bluuebunny/crossref_metadata_2025 huggingface dataset:
The chicken RH map: current state of progress and microchromosome mapping
Authors: Morisson M. , Denis M. , Milan D. , Klopp C. , Leroux S. , Bardes S. , Pitel F. , Vignoles F. , Gérus M. , Fillon V. , Douaud M. , Vignal A.
Published: July 2007

The ChickRH6 radiation hybrid panel has been used to construct consensus chromosome radiation hybrid (RH) maps of the chicken genome. Markers genotyped were either from throughout the genome or targeted to specific chromosomes and a large proportion (one third) of data was the result of collaborative efforts. Altogether, 2,531 markers were genotyped, allowing the construction of RH reference maps for 20 chromosomes and linkage groups for four other chromosomes. Amongst the markers, 581 belong to the framework maps, while 1,721 are on the comprehensive maps. Around 800 markers still have to be assigned to linkage groups. Our attempt to assign the supercontigs from the chrun (virtual chromosome containing all the genome sequence that could not be attributed to a chromosome) as well as EST (Expressed Sequence Tag) contigs that do not have a BLAST hit in the genome assembly led to the construction of new maps for microchromosomes either absent or for which very little data is present in the genome assembly. RH data is presented through our ChickRH webserver (http://chickrh.toulouse.inra.fr/), which is a mapping tool as well as the official repository RH database for genotypes. It also displays the RH reference maps and comparison charts with the sequence thus highlighting the possible discrepancies. Future improvements of the RH maps include complete coverage of the sequence assigned to chromosomes, further mapping of the chrun and mapping of EST contigs absent from the assembly. This will help finish the mapping of the smallest gene-rich microchromosomes.
A high-resolution linkage map for the Z chromosome in chicken reveals hot spots for recombination
Authors: Wahlberg P. , Strömstedt L. , Tordoir X. , Foglio M. , Heath S. , Lechner D. , Hellström A.R. , Tixier-Boichard M. , Lathrop M. , Gut I.G. , Andersson L.
Published: July 2007

A comprehensive linkage map for chicken chromosome Z was constructed as the result of a large-scale screening of single nucleotide polymorphisms (SNPs). A total of 308 SNPs were assigned to Z based on the genotype distribution among 182 birds representing several populations. A linkage map comprising 210 markers and spanning 200.9 cM was established by analyzing a small Red junglefowl/White Leghorn intercross. There was excellent agreement between the linkage map for Z and a recently released assembly of the chicken genome (May 2006). Almost all SNPs assigned to chromosome Z in the present study are on Z in the new genome assembly. The remaining 12 loci are all found on unassigned contigs that can now be assigned to Z. The average recombination rate was estimated at 2.7 cM/Mb but there was a very uneven distribution of recombination events with both cold and hot spots of recombination. The existence of one of the major hot spots of recombination, located around position 39.4 Mb, was supported by the observed pattern of linkage disequilibrium. Thirteen markers from unassigned contigs were shown to be located on chromosome W. Three of these contigs included genes that have homologues on chromosome Z. The preliminary assignment of three more genes to the gene-poor W chromosome may be important for studies on the mechanism of sex determination and dosage compensation in birds.
GEISHA: an in situ hybridization gene expression resource for the chicken embryo
Authors: Darnell D.K. , Kaur S. , Stanislaw S. , Davey S. , Konieczka J.H. , Yatskievych T.A. , Antin P.B.
Published: July 2007

An important and ongoing focus of biomedical and agricultural avian research is to understand gene function, which for a significant fraction of genes remains unknown. A first step is to determine when and where genes are expressed during development and in the adult. Whole mount in situ hybridization gives precise spatial and temporal resolution of gene expression throughout an embryo, and a comprehensive analysis and centralized repository of in situ hybridization information would provide a valuable research tool. The GEISHA project (gallus expression in situ hybridization analysis) was initiated to explore the utility of using high-throughput in situ hybridization as a means for gene discovery and annotation in chicken embryos, and to provide a unified repository for in situ hybridization information. This report describes the design and implementation of a new GEISHA database and user interface (www.geisha.arizona.edu), and illustrates its utility for researchers in the biomedical and poultry science communities. Results obtained from a high throughput screen of microRNA expression in chicken embryos are also presented.
Chromosome repatterning in three representative parrots (Psittaciformes) inferred from comparative chromosome painting
Authors: Nanda I. , Karl E. , Griffin D.K. , Schartl M. , Schmid M.
Published: July 2007

