Defects in tracheoesophageal and lung morphogenesis in Nkx2.1(-/-) mouse embryos

NKX2.1 is a homeodomain transcriptional factor expressed in thyroid, lung, and parts of the brain. We demonstrate that septation of the anterior foregut along the dorsoventral axis, into distinct tracheal and esophageal structures, is blocked in mouse embryos carrying a homozygous targeted disruption of the Nkx2.1 locus. This is consistent with the loss of Nkx2.1 expression, which defines the dorsoventral boundary within the anterior foregut in wild-type E9 embryos. Failure in septation between the trachea and the esophagus in Nkx2.1(-/-) mice leads to the formation of a common lumen that connects the pharynx to the stomach, serving both as trachea and as esophagus, similar in phenotype to a human pathologic condition termed tracheoesophageal fistula. The main-stem bronchi bifurcate from this common structure and connect to profoundly hypoplastic lungs. The mutant lungs fail to undergo normal branching embryogenesis, consist of highly dilated sacs that are not capable of sustaining normal gas exchange functions, and lead to immediate postnatal death. In situ hybridization suggests reduced Bmp-4 expression in the mutant lung epithelium, providing a possible mechanistic clue for impaired branching. Functional deletion of Nkx2. 1 blocks pulmonary-specific epithelial cell differentiation marked by the absence of pulmonary surfactant protein gene expression. Altered expression of temporally regulated genes such as Vegf demonstrates that the lung in Nkx2.1(-/-) mutant embryos is arrested at early pseudoglandular (E11-E15) stage. These results demonstrate a critical role for Nkx2.1 in morphogenesis of the anterior foregut and the lung as well as in differentiation of pulmonary epithelial cells.

Relationships in broiler chickens between lameness, liveweight, growth rate and age

Thirteen genotypes of poultry were selected to represent a wide range of growth profiles and were fed either a non-limiting or Label Rouge diet. The birds' degree of lameness and liveweight were measured after 54 and 81 days. The birds reared on the Label Rouge diets were less lame than birds of the same genotype reared on the non-limiting diet. More traditional and slower growing genotypes tended to be less lame than the modern genotypes reared on the same feeding regimen. All the birds, irrespective of their genotype or diet, were less lame after 54 days than after 81 days. However, when liveweight was included in the analysis as a covariable, many of the differences disappeared. Only age at assessment significantly affected the walking ability of the birds, with the birds being approximately 0.6 units of gait score worse at 54 days of age than at 81 days. The regression coefficient between gait score and liveweight was 1.262 at 54 days and 1.128 at 84 days. The results indicated that liveweight was an important determinant of lameness in the diverse range of genotypes examined, that growth rate was also an important determinant of lameness and that younger birds may be more sensitive to differences in liveweight than older birds.

Effects of age and stocking density on leg weakness in broiler chickens

The effects of stocking density (STD) on leg weakness in broiler chickens was assessed in two trials. The interaction between age and STD on leg weakness was further evaluated in one trial. In Trial 1, walking ability was assessed at 28, 42, and 49 d of age. Birds were stocked at 833, 625, or 435 cm2 per bird. In Trial 2, birds were stocked at 625 or 455 cm2 per bird and assessed for tibial dyschondroplasia (TD) by radiographic examination at 28 d and walking ability at 35 d. Foot pad burn, hock burn, and angulation of the hock joint were also assessed at slaughter on Day 42. Body weight was measured during both trials. At 4 wk of age, leg weakness was a relatively minor problem; few severely lame birds had a gait score (GS) of 4 or 5 at any density. However, 2 wk later, the birds had substantially poorer walking ability. Further deterioration had occurred by 7 wk of age. At all ages, males exhibited greater leg weakness than did females, and the proportion of severely lame birds increased with age of assessment. The effect of STD was consistent across both trials; higher STD were associated with poorer walking ability and reduced live weights. In Trial 2, higher STD resulted in more foot and hock burns. Females were more sensitive to STD than were males However, there was no effect of STD on the prevalence of TD or angulation of the hock joint. The effect of high STD on walking ability was apparent even at 4 wk of age. Adjusting the observations for differences in BW did not alter the findings. It was concluded that the lower STD substantially reduced the prevalence of leg weakness.

