Using selection index theory to estimate consistency of multi-locus linkage disequilibrium across populations
Wientjes, Y.C.J. ; Veerkamp, R.F. ; Calus, M.P.L. - \ 2015
BMC Genetics 16 (2015). - ISSN 1471-2156
genomic breeding values - genetic-relationship information - quantitative trait loci - dairy-cattle breeds - prediction - accuracy - haplotype - markers - impact - lines
The potential of combining multiple populations in genomic prediction is depending on the consistency of linkage disequilibrium (LD) between SNPs and QTL across populations. We investigated consistency of multi-locus LD across populations using selection index theory and investigated the relationship between consistency of multi-locus LD and accuracy of genomic prediction across different simulated scenarios. In the selection index, QTL genotypes were considered as breeding goal traits and SNP genotypes as index traits, based on LD among SNPs and between SNPs and QTL. The consistency of multi-locus LD across populations was computed as the accuracy of predicting QTL genotypes in selection candidates using a selection index derived in the reference population. Different scenarios of within and across population genomic prediction were evaluated, using all SNPs or only the four neighboring SNPs of a simulated QTL. Phenotypes were simulated using different numbers of QTL underlying the trait. The relationship between the calculated consistency of multi-locus LD and accuracy of genomic prediction using a GBLUP type of model was investigated.
The accuracy of predicting QTL genotypes, i.e. the measure describing consistency of multi-locus LD, was much lower for across population scenarios compared to within population scenarios, and was lower when QTL had a low MAF compared to QTL randomly selected from the SNPs. Consistency of multi-locus LD was highly correlated with the realized accuracy of genomic prediction across different scenarios and the correlation was higher when QTL were weighted according to their effects in the selection index instead of weighting QTL equally. By only considering neighboring SNPs of QTL, accuracy of predicting QTL genotypes within population decreased, but it substantially increased the accuracy across populations.
Consistency of multi-locus LD across populations is a characteristic of the properties of the QTL in the investigated populations and can provide more insight in underlying reasons for a low empirical accuracy of across population genomic prediction. By focusing in genomic prediction models only on neighboring SNPs of QTL, multi-locus LD is more consistent across populations since only short-range LD is considered, and accuracy of predicting QTL genotypes of individuals from another population is increased.
Copy number variation in Fayoumi and Leghorn chickens analyzed using array comparative genomic hybridization
Abernathy, J. ; Li, X. ; Jia, X. ; Chou, W. ; Lamont, S.J. ; Crooijmans, R.P.M.A. ; Zhou, H. - \ 2014
Animal Genetics 45 (2014)3. - ISSN 0268-9146 - p. 400 - 411.
major histocompatibility complex - large gene lists - expression profiles - avian evolution - snp beadchip - human health - v-atpases - ncbi geo - disease - lines
Copy number variation refers to regions along chromosomes that harbor a type of structural variation, such as duplications or deletions. Copy number variants (CNVs) play a role in many important traits as well as in genetic diversity. Previous analyses of chickens using array comparative genomic hybridizations or single-nucleotide polymorphism chip assays have been performed on various breeds and genetic lines to discover CNVs. In this study, we assessed individuals from two highly inbred (inbreeding coefficiency > 99.99%) lines, Leghorn G-B2 and Fayoumi M15.2, to discover novel CNVs in chickens. These lines have been previously studied for disease resistance, and to our knowledge, this represents the first global assessment of CNVs in the Fayoumi breed. Genomic DNA from individuals was examined using the Agilent chicken 244 K comparative genomic hybridization array and quantitative PCR. We identified a total of 273 CNVs overall, with 112 CNVs being novel and not previously reported. Quantitative PCR using the standard curve method validated a subset of our array data. Through enrichment analysis of genes within CNV regions, we observed multiple chromosomes, terms and pathways that were significantly enriched, largely dealing with the major histocompatibility complex and immune responsiveness. Using an additional round of computational and statistical analysis with a different bioinformatic pipeline, we identified 43 CNVs among these as high-confidence regions, 14 of which were found to be novel. We further compared and contrasted individuals of the two inbred lines to discover regions that have a significant difference in copy number between lines. A total of 40 regions had significant deletions or duplications between the lines. Gene Ontology analysis of genomic regions containing CNVs between lines also was performed. This between-line candidate CNV list will be useful in studies with these two unique genetic lines, which may harbor variations that underlie quantitative trait loci for disease resistance and other important traits. Through the global discovery of novel CNVs in chicken, these data also provide resources for further genetic and functional genomics studies.
Hybrid recreation by reverse breeding in Arabidopsis thaliana
Wijnker, T.G. ; Deurhof, L. ; Belt, J. van de; Snoo, B. de; Vries, M.H.C. de; Becker, F.F.M. ; Ravi, M. ; Chan, S.W.L. ; Dun, van, K. ; Lelivelt, C.L.C. ; Jong, J.H.S.G.M. de; Dirks, R. ; Keurentjes, J.J.B. - \ 2014
Nature protocols 9 (2014)4. - ISSN 1754-2189 - p. 761 - 772.