Parrots (order: Psittaciformes) are the most common captive birds and have attracted human fascination since ancient times because of their remarkable intelligence and ability to imitate human speech. However, their genome organization, evolution and genomic relation with other birds are poorly understood. Chromosome painting with DNA probes derived from the flow-sorted macrochromosomes (1–10) of chicken (Gallus gallus, GGA) has been used to identify and distinguish the homoeologous chromosomal segments in three species of parrots, i.e., Agapornis roseicollis (peach-faced lovebird); Nymphicus hollandicus (cockatiel) and Melopsittacus undulatus (budgerigar). The ten GGA macrochromosome paints unequivocally recognize 14 to 16 hybridizing regions delineating the conserved chromosomal segments for the respective chicken macrochromosomes in these representative parrot species. The cross-species chromosome painting results show that, unlike in many other avian karyotypes with high homology to chicken chromosomes, dramatic rearrangements of the macrochromosomes have occurred in parrot lineages. Among the larger GGA macrochromosomes (1–5), chromosomes 1 and 4 are conserved on two chromosomes in all three species. However, the hybridization pattern for GGA 4 in A. roseicollis and M. undulatus is in sharp contrast to the most common pattern known from hybridization of chicken macrochromosome 4 in other avian karyotypes. With the exception of A. roseicollis, chicken chromosomes 2, 3 and 5 hybridized either completely or partially to a single chromosome. In contrast, the smaller GGA macrochromosomes 6, 7 and 8 displayed a complex hybridization pattern: two or three of these macrochromosomes were found to be contiguously arranged on a single chromosome in all three parrot species. Overall, the study shows that translocations and fusions in conjunction with intragenomic rearrangements have played a major role in the karyotype evolution of parrots. Our inter-species chromosome painting results unequivocally illustrate the dynamic reshuffling of ancestral chromosomes among the karyotypes ofPsittaciformes.
Chromosomal mapping of chicken mega-telomere arrays to GGA9, 16, 28 and W using a cytogenomic approach
Authors: Delany M.E. , Gessaro T.M. , Rodrigue K.L. , Daniels L.M.
Published: July 2007

Four mega-telomere loci were mapped to chicken chromosomes 9, 16, 28, and the W sex chromosome by dual-color fluorescence in situ hybridization using a telomeric sequence probe and BAC clones previously assigned to chicken chromosomes. The in-common features of the mega-telomere chromosomes are that microchromosomes are involved rather than macrochromosomes; in three cases (9, 16, 28) acrocentrics are involved with the mega-telomeres mapping to the p arms. Three of the four chromosomes (9, 16, W) encode tandem repeats which in two cases (9 and 16) involve the ribosomal DNA arrays (the 5S and 18S-5.8S-28S gene repeats, respectively). All involved chromosomes have a typical-sized telomere on the opposite terminus. Intra- and interindividual variation for mega-telomere distribution are discussed in terms of karyotype abnormalities and the potential for mitotic instability of some telomeres. The diversity and distribution of telomere array quantity in the chicken genome should be useful in contributing to research related to telomere length regulation – how and by what mechanism genomes and individual chromosomes establish and maintain distinct sets of telomere array sizes, as well as for future studies related to stability of the chicken genome affecting development, growth, cellular lifespan and disease. An additional impact of this study includes the listing of BAC clones (26 autosomal and six W BACs tested) that were cytogenetically verified; this set of BACs provide a useful tool for future cytogenetic analyses of the microchromosomes.
ZP genes in avian species illustrate the dynamic evolution of the vertebrate egg envelope
Authors: Hughes D.C.
Published: July 2007

The vertebrate egg envelope is composed of a set of related proteins, encoded by the ZP genes. The apparent simplicity of the egg envelope is in contrast to the number of ZP genes identified by conventional cloning and data mining of genome sequences from a number of vertebrates. The vertebrate ZP genes fall into five classes, ZP1, ZP2, ZP3, ZPD and ZPAX. Analysis of chicken genome and EST sequence data has revealed the presence of seven distinct ZP genes, falling into these classes that are expressed in the female reproductive system. Comparison with the repertoire of ZP genes in other vertebrates suggests a major source of diversity in the composition of the egg envelope is a continual process of amplification, diversification and attrition of ZP gene sequences.
Different origins of bird and reptile sex chromosomes inferred from comparative mapping of chicken Z-linked genes
Authors: Kawai A. , Nishida-Umehara C. , Ishijima J. , Tsuda Y. , Ota H. , Matsuda Y.
Published: July 2007