Divergent selection on feather pecking behaviour in laying hens (Gallus gallus domesticus)

A selection experiment was initiated in 1996 in which selection for (HP line) and against (LP line) feather pecking was performed. The foundation stock was a White Leghorn layer strain established in 1970 and maintained since then as a random bred control line at the Institute. Six hatches were produced over three generations. At the age of 68 weeks (generation 0, 1996), 35 weeks (generation 1, 1997), 30 weeks (generation 2, 1998), and 27 weeks (generation 3, 1999) female birds were transferred to observation pens and their feather pecking behaviour was recorded. In each generation, 30 females and 8 males were selected from approximately 200 females and 60 males. The selection criterion was breeding value estimated by animal model on the trait 'number of bouts of feather pecking per bird per hour'.Feather pecking behaviour in adult hens was significantly higher in HP than in LP. In generation 2 the following was recorded: 3.10 versus 1.37 bouts per bird per hour (P<0.01), 7.04 versus 3.58 pecks per bird per hour (P<0.05) and the proportion of hens recorded feather pecking in the 180min observation period was 67 versus 56% (P<0.05). In generation 3 the following was recorded: 4.56 versus 0.63 bouts per bird per hour (P<0.001), 13.9 versus 2.51 pecks per bird per hour (P<0.001) and the proportion of hens recorded feather pecking in the 180min observation period was 75 versus 49% (P<0.001).In generation 3, plumage condition was better in LP on neck, breast, back, wings and tail, as well as overall (P<0.001). Body weight did not differ between lines in generation 2, but in generation 3, HP hens were on average heavier than LP hens at the age of 27 weeks (1435g versus 1371g, P<0.001).

Heterogeneity of gene expression in stromal fibroblasts of human breast carcinomas and normal breast

Breast carcinoma invasion is associated with prominent alterations in stromal fibroblasts. Carcinoma-associated fibroblasts (CAF) support and promote tumorigenesis, whereas normal mammary fibroblasts (NF) are thought to suppress tumor progression. Little is known about the difference in gene expression between CAF and NF or the patient-to-patient variability in gene expression. Paired CAF and NF were isolated from six primary human breast carcinoma specimens. RNA was extracted from low-passage cultures of CAF and NF and analyzed with Affymetrix Human Genome U133 Plus 2.0 arrays. The array data were examined with an empirical Bayes model and filtered according to the posterior probability of equivalent expression and fold difference in expression. Twenty-one genes (27 probe sets) were up-regulated in CAF, as compared to NF. Known functions of these genes relate to paracrine or intracellular signaling, transcriptional regulation, extracellular matrix and cell adhesion/migration. Ten genes (14 probe sets) were down-regulated in CAF, including the pluripotency transcription factor KLF4. Quantitative RT-PCR analysis of 10 genes validated the array results. Immunohistochemical staining for three gene products confirmed stromal expression in terms of location and relative quantity. Surprisingly, the variability of gene expression was slightly higher in NF than in CAF, suggesting inter-individual heterogeneity of normal stroma.

Quantitative trait loci markers derived from whole genome sequence data increases the reliability of genomic prediction

This study investigated the effect on the reliability of genomic prediction when a small number of significant variants from single marker analysis based on whole genome sequence data were added to the regular 54k single nucleotide polymorphism (SNP) array data. The extra markers were selected with the aim of augmenting the custom low-density Illumina BovineLD SNP chip (San Diego, CA) used in the Nordic countries. The single-marker analysis was done breed-wise on all 16 index traits included in the breeding goals for Nordic Holstein, Danish Jersey, and Nordic Red cattle plus the total merit index itself. Depending on the trait's economic weight, 15, 10, or 5 quantitative trait loci (QTL) were selected per trait per breed and 3 to 5 markers were selected to tag each QTL. After removing duplicate markers (same marker selected for more than one trait or breed) and filtering for high pairwise linkage disequilibrium and assaying performance on the array, a total of 1,623 QTL markers were selected for inclusion on the custom chip. Genomic prediction analyses were performed for Nordic and French Holstein and Nordic Red animals using either a genomic BLUP or a Bayesian variable selection model. When using the genomic BLUP model including the QTL markers in the analysis, reliability was increased by up to 4 percentage points for production traits in Nordic Holstein animals, up to 3 percentage points for Nordic Reds, and up to 5 percentage points for French Holstein. Smaller gains of up to 1 percentage point was observed for mastitis, but only a 0.5 percentage point increase was seen for fertility. When using a Bayesian model accuracies were generally higher with only 54k data compared with the genomic BLUP approach, but increases in reliability were relatively smaller when QTL markers were included. Results from this study indicate that the reliability of genomic prediction can be increased by including markers significant in genome-wide association studies on whole genome sequence data alongside the 54k SNP set.

Selection for litter size at day five to improve litter size at weaning and piglet survival rate

