Bowman-Birk inhibitor affects pathways associated with energy metabolism in Drosophila melanogaster

Bowman-Birk inhibitor (BBI) is toxic when fed to certain insects, including the fruit fly, Drosophila melanogaster. Dietary BBI has been demonstrated to slow growth and increase insect mortality by inhibiting the digestive enzymes trypsin and chymotrypsin, resulting in a reduced supply of amino acids. In mammals, BBI influences cellular energy metabolism. Therefore, we tested the hypothesis that dietary BBI affects energy-associated pathways in the D. melanogaster midgut. Through microarray and metabolomic analyses, we show that dietary BBI affects energy utilization pathways in the midgut cells of D. melanogaster. In addition, ultrastructure studies indicate that microvilli are significantly shortened in BBI-fed larvae. These data provide further insights into the complex cellular response of insects to dietary protease inhibitors.

Precision genetics for complex objectives in animal agriculture

Indirect modification of animal genomes by interspecific hybridization, cross-breeding, and selection has produced an enormous spectrum of phenotypic diversity over more than 10,000 yr of animal domestication. Using these established technologies, the farming community has successfully increased the yield and efficiency of production in most agricultural species while utilizing land resources that are often unsuitable for other agricultural purposes. Moving forward, animal well-being and agricultural sustainability are moral and economic priorities of consumers and producers alike. Therefore, these considerations will be included in any strategy designed to meet the challenges produced by global climate change and an expanding world population. Improvements in the efficiency and precision of genetic technologies will enable a timely response to meet the multifaceted food requirements of a rapidly increasing world population.

A mixture model approach for the analysis of small exploratory microarray experiments

The microarray is an important and powerful tool for prescreening of genes for further research. However, alternative solutions are needed to increase power in small microarray experiments. Use of traditional parametric and even non-parametric tests for such small experiments lack power and have distributional problems. A mixture model is described that is performed directly on expression differences assuming that genes in alternative treatments are expressed or not in all combinations (i) not expressed in either condition, (ii) expressed only under the first condition, (iii) expressed only under the second condition, and (iv) expressed under both conditions, giving rise to 4 possible clusters with two treatments. The approach is termed a Mean-Difference-Mixture-Model (MD-MM) method. Accuracy and power of the MD-MM was compared to other commonly used methods, using both simulations, microarray data, and quantitative real time PCR (qRT-PCR). The MD-MM was found to be generally superior to other methods in most situations. The advantage was greatest in situations where there were few replicates, poor signal to noise ratios, or non-homogenous variances.

Transcriptional signatures in response to wheat germ agglutinin and starvation in Drosophila melanogaster larval midgut

One function of plant lectins such as wheat germ agglutinin is to serve as defences against herbivorous insects. The midgut is one critical site affected by dietary lectins. We observed marked cellular, structural and gene expression changes in the midguts of Drosophila melanogaster third instar larvae that were fed wheat germ agglutinin. Some of these changes were similar to those observed in the midguts of starved D. melanogaster. Dietary wheat germ agglutinin caused shortening, branching, swelling, distortion and in some cases disintegration of the midgut microvilli. Starvation was accompanied primarily by shortening of the microvilli. Microarray analyses revealed that dietary wheat germ agglutinin evoked differential expression of 61 transcripts; seven of these were also differentially expressed in starved D. melanogaster. The differentially transcribed gene clusters in wheat germ agglutinin-fed larvae were associated with (1) cytoskeleton organization; (2) digestive enzymes; (3) detoxification reactions; and (4) energy metabolism. Four possible transcription factor binding motifs were associated with the differentially expressed genes. One of these exhibited substantial similarity to MyoD, a transcription factor binding motif associated with cellular structures in mammals. These results are consistent with the hypothesis that wheat germ agglutinin caused a starvation-like effect and structural changes of midgut cells of D. melanogaster third-instar larvae.

Fitness components and ecological risk of transgenic release: a model using Japanese medaka (Oryzias latipes)

Any release of transgenic organisms into nature is a concern because ecological relationships between genetically engineered organisms and other organisms (including their wild-type conspecifics) are unknown. To address this concern, we developed a method to evaluate risk in which we input estimates of fitness parameters from a founder population into a recurrence model to predict changes in transgene frequency after a simulated transgenic release. With this method, we grouped various aspects of an organism's life cycle into six net fitness components: juvenile viability, adult viability, age at sexual maturity, female fecundity, male fertility, and mating advantage. We estimated these components for wild-type and transgenic individuals using the fish, Japanese medaka (Oryzias latipes). We generalized our model's predictions using various combinations of fitness component values in addition to our experimentally derived estimates. Our model predicted that, for a wide range of parameter values, transgenes could spread in populations despite high juvenile viability costs if transgenes also have sufficiently high positive effects on other fitness components. Sensitivity analyses indicated that transgene effects on age at sexual maturity should have the greatest impact on transgene frequency, followed by juvenile viability, mating advantage, female fecundity, and male fertility, with changes in adult viability, resulting in the least impact.

Comparison of genomic and traditional BLUP-estimated breeding value accuracy and selection response under alternative trait and genomic parameters

Accuracy of prediction of estimated breeding values based on genome-wide markers (GEBV) and selection based on GEBV as compared with traditional Best Linear Unbiased Prediction (BLUP) was examined for a number of alternatives, including low heritability, number of generations of training, marker density, initial distributions, and effective population size (Ne). Results show that the more the generations of data in which both genotypes and phenotypes were collected, termed training generations (TG), the better the accuracy and persistency of accuracy based on GEBV. GEBV excelled for traits of low heritability regardless of initial equilibrium conditions, as opposed to traditional marker-assisted selection, which is not useful for traits of low heritability. Effective population size is critical for populations starting in Hardy-Weinberg equilibrium but not for populations started from mutation-drift equilibrium. In comparison with traditional BLUP, GEBV can exceed the accuracy of BLUP provided enough TG are included. Unfortunately selection rapidly reduces the accuracy of GEBV. In all cases examined, classic BLUP selection exceeds what was possible for GEBV selection. Even still, GEBV could have an advantage over traditional BLUP in cases such as sex-limited traits, traits that are expensive to measure, or can only be measured on relatives. A combined approach, utilizing a mixed model with a second random effect to account for quantitative trait loci in linkage equilibrium (the polygenic effect) was suggested as a way to capitalize on both methodologies.