Recent progress of chicken genome projects has revealed that bird ZW and mammalian XY sex chromosomes were derived from different autosomal pairs of the common ancestor; however, the evolutionary relationship between bird and reptilian sex chromosomes is still unclear. The Chinese soft-shelled turtle (Pelodiscus sinensis) exhibits genetic sex determination, but no distinguishable (heteromorphic) sex chromosomes have been identified. In order to investigate this further, we performed molecular cytogenetic analyses of this species, and thereby identified ZZ/ZW-type micro-sex chromosomes. In addition, we cloned reptile homologues of chicken Z-linked genes from three reptilian species, the Chinese soft-shelled turtle and the Japanese four-striped rat snake (Elaphe quadrivirgata), which have heteromorphic sex chromosomes, and the Siam crocodile (Crocodylus siamensis), which exhibits temperature-dependent sex determination and lacks sex chromosomes. We then mapped them to chromosomes of each species using FISH. The linkage of the genes has been highly conserved in all species: the chicken Z chromosome corresponded to the turtle chromosome 6q, snake chromosome 2p and crocodile chromosome 3. The order of the genes was identical among the three species. The absence of homology between the bird Z chromosome and the snake and turtle Z sex chromosomes suggests that the origin of the sex chromosomes and the causative genes of sex determination are different between birds and reptiles.
Molecular evolutionary genomics of birds
Authors: Ellegren H.
Published: July 2007

Insight into the molecular evolution of birds has been offered by the steady accumulation of avian DNA sequence data, recently culminating in the first draft sequence of an avian genome, that of chicken. By studying avian molecular evolution we can learn about adaptations and phenotypic evolution in birds, and also gain an understanding of the similarities and differences between mammalian and avian genomes. In both these lineages, there is pronounced isochore structure with highly variable GC content. However, while mammalian isochores are decaying, they are maintained in the chicken lineage, which is consistent with a biased gene conversion model where the high and variable recombination rate of birds reinforces heterogeneity in GC. In Galliformes, GC is positively correlated with the rate of nucleotide substitution; the mean neutral mutation rate is 0.12–0.15% at each site per million years but this estimate comes with significant local variation in the rate of mutation. Comparative genomics reveals lower dN/dS ratios on micro- compared to macrochromosomes, possibly due to population genetic effects or a non-random distribution of genes with respect to chromosome size. A non-random genomic distribution is shown by genes with sex-biased expression, with male-biased genes over-represented and female-biased genes under-represented on the Z chromosome. A strong effect of selection is evident on the non-recombining W chromosome with high dN/dS ratios and limited polymorphism. Nucleotide diversity in chicken is estimated at 4–5 × 10–3 which might be seen as surprisingly high given presumed bottlenecks during domestication, but is lower than that recently observed in several natural populations of other species. Several important aspects of the molecular evolutionary process of birds remain to be understood and it can be anticipated that the upcoming genome sequence of a second bird species, the zebra finch, as well as the integration of data on gene expression, shall further advance our knowledge of avian evolution.
Manipulation of small RNAs to modify the chicken transcriptome and enhance productivity traits
Authors: Tizard M.L.V. , Moore R.J. , Lambeth L.S. , Lowenthal J.W. , Doran T.J.
Published: July 2007

In recent years there has been a revolution in our understanding of genes and how they come to control the physical outcomes of development. Central to this has been the understanding of the cellular processes of RNA interference (RNAi), for which the Nobel Prize for Physiology or Medicine was awarded in 2006. Coupled with this has been the recognition that microRNAs are key mediators of this process within cells. RNAi whether mediated exogenously by synthetic oligonucleotides or vector-delivered double stranded RNA or endogenously by microRNAs can have a profound and specific effect on gene expression. Elucidating and understanding these processes in the chicken will provide critical information to enable more precise control over breeding strategies for improvement of traits in production poultry, either by direct or indirect means. It will also provide alternative strategies for the control and prevention of important avian diseases.
Avian sex determination: what, when and where?
Authors: Smith C.A. , Roeszler K.N. , Hudson Q.J. , Sinclair A.H.
Published: July 2007