Selection for total number of piglets born (TNB) since 1992 has led to a significant increase in this trait in Danish Landrace and Danish Yorkshire but has also been accompanied by an increase in piglet mortality. The objective of this study was to estimate the genetic and phenotypic parameters for litter size and survival to find alternative selection criteria to improve litter size at weaning. Data from Landrace (9,300 litters) and Yorkshire (6,861 litters) were analyzed using REML based on a linear model including genetic effects of sow and service-sire. The estimates of heritability (based on the sow component) for TNB, number born alive (NBA), and number alive at d 5 after birth (N5D) and at weaning (about 3 wk, N3W) ranged from 0.066 to 0.090 in Landrace and 0.050 to 0.070 in Yorkshire. Genetic correlations between TNB and N3W were 0.289 in Landrace and 0.561 in Yorkshire, but between N5D and N3W the estimated genetic correlation was 0.995 in both populations. The approximate estimates of heritability for survival rate per litter at birth (SVB = NBA/TNB), from birth to d 5 (SV5 = N5D/NBA), and from d 5 to weaning (SVW = N3W/N5D) were 0.130, 0.131, and 0.023, respectively, in Landrace, and 0.095, 0.043, and 0.009, respectively, in Yorkshire. Genetic correlations between TNB and survival rates at different stages were negative. On the other hand, genetic correlations between N5D and survival rates and between N3W and survival rates were strongly or moderately positive, except for the correlations with SVW in Yorkshire. The results suggest that selection for N5D could be an interesting alternative to improve litter size at weaning and piglet survival for Danish Landrace and Danish Yorkshire.

Different commercial broiler crosses have different susceptibilities to leg weakness

A trial was conducted to investigate the susceptibility of different genotypes of broilers to leg weakness. Four crosses of commercial broiler lines were assessed. Birds were reared on commercial diets at commercial stocking densities. Indices of leg weakness examined included: walking ability, tibial dyschondroplasia (TD), foot pad burn, hock burn, and angulation of the hock joint. Body weight and feed efficiency were also measured. There were small differences in BW and feed efficiency among the commercial crosses; however, there were large differences in some of the indices of leg weakness among the crosses. Three crosses had similar prevalence of TD; one cross had much less TD than the others. There were large differences in walking ability among crosses. There were also differences among crosses in the prevalence of foot pad and hock burn and angulation of the hock joint. Adjusting the observations for differences in BW did not substantially alter the findings. There were differences among genotypes regarding the correlation coefficients between walking ability and BW, walking ability and hock burn, and TD and BW. It was concluded that there were large differences in some important traits associated with leg weakness among the commercial line crosses.

Comparison of genomic predictions using medium-density (∼54,000) and high-density (∼777,000) single nucleotide polymorphism marker panels in Nordic Holstein and Red Dairy Cattle populations

This study investigated genomic prediction using medium-density (∼54,000; 54K) and high-density marker panels (∼777,000; 777K), based on data from Nordic Holstein and Red Dairy Cattle (RDC). The Holstein data comprised 4,539 progeny-tested bulls, and the RDC data 4,403 progeny-tested bulls. The data were divided into reference data and test data using October 1, 2001, as a cut-off date (birth date of the bulls). This resulted in about 25% genotyped bulls in the Holstein test data and 20% in the RDC test data. For each breed, 3 data sets of markers were used to predict breeding values: (1) 54K data set with missing genotypes, (2) 54K data set where missing genotypes were imputed, and (3) imputed high-density (HD) marker data set created by imputing the 54K data to the HD data based on 557 bulls genotyped using a 777K single nucleotide polymorphism chip in Holstein, and 706 bulls in RDC. Based on the 3 marker data sets, direct genomic breeding values (DGV) for protein, fertility, and udder health were predicted using a genomic BLUP model (GBLUP) and a Bayesian mixture model with 2 normal distributions. Reliability of DGV was measured as squared correlations between deregressed proofs (DRP) and DGV corrected for reliability of DRP. Unbiasedness was assessed by regression of DRP on DGV, based on the bulls in the test data sets. Averaged over the 3 traits, reliability of DGV based on the HD markers was 0.5% higher than that based on the 54K data in Holstein, and 1.0% higher than that in RDC. In addition, the HD markers led to an improvement of unbiasedness of DGV. The Bayesian mixture model led to 0.5% higher reliability than the GBLUP model in Holstein, but not in RDC. Imputing missing genotypes in the 54K marker data did not improve genomic predictions for most of the traits.

Foot Pad Dermatitis and Hock Burn in Broiler Chickens and Degree of Inheritance

A total of 2,118 birds from 2 strains were allocated to 12 groups of 93 to 100 each in 2 time-separated replicates. The development of foot pad dermatitis (FPD) and hock burn (HB) were recorded weekly from d 8 to slaughter on a set sample of live animals (7 per group). In addition, feet and hocks of all birds were investigated at slaughter at either 4, 6 (fast-growing strain), 8, or 10 (slow-growing strain) wk of age. Lesions were scored for both the left and right foot and classified according to a scale from 1 (no lesion) to 9 (very severe lesions) for FPD and from 1 (no lesion) to 3 (very severe lesions) for HB. No FPD lesions and very few low-grade HB lesions were found in chickens from the slow-growing strain. In the fast-growing strain, the first signs of FPD and HB were seen in wk 2. The incidence of both types of lesions increased thereafter. Foot pad dermatitis was more frequent in females (49 vs. 36%, P < 0.05). Body weight did not affect FPD, but more HB were found at higher BW (P < 0.01). Egg weight influenced neither FPD nor HB. Variance and covariance components were analyzed using a multivariate animal model, in which scores for FPD and HB were transformed into logarithmic scale. The analyses were carried out using restricted maximum likelihood algorithm. Heritabilities were estimated to be 0.31 +/- 0.12 (SE) for FPD, 0.08 +/- 0.08 for HB, and 0.38 +/- 0.13 for BW. Genetic correlations among these traits were low and nonsignificant. Phenotypic correlation between BW and FPD was low and nonsignificant and between BW and HB was 0.17 +/- 0.05 (P < 0.01). The relative high heritability of FPD and the low genetic correlation to BW suggested that genetic selection against susceptibility to FPD should be possible without negative effects on BW gain.