chromosome substitution strains - pcr analysis - dna - lines - plant - extraction - protocol - ecotypes - traits - genome
Hybrid crop varieties are traditionally produced by selecting and crossing parental lines to evaluate hybrid performance. Reverse breeding allows doing the opposite: selecting uncharacterized heterozygotes and generating parental lines from them. With these, the selected heterozygotes can be recreated as F1 hybrids, greatly increasing the number of hybrids that can be screened in breeding programs. Key to reverse breeding is the suppression of meiotic crossovers in a hybrid plant to ensure the transmission of nonrecombinant chromosomes to haploid gametes. These gametes are subsequently regenerated as doubled-haploid (DH) offspring. Each DH carries combinations of its parental chromosomes, and complementing pairs can be crossed to reconstitute the initial hybrid. Achiasmatic meiosis and haploid generation result in uncommon phenotypes among offspring owing to chromosome number variation. We describe how these features can be dealt with during a reverse-breeding experiment, which can be completed in six generations (~1 year)
The fearful feather pecker : applying the principles to practice to prevent feather pecking in laying hens
Haas, E.N. de - \ 2014
Wageningen University. Promotor(en): Bas Kemp; A.G.G. Groothuis, co-promotor(en): Bas Rodenburg; Liesbeth Bolhuis. - Wageningen : Wageningen University - ISBN 9789462570429 - 285
hennen - verenpikken - bangheid - gedragsproblemen - lijnen - hormonale controle - stressreactie - ontogenie - legresultaten - dierenwelzijn - diergedrag - dierfysiologie - hens - feather pecking - fearfulness - behaviour problems - lines - hormonal control - stress response - ontogeny - laying performance - animal welfare - animal behaviour - animal physiology
Billions of laying hens are kept worldwide. Severe feather pecking (SFP) is a behaviour which occurs with a high prevalence on commercial farms. SFP, the pecking and plucking of feathers of another bird, induces pain and stress and can ultimately lead to cannibalism. Moreover, SFP can occur if a bird is unable to cope with fear and stress and is living in an inappropriate environment. SFP thus reduces the welfare of many laying hens worldwide. To prevent SFP it is essential to know the risk factors in its development. To that aim, first, two experimental studies were conducted to gain insight in the principles of SFP, and three on-farm studies were conducted to assess the risk factors of SFP under commercial conditions.
Factors which relate to SFP are high fearfulness as young and low levels of brain and peripheral serotonin (5-HT) and brain dopamine (DA). Furthermore, commercial laying hen lines can differ in SFP tendencies and associated traits indicating that SFP has a genetic component. In chapters 2 and 3, fear response as young and adult, and stress response, 5-HT and DA brain levels as adult were
compared in hens of two lines: the low mortality line (LML) selected on low levels of mortality due to cannibalism and individual performance vs. the control line (CL) which was selected on individual performance only. Hens were exposed to an Open Field (OF) test at 5 weeks of age and a Manual Restraint (MR) test at 33 weeks of age. At 33 weeks of age, levels of corticosterone (CORT) post MR and 5-HT and DA levels in four brain areas were determined. Hens of the LML were less fearful at both ages and had lower levels of DA in the arcopallium, a somatomotor area involved in fear and motor control, compared to hens of the CL. In chapter 2, it was also shown that fearful chicks had higher levels of CORT and higher activity levels as adult, compared to non-fearful chicks. Moreover,
presence of fearful animals in the group was related to average CORT levels of their pen members. Fearful hens may induce social instability in a group, and thereby affecting the stress-sensitivity of their group mates. These results indicate that groups differ in levels of fear and stress-sensitivity, and that fearfulness at a young age can lead to stress-sensitivity as adults, which create a risk for development of SFP.
In chapters 4, 5 and 6, the laying hen production chain consisting of parent stock, rearing flocks and laying flocks was studied. Risk factors for SFP could originate from previous parts in the chain. Therefore, in all on-farm studies, measurements of SFP, fearfulness, basal CORT and peripheral 5-HT system were obtained, and related to housing conditions and to previous parts in the chain. Fearfulness was assessed, on a flock level, by distance to a stationary person (SP) test and latency
of bird to approach a novel object (NO). Dekalb White (DW) and ISA brown (ISA) crosses whose pure lines differ in levels of fear, CORT, 5-HT and DA, were compared. First, parent stock (PS) flocks were studied and associations between production performance and measurements of fear, stress and 5-HT were conducted and related to group size conditions (chapter 4). Second, rearing flocks originating from PS flocks were studied throughout the rearing period (chapter 5). High levels of feather damage, CORT and 5-HT in the mothers were related to fearfulness and SFP in their offspring at flock level. Especially, a large flock size and limitation and/or disruption in litter supply affected SFP and levels of fearfulness and 5-HT (chapter 5). Finally, high levels of feather damage during the laying period were related to high SFP rearing, and high fearfulness during rearing and laying (chapter 6). These studies together aimed to determine the risk factors for the development of SFP and the resulting feather damage. The main outcomes of these studies are as follows.
