissue identifies candidate genes in pigs.

Background Nearly 6,000 QTL have been reported for 588 different traits in pigs, more than in any other livestock species. However, this effort has translated into only a few confirmed causative variants. A powerful strategy for revealing candidate genes involves expression QTL (eQTL) mapping, where the mRNA abundance of a set of transcripts is used as the response variable for a QTL scan. Methodology/Principal Findings We utilized a whole genome expression microarray and an F2 pig resource population to conduct a global eQTL analysis in loin muscle tissue, and compared results to previously inferred phenotypic QTL (pQTL) from the same experimental cross. We found 62 unique eQTL (FDR <10%) and identified 3 gene networks enriched with genes subject to genetic control involved in lipid metabolism, DNA replication, and cell cycle regulation. We observed strong evidence of local regulation (40 out of 59 eQTL with known genomic position) and compared these eQTL to pQTL to help identify potential candidate genes. Among the interesting associations, we found aldo-keto reductase 7A2 (AKR7A2) and thioredoxin domain containing 12 (TXNDC12) eQTL that are part of a network associated with lipid metabolism and in turn overlap with pQTL regions for marbling, % intramuscular fat (% fat) and loin muscle area on Sus scrofa (SSC) chromosome 6. Additionally, we report 13 genomic regions with overlapping eQTL and pQTL involving 14 local eQTL. Conclusions/Significance Results of this analysis provide novel candidate genes for important complex pig phenotypes.

Componentes de (co)variância e parâmetros genéticos para caracteres produtivos à desmama de bezerros Angus criados no Estado do Rio Grande do Sul

(Co) variance components and genetic parameters for birth weight (BW), adjusted weaning gain (AWG) and for conformation (WC), precocity (WP), muscling (WM) and size (WS) scores at weaning were estimated, from records of 40,915 Angus calves, raised in the state of Rio Grande do Sul, southern Brazil. From that data, 12,706 had birth weight records and 11,863 had complete records for visual scores (VS). The data were analyzed using an animal model, in uni and multivariate analyses, and the variance components estimated by restrict maximum likelihood. The direct additive heritabilities estimated were 0.29, 0.25, 0.18, 0.19, 0.19 and 0.21, respectively for BW, AWG, WC, WP, WM and WS. Maternal heritability for AWG was 0.16 and genetic correlation between direct and maternal effects was ¾0.51. This high negative correlation indicates antagonism between these effects and decreases total heritability for AWG to 0.18. The contribution of dam permanent environment to phenotypic variance was between a minimum of 0.05 for BW and a maximum of 0.12 for AWG. Genetic correlation between BW and AWG was ¾0.06, showing that these traits are genetically non-dependent. The genetic correlations found between AWG and VS were from 0.71 to 0.86, and among VS traits from 0.58 to 0.91. These positive associations among VS traits and these with pre-weaning growth phase, support the simultaneous selection of these traits, by means of selection indexes.

Genotype by environment interaction characterization and model comparison for post weaning gain adjustment of Devon cattle via reaction norms

The objectives of this study were to verify the presence of the genotype by environment interaction and to compare different models to fit Devon cattle post weaning gain standardized to 345 days, via reaction norms obtained by random regression. Data from 14,973 calves collected by the beef cattle improvement program from 1980 to 2005 were used. The INTERGEN program was used for data analysis. First, a standard animal model (AM) was fitted to serve as comparison basis and to provide estimates of the environmental gradient, based on contemporary group (CG) deviations and, next, the reaction norms hierarchical models with homogeneous (RNHM) and heterogeneous (RNHMH) residual variances were run. In these last two models, fixed effects of age of dam and age of calf at yearling and random contemporary group and genetic effects (level and slope of animals reaction norms) were included. For the RNHM estimates of residual variance, reaction norm level and slope additive genetic variances and their genetic correlation were, respectively, 272.02 ± 8.51; 340.38 ± 17.11; 0.119 ± 0.006 and 0.83 ± 0.01, while for the RNHHM were 401.96 ± 11.91; 177.86 ± 16.60; 0.076 ± 0.006 and 0.72 ± 0.02, respectively. The heritability asa well as the genetic variance increased on the environmental gradient, characterizing that there is genotype by environment interaction. Based on the Deviance Information Criterion, Bayes Factors and Pseudo Bayes Factors, the NRHM provided superior fit to the data, being the most appropriate model to consider the genotype by environmental interaction of this population.

Fatores ambientais sobre escores de avaliação visual à desmama em bezerros angus criados no Rio Grande do Sul

The objectives of this study were to determine the importance of the effects of age of dam (AoD), sex (S) and age of calf (AC), month of birth (M) and the interaction between age of dam and sex (AoD*S) on visual scores (VS) for weaning conformation (WC), precocity (WP), muscling (WM) and size (WS) of Angus cattle, and to estimate correction factors for these effects. Data from 11,863 calves, controlled by the Beef Cattle Improvement Program (PROMEBO), between 1989 and 1997, were used. The data were analyzed using PROC MIXED of SAS. The model included the effects of contemporary group, M, AoD, S, AC (linear and quadratic), AoD*S and the random effect of sire. From the least square means of WC, WP, WM and WS, regression equations for M and AoD*S were estimated. The VS showed response to the effects of AoD, S and AC similar to the weight gain at the weaning phase. The age of calf was the factor responsible for the largest non-genetic variation in VS. Correction factors for AoD, AC and Julian birth date were proposed.

Accuracy of genome-wide imputation in Braford and Hereford beef cattle

BackgroundStrategies for imputing genotypes from the Illumina-Bovine3K, Illumina-BovineLD (6K), BeefLD-GGP (8K), a non-commercial-15K and IndicusLD-GGP (20K) to either Illumina-BovineSNP50 (50K) or to Illumina-BovineHD (777K) SNP panel, as well as for imputing from 50K, GGP-IndicusHD (90iK) and GGP-BeefHD (90tK) to 777K were investigated. Imputation of low density (<50K) genotypes to 777K was carried out in either one or two steps. Imputation of ungenotyped parents (n = 37 sires) with four or more offspring to the 50K panel was also assessed. There were 2,946 Braford, 664 Hereford and 88 Nellore animals, from which 71, 59 and 88 were genotyped with the 777K panel, while all others had 50K genotypes. The reference population was comprised of 2,735 animals and 175 bulls for 50K and 777K, respectively. The low density panels were simulated by masking genotypes in the 50K or 777K panel for animals born in 2011. Analyses were performed using both Beagle and FImpute software. Genotype imputation accuracy was measured by concordance rate and allelic R2 between true and imputed genotypes.ResultsThe average concordance rate using FImpute was 0.943 and 0.921 averaged across all simulated low density panels to 50K or to 777K, respectively, in comparison with 0.927 and 0.895 using Beagle. The allelic R2 was 0.912 and 0.866 for imputation to 50K or to 777K using FImpute, respectively, and 0.890 and 0.826 using Beagle. One and two steps imputation to 777K produced averaged concordance rates of 0.806 and 0.892 and allelic R2 of 0.674 and 0.819, respectively. Imputation of low density panels to 50K, with the exception of 3K, had overall concordance rates greater than 0.940 and allelic R2 greater than 0.919. Ungenotyped animals were imputed to 50K panel with an average concordance rate of 0.950 by FImpute.ConclusionFImpute accuracy outperformed Beagle on both imputation to 50K and to 777K. Two-step outperformed one-step imputation for imputing to 777K. Ungenotyped animals that have four or more offspring can have their 50K genotypes accurately inferred using FImpute. All low density panels, except the 3K, can be used to impute to the 50K using FImpute or Beagle with high concordance rate and allelic R2.