Sex is determined genetically in all birds, but the underlying mechanism remains unknown. All species have a ZZ/ZW sex chromosome system characterised by female (ZW) heterogamety, but the chromosomes themselves can be heteromorphic (in most birds) or homomorphic (in the flightless ratites). Sex in birds might be determined by the dosage of a Z-linked gene (two in males, one in females) or by a dominant ovary-determining gene carried on the W sex chromosome, or both. Sex chromosome aneuploidy has not been conclusively documented in birds to differentiate between these possibilities. By definition, the sex chromosomes of birds must carry one or more sex-determining genes. In this review of avian sex determination, we ask what, when and where? What is the nature of the avian sex determinant? When should it be expressed in the developing embryo, and where is it expressed? The last two questions arise due to evidence suggesting that sex-determining genes in birds might be operating prior to overt sexual differentiation of the gonads into testes or ovaries, and in tissues other than the urogenital system.
Genomics of antiviral defenses in the duck, a natural host of influenza and hepatitis B viruses
Authors: MacDonald M.R.W. , Veniamin S.M. , Guo X. , Xia J. , Moon D.A. , Magor K.E.
Published: July 2007

We review our progress using genomics approaches to examine key antiviral defenses of the White Pekin mallard duck, Anas platyrhynchos. Our interest stems from the fact that ducks are the natural host of avian influenza, and are an important animal model for hepatitis B research. First, we have conducted an expressed sequence tag (EST) project and identified more than 200 immune relevant genes in the duck. Our analysis of these genes allows us to evaluate the homology between ducks and their closest genetic model organism, the chicken. We have also constructed genomic and cDNA libraries from the same individual duck, allowing us to directly compare expressed sequences with those present in the genome. These resources allow us to determine the organization and expression of regions of the genome important in antiviral defenses. Here we examine the organization of the immunoglobulin heavy chain locus, the Major Histocompatibility Complex class I region, the lectin immunoreceptors and Toll-like receptor 7. We discuss our research-in-progress in the context of the immune defense against viruses, particularly influenza.
Characterization of the turkey MHC chromosome through genetic and physical mapping
Authors: Chaves L.D. , Krueth S.B. , Reed K.M.
Published: July 2007

Previous studies in the chicken have identified a single microchromosome (GGA16) containing the ribosomal DNA (rDNA) and two genetically unlinked MHC regions, MHC-B and MHC-Y. Chicken DNA sequence from these loci was used to develop PCR primers for amplification of homologous fragments from the turkey (Meleagris gallopavo). PCR products were sequenced and overgo probes were designed to screen the CHORI 260 turkey BAC library. BAC clones corresponding to the turkey rDNA, MHC-B and MHC-Y were identified. BAC end and subclone sequencing confirmed identity and homology of the turkey BAC clones to the respective chicken loci. Based on subclone sequences, single-nucleotide polymorphisms (SNPs) segregating within the UMN/NTBF mapping population were identified and genotyped. Analysis of SNP genotypes found the B and Y to be genetically unlinked in the turkey. Silver staining of metaphase chromosomes identified a single pair of microchromosomes with nucleolar organizer regions (NORs). Physical locations of the rDNA and MHC loci were determined by fluorescence in situ hybridization (FISH) of the BAC clones to metaphase chromosomes. FISH clearly positioned the rDNA distal to the Y locus on the q-arm of the MHC chromosome and the MHC-B on the p-arm. An internal telomere array on the MHC chromosome separates the B and Y loci.
Low density lipoprotein receptor relatives in chicken ovarian follicle and oocyte development
Authors: Schneider W.J.
Published: July 2007

The normal development of the chicken oocyte within the ovarian follicle depends on the coordinated expression and function of several members of the low density lipoprotein receptor gene family. The human low density lipoprotein receptor is the prototype of the gene family; since its discovery and the elucidation of the medical significance of mutations in the LDLR gene, many additional family members have been discovered and characterized, and some important advances have resulted from studies in the chicken. I describe the analogies as well as the differences that exist between the molecular genetics of the mammalian and avian members of this important gene family, with emphasis on receptor-mediated oocyte growth. Recent progress in the molecular characterization of the chicken genes whose products mediate oocyte growth, follicle development, and accessory pathways is described in detail, and emerging information of preliminary nature is included. As the availability of chicken genome sequence data has enhanced the rate of progress in the field, our understanding of the physiological roles of members of this receptor family in general has already gained from studies in the avian model system.
Characterising alternate splicing and tissue specific expression in the chicken from ESTs
Authors: Tang H. , Heeley T. , Morlec R. , Hubbard S.J.
Published: July 2007