Genetic variation at the tumour virus B locus in commercial and laboratory chicken populations assessed by a medium-throughput or a high-throughput assay

The tumour virus B (TVB) locus encodes cellular receptors mediating infection by three subgroups of avian leukosis virus (B, D, and E). Three major alleles, TVB*S1, TVB*S3, and TVB*R, have been described. TVB*S1 encodes a cellular receptor mediating infection of subgroups B, D, and E. TVB*S3 encodes the receptor for two subgroups, B and D, and TVB*R encodes a dysfunctional receptor that does not permit infection by any of the subgroups, B, D, or E. Genetic diversity at the TVB locus of chickens was investigated in both layer and broiler commercial pure lines and laboratory lines. Genotyping assays were developed for both medium-throughput and high-throughput analysis. Of the 36 broiler lines sampled, 14 were fixed for the susceptible allele TVB*S1. Across all broiler lines, 83% of chickens were typed as TVB*S1/*S1, 3% as TVB*R/*R, and 14% as TVB*S1/*R. In the egg-layer lines, five of the 16 tested were fixed for TVB*S1/*S1. About 44% of egg-layers were typed as TVB*S1/*S1, 15% as TVB*R/*R, with the rest segregating for two or three of the alleles. In the laboratory chickens, 60% were fixed for TVB*S1/*S1, 6% for TVB*S3/*S3, 14% for TVB*R/*R, and the rest were heterozygotes (TVB*S1/*S3 or TVB*S1/*R). All commercial pure lines examined in this study carry the TVB*S1 allele that sustains the susceptibility to avian leukosis viruses B, D, and E. More importantly, the TVB*R allele was identified in multiple populations, thus upholding the opportunities for genetic improvement through selection.

Changes in Drosophila melanogaster midgut proteins in response to dietary Bowman-Birk inhibitor

The midgut proteome of Drosophila melanogaster was compared in larvae fed dietary Bowman-Birk inhibitor (BBI) vs. larvae fed a control diet. By using two-dimensional gel electrophoresis, nine differentially expressed proteins were observed, which were associated with enzymes or transport functions such as sterol carrier protein X (SCPX), ubiquitin-conjugating enzyme, endopeptidase, receptor signalling protein kinase, ATP-dependent RNA helicase and alpha-tocopherol transport. Quantitative real-time PCR verified differential expression of transcripts coding for six of the proteins observed from the proteomic analysis. BBI evidently affects expression of proteins associated with protein degradation, transport and fatty acid catabolism. We then tested the hypothesis that SCPX was critical for the Drosophila third instars' response to BBI treatment. Inhibition of SCPX caused the third instars to become more susceptible to dietary BBI.

Evidence for widespread epistatic interactions influencing Marek’s disease virus viremia levels in chicken

Marek's disease (MD), a T cell lymphoma induced by the Marek's disease virus (MDV), is the main chronic infectious disease concern threatening the poultry industry. Enhancing genetic resistance to MD in commercial poultry is an attractive method to augment MD vaccines, which is currently the control method of choice. In order to implement this control strategy through marker-assisted selection (MAS), it is necessary to identify quantitative trait loci (QTL) or genes that influence MD incidence. Previous studies have demonstrated that it is possible to identify QTL that confer MD resistance in both experimental and commercial chickens. With the advent of the chicken genome sequence and new genomic tools, and evidence that interactions are important in understanding complex traits, the line 6 x 7 F(2) experimental resource population was re-evaluated with finer resolution for epistatic interactions. The F(2) population, consisting of 272 individuals and previously genotyped with 133 genetic markers, was combined along with 576 additional single nucleotide polymorphisms (SNPs) genotyped on 80 individuals in each of the distribution tails for MD and other associated traits, and tested for the presence of main effects and two-way epistatic interactions accounting for MD incidence, viremia titers, and length of survival. Main effects were generally not significant but a large number of highly significant interactions, involving loci located throughout the genome, were identified that account for MDV viremia titers in infected birds. These results suggest that resistance to MD is highly complex and will require the incorporation of epistatic interaction analyses and functional genomic approaches to reveal the underlying genetic basis.

Genome-wide analysis of phenobarbital-inducible genes in Drosophila melanogaster

An oligoarray analysis was conducted to determine the differential expression of genes due to phenobarbital exposure in Drosophila melanogaster (w(1118) strain) third instar larvae. Seventeen genes were observed to be induced with increased expression by a statistical analysis of microarrays approach with a q < or = 0.05. At q < or = 0.12, four more genes (Cyp12d1, DmGstd4, and two genes with unknown function) were found to be up-regulated, and 11 genes with unknown function were found to be down-regulated. Fifteen of these genes, Cyp4d14, Cyp6a2, Cyp6a8, Cyp12d1, Cyp6d5, Cyp6w1, CG2065, DmGstd6, DmGstd7, Amy-p/Amy-d, Ugt86Dd, GC5724, Jheh1, Jheh2 and CG11893, were verified using quantitative real time polymerase chain reaction. Some of these genes have been shown to be over-transcribed in metabolically DDT-resistant Drosophila strains.

Application of One Sided t-tests and a Generalized Experiment Wise Error Rate to High-Density Oligonucleotide Microarray Experiments: An Example Using Arabidopsis

MOTIVATION: A formidable challenge in the analysis of microarray data is the identification of those genes that exhibit differential expression. The objectives of this research were to examine the utility of simple ANOVA, one sided t tests, natural log transformation, and a generalized experiment wise error rate methodology for analysis of such experiments. As a test case, we analyzed a Affymetrix GeneChip microarray experiment designed to test for the effect of a CHD3 chromatin remodeling factor, PICKLE, and an inhibitor of the plant hormone gibberellin (GA), on the expression of 8256 Arabidopsis thaliana genes. RESULTS: The GFWER(k) is defined as the probability of rejecting k or more true null hypothesis at a given p level. Computing probabilities by GFWER(k) was shown to be simple to apply and, depending on the value of k, can greatly increase power. A k value as small as 2 or 3 was concluded to be adequate for large or small experiments respectively. A one sided t-test along with GFWER(2)=.05 identified 43 genes as exhibiting PICKLE-dependent expression. Expression of all 43 genes was re-examined by qRT-PCR, of which 36 (83.7%) were confirmed to exhibit PICKLE-dependent expression.