Ø Parent stock flocks
DW flocks were more fearful of an SP and hens had higher levels of feather damage than in ISA flocks. ISA flocks, in turn, were more fearful of the NO and hens had higher 5-HT levels than in DW flocks. A small flock size led to higher feed conversion, mortality levels, and smothering events in ISA but not in DW flocks. These results indicate that DW and ISA PS flocks differ in levels of fear and
feather damage, and respond differently to their social environment. For both crosses, fear of an SP related to high mortality and fear of the NO related to low hen body weight, egg weight, and feed intake. High basal CORT related to low egg weight. High fear and stress levels in PS flocks may, thus, negatively affect (re)production, and thereby potentially negatively influence the developing
Ø Rearing flocks
In the DW cross, high CORT, feather damage, and 5-HT of mother hens related to high SFP and fearfulness of their rearing flocks at 1 week of age. At 5 weeks of age, a peak in both gentle feather pecking (GFP) and SFP was recorded, coinciding with a disruption in substrate availability (i.e. a temporal absence of substrate) and a limitation of substrate (i.e. limited amounts of substrate
provided) in some of the farms. Especially, ISA pullets showed higher SFP under substrate limitation and became more fearful under substrate disruption than DW pullets. ISA pullets had higher 5-HT levels than DW pullets. Only in the ISA cross, high 5-HT related to high fearfulness, specifically under substrate disruption. For both crosses, high fearfulness was related to high feather damage. Furthermore, in a level system (floor system where levels are gradually added) higher levels of SFP and feather damage were found compared to an aviary system (a tier-system with cages and litter area). These results highlight that; 1) parental effects exist in the development of fearfulness and SFP, 2) disruption and limitation in substrate availability can lead to high SFP at 5 weeks of age, 3) ISA pullets are more strongly influenced by environmental conditions than DW pullets and 4) a level housing, which coincided with a large group size, increase the risk of SFP and feather damage during rearing.
Ø Laying flocks
In our sample, 49% of the laying flocks had severe damage at 40 weeks of age, compared with 71%, 65% and 53% of the rearing flocks at 15, 10 and 5 weeks of age, respectively. High fear of a SP at rearing and high SFP at 5 weeks of age related to high levels of feather damage at lay. In a floor system and at a large flock size higher levels of feather damage were recorded than in an aviary system and at a small flock size. An adjusted management on the laying farm (i.e. aerated blocks, presence of roosters or a radio playing) reduced levels of feather damage compared to standard management. DW flocks were more fearful of the SP and NO than ISA flocks. This study showed that factors during rearing and laying contributed to feather damage at 40 weeks of age.
With the knowledge from the experimental and on-farm studies in this thesis, an assessment of the risk factors for SFP could be established. Risk factors for SFP are: high fear, stress and feather damage in DW parent stock, high fear of humans, especially for DW hens, litter disruption or limitation during rearing, large group sizes, and a floor or level system.
Using pooled data to estimate variance components and breeding values for traits affected by social interactions
Peeters, K.L.M. ; Ellen, E.D. ; Bijma, P. - \ 2013
Genetics, Selection, Evolution 45 (2013)1. - ISSN 0999-193X - 10 p.
average daily gain - genetic-parameters - group selection - laying hens - competition - survival - lines - pigs
Background Through social interactions, individuals affect one another’s phenotype. In such cases, an individual’s phenotype is affected by the direct (genetic) effect of the individual itself and the indirect (genetic) effects of the group mates. Using data on individual phenotypes, direct and indirect genetic (co)variances can be estimated. Together, they compose the total genetic variance that determines a population’s potential to respond to selection. However, it can be difficult or expensive to obtain individual phenotypes. Phenotypes on traits such as egg production and feed intake are, therefore, often collected on group level. In this study, we investigated whether direct, indirect and total genetic variances, and breeding values can be estimated from pooled data (pooled by group). In addition, we determined the optimal group composition, i.e. the optimal number of families represented in a group to minimise the standard error of the estimates. Methods This study was performed in three steps. First, all research questions were answered by theoretical derivations. Second, a simulation study was conducted to investigate the estimation of variance components and optimal group composition. Third, individual and pooled survival records on 12 944 purebred laying hens were analysed to investigate the estimation of breeding values and response to selection. Results Through theoretical derivations and simulations, we showed that the total genetic variance can be estimated from pooled data, but the underlying direct and indirect genetic (co)variances cannot. Moreover, we showed that the most accurate estimates are obtained when group members belong to the same family. Additional theoretical derivations and data analyses on survival records showed that the total genetic variance and breeding values can be estimated from pooled data. Moreover, the correlation between the estimated total breeding values obtained from individual and pooled data was surprisingly close to one. This indicates that, for survival in purebred laying hens, loss in response to selection will be small when using pooled instead of individual data. Conclusions Using pooled data, the total genetic variance and breeding values can be estimated, but the underlying genetic components cannot. The most accurate estimates are obtained when group members belong to the same family.
Genetic parameters of natural antibody isotypes and survival analysis in beak-trimmed and non-beak-trimmed crossbred laying hens
Sun, Y. ; Ellen, E.D. ; Parmentier, H.K. ; Poel, J.J. van der - \ 2013
Poultry Science 92 (2013)8. - ISSN 0032-5791 - p. 2024 - 2033.