Bayesian analysis of the linear reaction norm model with unknown covariates

The reaction norm model is becoming a popular approach for the analysis of genotype x environment interactions. In a classical reaction norm model, the expression of a genotype in different environments is described as a linear function (a reaction norm) of an environmental gradient or value. An environmental value is typically defined as the mean performance of all genotypes in the environment, which is usually unknown. One approximation is to estimate the mean phenotypic performance in each environment and then treat these estimates as known covariates in the model. However, a more satisfactory alternative is to infer environmental values simultaneously with the other parameters of the model. This study describes a method and its Bayesian Markov Chain Monte Carlo implementation that makes this possible. Frequentist properties of the proposed method are tested in a simulation study. Estimates of parameters of interest agree well with the true values. Further, inferences about genetic parameters from the proposed method are similar to those derived from a reaction norm model using true environmental values. On the other hand, using phenotypic means as proxies for environmental values results in poor inferences.

Host Specialization in the Charcoal Rot Fungus, Macrophomina phaseolina

ABSTRACT To investigate host specialization in Macrophomina phaseolina, the fungus was isolated from soybean, corn, sorghum, and cotton root tissue and soil from fields cropped continuously to these species for 15 years in St. Joseph, LA. Chlorate phenotype of each isolate was determined after growing on a minimal medium containing 120 mM potassium chlorate. Consistent differences in chlorate sensitivity were detected among isolates from different hosts and from soil versus root. To further explore genetic differentiation among fungal isolates from each host, these isolates were examined by restriction fragment length polymorphism and random amplified polymorphic DNA (RAPD) analysis. No variations were observed among isolates in restriction patterns of DNA fragments amplified by polymerase chain reaction covering the internal transcribed spacer region, 5.8S rRNA and part of 25S rRNA, suggesting that M. phaseolina constitutes a single species. Ten random primers were used to amplify the total DNA of 45 isolates, and banding patterns resulting from RAPD analysis were compared with the neighbor-joining method. Isolates from a given host were genetically similar to each other but distinctly different from those from other hosts. Chlorate-sensitive isolates were distinct from chlorate-resistant isolates within a given host. In greenhouse tests, soybean, sorghum, corn, and cotton were grown separately in soil infested with individual isolates of M. phaseolina that were chosen based on their host of origin and chlorate phenotype. Root colonization and plant weight were measured after harvesting. More colonization of corn roots occurred when corn was grown in soil containing corn isolates compared with isolates from other hosts. However, there was no host specialization in isolates from soybean, sorghum, or cotton. More root colonization in soybean occurred with chlorate-sensitive than with chlorate-resistant isolates.

Meal feeding is more effective than early feed restriction at reducing the prevalence of leg weakness in broiler chickens

Two trials were conducted to investigate whether manipulation of feeding pattern or early feed intake affected the prevalence of leg weakness in broiler chickens. In Trial 1, the birds were offered two, three, or four meals per day or consumed feed ad libitum. In Trial 2, a multifactorial design was used with age at start, duration of restriction, and severity of restriction as factors. The start of restrictions were at 5, 7, or 9 d, duration of restriction was 5 or 7 d, and feed was restricted to achieve 25, 50, and 75% of predicted growth during the restriction period. Ad libitum birds served as controls. Leg weakness was assessed by gait scoring (GS) and tibial dyschondroplasia (TD) by radiography. Foot burn, hock burn, angulation of the hock joint, feed consumption, and body weight gain were also assessed. The response of the birds to meal feeding was clear. Fewer meals per day was associated with less TD, less hock burn, better walking ability, lower body weight, and better feed conversion. The response of the birds to feed restriction was also clear. Earlier restriction, longer duration, and more severe level of restriction were all associated with lower prevalence of TD, better walking ability, lower body weight, and better relative growth rates and feed efficiency. However, adjusting the observations for differences in body weight removed many of the significant differences; only birds that started feed restriction earlier had less TD. From these trials, it was concluded that meal feeding can beneficially affect the prevalence of leg weakness, and that the major part of this effect is independent of changes in body weight. It was also concluded that early feed restriction reduced many aspects of leg weakness, but that these effects were mainly a result of reduced body weight. Meal feeding and early feed restriction improved feed efficiency.