Chronic social stress differentially regulates neuroendocrine responses in laying hens: II. Genetic basis of adrenal responses under three different social conditions

Chicken lines were divergently selected for both high (HGPS) or low (LGPS) group productivity and survivability resulting from cannibalism and flightiness in colony cages. Each line has unique characteristics in physical indexes, domestic behavior, and physiological responsiveness to stress. The differences between the selected lines could be reflected in differing regulation of the neuroendocrine system such as the hypothalamic-pituitary-adrenal axis. Change of the adrenal function is a key initial event in response to stress in animals, which differs for this trait. Comparisons between the selected lines showed that adrenal function was stable in HGPS hens but not in LGPS hens in response to chronic social stress. Social stress-induced adrenal hypertrophy and its positive correlation with plasma corticosterone concentrations were found in the LGPS hens but not in the HGPS hens. The data demonstrated that chickens selected for variations in productivity and survivability variously altered the adrenal system in response to social stressors. The results suggest that these chicken lines could be valuable animal models for biomedical investigation of the effect of genetic-environmental interactions on the neuroendocrine function in controlling stress responses.

Social stress differentially regulates neuroendocrine responses in laying hens: I. Genetic basis of dopamine responses under three different social conditions

Effects of genetic-environmental interactions on plasma dopamine (DA) concentrations were studied in White Leghorn chickens selected for both high (HGPS) or low (LGPS) group productivity and survivability resulting from cannibalism and flightiness. Plasma DA levels were measured from chickens in three social treatments: single-, two-, or ten-hen cages. The two-hen treatment consisted of paired chickens from three genetic lines: HGPS, LGPS and a commercial strain, Dekalb XL (DXL). In HGPS/DXL and LGPS/DXL pairs, the DXL hen was used as a standardized genetic competitor. The ten-hen treatment contained only hens from the same line, which is similar to the original selection condition. After 7 weeks housing in the social environments, LGPS hens in the ten-hen treatment had greater plasma DA concentrations than HGPS hens (P<0.05). Compared to levels in the ten-hen treatment from the same line, plasma DA concentrations in both HGPS and LGPS hens were significantly lower in the two-hen treatment (average mean, 0.09 vs. 0.15 ng/ml and 0.22 vs. 0.44 ng/ml, P<0.05, respectively), but significantly higher in the single-hen treatment (average mean, 0.44 vs. 0.15 ng/ml and 1.78 vs. 0.44 ng/ml, P<0.05 and P<0.01, respectively). In the single-hen treatment, LGPS hens had greater plasma DA levels than HGPS hens (P<0.05). The results provide evidence of genetically related differences in the regulation of chickens' plasma DA concentrations in response to social stress. These differences may magnify the behavioral and physiological differences observed in the lines under basal and challenged conditions. These results suggest that these chicken lines may provide a new model for investigating effects of DA on the control of behavioral, neural and endocrine responses to stress.

Social stress in laying hens: differential effect of stress on plasma dopamine concentrations and adrenal function in genetically selected chickens

Genetic selection for high or low group productivity and survivability (HGPS, LGPS) has created two phenotypically distinct chicken lines. Each line has unique characteristics in behavioral and physiological adaptability to multiple-bird cage system. The present study was designed to examine whether these differences reflect genetic variation in the control of plasma dopamine (DA) concentrations and adrenal function in response to social stress. Chickens from the HGPS and LGPS lines were randomly assigned to single- or 10-bird cages at 17 wk of age. The 10-bird cages were the same as those used in the development of the two lines. Differences in regulation of DA concentrations and adrenal function in response to different social environments were measured between the two lines when the study was conducted at 24 wk of age. In the 10-bird cages, the HGPS line had lower levels of DA (P < 0.05) and heavier adrenal glands (AG, P < 0.05) than those of the LGPS line, but concentrations of corticosterone (CORT) from the two lines were not significantly different. In the single-bird cages, DA levels in both lines were greater than in that of their siblings in the 10-bird cages, but a greater increase was found in the LGPS line (P < 0.01 and P < 0.05, 405% vs. 293%). Likewise, both lines had lower concentrations of CORT (P < 0.05) in the single- vs. 10-bird cages, but the AG were less heavy in the LGPS line but not in HGPS line in the single-bird cages (P < 0.05). The results indicated that the two strains reacted differently in terms of their stress hormone levels in the two different environments. These differences could contribute to the behavioral and physiological differences existing between the two lines.

Social stress in laying hens: differential dopamine and corticosterone responses after intermingling different genetic strains of chickens

White Leghorn chickens were genetically selected for high (HGPS) or low (LGPS) group productivity and survivability. The selection resulted in two genetic lines with marked opposite changes in cannibalism and flightiness when housed in multiple-colony battery cages without beak trimming. The objective of the study was to examine whether the genetic selection differentially affected the neuroendocrine system of chickens from different strains in response to social stress. Based on the previous studies, social stress was induced by randomly pairing 17-wk-old hens from three genetic lines, i.e., HGPS, LGPS, and Dekalb XL (DXL), to form three mixed-line combinations. At 24 wk of age, the concentrations of plasma dopamine (DA) and corticosterone (CORT) showed no differences in DXL hens housed with HGPS or LGPS hens (P > 0.05). However, different regulations of DA and adrenal function were found between HGPS and LGPS hens when paired with DXL hens. Compared to HGPS hens, LGPS hens had greater levels of DA and CORT (P < 0.01 and P < 0.05, respectively). In addition, under the HGPS-LGPS social treatment, the concentrations of DA but not CORT were greater in LGPS hens than in HGPS hens (P < 0.05 and P > 0.05, respectively). The results indicated genetic selection for production and survivability differentially altered DA and CORT systems in response to social stress. The data suggested, compared to LGPS hens, HGPS hens had a better coping capability to social stress, which might have been responsible for their higher productivity and survivability.

Possible ecological risks of transgenic organism release when transgenes affect mating success: sexual selection and the Trojan gene hypothesis

Widespread interest in producing transgenic organisms is balanced by concern over ecological hazards, such as species extinction if such organisms were to be released into nature. An ecological risk associated with the introduction of a transgenic organism is that the transgene, though rare, can spread in a natural population. An increase in transgene frequency is often assumed to be unlikely because transgenic organisms typically have some viability disadvantage. Reduced viability is assumed to be common because transgenic individuals are best viewed as macromutants that lack any history of selection that could reduce negative fitness effects. However, these arguments ignore the potential advantageous effects of transgenes on some aspect of fitness such as mating success. Here, we examine the risk to a natural population after release of a few transgenic individuals when the transgene trait simultaneously increases transgenic male mating success and lowers the viability of transgenic offspring. We obtained relevant life history data by using the small cyprinodont fish, Japanese medaka (Oryzias latipes) as a model. Our deterministic equations predict that a transgene introduced into a natural population by a small number of transgenic fish will spread as a result of enhanced mating advantage, but the reduced viability of offspring will cause eventual local extinction of both populations. Such risks should be evaluated with each new transgenic animal before release.