immune-system - pineal-gland - chickens - lines - autoantibodies - repertoire - responses - antigens - disease - stress
Natural antibodies (NAb) are important humoral components of innate immunity. As the first line of defense, NAb provide protection against infection and support adaptive immunity. An earlier study indicated that serum levels of NAb isotypes IgM and IgG at a young age were predictive for survival in non-beak-trimmed purebred laying hens during the laying period. In the present study, genetic parameters of NAb isotypes were estimated and relationships between survival and NAb isotypes levels in crossbred laying hens were investigated. In total, 1,555 beak-trimmed and 1,169 non-beak-trimmed crossbred laying hens were used. Genetic parameters of IgM and IgG titers binding keyhole limpet hemocyanin at 24 wk of age were estimated with a linear animal model. The heritabilities of NAb isotypes IgG and IgM were 0.21 (SE = 0.04) and 0.26 (SE = 0.04), respectively. The genetic correlation between IgG and IgM isotypes was 0.43 (SE = 0.11). These results indicated that NAb isotype titers were heritable traits in the crossbred laying hens. Both NAb isotypes can be selected for simultaneously because the detected positive genetic correlation (0.43, SE = 0.11) between them is positive. Both row and level of the cage were indicated to be associated environmental factors for NAb isotype titers. Different from an earlier study with purebred hens, survival analysis showed no significant associations of survival with NAb isotype titers in beak-trimmed or non-beak-trimmed crossbred hens. Non-health-related causes of mortality, especially in birds with intact beaks, overruled the anticipated relationships between NAb isotype titers and survival.
Transcriptomics Research in Chicken
Yang, D.Y. ; Gao, C. ; Zhu, L.Q. ; Tang, L.G. ; Liu, J. ; Nie, H. - \ 2012
Journal of Animal and Veterinary Advances 11 (2012)16. - ISSN 1680-5593 - p. 2945 - 2947.
gene-expression responses - human housekeeping genes - salmonella infection - eimeria-maxima - lines - fabricius - intestine - bursa - array
The chicken (Gallus gallus) is an important model organism in genetics, developmental biology, immunology and evolutionary research. Moreover, besides being an important model organism the chicken is also a very important agricultural species and an important source of food (eggs and meat). The availability of the draft chicken genome sequence provided many possibilities to in detail study a variety of genomic changes during evolution using a comparison between chicken and mammals. For example, compared to mammals, the use of a Z/W sex determination system is a special aspect of the avian genome where the female is the heterogametic sex (ZW) and the male is the homogametic (ZZ) sex. A comparison of the genomic sequences of platypus, chicken and human showed that sex chromosomes evolved separately in birds and mammals
Genetic correlation between heart ratio and body weight as a function of ascites frequency in broilers split up into sex and health status
Closter, A.M. ; As, P. van; Elferink, M.G. ; Crooijmans, R.P.M.A. ; Groenen, M.A.M. ; Vereijken, A.L.J. ; Arendonk, J.A.M. van; Bovenhuis, H. - \ 2012
Poultry Science 91 (2012)3. - ISSN 0032-5791 - p. 556 - 564.
pulmonary-hypertension syndrome - right ventricular hypertrophy - normal mixture model - somatic-cell scores - carcass traits - chickens - growth - parameters - lines - selection
Ascites or pulmonary hypertension syndrome is a metabolic disorder in broilers. Male broilers have a higher BW and are therefore expected to be more prone to developing ascites than females. As genetic parameters might be affected by the ascites incidence, genetic parameters might differ between male and female broilers. The aims of this study were to estimate the heritability for the ratio of right ventricular weight to total ventricular weight (RATIO) and BW in male and female broilers, the genetic correlation between RATIO and BW separately for male and female broilers, and the genetic correlations between BW for ascitic and nonascitic broilers. Data were available from 7,856 broilers (3,819 males and 4,037 females). The broilers in the experiment were kept under a cold temperature regimen and increased CO2 levels. In this study, we showed that the incidence of ascites is higher in male than in female broilers. Heritability estimates for BW at 7 wk of age were higher for male (0.22) than for female (0.17) broilers, and for RATIO heritability, estimates were higher for female (0.44) than for male (0.32) broilers. The genetic correlations between RATIO and BW measured at different ages changed from slightly positive at 2 wk of age to moderately negative at 7 wk. The change in genetic correlation was more extreme for male (from 0.01 to -0.62) than for female (from 0.13 to -0.24) broilers. The difference in ascites incidence between male and female broilers is the most likely reason for the difference in genetic correlations. The genetic correlation between BW traits measured in broilers with fluid in the abdomen and without fluid in the abdomen decreased from 0.91 at 2 wk to 0.69 at 7 wk. We conclude that under circumstances with ascites, data from male and female broilers should be analyzed separately.
Comparison of the exomes of common carp (Cyprinus carpio) and zebrafish (Danio rerio)
Henkel, C.V. ; Dirks, R.P. ; Jansen, H.J. ; Forlenza, M. ; Wiegertjes, G.F. ; Howe, K. ; Thillart, G.E. van den; Spaink, H.P. - \ 2012
Zebrafish 9 (2012)2. - ISSN 1545-8547 - p. 59 - 67.
transcriptome analysis - genetic-variability - antibody-production - nitrosative stress - dna-sequences - genome - fish - macrophages - lines - microsatellite
Research on common carp, Cyprinus carpio, is beneficial for zebrafish research because of resources available owing to its large body size, such as the availability of sufficient organ material for transcriptomics, proteomics, and metabolomics. Here we describe the shot gun sequencing of a clonal double-haploid common carp line. The assembly consists of 511891 scaffolds with an N50 of 17¿kb, predicting a total genome size of 1.4–1.5¿Gb. A detailed analysis of the ten largest scaffolds indicates that the carp genome has a considerably lower repeat coverage than zebrafish, whilst the average intron size is significantly smaller, making it comparable to the fugu genome. The quality of the scaffolding was confirmed by comparisons with RNA deep sequencing data sets and a manual analysis for synteny with the zebrafish, especially the Hox gene clusters. In the ten largest scaffolds analyzed, the synteny of genes is almost complete. Comparisons of predicted exons of common carp with those of the zebrafish revealed only few genes specific for either zebrafish or carp, most of these being of unknown function. This supports the hypothesis of an additional genome duplication event in the carp evolutionary history, which—due to a higher degree of compactness—did not result in a genome larger than that of zebrafish.