Historical and contemporary multilocus population structure of Ascochyta rabiei (teleomorph: Didymella rabiei) in the Pacific Northwest of the United States

The historical and contemporary population genetic structure of the chickpea Ascochyta blight pathogen, Ascochyta rabiei (teleomorph: Didymella rabiei), was determined in the US Pacific Northwest (PNW) using 17 putative AFLP loci, four genetically characterized, sequence-tagged microsatellite loci (STMS) and the mating type locus (MAT). A single multilocus genotype of A. rabiei (MAT1-1) was detected in 1983, which represented the first recorded appearance of Ascochyta blight of chickpea in the PNW. During the following year many additional alleles, including the other mating type allele (MAT1-2), were detected. By 1987, all alleles currently found in the PNW had been introduced. Highly significant genetic differentiation was detected among contemporary subpopulations from different hosts and geographical locations indicating restricted gene flow and/or genetic drift occurring within and among subpopulations and possible selection by host cultivar. Two distinct populations were inferred with high posterior probability which correlated to host of origin and date of sample using Bayesian model-based population structure analyses of multilocus genotypes. Allele frequencies, genotype distributions and population assignment probabilities were significantly different between the historical and contemporary samples of isolates and between isolates sampled from a resistance screening nursery and those sampled from commercial chickpea fields. A random mating model could not be rejected in any subpopulation, indicating the importance of the sexual stage of the fungus both as a source of primary inoculum for Ascochyta blight epidemics and potentially adaptive genotypic diversity.

Reduction in the risk of clinical fractures after a single dose of zoledronic Acid 5 milligrams

CONTEXT

Annual infusions of zoledronic acid 5 mg over 3 years have been shown to reduce fracture incidence. There is now evidence that the effects of a single dose of zoledronic acid on bone mineral density and bone turnover last for much more than a year. Whether this is associated with sustained fracture prevention is not known.

OBJECTIVE

The objective of the study was to assess fracture incidence after only 1 infusion of zoledronic acid.

DESIGN

The design of the study included post hoc analysis of subgroups of subjects from 2 trials, who received only 1 study infusion.

SETTING

The study included multicenter, randomized controlled trials.

PARTICIPANTS

A total of 1367 subjects from HORIZON-PFT and HORIZON-RFT studies who received only 1 of the planned annual infusions participated in the study.

INTERVENTION

The intervention of the study consisted of 1 infusion of zoledronic acid or placebo.

MAIN OUTCOME MEASURE

Clinical fracture was the main outcome measure of the study.

RESULTS

Mean follow-up period was 1.5 years. In patients who received only a single infusion, there was a 32% reduction in clinical fracture comparing zoledronic acid with placebo over 3 years of follow-up (95% confidence interval 2-53%, P = .04), comparable with the fracture reduction seen in those who had 3 or more annual infusions (34%; 95% confidence interval, 23-43%, P < .0001). New morphometric vertebral fractures were reduced by 68% in the single-infusion group (P = .004). The between-group differences in total hip bone mineral density at 3 years were 3.8% in those receiving 1 infusion and 6.2% in those receiving 3 infusions.

CONCLUSIONS

In this post hoc analysis based on postrandomization subgroups, fracture risk appears to be reduced for more than 1 year after a single infusion of zoledronic acid. Prospective studies designed to assess this possibility are now warranted.

Effect of imputing markers from a low-density chip on the reliability of genomic breeding values in Holstein populations

The purpose of this study was to investigate the imputation error and loss of reliability of direct genomic values (DGV) or genomically enhanced breeding values (GEBV) when using genotypes imputed from a 3,000-marker single nucleotide polymorphism (SNP) panel to a 50,000-marker SNP panel. Data consisted of genotypes of 15,966 European Holstein bulls from the combined EuroGenomics reference population. Genotypes with the low-density chip were created by erasing markers from 50,000-marker data. The studies were performed in the Nordic countries (Denmark, Finland, and Sweden) using a BLUP model for prediction of DGV and in France using a genomic marker-assisted selection approach for prediction of GEBV. Imputation in both studies was done using a combination of the DAGPHASE 1.1 and Beagle 2.1.3 software. Traits considered were protein yield, fertility, somatic cell count, and udder depth. Imputation of missing markers and prediction of breeding values were performed using 2 different reference populations in each country: either a national reference population or a combined EuroGenomics reference population. Validation for accuracy of imputation and genomic prediction was done based on national test data. Mean imputation error rates when using national reference animals was 5.5 and 3.9% in the Nordic countries and France, respectively, whereas imputation based on the EuroGenomics reference data set gave mean error rates of 4.0 and 2.1%, respectively. Prediction of GEBV based on genotypes imputed with a national reference data set gave an absolute loss of 0.05 in mean reliability of GEBV in the French study, whereas a loss of 0.03 was obtained for reliability of DGV in the Nordic study. When genotypes were imputed using the EuroGenomics reference, a loss of 0.02 in mean reliability of GEBV was detected in the French study, and a loss of 0.06 was observed for the mean reliability of DGV in the Nordic study. Consequently, the reliability of DGV using the imputed SNP data was 0.38 based on national reference data, and 0.48 based on EuroGenomics reference data in the Nordic validation, and the reliability of GEBV using the imputed SNP data was 0.41 based on national reference data, and 0.44 based on EuroGenomics reference data in the French validation.