Improving animal well-being through genetic selection

This paper reviews the possibilities of adapting laying hens to cages by means of genetic selection. By selecting separately for rate of lay and longevity using a kin selection method, a strain of laying hen has been developed that shows much less feather pecking and cannibalism than a control strain, and with no decrease in productivity. This experimental strain enjoys a higher level of welfare in cages because it does not require beak trimming.

Selection index updating for maximizing rate of annual genetic gain in laying hens

Four selection strategies aimed at maximizing egg production in laying hens were compared with respect to expected annual genetic gain (GA). The selection strategies were: 1) (S1P) Traditional single-stage selection based on a single-house production system using partial records for both the individual and its ancestors, 2) Single-stage selection based on a single-house production system using full records for both the individual and its ancestors (S1F), 3) Single-stage selection based on a two-house production system using partial records for the individual and full records for its ancestors (S2P), and 4) Multistage selection based on a two-house production system using partial records for the individual and all available ancestral records (M2P). Strategy M2P resulted in the shortest generation interval (0.538 yr) and was the most efficient (deltaGA4 = 3.620 eggs per year), whereas strategy S1F generated the longest generation interval (2 yr) and was the least efficient (deltaGA2 = 1.334 eggs per year). Strategies S1P and S2P resulted in generation intervals of 1 yr, and were intermediate in efficiency (deltaGA1 = 2.232 eggs per year, deltaGA3 = 2.593 eggs per year). It was concluded that a two-house production system utilizing multistage selection was the most effective selection methodology. Further, selection based on M2P is expected to improve persistency of lay, whereas selection on S1P will not.

Genetic selection strategies: computer modeling

There are four primary factors to consider in genetic selection strategies: 1) accuracy of selection, 2) selection intensity, 3) effective population size, and 4) mating system. Current theory indicates that optimum response to selection is achieved by maximizing the first three factors and using a mating systems that allows optimization of reproductive characteristics in dam lines and production characteristics in sire lines. However, with limited resources, compromises among the first three factors are needed. Simulations are useful for examining those compromises. Unrealistic simplifying assumptions are necessary for analytic theoretical results and thus do not address real world breeding problems. Using simulations, the relationship between selection accuracy, which is increased by use of family selection indices or Best Linear Unbiased Prediction (BLUP), and response to selection was examined. Results show that those procedures place a great restriction on effective population size, which offsets most of their advantage, i.e., there is too little emphasis on effective population size. A revision of the methodology and a reappraisal of the results of selection theory for optimization of genetic response is required. Another relationship that is of fundamental importance in breeding programs is that between selection intensity and effective population size. Analytical results for the additive case have been developed but have never been extended to heterotic traits. A gene level simulation program was developed to examine that relationship. Results show that the optimal selection strategy depends on the trait being selected. For additive traits and in the short term (20 generations), one should maximize selection intensity. For heterotic traits, an intermediate proportion (25% of each sex) gives optimal response. In all breeding strategies, primary attention must be given to the rate of inbreeding, which is increased by increasing either accuracy of selection or selection intensity. Inbreeding reduces response to selection in two ways. First, for both additive and nonadditive traits, inbreeding is a measure of the amount of random genetic drift that has occurred. Genetic drift causes loss of favorable alleles. Once lost, those alleles can never be recovered and thus genetic drift lowers the selection limit. Second, for heterotic traits, inbreeding results in a depression of the mean caused by directional dominance.

Group selection for adaptation to multiple-hen cages: hematology and adrenal function

A selected line of White Leghorns that has shown improved survivability and productivity and reduced feather loss in multiple-hen cages was evaluated for hematological and adrenal responses under both stressed and unstressed conditions. It was hypothesized that hens selected for adaptation to multiple-bird cages would react less intensely to stressors. Three lines of chickens (selected, control, and commercial) were housed in either single-hen (1 hen) or multiple-hen cages (12 hens, social competition) at 16.7 or 17.1 wk of age. They were subsequently subjected to cold exposure at 33 wk of age and heat exposure at 44 wk of age. Genetic stock as a main effect, and the interaction of genetic stock with either a cold or heated environment or with cage size, had no effect on plasma levels of cholesterol and corticosterone. At the time of transfer to laying cages, the selected line of pullets, as indicated by a decrease in packed cell volume, appeared to adapt more quickly to the new waterer system of multiple-hen cages than did the control and commercial lines. At 33 wk of age, the control and commercial lines in multiple-hen cages experienced heterophilia and increased heterophil to lymphocyte ratios, whereas the selected line did not, when compared with these same lines in single-hen cages. This leucocytic response could be interpreted to mean that the selected line of chickens adapted better to social competition than either the control or commercial lines; however, a similar leucocytic response was not observed at 18 or 44 wk of age. In conclusion, the physiological characterization of the selected line of Leghorns showed evidence of improved adaptation to multiple-hen cages when compared to the other stocks. In some cases, the selected line responded less intensely to stress; however, trends were not always consistent.

Group selection for adaptation to multiple-hen cages: humoral immune response

A selected line of White Leghorns, which has shown improved survivability and reduced feather loss in large multiple-hen cages, was evaluated for humoral immune response to SRBC under both stressed and unstressed conditions. Three lines of chickens (selected, control, and commercial) were housed in either single- (1 hen) or multiple-hen cages (12 hens, social competition) and subjected to a cold ambient temperature (0 C) at 33 wk of age and to two heating episodes (38 C) at 44 wk of age. Each hen was challenged intravenously with 1 mL of a 7% saline suspension of SRBC at the time that cold exposure was initiated. Hens subjected to high ambient temperatures had been exposed previously to a cold temperature, but were not challenged with SRBC until 16 to 18 h following the end of the second heating episode. Exposure to cold caused immunosuppression in single-caged hens, but not in hens in colony cages. Single- vs colony-caged hens of the control environment challenged with SRBC at 33 wk of age had similar primary hemagglutinin responses to SRBC. Hens subjected to heat experienced immunosuppression at 9 and 12 d following challenge to SRBC when compared to the controls. Hens of multiple-bird cages challenged with antigen at 44 wk of age had a significantly lower hemagglutinin response to SRBC than those reared in single-bird cages. The three lines of genetic stock had similar primary hemagglutinin responses to SRBC; the interactions of genetic stock with cage size or environmental temperature were not significant. It was concluded that genetically selecting hens for survival in multiple-hen cages did not affect their humoral immune response to SRBC.