Alternate splicing is believed to produce the greatest diversity in transcriptional complexity and function in eukaryotic species. In this study, we present an analysis of alternative splicing events that occur in the chicken, using the recently sequenced genomic sequence and over 580,000 EST sequences mapped back to the genome. A carefully controlled EST-to-genome mapping pipeline is presented, based around the EXONERATE program using the est2genome model, which also considers several quality control steps to filter out erroneous matches. The data is then used to estimate the level of alternate splicing events with respect to Ensembl predicted transcripts. The EST-genome mappings are characterised at the exon level, in order to classify individual splicing events and provide estimates of novel transcripts not currently annotated by the Ensembl genome database. This is the first large scale analysis of this kind in an avian species, and suggests that chicken displays a similar level of alternate splicing as that found in other higher vertebrates such as human and mouse, both in terms of the number of genes that undergo alternate splicing events, and the average number of transcripts produced per gene. The EST data suggests alternate splicing may occur in some 50–60% of the chicken gene set and with an average of around 2.3 transcripts per gene which undergo this process. The EST data is also used to look at gene and transcript usage in the tissues sequenced in embryonic and adult libraries. Genes which display notable biases were analysed in more detail, including twinfilin-2 and embryonic heavy chain myosin. This also highlights several as yet functionally un-annotated genes which appear to be important in embryonic tissues and also undergo alternate splicing events. The analysis also demonstrates some of the difficulties involved in using EST-based data to annotate transcriptional activity in eukaryotic genes, where a broad spectrum of tissues and a large number of sequenced transcripts are required in order to fully characterise alternate splicing and differential expression.
GOing from functional genomics to biological significance
Authors: McCarthy F.M. , Bridges S.M. , Burgess S.C.
Published: July 2007

The chicken genome is sequenced and this, together with microarray and other functional genomics technologies, makes post-genomic research possible in the chicken. At this time, however, such research is hindered by a lack of genomic structural and functional annotations. Bio-ontologies have been developed for different annotation requirements, as well as to facilitate data sharing and computational analysis, but these are not yet optimally utilized in the chicken. Here we discuss genomic annotation and bio-ontologies. We focus specifically on the Gene Ontology (GO), chicken GO annotations and how these can facilitate functional genomics in the chicken. The GO is the most developed and widely used bio-ontology. It is the de facto standard for functional annotation. Despite its critical importance in analyzing microarray and other functional genomics data, relatively few chicken gene products have any GO annotation. When these are available, the average quality of chicken gene products annotations (defined using evidence code weight and annotation depth) is much less than in mouse. Moreover, tools allowing chicken researchers to easily and rapidly use the GO are either lacking or hard to use. To address all of these problems we developed ChickGO and AgBase. Chicken GO annotations are provided by complementary work at MSU-AgBase and EBI-GOA. The GO tools pipeline at AgBase uses GO to derive functional and biological significance from microarray and other functional genomics data. Not only will improved genomic annotation and tools to use these annotations benefit the chicken research community but they will also facilitate research in other avian species and comparative genomics.
Identification of quantitative trait loci affecting shank length, body weight and carcass weight from the Japanese cockfighting chicken breed, Oh-Shamo (Japanese Large Game)
Authors: Tsudzuki M. , Onitsuka S. , Akiyama R. , Iwamizu M. , Goto N. , Nishibori M. , Takahashi H. , Ishikawa A.
Published: July 2007

We performed a quantitative trait locus (QTL) analysis to map QTLs controlling shank length, body weight, and carcass weight in a resource family of 245 F2 birds developed from a cross of the large-sized, native, Japanese cockfighting breed, Oh-Shamo (Japanese Large Game), and the White Leghorn breed of chickens. Interval mapping revealed three significant QTLs for shank length on chromosomes 1, 4 and 24 at the experiment-wise 5% level, and a suggestive shank length QTL on chromosome 27 at the experiment-wise 10% level. For body weight two QTLs, one significant and the other suggestive, were identified on chromosomes 4 and 24, respectively. As expected, QTLs for carcass weight, which was highly correlated with body weight (r = 0.95), were detected at the same chromosomal locations as the detected body weight QTLs. Interestingly, the chromosomal locations containing these body weight and carcass weight QTLs coincided with those of two of the four shank length QTLs detected. No QTL with an epistatic interaction effect was discovered for any trait. The total contribution of all detected QTLs to genetic variance was 98.4%, 27.0% and 25.9% for shank length, body weight and carcass weight, respectively, indicating that most shank length QTLs have been identified but many body weight and carcass weight QTLs have been overlooked by the present analysis because of a low coverage rate of the 88 microsatellite markers used here (approximately 46% of the whole genome).
Quantitative trait loci for bone traits segregating independently of those for growth in an F2 broiler × layer cross
Authors: Sharman P.W.A. , Morrice D.R. , Law A.S. , Burt D.W. , Hocking P.M.
Published: July 2007