Functional analysis of two inhibitor of apoptosis (iap) orthologs from Helicoverpa armigera nucleopolyhedrovirus
Liang, Ch.Y. ; Lange, J. de; Chen, X.W. ; Oers, M.M. van; Vlak, J.M. ; Westenberg, M. - \ 2012
Virus Research 165 (2012)1. - ISSN 0168-1702 - p. 107 - 111.
programmed cell-death - baculovirus gene - insect cells - p35 gene - proteins - lines - identification - establishment - expression - tolerance
Baculoviruses induce apoptotic responses in cultured insect cells, which can severely limit viral replication. To overcome this host response baculoviruses carry anti-apoptotic genes, including members of the p35 and inhibitor of apoptosis (iap) gene families. The baculovirus Helicoverpa armigera nucleopolyhedrovirus (HearNPV) carries two putative apoptosis suppressor genes (iap2 and iap3), which we studied in more detail. IAPs are believed to be functional in the cytoplasm, but surprisingly, when transiently expressed as EGFP fusions, IAP2 was evenly distributed throughout the cell, while IAP3 was mainly found in the nucleus. The latter became evenly distributed in both compartments in HearNPV infected cells. When iap2 was deleted, HearNPV could be propagated in Hz2e5 cells, while an iap3 deletion was lethal. The HearNPV ¿iap3 mutant could be rescued by reinsertion of the HearNPV iap3 gene and by the well-studied anti-apoptotic genes Autographa californica (Ac)MNPV p35 or Orgyia pseudotsugata (Op)MNPV iap3. RNAi analysis showed that HearNPV induced apoptosis in Hz2e5 cells transfected with iap3 dsRNA, while silencing of iap2 did not lead to apoptosis. Finally, IAP3 was able to inhibit actinomycin-D induced apoptosis when transiently expressed in Sf21 cells. These results together indicate that HearNPV IAP3 is a functional apoptosis suppressor, while the function of IAP2 remains elusive.
Effect of natural and chimeric haemagglutinin genes on influenza A virus replication in baby hamster kidney cells.
Wielink, R. van; Harmsen, M.M. ; Martens, D.E. ; Leeuw, O.S. de; Peeters, B.P.H. ; Wijffels, R.H. - \ 2012
Journal of Biotechnology 162 (2012)2-3. - ISSN 0168-1656 - p. 197 - 201.
candidate vaccine viruses - system - generation - molecules - growth - lines
Baby hamster kidney (BHK21) cells are used to produce vaccines against various viral veterinary diseases, including rabies and foot-and-mouth-disease. Although particular influenza virus strains replicate efficiently in BHK21 cells the general use of these cells for influenza vaccine production is prohibited by the poor replication of most strains, including model strain A/PR/8/34 [H1N1] (PR8). We now show that in contrast to PR8, the related strain A/WSN/33 [H1N1] (WSN) replicates efficiently in BHK21 cells. This difference is determined by the haemagglutinin (HA) protein since reciprocal reassortant viruses with swapped HAs behave similarly with respect to growth on BHK21 cells as the parental virus from which their HA gene is derived. The ability or inability of six other influenza virus strains to grow on BHK21 cells appears to be similarly dependent on the nature of the HA gene since reassortant PR8 viruses containing the HA of these strains grow to similar titres as the parental virus from which the HA gene was derived. However, the growth to low titres of a seventh influenza strain was not due to the nature of the HA gene since a reassortant PR8 virus containing this HA grew efficiently on BHK21 cells. Taken together, these results suggest that the HA gene often primarily determines influenza replication efficiency on BHK21 cells but that in some strains other genes are also involved. High virus titres could be obtained with reassortant PR8 strains that contained a chimeric HA consisting of the HA1 domain of PR8 and the HA2 domain of WSN. HA1 contains most antigenic sites and is therefore important for vaccine efficacy. This method of producing the HA1 domain as fusion to a heterologous HA2 domain could possibly also be used for the production of HA1 domains of other viruses to enable the use of BHK21 cells as a generic platform for veterinary influenza vaccine production.
Meta-analysis of Chicken - Salmonella infection experiments
Pas, M.F.W. te; Hulsegge, B. ; Schokker, D.J. ; Smits, M.A. ; Fife, M. ; Zoorob, R. ; Endale, M.L. ; Rebel, J.M.J. - \ 2012
BMC Genomics 13 (2012). - ISSN 1471-2164 - 28 p.