Group selection for adaptation to multiple-hen cages: production traits during heat and cold exposures

A selected line of White Leghorns that has shown improved survivability and productivity and reduced feather loss in multiple-hen cages was evaluated for production traits under both stressed and unstressed conditions. It was hypothesized that hens selected for adaptation to multiple-bird cages would react less intensely to stressors and therefore lay more eggs and have lower mortality under stressed conditions. Three lines of chickens (selected, control, and commercial) were housed in either single-hen (1 hen) or multiple-hen cages (12 hens, social competition) at 16.7 or 17.1 wk of age. They were subsequently subjected to cold exposure at 33 wk of age and heat exposure at 44 wk of age. The selected line of chickens in multiple-hen cages showed an increased resistance to heat exposure, as indicated by lower mortality, when compared to the control and commercial lines housed in multiple-hen cages. Egg production 8 d prior to, during, and 8 d following either cold or heat exposures indicated that the selected line of chickens withstood social, handling, and environmental stressors better than the control line and, in some cases, the commercial line of chickens. It was concluded that the selected line of Leghorns showed evidence of stress resistance through lowered mortality and improved production.

Group selection for adaptation to multiple-hen cages: behavioral responses

Three stocks of White Leghorns were compared for behavioral traits when kept in single-bird (1H) and 12-hen (12H) layer-house cages. Genetic stocks consisted of a commercial strain (X), a randombred control (C), and a stock derived from C and selected on the basis of kin's group performance information for increased survival and egg production over seven generations (S). Experimental units consisted of four consecutive 1H cages or a single 12H cage. All birds within a unit had intact beaks and were of the same stock. Each stock was represented by hens in 48 units of both 1H and 12H cages, and by 48 males (C and S stocks only) in 1H cages. Birds that died were replaced. Observations involved hens in their home cages except for tonic immobility (TI) and pair contests. Observations carried out soon after birds were placed in layer-house cages indicated that avoidance of the observer was essentially absent after pullets were observed on the 1st and 2nd d. Behavioral profile frequencies differed for nearly all behaviors compared in 1H and 12H environments. Following initially high crouching and low feeding frequencies, apparently normal levels were present by Days 15 and 16 posthousing. During the initial adaptation phase, genetic stock differences were not found within 1H cages and were present in only 2 of 10 categories in 12H cages. Young adult profiles also indicated no differences among stocks in 1H cages, but stock differences were found in 6 of 12 categories in 12H cages. In those cases, X strain hens differed from hens of the C and S stocks, but C and S hens did not differ from each other. Comparisons carried out between hens in 1H and 12H cages revealed that fearfulness was greater in 12H cages. Genetic stock comparisons, involving relative fearfulness and feeding and movement in a frustrating situation indicated that the X stock frequently differed from both C and S, but C and S did not usually differ from each other. However, observations of hens' agonistic activity in the 12H home cage environment revealed that the S stock had fewer agonistic acts than the C stock from which it was derived, and both C and S had less agonistic activity than the X stock. Pair contests carried out within and between C and S stocks in both sexes yielded results inconsistent with those for agonistic activity in 12H cages. The C and S hens did not differ, but S males were more aggressive and, in between-strain contests, were more dominant.

Useful DNA polymorphisms are identified by snapback, a midrepetitive element in Tribolium castaneum

The red flour bettle, Tribolium castaneum, is both a pest of stored grain products and an important experimental organism. To improve its facility as a genetic model, we are developing DNA fingerprinting methods for this insect. A Tribolium DNA fragment, snapback-1 (SBI), identified among sequences that reassociate before a Cot of 0.03 mol.s/L, was found to produce a banding pattern in restriction endonuclease digested genomic DNA that is characteristic of a midrepetitive element. DNA fingerprints of individual beetles demonstrated that unvarying inherited DNA polymorphism is revealed, and that polymorphism is inherited in a dominant Mendelian fashion. Linkage between bands was minimal. The sequence of SBI was determined, and hybridization experiments indicated that SBI is a fragment of a larger midrepetitive element. Fingerprinting individuals with known inbreeding coefficients indicated that SBI loci have relatively high mutation rates. The possibility that SBI is a fragment of a transposable element is discussed.

Group selection for adaptation to multiple-hen cages: selection program and direct responses

A selection experiment was initiated with a synthetic line of White Leghorns in 1982 to improve adaptability and well-being of layers in large multiple-bird cages by use of a selection procedure termed "group selection". With this procedure, each sire family was housed as a group in a multiple-bird cage and selected or rejected as a group. An unselected control, with approximately the same number of breeders as the selected line, was maintained for comparison and housed in one-third cages. Annual percentage mortality of the selected line in multiple-bird cages decreased from 68% in Generation (G)2 to 8.8% in G6. Percentage mortality in G6 of the selected line in multiple-bird cages was similar to that of the unselected control in one-bird cages (9.1%). Annual days survival improved from 169 to 348 d, eggs per hen per day (EHD) from 52 to 68%, eggs per hen housed from 91 to 237 eggs, and egg mass (EM) from 5.1 to 13.4 kg, whereas annual egg weight remained unchanged. The dramatic improvement in livability demonstrates that adaptability and well-being of these birds were improved by group selection. The similar survival of the selected line in multiple-bird cages and the control in one-bird cages suggests that break-trimming of the selected line would not further reduce mortalities, which implies that group selection may have eliminated the need to beak-trim. Corresponding improvements in EHD and EM demonstrate that such changes can also be profitable. The most surprising finding was the rate of which such improvement took place, with the majority of change in survival occurring by the third generation. However, EHD continued to improve at the rate of 4% per generation.