Comparison of different methods for imputing genome-wide marker genotypes in Swedish and Finnish Red Cattle

This study investigated the imputation accuracy of different methods, considering both the minor allele frequency and relatedness between individuals in the reference and test data sets. Two data sets from the combined population of Swedish and Finnish Red Cattle were used to test the influence of these factors on the accuracy of imputation. Data set 1 consisted of 2,931 reference bulls and 971 test bulls, and was used for validation of imputation from 3,000 markers (3K) to 54,000 markers (54K). Data set 2 contained 341 bulls in the reference set and 117 in the test set, and was used for validation of imputation from 54K to high density [777,000 markers (777K)]. Both test sets were divided into 4 groups according to their relationship to the reference population. Five imputation methods (Beagle, IMPUTE2, findhap, AlphaImpute, and FImpute) were used in this study. Imputation accuracy was measured as the allele correct rate and correlation between imputed and true genotypes. Results demonstrated that the accuracy was lower when imputing from 3K to 54K than from 54K to 777K. Using various imputation methods, the allele correct rates varied from 93.5 to 97.1% when imputing from 3K to 54K, and from 97.1 to 99.3% when imputing from 54K to 777K; IMPUTE2 and Beagle resulted in higher accuracies and were more robust under various conditions than the other 3 methods when imputing from 3K to 54K. The accuracy of imputation using FImpute was similar to those results from Beagle and IMPUTE2 when imputing from 54K to high density, and higher than the remaining 2 methods. The results also showed that a closer relationship between test set and reference set led to a higher accuracy for all the methods. In addition, the correct rate was higher when the minor allele frequency was lower, whereas the correlation coefficient was lower when the minor allele frequency was lower. The results indicate that Beagle and IMPUTE2 provide the most robust and accurate imputation accuracies, but considering computing time and memory usage, FImpute is another alternative method.

Influence of early or late start of first feeding on growth and immune phenotype of broilers

1. The changes in body weight (BW) gain, immune phenotype and viability of commercial broilers, either given feed and water immediately after hatch or food-deprived for 24 or 48 h, were analysed in order to study the effect of early or late start of first feeding. 2. Chickens fed immediately had a 6.1% higher BW at slaughter age than those food-deprived for 48 h, while those chickens food-deprived for 24 h only had a 1.4% higher weight than those deprived for 48 h. 3. Those fed immediately and those food-deprived for 24 h did not differ significantly in BW. 4. Humoral immune status was measured as specific IgG antibody production and concentration of IgM and IgG in serum. Cellular immunological variables were the proportion of circulating leukocyte subpopulations and the relative expression of leukocyte surface markers, including the relative expression of Major Histocompatibility Complex (MHC) antigens. 5. Differences were found between the three feeding treatments in the relative expression of MHC class II molecules, the relative expression of BU-1 molecules, and the ratio of CD4:CD8 single positive cells. 6. For the MHC class II molecules, a lower expression was found on the surface of mainly B-cells in chickens fed immediately compared with the two other feeding regimes. 7. These results suggest that food deprivation for 48 h may be unfavourable to the growth, viability, and the immune performance of broilers, whereas deprivation for 24 h appears to be acceptable for growth and normal immunological performance.

The effect of photoperiod:scotoperiod on leg weakness in broiler chickens

Four trials were conducted to investigate whether manipulations of photoperiod:scotoperiod affected the prevalence of leg weakness in broiler chickens. Modified photoperiods were applied from 3 until 21 d of age, followed by gradual or immediate return to 23 h light. The photoperiods tested were 8, 16, 21, and 23 h light. Leg weakness was assessed by measuring walking ability by gait scoring (GS) and tibial dyschondroplasia by x-ray (TD). Foot burn, hock burn, angulation of the hock joint, and BW were also measured. In total, 4,640 birds were assessed. The responses of the birds across the four trials were consistent. Increased photoperiod was associated with increased BW and prevalence of TD. There was no clear relationship between photoperiod and GS but foot pad burns were reduced by longer photoperiod. When the data were adjusted for differences in BW, increased photoperiod was associated with increased prevalence of TD, better walking ability (GS), and fewer hock and foot pad burns. Strong correlations were found between GS and live weight, and weak correlations with hock burn and TD. Tibial dyschondroplasia was weakly correlated with BW. The linear regressions of GS on live weight, within sex, across trials, were not different, but there was a difference between sexes, with males having a higher intercept but lower slope than females. It was concluded that shorter photoperiod affected walking ability and TD, but that these effects were largely a result of BW.