gene-expression responses - wd-repeat proteins - typhimurium infection - jejunal development - actin cytoskeleton - immune-response - enteritidis - resistance - enterica - lines
Background: Chicken meat and eggs can be a source of human zoonotic pathogens, especially Salmonella species. These food items contain a potential hazard for humans. Chickens lines differ in susceptibility for Salmonella and can harbor Salmonella pathogens without showing clinical signs of illness. Many investigations including genomic studies have examined the mechanisms how chickens react to infection. Apart from the innate immune response, many physiological mechanisms and pathways are reported to be involved in the chicken host response to Salmonella infection. The objective of this study was to perform a meta-analysis of diverse experiments to identify general and host specific mechanisms to the Salmonella challenge. Results: Diverse chicken lines differing in susceptibility to Salmonella infection were challenged with different Salmonella serovars at several time points. Various tissues were sampled at different time points post-infection, and resulting host transcriptional differences investigated using different microarray platforms. The meta-analysis was performed with the R-package metaMA to create lists of differentially regulated genes. These gene lists showed many similarities for different chicken breeds and tissues, and also for different Salmonella serovars measured at different times post infection. Functional biological analysis of these differentially expressed gene lists revealed several common mechanisms for the chicken host response to Salmonella infection. The meta-analysis-specific genes (i.e. genes found differentially expressed only in the meta-analysis) confirmed and expanded the biological functional mechanisms. Conclusions: The meta-analysis combination of heterogeneous expression profiling data provided useful insights into the common metabolic pathways and functions of different chicken lines infected with different Salmonella serovars.
Whole genome QTL mapping for growth, meat quality and breast meat yield traits in turkey
Aslam, M.L. ; Bastiaansen, J.W.M. ; Crooijmans, R.P.M.A. ; Vereijken, J.M. ; Groenen, M. - \ 2011
BMC Genetics 12 (2011). - ISSN 1471-2156 - 10 p.
quantitative trait - body-composition - chicken - loci - linkage - weight - lines - cross - identification - selection
Background The turkey (Meleagris gallopavo) is an important agricultural species and is the second largest contributor to the world's poultry meat production. Demand of turkey meat is increasing very rapidly. Genetic markers linked to genes affecting quantitative traits can increase the selection response of animal breeding programs. The use of these molecular markers for the identification of quantitative trait loci, and subsequently fine-mapping of quantitative trait loci regions, allows for pinpointing of genes that underlie such economically important traits. Results The quantitative trait loci analyses of the growth curve, body weight, breast yield and the meat quality traits showed putative quantitative trait loci on 21 of the 27 turkey chromosomes covered by the linkage map. Forty-five quantitative trait loci were detected across all traits and these were found in 29 different regions on 21 chromosomes. Out of the 45 quantitative trait loci, twelve showed significant (p <0.01) evidence of linkage while the remaining 33 showed suggestive evidence (p <0.05) of linkage with different growth, growth curve, meat quality and breast yield traits. Conclusion A large number of quantitative trait loci were detected across the turkey genome, which affected growth, breast yield and meat quality traits. Pleiotropic effects or close linkages between quantitative trait loci were suggested for several of the chromosomal regions. The comparative analysis regarding the location of quantitative trait loci on different turkey, and on the syntenic chicken chromosomes, along with their phenotypic associations, revealed signs of functional conservation between these species
Effects of genetic origin and social environment on behavioral response to manual restraint and monoamine functioning in laying hens
Uitdehaag, K.A. ; Rodenburg, T.B. ; Reenen, C.G. van; Koopmanschap, R.E. ; Vries Reilingh, G. de; Engel, B. ; Buist, W.G. ; Komen, J. ; Bolhuis, J.E. - \ 2011
Poultry Science 90 (2011)8. - ISSN 0032-5791 - p. 1629 - 1636.
feather pecking behavior - open-field - dopamine turnover - tonic immobility - group selection - serotonin - chicks - corticosterone - platelets - lines
Purebred laying hen lines of White Leghorn (WL) origin have been found to be more flighty and to show more feather pecking than lines of Rhode Island Red (RIR) origin. It has been found, however, that when RIR birds were housed together with WL birds, RIR birds became more flighty and those mixed groups developed more feather damage than pure-line cage-housed groups. It is unknown, however, whether this effect of social environment is accompanied by changes in stress-related behavior and neurophysiological activity, which are assumed to be associated with increased feather damage. The objective of this study was therefore to investigate the effects of genetic origin (WL or RIR) and social environment (mixed or pure groups) on behavioral response to manual restraint and monoamine functioning. Monoamine functioning was measured by brain serotonin (5-HT) and dopamine turnover. Furthermore, correlations between 5-HT turnover in the brain and peripheral measures of 5-HT in the blood were calculated. Experimental birds, housed either with other birds from the same genetic origin (pure groups) or with both RIR and WL birds (mixed groups) from hatching onward, were subjected to a manual restraint test at 47 wk of age. The WL birds struggled less during restraint and had higher dopamine and 5-HT turnover levels after restraint than did RIR birds. The WL birds also showed higher levels of platelet 5-HT uptake than did RIR birds. No effects of social environment were found. Blood and brain 5-HT measures were found to be correlated, with correlations ranging from 0.34 to 0.57, which seems to offer opportunities for less invasive peripheral indicators of 5-HT activity. In conclusion, genetic origin, but not social environment, affected the behavioral response to manual restraint and monoamine functioning in laying hens
The development of a cisgenic apple plant
Vanblaere, T. ; Szankowski, Iris ; Schaart, J. ; Schouten, H.J. ; Flachowsky, H. ; Broggini, G.A.L. ; Gessler, C. - \ 2011
Journal of Biotechnology 154 (2011)4. - ISSN 0168-1656 - p. 304 - 311.
scab resistance - gene - dna - transformation - expression - growth - lines - l.