Group selection for adaptation to multiple-hen cages: beak-related mortality, feathering, and body weight responses

The hypothesis was tested that selection on the basis of family means for increased survival and hen-housed egg production, when sisters with intact beaks were kept together in multiple-bird cage, would cause adaptive changes in behavior. Specifically, it was posited that beak-inflicted injuries causing cannibalistic mortality and feather loss and damage would be reduced. Body weight effects were not predicted, but were examined. Three stocks were compared; the Selected (S), representing the seventh generation of selection, the Randombred Control (C) from which S was derived, and a commercial stock (X), known to be highly productive and peak-trimmed by commercial producers. Pullets were placed in single-bird (1H) as well as in 12-hen (12H) cages using a completely randomized block experimental design. Mortality from beak-inflicted injuries differed among stocks in total hens lost (P < 0.005). Of 576 per stock in 12H cages 287, 128, and 46 replacements were used from 17 to 44 wk in X, C, and S, respectively, to maintain group size. The C and S hens also differed from 44 to 59 wk and 17 to 59 wk. X hens were not included in comparisons of mortality beyond 44 wk. Relative incidence of mortality caused by vent-cloacal injuries differed with X > C = S (P < 0.005 for X vs C and S). For cages with > or = 1 cannibalistic death, X had twice (P < 0.025) and C 1.6 times (P < 0.10) as many with repeated losses as S. Means and variances of feather scores were different for 1H vs 12H cages, ages, and genetic stocks. Greater variances were observed in 12H cages and among older birds. Within 1H units, genetic stocks did not differ in general, but in 12H cages X and C were always more variable than S. In 12H cages, mean feather scores and body weights were decreased and S hens had better feathering than either C or X. The evidence supported the hypothesis.

Multistage selection for maximum economic return with an application to beef cattle breeding

Methodology for selection index updating was developed to allow multistage selection. The program determines truncation points for each stage of selection that will maximize either profit or the ratio of aggregate economic gain to cost (R = delta H/C). Either maximum profit or R may be attained by reducing the cost of performance testing in later stages of a multistage program. In order to eliminate the need for multiple integration and assure convergence, a piecewise algorithm was developed. Examples of beef bull selection compared single-stage selection at 1 yr of age, two-stage selection at birth and 1 yr, two-stage selection at 205 d and 1 yr, and three-stage selection at birth, 205 d, and 1 yr. Selection based on three traits (birth weight, gain birth to 205 d, and gain 205 to 365 d) was compared with selection based on four traits (the above three plus ultrasound fat depth) and selection based on five traits (the above four plus feed:gain ratio). Five scenarios were used that allowed variation in proportion of candidates selected for breeding, number of progeny per selected bull, and proportion of profit returned to the nucleus herd. General conclusions based on the examples were 1) multistage selection reduced aggregate economic gain relative to that attained by single-stage selection, 2) inclusion of feed conversion in the index of traits resulted in reduced profit and aggregate economic gain, 3) measurement of feed conversion could be justified when selected bulls produced a large number of progeny, and 4) three-trait selection produced greater profit in all five scenarios than did four- or five-trait selection. Use of the selection updating program described here provides a new source of information that can be used in developing economically sound performance testing and selection programs.

Partial and conditional maximum likelihood for variance-component estimation

SUMMARY

Patterson and Thompson's idea of 'error contrasts' (or restricted maximum likelihood) (1971) was extended to multiple sets of linear contrasts for variance component estimtion. The error contrasts were established in such a way that only errors are retained in the model. The error variance was then estimated by maximizing the likelihood function obtained from the error contrasts. More sets of linear contrasts were then progressively established such that each set of linear contrasts contains only one class of random effects and the errors. A likelihood function was constructed and maximized for each variance of random effects given the error variance held at its estimated value. The likelihood function for estimating the covariance component between two classes of random effects was established such that all other random effects are treated as fixed effects. The likelihood function was then maximized with respect to the covariance given the two variance components fixed at their estimated values. The multidimensional optimization problem in the traditional restricted maximum-likelihood problem was then turned into several one-dimensional optimization problems by using this technique. Inasmuch as the error variance was estimated using a partial likelihood function and the other variance components are estimated using likelihood functions conditional on the estimated error variance, the method is referred to as partial and conditional maximum likelihood (PCML). ZUSAMMENFASSUNG: Partielle und bedingte Maximum Likelihood zur Schätzung von Varianzkomponenten Die Patterson und Thompson Vorstellungen von 'Fehlerkontrasten' (1971) (oder beschränkte maximale Likelihood) wurde auf multiple Gruppen linearer Kontraste für Varianzkomponenten- schätzung ausgedehnt. Die Fehlerkontraste erfolgen in der Form, daß nur Fehler im Modell verbleiben. Die Fehlervarianz wurde dann durch Maximierung der Likelihood Funktion von Fehlerkontrasten geschätzt. Weitere Gruppen linearer Kontraste wurden nacheinander etabliert dergestalt, daß jede Gruppe linearer Kontraste nur eine Klasse zufälliger Wirkungen und die Fehler enthält. Eine Likelihood Funktion wurde konstruiert und für jede Varianz von Zufallsgrößen maximiert unter der Voraussetzung, daß die Fehlervarianz auf ihrem geschätzten Wert verbleibt. Die Likelihood Funktion zur Schätzung der Ko-Varianzkomponenten zwischen zwei Klassen zufälliger Wirkungen wurde in der Form aufgestellt, daß alle anderen Zufallswirkungen als fixe behandelt werden. Die Likelihood Funktion wurde maximiert im Hinblick auf Ko-Varianz bei gegebenen geschätzten Varianzkomponenten. Das multidimensionale Optimierungsproblem der traditionellen restringierten Maximum Likelihood wurde auf diese Weise in ein eindimensionales Optimierungsproblem verwandelt. Nachdem die Fehlervarianz aus der partiellen Likelihood Funktion und die anderen Varianzkomponenten unter Verwendung der bedingten Likelihood Funktionen geschätzt worden waren, wurde die Methode als partielle und bedingte Maximum Likelihood (pcml) bezeichnet.