Regulation of Na(+)-K(+)-Cl(-) cotransporter in primary astrocytes by dibutyryl cAMP and high [K(+)](o)

In this study, we examined the Na(+)-K(+)-Cl(-) cotransporter activity and expression in rat cortical astrocyte differentiation. Astrocyte differentiation was induced by dibutyryl cAMP (DBcAMP, 0. 25 mM) for 7 days, and cells changed from a polygonal to process-bearing morphology. Basal activity of the cotransporter was significantly increased in DBcAMP-treated astrocytes (P < 0.05). Expression of an approximately 161-kDa cotransporter protein was increased by 91% in the DBcAMP-treated astrocytes. Moreover, the specific [(3)H]bumetanide binding was increased by 67% in the DBcAMP-treated astrocytes. Inhibition of protein synthesis by cyclohexamide (2-3 microgram/ml) significantly attenuated the DBcAMP-mediated upregulation of the cotransporter activity and expression. The Na(+)-K(+)-Cl(-) cotransporter in astrocytes has been suggested to play a role in K(+) uptake. In 75 mM extracellular K(+) concentration, the cotransporter-mediated K(+) influx was stimulated by 147% in nontreated cells and 79% in DBcAMP-treated cells (P < 0.05). To study whether this high K(+)-induced stimulation of the cotransporter is attributed to membrane depolarization and Ca(2+) influx, the role of the L-type voltage-dependent Ca(2+) channel was investigated. The high-K(+)-mediated stimulation of the cotransporter activity was abolished in the presence of either 0.5 or 1.0 microM of the L-type channel blocker nifedipine or Ca(2+)-free HEPES buffer. A rise in intracellular free Ca(2+) in astrocytes was observed in high K(+). These results provide the first evidence that the Na(+)-K(+)-Cl(-) cotransporter protein expression can be regulated selectively when intracellular cAMP is elevated. The study also demonstrates that the cotransporter in astrocytes is stimulated by high K(+) in a Ca(2+)-dependent manner.

Comparison between genomic predictions using daughter yield deviation and conventional estimated breeding value as response variables

This study compared genomic predictions using conventional estimated breeding values (EBV) and daughter yield deviations (DYD) as response variables based on simulated data. Eight scenarios were simulated in regard to heritability (0.05 and 0.30), number of daughters per sire (30, 100, and unequal numbers with an average of 100 per sire) and numbers of genotyped sires (all or half of sires were genotyped). The simulated genome had a length of 1200 cM with 15,000 equally spaced Single-nucleotide polymorphism (SNP) markers and 500 randomly distributed Quantitative trait locus (QTL). In the simulated scenarios, the EBV approach was as effective as or slightly better than the DYD approach at predicting breeding value, dependent on simulated scenarios and statistical models. Applying a Bayesian common prior model (the same prior distribution of marker effect variance) and a linear mixed model (GBLUP), the EBV and DYD approaches provided similar genomic estimated breeding value (GEBV) reliabilities, except for scenarios with unequal numbers of daughters and half of sires without genotype, for which the EBV approach was superior to the DYD approach (by 1.2 and 2.4%). Using a Bayesian mixture prior model (mixture prior distribution of marker effect variance), the EBV approach resulted in slightly higher reliabilities of GEBV than the DYD approach (by 0.3-3.6% with an average of 1.9%), and more obvious in scenarios with low heritability, small or unequal numbers of daughters, and half of sires without genotype. Moreover, the results showed that the correlation between GEBV and conventional parent average (PA) was lower (corresponding to a relatively larger gain by including PA) when using the DYD approach than when using the EBV approach. Consequently, the two approaches led to similar reliability of an index combining GEBV and PA in most scenarios. These results indicate that EBV can be used as an alternative response variable for genomic prediction.

Stimulation of Na-K-2Cl cotransporter in neurons by activation of Non-NMDA ionotropic receptor and group-I mGluRs