An F2 broiler–layer cross was phenotyped for 18 skeletal traits at 6, 7 and 9 weeks of age and genotyped with 120 microsatellite markers. Interval mapping identified 61 suggestive and significant QTL on 16 of the 25 linkage groups for 16 traits. Thirty-six additional QTL were identified when the assumption that QTL were fixed in the grandparent lines was relaxed. QTL with large effects on the lengths of the tarsometatarsus, tibia and femur, and the weights of the tibia and femur were identified on GGA4 between 217 and 249 cM. Six QTL for skeletal traits were identified that did not co-locate with genome wide significant QTL for body weight and two body weight QTL did not coincide with skeletal trait QTL. Significant evidence of imprinting was found in ten of the QTL and QTL × sex interactions were identified for 22 traits. Six alleles from the broiler line for weight- and size-related skeletal QTL were positive. Negative alleles for bone quality traits such as tibial dyschondroplasia, leg bowing and tibia twisting generally originated from the layer line suggesting that the allele inherited from the broiler is more protective than the allele originating from the layer.
Parent-of-origin specific QTL – a possibility towards understanding reciprocal effects in chicken and the origin of imprinting
Authors: Tuiskula-Haavisto M. , Vilkki J.
Published: July 2007

Reciprocal effects for sexual maturity, egg production, egg quality traits and viability are well known in poultry crosses. They have been used in an optimal way to form profitable production hybrids. These effects have been hypothesized to originate from sex-linked genes, maternal effects or a combination of both. However, these may not be the only explanations for reciprocal effects. Recent mapping of quantitative trait loci (QTL) has revealed autosomal areas with parent-of-origin specific effects in the chicken. In mammals, parental imprinting, i.e. the specifically regulated expression of either maternal or paternal allele in the offspring, is the main cause of such effects. The most commonly accepted hypothesis for the origin of imprinting, the conflict hypothesis, assumes a genetic conflict of interest between the maternal and paternal genomes regarding the allocation of resources to the offspring. It also intrinsically implies that imprinting should not occur in oviparous taxa. However, new molecular genetic information has raised a need to review the possible involvement of imprinting or some related phenomena as a putative cause of reciprocal effects in poultry. Comparative mapping provides strong evidence for the conservation of orthologous imprinted gene clusters on chicken macrochromosomes. Furthermore, these gene clusters exhibit asynchronous DNA replication, an epigenetic mark specific for all imprinted regions. It has been proposed that these intrinsic chromosomal properties have been important for the evolution of imprinted gene expression in the mammalian lineage. Many of the mapped parent-of-origin specific QTL effects in chicken locate in or close to these conserved regions that show some of the basic features involved in monoallelic expression. If monoallelic expression in these regions would be observed in birds, the actual mechanism and cause may be different from the imprinting that evolved later in the mammalian lineage. In this review we discuss recent molecular genetic results that may provide tools for understanding of reciprocal differences in poultry breeding and the evolution of imprinting.
Evidence for widespread epistatic interactions influencing Marek’s disease virus viremia levels in chicken
Authors: Cheng H.H. , Zhang Y. , Muir W.M.
Published: July 2007

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 × 7 F2 experimental resource population was re-evaluated with finer resolution for epistatic interactions. The F2 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.
Biodiversity of 20 chicken breeds assessed by SNPs located in gene regions
Authors: Twito T. , Weigend S. , Blum S. , Granevitze Z. , Feldman M.W. , Perl-Treves R. , Lavi U. , Hillel J.
Published: July 2007