Selection index updating

When traits become evident at different ages or there are large differences in the costs of measuring various traits, selection by independent culling levels may give a higher aggregate economic return than index selection because not all traits need to be measured on all individuals. The problems with optimum independent culling selection is that general solutions are not possible and numerical integration is needed for specific cases. Recently, Xu and Muir (1991) developed a new independent culling level procedure by use of orthogonal transformation of the original characters. With their procedure, explicit solutions for optimum truncation points are possible without numerical integration. As such, the procedure is proficient for any number of stages, and generalized theoretical comparisons of alternative breeding strategies are possible. However, their procedure was limited to the case where selection is for one character at each stage. In this paper, our previous results are extended to the general case of multi-stage index selection, called selection index updating. This procedure is called selection index updating because as traits become available in latter stages, each subsequent index contains all of the traits available up to that stage.The procedure is to develop sequential indices for each stage such that correlations among indices at different stages are zero. Optimum culling points are obtained for the updating procedure by using Xu and Muir's (1991) iterative equations. Due to the property of orthogonality of the updated indices, aggregate gain can be partitioned into gains due to various stages of selection. Partitioning of aggregate economic gain is useful to breeders who desire to adjust individual trait selection intensity based on facilities available at that stage. Methods are discussed to modify the procedure to obtain maximum aggregate economic return per unit of cost associated with obtaining measures on each trait. An application of multi-stage selection is demonstrated using a set of data for Rhode Island Red layer type chickens. A second example demonstrates the use of multi-stage selection optimized with respect to aggregate economic gain and costs associated with obtaining measurements.

Multistage selection for genetic gain by orthogonal transformation

An exact transformed culling method for any number of traits or stages of selection with explicit solution for multistage selection is described in this paper. This procedure does not need numerical integration and is suitable for obtaining either desired genetic gains for a variable proportion selected or optimum aggregate breeding value for a fixed total proportion selected. The procedure has similar properties to multistage selection index and, as such, genetic gains from use of the procedure may exceed ordinary independent culling level selection. The relative efficiencies of transformed to conventional independent culling ranged from 87% to over 300%. These results suggest that for most situations one can chose a multistage selection scheme, either conventional or transformed culling, which will have an efficiency close to that of selection index. After considering cost savings associated with multistage selection, there are many situations in which economic returns from use of independent culling, either conventional or transformed, will exceed that of selection index.

Research note: genetic adaptation to multiple-bird cage environment is less evident with effective beak trimming

Selection of hens with intact beaks for high performance in multiple-bird cages has produced a stock that clearly exceeds its unselected control when hens have intact beaks but shows less advantage when comparisons involve effectively beak-trimmed birds. The selected stock performed at about the same level as a stock recently derived from a commercial source (but with two generations of relaxed selection) when birds had intact beaks but at a lower level when birds had their beaks trimmed. Relative incidences of deaths from cannibalistic pecking were partially responsible for the results obtained.

An approximate method for optimum independent culling level selection for n stages of selection with explicit solutions

An approximate method with explicit solutions to apply independent culling levels for multiple traits in n-stages of selection was developed. An approximate solution was found for sequentially selected traits. Two assumptions were necessary. The first was to assume that subsequent selection would not appreciably change the mean of traits already selected, and the second was to approximate the variance of a correlated trait in a selected population with an upward biased projection. The procedure was shown to give near optimal results regardless of selection intensity or genetic correlations if phenotypic correlations among traits were low. The procedure gave poor results only for certain sequences of selection when phenotypic correlations were high. However, in those cases good results were obtained using a different sequence of selection. With high correlations, the procedure is recommended only after comparing solutions and expected genetic gain for all sequences of selection. If the expected aggregate gain for the sequence of selection desired is less than that of another order, culling points associated with the optimal ordering must be determined. Genetic gain from use of culling points is independent of order of selection. The procedure is recommended for use with computer programs that attempt to find optimal culling points to reduce computational time and to check results.

Selection and beak-trimming effects on behavior, cannibalism, and short-term production traits in White Leghorn pullets

Pullets of stocks derived from the North Central Randombred White Leghorn population without selection (C) or selected (S) on family performance when kept with beaks intact in multiple-hen cages were compared. Pullets had intact, one-fourth, or one-half of the beak removed (IN, 1/4R, and 1/2R, respectively). No stock differences were detected for behavior traits or other measures during the rearing period. However, beak-trimmed pullets were more inactive and feeding behavior was depressed in 1/2R pullets 1 wk after beak trimming. At 16 wk, 1/4R pullets' beaks had regrown but 1/2R pullets' beaks continued to be shorter than IN pullets' beaks. No differences in fearfulness were found between genetic stocks or among beak length treatments early in the laying period. Deaths from beak-inflicted injuries accumulated steadily from 18 wk until the study was ended at 40 wk. Cannibalistic deaths occurred less frequently in S as compared with C pullets within each beak treatment. As the amount of beak removal increased, beak-inflicted mortality decreased. The S pullets had earlier sexual maturity, lighter egg weights, and greater hen-housed egg production and egg mass than C pullets, and 1/2R pullets had greater egg production than 1/4R and IN pullets. Genetic stock by age and beak treatment by age interactions were present for hen-housed production and egg mass, and the interactions appeared to result primarily from increased mortality from cannibalistic pecking with increased age.

Multiple vital functions of the daughterless (da) gene in Drosophila melanogaster and factors influencing its expression

Multiple sub-vital effects, here designated as reductions in fitness S1-S5, for the second chromosome gene 'daughterless' (da) of Drosophila melanogaster were described as (S1) a recessive maternal lethality for daughters, (S2) a reduced fertility of da/da females, (S3) a recessive sub-vital zygotic effect, (S4) a recessive female-specific zygotic effect and (S5) a recessive maternal interaction effect on sons. (For S1-3 see also: Bell, 1954; Sandler, 1972; Cline, 1976). These five distinct effects were initially quantified from estimates of viability in single generation crossing experiments. Dynamic estimates of these fitness parameters were obtained by fitting the elimination rate of da from a series of large random mating cage populations to a recurrence equation by the method of minimum chi-square. The stability of these estimates discerns those effects which are truly pleiotropic versus those due to linked genes. The dynamic estimates supported only S1 and S4 effects. Evidence for S2 and S5 was indeterminate, but the S3 effect was rejected (P less than 0.01). The observed reduction in fitness, supposedly due to this recessive zygotic effect for da, was most likely the result of linked deleterious genes. These results indicate that pleiotropic vital effects observed in single generation test-cross matings may be caused by linked genes rather than the specific mutant per se. This problem is of particular importance when the mutant allele has been maintained with a balancer chromosome. Experiments on the rescue of daughters from da/da mothers with low temperatures during embryogenesis and with dechorionation of eggs were described in which the findings failed to confirm previously reported actions of the da gene. Modifying genes rather than environmental variables were cited as the probable cause for these conflicting results.