Cisgenesis represents a step toward a new generation of GM crops. The lack of selectable genes (e.g. antibiotic or herbicide resistance) in the final product and the fact that the inserted gene(s) derive from organisms sexually compatible with the target crop should rise less environmental concerns and increase consumer's acceptance. Here we report the generation of a cisgenic apple plant by inserting the endogenous apple scab resistance gene HcrVf2 under the control of its own regulatory sequences into the scab susceptible apple cultivar Gala. A previously developed method based on Agrobacterium-mediated transformation combined with a positive and negative selection system and a chemically inducible recombination machinery allowed the generation of apple cv. Gala carrying the scab resistance gene HcrVf2 under its native regulatory sequences and no foreign genes. Three cisgenic lines were chosen for detailed investigation and were shown to carry a single T-DNA insertion and express the target gene HcrVf2. This is the first report of the generation of a true cisgenic plant
Transgressive segregation for very low and high levels of basal resistance to powdery mildew in barley
Aghnoum, R. ; Niks, R.E. - \ 2011
Journal of Plant Physiology 168 (2011)1. - ISSN 0176-1617 - p. 45 - 50.
marker-assisted selection - quantitative trait loci - adult-plant resistance - erysiphe-graminis - puccinia-hordei - spring barley - host-resistance - stripe rust - lines - map
Basal resistance of barley to powdery mildew is a quantitatively inherited trait that limits the growth and sporulation of barley powdery mildew pathogen by a non-hypersensitive mechanism of defense. Two experimental barley lines were developed with a very high (ErBgh) and low (EsBgh) level of basal resistance to powdery mildew by cycles of convergent crossing and phenotypic selection between the most resistant and between the most susceptible lines, respectively, from four mapping populations of barley. Phenotypic selection in convergent crossing was highly effective in producing contrasting phenotypes for basal resistance and susceptibility. In ErBgh, almost 90% of infection units failed to form a primary haustorium in the epidermal cells in association with papilla formation, but in EsBgh only 33% of infection units failed to form a primary haustorium. The contrast between ErBgh and EsBgh for successful formation of secondary and subsequent haustoria was much less obvious (69% versus 79% successful secondary haustorium formation). In an earlier investigation, we determined seven QTLs for basal resistance in the four mapping populations. Checking the peak markers of these QTLs indicated that only four out of seven QTLs were confirmed to be present in the selected resistant lines and only four QTLs for susceptibility were confirmed to be present in the selected susceptible lines. Surprisingly, none of the expected QTLs could be detected in the resistant line ErBgh. We discuss some reasons why marker aided selection might be less efficient in raising levels of basal resistance than phenotypic selection. The very resistant and susceptible lines developed here are valuable material to be used in further experiments to characterize the molecular basis of basal resistance to powdery mildew
A quantitative trait locus for a primary antibody response to keyhole limpet hemocyanin on chicken chromosome 14-Confirmation and candidate gene approach
Siwek, M. ; Slawinska, A. ; Nieuwland, M.G.B. ; Witkowski, A. ; Zieba, G. ; Minozzi, G. ; Knol, E.F. ; Bednarczyk, M. - \ 2010
Poultry Science 89 (2010)9. - ISSN 0032-5791 - p. 1850 - 1857.
red-blood-cells - infectious pancreatic necrosis - salmon salmo-salar - unselected traits - disease virus - laying hens - major qtl - lines - confirmation - resistance
A QTL involved in the primary antibody response toward keyhole limpet hemocyanin (KLH) was detected on chicken chromosome 14 in the experimental population, which was created by crossing commercial White Leghorn and a Polish native chicken breed (green-legged partridgelike). The current QTL location is a validation of previous experiments pointing to the same genomic location for the QTL linked to a primary antibody response to KLH. An experimental population was typed with microsatellite markers distributed over the chicken chromosome 14. Titers of antibodies binding KLH were measured for all individuals by ELISA. Statistical models applied in the Grid QTL Web-based software were used to analyze the data: a half-sib model, a line-cross model, and combined analysis in a linkage disequilibrium and linkage analysis model. Candidate genes that have been proposed were genotyped with SNP located in genes exons. Statistical analyses of single SNP associations were performed pointing out 2 SNP of an axis inhibitor protein (AXIN1) gene as significantly associated with the trait of an interest
The use of blood gas parameters to predict ascites susceptibility in juvenile broilers
As, P. van; Elferink, M.G. ; Closter, A.M. ; Vereijken, A. ; Crooijmans, R.P.M.A. ; Bovenhuis, H. ; Decuypere, E. ; Groenen, M.A.M. - \ 2010
Poultry Science 89 (2010). - ISSN 0032-5791 - p. 1684 - 1691.