Twenty-five single nucleotide polymorphisms (SNPs) were analyzed in 20 distinct chicken breeds. The SNPs, each located in a different gene and mostly on different chromosomes, were chosen to examine the use of SNPs in or close to genes (g-SNPs), for biodiversity studies. Phylogenetic trees were constructed from these data. When bootstrap values were used as a criterion for the tree repeatability, doubling the number of SNPs from 12 to 25 improved tree repeatability more than doubling the number of individuals per population, from five to ten. Clustering results of these 20 populations, based on the software STRUCTURE, are in agreement with those previously obtained from the analysis of microsatellites. When the number of clusters was similar to the number of populations, affiliation of birds to their original populations was correct (>95%) only when at least the 22 most polymorphic SNP loci (out of 25) were included. When ten populations were clustered into five groups based on STRUCTURE, we used membership coefficient (Q) of the major cluster at each population as an indicator for clustering success level. This value was used to compare between three marker types; microsatellites, SNPs in or close to genes (g-SNPs) and SNPs in random fragments (r-SNPs). In this comparison, the same individuals were used (five to ten birds per population) and the same number of loci (14) used for each of the marker types. The average membership coefficients (Q) of the major cluster for microsatellites, g-SNPs and r-SNPs were 0.85, 0.7, and 0.64, respectively. Analysis based on microsatellites resulted in significantly higher clustering success due to their multi-allelic nature. Nevertheless, SNPs have obvious advantages, and are an efficient and cost-effective genetic tool, providing broader genome coverage and reliable estimates of genetic relatedness.
Detection of agriculturally important QTLs in chickens and analysis of the factors affecting genotyping strategy
Authors: Atzmon G. , Blum S. , Feldman M. , Lavi U. , Hillel J.
Published: July 2007

Three single cross populations were generated in order to analyze factors affecting the ability to detect true linkage with minimum false positive or false negative associations, and to detect associations between markers and quantitative traits. The three populations are: (1) a broiler × broiler cross of a single sire and 34 dams, resulting in 266 progeny; (2) a broiler × broiler cross of a single sire and 41 dams resulting in 360 progeny; and (3) a broiler × layer cross of a single sire with 56 dams resulting in 1180 progeny. Based on these three resource populations we show that: a) gradient selective genotyping was more effective than the random selective genotyping; b) selective genotyping was significant at a selected proportion less than 62% of the cumulative truncation point; c) as few as 10% of selected individuals (5% of each of the two tails) were sufficient to show significant association between markers and phenotypes; d) a gradient slices approach was more powerful than using replicates of the extreme groups; and e) in resource populations resulting from crosses between lines of different backgrounds, most of the microsatellite markers used are polymorphic. We also used simulation to test factors affecting power to detect true associations between markers and traits that are hard to detect in experimental resource populations. Using defined populations in the simulation, we concluded that the following guidelines provide reliable detection of linked QTLs: 1) the resource population size should be larger than 100; 2) a QTL effect larger than 0.4 SD is detectable with a reasonable number of markers (>100) and resource population size (>200 subjects); 3) the DNA pool from each tail of the trait distribution should contain at least 10% of the resource family; 4) each of the two DNA pools should include more than 35 individuals. Some of these guidelines that were deduced from the simulation analysis have been confirmed in the experimental part of this study.
Extent of linkage disequilibrium in chicken
Authors: Aerts J. , Megens H.J. , Veenendaal T. , Ovcharenko I. , Crooijmans R. , Gordon L. , Stubbs L. , Groenen M.
Published: July 2007

Many of the economically important traits in chicken are multifactorial and governed by multiple genes located at different quantitative trait loci (QTLs). The optimal marker density to identify these QTLs in linkage and association studies is largely determined by the extent of linkage disequilibrium (LD) around them. In this study, we investigated the extent of LD on two chromosomes in a white layer and two broiler chicken breeds. Pairwise levels of LD were calculated for 33 and 36 markers on chromosomes 10 and 28, respectively. We found that useful LD (i.e. an r2 value higher than 0.3) in Nutreco chicken breed E5 (inbred) can extend to around 1 cM on chromosomes 10 and 28, although in a second region on chromosome 28 it extends to about 2.5 cM. The extent in breed Nutreco E3 (outbred) was very short in chromosome 10 (15 kb) but very much larger on chromosome 28, particularly in one region of depressed heterozygosity. The layer breed E2 (inbred) showed an extent of useful LD up to 4 cM on chromosome 10; the extent on chromosome 28 could not be assessed due to an erratic pattern of LD on that chromosome, although in one region LD appears to be in the order of 0.8 cM. This indicates that there may be very large differences in patterns of LD between different chicken breeds and different genomic regions.
Modulation of macrophages by infectious bursal disease virus
Authors: Khatri M. , Sharma J.M.
Published: July 2007