In a previous study, we found that Na(+)-K(+)-2Cl(-) cotransporter in immature cortical neurons was stimulated by activation of the ionotropic N-methyl-D-aspartate (NMDA) glutamate receptor in a Ca(2+)-dependent manner. In this report, we investigated whether the Na(+)-K(+)-2Cl(-) cotransporter in immature cortical neurons is stimulated by non-NMDA glutamate receptor-mediated signaling pathways. Expression of the Na(+)-K(+)-2Cl(-) cotransporter and metabotropic glutamate receptors (mGluR1 and 5) was detected in cortical neurons via immunoblotting and immunofluorescence staining. Significant stimulation of cotransporter activity was observed in the presence of both trans-(+/-)-1-aminocyclopentane-trans-1,3-dicarboxylic acid (trans-ACPD) (10 microM), a metabotropic glutamate receptor (mGluR) agonist, and (RS)-3,5-dihydroxyphenylglycine (DHPG) (20 microM), a selective group-I mGluR agonist. Both trans-ACPD and DHPG-mediated effects on the cotransporter were eradicated by bis-(o-aminophenoxy)-N,N,N',N'-tetraacetic acid-AM, a Ca(2+) chelator. In addition, DHPG-induced stimulation of the cotransporter activity was inhibited in the presence of mGluRs antagonist (RS)-1-aminoindan-1,5-dicarboxylic acid (AIDA) (1 mM) and also with selective mGluR1 antagonist 7-(hydroxyimino)cyclopropa[b]chromen-1a-carboxylate ethyl ester (CPCCOEt) (100 microM). A DHPG-induced rise in intracellular Ca(2+) in cortical neurons was detected with Fura-2. Moreover, DHPG-mediated stimulation of the cotransporter was abolished by inhibition of Ca(2+)/CaM kinase II. Interestingly, the cotransporter activity was increased by activation of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor. These results suggest that the Na(+)-K(+)-2Cl(-) cotransporter in immature cortical neurons is stimulated by group-I mGluR- and AMPA-mediated signal transduction pathways. The effects are dependent on a rise of intracellular Ca(2+).

Selection for increased number of piglets at d 5 after farrowing has increased litter size and reduced piglet mortality

Selection for litter size at d 5 after farrowing (LS5) was introduced in 2004 to increase the number of piglets weaned and to reduce piglet mortality in Danish Landrace and Yorkshire. The objective of this study was to investigate selection responses for LS5, total number born (TNB), and mortality [MORT, defined as (TNB - LS5)/TNB] when selection for increasing LS5 was a part of the breeding goal. Data were collected from nucleus herds recorded from 2004 to 2010, including first litters of 42,807 Landrace sows and 33,225 Yorkshire sows. The data were analyzed using a 3-trait animal model of TNB, MORT, and LS5. Significant (co) variances were estimated between the 3 traits in both populations. The heritabilities of TNB, MORT, and LS5 were 0.10, 0.09, and 0.09 in Landrace and 0.12, 0.10, and 0.10 in Yorkshire. The genetic correlations were 0.28 and 0.22 between TNB and MORT, 0.74 and 0.68 between TNB and LS5, and -0.43 and -0.57 between MORT and LS5 in Landrace and Yorkshire, respectively. The results show that the genetic improvement of LS5 was a combination of increased TNB and reduced MORT. During the observation period, the genetic improvement was 1.7 piglets per litter for LS5, 1.3 piglets per litter for TNB, and 4.7% for MORT in Landrace and 2.2 piglets per litter, 1.9 piglets per litter, and 5.9% in Yorkshire. Phenotypic improvement was 1.4 piglets per litter for LS5, 0.3 piglets per litter for TNB, and 7.9% for MORT in Landrace and 2.1 piglets per litter, 1.3 piglets per litter, and 7.6% in Yorkshire. In addition, genetic gain was evaluated in 3 phenotypic groups of TNB, representing the 25% smallest litters, the 50% medium litters, and the 25% largest litters. In all 3 groups, the genetic and phenotypic gains of TNB and LS5 increased, whereas MORT reduced in both populations.

Improvement in genetic evaluation of female fertility in dairy cattle using multiple-trait models including milk production traits

This study investigated the improvement in genetic evaluation of fertility traits by using production traits as secondary traits (MILK = 305-d milk yield, FAT = 305-d fat yield, and PROT = 305-d protein yield). Data including 471,742 records from first lactations of Denmark Holstein cows, covering the years of inseminations during first lactations from 1995 to 2004, were analyzed. Six fertility traits (i.e., interval in days from calving to first insemination, calving interval, days open, interval in days from first to last insemination, numbers of inseminations per conception, and nonreturn rate within 56 d after first service) were analyzed using single- and multiple-trait sire models including 1 or 3 production traits. Model stability was evaluated by correlation between EBV from 2 sub-data sets (DATA(A) and DATA(B)). Model predictive ability was assessed by the correlation between EBV from training data (DATA(A) or DATA(B)) and daughter performance (yield deviation, defined as average of daughter-records adjusted for nongenetic effects) from test data (DATA(B) or DATA(A)) in a cross-validation procedure, and correlation between EBV obtained from the whole data set (DATA(T)) and from a reduced data set (DATA(C1), which only contained the first crop daughters) for proven bulls. In addition, the superiority of the models was evaluated by expected reliability of EBV, calculated from the prediction error variance of EBV. Based on these criteria, the models combining milk production traits showed better model stability and predictive ability than single-trait models for all the fertility traits, except for nonreturn rate within 56 d after first service. The stability and predictive ability for the model including MILK or PROT were similar to the model including all 3 milk production traits and better than the model including FAT. In addition, it was found that single-trait models underestimated genetic trend of fertility traits. These results suggested that genetic evaluation of fertility traits would be improved using a multiple-trait model including MILK or PROT.