carbon-dioxide tensions - growth-rate - chickens - lines - traits - hematocrit - resistant - failure - weight
Ascites syndrome is a metabolic disorder found in modern broilers that have insufficient pulmonary vascular capacity. Commercial breeding programs have heavily focused on high growth rate, which led to fast-growing chickens, but as a negative consequence, the incidence of ascites syndrome increased. However, not all birds with a high growth rate will suffer from ascites syndrome, which might indicate a genetic susceptibility to ascites. Information on blood gas parameters measured early in life and their relation to ascites susceptibility is expected to contribute to identification on the cause of ascites syndrome. In this study, several physiological parameters, such as blood gas parameters [pH, partial pressure of CO2 in venous blood (pvCO2), and partial pressure of O2 in venous blood], hematocrit, electrolytes (Na+, Ca2+, and K+), metabolites (lactate and glucose), were measured at d 11 to 12 of age from 100 female and 100 male broilers. From d 14 onward, the birds were challenged to provoke the development of ascites syndrome. Our results showed that high pvCO2 values together with low pH values (males) or high pH values (females) in the venous blood of juvenile broilers coincided with ascites. Therefore, blood pvCO2 and pH in both juvenile male and female broilers seem to be critical factors in ascites pathophysiology and can be used as phenotypic traits to predict ascites susceptibility in juvenile broilers at d 11 to 12. A prediction model was built on a subpopulation of the broilers without any loss in sensitivity (0.52) and specificity (0.78) when applied to the validation population. The parameter sex was included in the prediction model because levels of pvCO2 and pH that associated with ascites susceptibility are different between males and females. Commercial breeders can include these phenotypic traits in their genetic selection programs to reduce the incidence of ascites syndrome.
Gene Expression in Chicken Reveals Correlation with Structural Genomic Features and Conserved Patterns of Transcription in the Terrestrial Vertebrates
Nie, H. ; Crooijmans, R.P.M.A. ; Lammers, A. ; Schothorst, E.M. van; Keijer, J. ; Neerincx, P. ; Leunissen, J.A.M. ; Megens, H.J.W.C. ; Groenen, M.A.M. - \ 2010
PLoS ONE 5 (2010)8. - ISSN 1932-6203 - 7 p.
human housekeeping genes - salmonella infection - eimeria-maxima - lines - responses - selection - evolution - intestine - clusters - tissues
Background - The chicken is an important agricultural and avian-model species. A survey of gene expression in a range of different tissues will provide a benchmark for understanding expression levels under normal physiological conditions in birds. With expression data for birds being very scant, this benchmark is of particular interest for comparative expression analysis among various terrestrial vertebrates. Methodology/Principal Findings - We carried out a gene expression survey in eight major chicken tissues using whole genome microarrays. A global picture of gene expression is presented for the eight tissues, and tissue specific as well as common gene expression were identified. A Gene Ontology (GO) term enrichment analysis showed that tissue-specific genes are enriched with GO terms reflecting the physiological functions of the specific tissue, and housekeeping genes are enriched with GO terms related to essential biological functions. Comparisons of structural genomic features between tissue-specific genes and housekeeping genes show that housekeeping genes are more compact. Specifically, coding sequence and particularly introns are shorter than genes that display more variation in expression between tissues, and in addition intergenic space was also shorter. Meanwhile, housekeeping genes are more likely to co-localize with other abundantly or highly expressed genes on the same chromosomal regions. Furthermore, comparisons of gene expression in a panel of five common tissues between birds, mammals and amphibians showed that the expression patterns across tissues are highly similar for orthologuous genes compared to random gene pairs within each pair-wise comparison, indicating a high degree of functional conservation in gene expression among terrestrial vertebrates. Conclusions - The housekeeping genes identified in this study have shorter gene length, shorter coding sequence length, shorter introns, and shorter intergenic regions, there seems to be selection pressure on economy in genes with a wide tissue distribution, i.e. these genes are more compact. A comparative analysis showed that the expression patterns of orthologous genes are conserved in the terrestrial vertebrates during evolution
Breeding amiable animals? Improving farm animal welfare by including social effects in breeding programmes
Rodenburg, T.B. ; Bijma, P. ; Ellen, E.D. ; Bergsma, R. ; Vries, S. de; Bolhuis, J.E. ; Kemp, B. ; Arendonk, J.A.M. van - \ 2010
Animal Welfare 19 (2010)Suppl. 1. - ISSN 0962-7286 - p. 77 - 82.
different coping characteristics - open-field response - laying hens - feather pecking - multilevel selection - behavioral-development - genetic-parameters - pigs - serotonin - lines
Social interactions between individuals, such as co-operation and competition, are key factors in evolution by natural selection. As a consequence, evolutionary biologists have developed extensive theories to understand the consequences of social interactions for response to natural selection. Current genetic improvement programmes in animal husbandry, in contrast, largely ignore the implications of social interactions for the design of breeding programmes. Recently, we have developed theoretical and empirical tools to quantify the magnitude of heritable social effects, ie the heritable effects that animals have on their group mates' traits, in livestock populations, and to utilise those effects in genetic improvement programmes. Results in commercial populations of pigs and laying hens indicate large heritable social effects, and the potential to substantially increase responses to selection in traits affected by social interactions. In pigs, including social effects into the breeding programme affected aggressive behaviour, both at mixing and in stable groups, indicating changes in the way dominance relationships are established and in aggressiveness. In laying hens, we applied selection between kin-groups to reduce mortality due to cannibalistic pecking. This resulted in a considerable difference in mortality between the low mortality line and the unselected control line in the first generation (20 vs 30%). Furthermore, changes in behavioural and neurobiological responses to stress were detected in the low mortality line, pointing to reduced fearfulness and stress sensitivity. These first results indicate that including social effects into breeding programmes is a promising way to reduce negative social interactions in farm animals, and possibly to also increase positive social interactions, by breeding animals with better social skills