Estimation of response to selection and utilization of control populations for additional information and accuracy

Problems associated with testing and estimation of response to selection are examined. An alternative procedure with increased power for testing hypotheses is given. The increased power results from a more precise method of estimating the variance about response. The new method is based on a Satterthwaite approximation which combines variance components estimated more precisely by other sources of variation in the analysis of variance. The expected variance about response and expected mean squares for the analysis of variance, used in the Satterthwaite procedure, are given. When intergeneration environmental trends cannot be ruled out, a control population must be used to estimate response to selection. However, if the experimental and control populations do not respond in the same direction and with the same magnitude to common environmental effects, then the usual method of estimating response by deviating the experimental values from the control will result in biased estimates. An alternative procedure, using the control as a covariate to adjust for environmental trends, gives relatively unbiased estimates of response in this situation. Some bias results from measurement error associated with the control. However, this bias is usually minimal.

The effect of dietary cholesterol, energy intake, and oxygen consumption on cholesterol metabolism in the chick

This experiment, involving 320 chicks, was conducted to determine the effects of dietary cholesterol, restricted caloric intake, and genetic lines on cholesterol metabolism in the bird. The two lines of chicks studied had been divergently selected for oxygen consumption and had been shown to differ significantly (P less than .01) in weight gain and carcass lipid deposition. The dietary treatments, administered for a 2-week period, consisted of two levels of dietary cholesterol (none and supplemented) for each of two levels of energy (ad libitum and restricted). At the end of this 2-week period, the birds were injected intravenously with 1-14C-acetate and their livers removed 4 hr later. Hepatic cholesterol and lipid synthesis were measured by the uptake of acetate. Added dietary cholesterol significantly (P less than .01) decreased hepatic cholesterol synthesis, lipid synthesis, and specific activity of hepatic cholesterol but increased plasma and liver cholesterol. However, the elevation in plasma and liver cholesterol represented only .9 and 1.8% respectively, of the increase in total intake of dietary cholesterol. Metabolizable energy of diets fed ad libitum was also significantly (P less than .01) reduced with supplemented dietary cholesterol. A significant (P less than .01) difference in body weight was present between the two lines, with low oxygen consuming (LOC) birds exhibiting heavier body weights than high oxygen consuming (HOC) birds. A significant interaction between line and energy intake (P less than .05) was present for hepatic cholesterol levels; LOC birds exhibited higher levels of hepatic cholesterol than HOC birds when both groups were fed at restricted levels.(ABSTRACT TRUNCATED AT 250 WORDS)

Cholesterol metabolism in the laying hen as influenced by dietary cholesterol, caloric intake, and genotype

Three trials, each with 24 hens, were conducted to determine the effects of dietary cholesterol, caloric intake, and genotype on the synthesis, storage, and excretion of cholesterol in the laying hen. The two genotypes of birds used in this experiment had been divergently selected for high and low oxygen consumption and had been shown to differ significantly (P less than .01) in body weight gain and carcass lipid deposition from 0 to 4 weeks of age. The dietary treatment, administered for a 2-week period to birds in each genotype, consisted of two levels of dietary cholesterol (0 and 1% added) and two energy intakes (ad libitum and 75% ad libitum). The experimental design was a 2 X 2 X 2 factorial. One percent added cholesterol versus none supplemented produced a significant (P less than .01) decrease in available metabolizable energy and uptake of acetate into liver cholesterol while causing significant (P less than .01) increases in egg and liver cholesterol but not in plasma cholesterol. Restricting caloric intake, as compared to ad libitum feeding, resulted in significantly (P less than .01) decreased egg production and total amount of cholesterol excreted via the egg with significantly (P less than .05) increased plasma and liver cholesterol levels but no change in egg cholesterol concentration. Differences were significant (P less than .05) between the two genotypes in feed intake and hepatic cholesterol and lipid synthesis.(ABSTRACT TRUNCATED AT 250 WORDS)

Performance of dwarf and normal laying hens as influenced by protein level and cage density

The performance of dwarf and normal White Leghorn laying hens with similar genotypes other than for the dwarf gene (dw) was observed over thirteen 28-day periods in a factorial arrangement involving four protein levels (20.0, 18.1, 16.4 or 14.3% protein plus supplemental methionine) and two densities (two or three birds per standard 10 X 16 in cage). The normal birds had significantly higher overall hen-day egg production, egg weight, and body weight, but the dwarf birds excelled for feed efficiency and adult viability. Significant genotype X ration interactions were observed for egg lay, egg weight, body weight, and feed efficiency, primarily due to the relatively poor performance of the dwarf birds on the 14% protein. A significant genotype X density interaction resulted for feed efficiency, due to a higher efficiency in 3-bird than in 2-bird cages for dwarf birds, while the reverse was true for normal birds. These results suggest that the potential of the dwarf gene for increasing the efficiency of commercial egg layers can be enhanced by further study as to optimal nutrition and management regimens.

Effect of dietary cholesterol and genotype on cholesterol metabolism in roosters

An experiment, involving 32 roosters, was designed to study the interaction of dietary cholesterol and genotype on cholesterol metabolism in roosters. The two lines of birds used in this study had been divergently selected for high and low oxygen consumption and had been shown to differ significantly (P less than .01) in body weight gain and carcass lipid deposition from hatch to 4 weeks of age. The dietary treatments, administered for a 2-week period, were 0 and 1% dietary cholesterol added to a basal mash diet. Two separate trials were run, each with 16 roosters, resulting in four replicates of each treatment per line for each trial (block). After the trial period, the birds were injected with 1-(14)C-acetate and livers were removed; hepatic cholesterol synthesis was measured by the uptake of labeled acetate into liver digitonin precipitable sterols. Plasma and liver cholesterol levels were also measured. The data were analyzed as a randomized complete block design. Added dietary cholesterol significantly (P less than .01) increased both plasma and liver cholesterol levels over the control while significantly (P less than .01) decreasing the uptake of acetate into hepatic cholesterol in both lines by about 7-fold. Plasma cholesterol was significantly (P less than .05) greater in the high than low oxygen-consuming birds, and liver cholesterol was higher (P less than .10) in the low than high oxygen-consuming line.(ABSTRACT TRUNCATED AT 250 WORDS)