Infectious bursal disease is one of the most important naturally occurring viral diseases of chickens worldwide. The causative agent, infectious bursal disease virus (IBDV), belongs to the family Birnaviridae. This viruscauses an acute, highly contagious and immunosuppressive disease in chickens. The virus infects and destroys actively dividing IgM-bearing B cells. Although B cells are the principal targets for IBDV, recent data show that the virus also infects macrophages. IBDV-infected macrophages produce various cytokines and chemokines which may play an important role in the protection and/or pathogenesis of IBDV. In this review, the modulatory effects of IBDV on macrophages will be discussed.
Genesis of pandemic influenza
Authors: Sorrell E.M. , Ramirez-Nieto G.C. , Gomez-Osorio I.G. , Perez D.R.
Published: July 2007

During the last decade the number of reported outbreaks caused by highly pathogenic avian influenza (HPAI) in domestic poultry has drastically increased. At the same time, low pathogenic avian influenza (LPAI) strains, such as H9N2 in many parts of the Middle East and Asia and H6N2 in live bird markets in California, have become endemic. Each AI outbreak brings the concomitant possibility of poultry-to-human transmission. Indeed, human illness and death have resulted from such occasional transmissions with highly pathogenic avian H7N7 and H5N1 viruses while avian H9N2 viruses have been isolated from individuals with mild influenza. The transmission of avian influenza directly from poultry to humans has brought a sense of urgency in terms of understanding the mechanisms that lead to interspecies transmission of influenza. Domestic poultry species have been previously overlooked as potential intermediate hosts in the generation of influenza viruses with the capacity to infect humans. In this review, we will discuss molecular and epidemiological aspects that have led to the recurrent emergence of avian influenza strains with pandemic potential, with a particular emphasis on the current Asian H5N1 viruses.
Food-Based Dietary Guidelines in Austria
Authors: Elmadfa I. , Freisling H.
Published: July 2007

The translation of nutrient-based dietary guidelines (NBDG) into food-based dietary guidelines (FBDG) is part of a nutrition policy at the national level to counteract the increasing prevalence of chronic diseases that are related to diet and physical activity. In Austria, first steps have already been taken and several promising FBDG have been introduced to the consumer. These FBDG are basically consistent as they use the same concept, a nutritive approach which is based on the ‘DACH Reference Values for Nutrient Intake’. Minor differences arise in the translation of this NBDG into food servings. The ‘Nutrition Circle’ and pyramids are the common forms used to visualize FBDG for the Austrian population. The ‘Three-Dimensional Food Pyramid’, which was introduced in 2005 by the German Nutrition Society and has been adopted by the Austrian Nutrition Society, combines quantitative and qualitative aspects. A not less promising approach has been introduced by the Austrian Nutrition Society – the ‘Module System’ as a visual aid to facilitate the promotion and dissemination of FBDG. Together with the Austrian Nutrition Reports, FBDG are important measures to improve the nutritional situation in Austria. Upcoming results of ongoing nutrition monitoring will evaluate the success of the current measures taken in Austrian nutrition policy.
Development of Food-Based Dietary Guidelines for Iran: A Preliminary Report
Authors: Safavi S.M. , Omidvar N. , Djazayery A. , Minaie M. , Hooshiarrad A. , Sheikoleslam R.
Published: July 2007

Iran is undergoing an epidemiological and nutritional transition. Over the last 2–3 decades, major changes in lifestyle and food consumption patterns have occurred, as well as in the socio-economic situation. Disease patterns have changed and some micronutrient deficiencies and chronic nutritional diseases, including obesity, are on the increase. Considering these, food habits, and the national food system, the Nutrition Department, Ministry of Health and Medical Education and the Iranian Nutrition Society jointly undertook to prepare food-based dietary guidelines (FBDGs). The process consisted of three phases: agreeing on food groups, designing pictorial FBDGs, and field testing them. Three working teams, supported by a large group of advisors consisting of nutritionists, epidemiologists, food/nutrition planners, and other relevant experts were formed. The first draft of the food groups consisted of 7 groups: Bread and Cereals; Meats and Eggs; Pulses; Fruits; Vegetables; Milk and Dairy Products; Miscellaneous (nuts, oils and fats, sugar and sweets, soft drinks). It was sent to 20 nutrition and public health experts for feedback. A suggestion was made to divide the Miscellaneous group into two – oils and fats, and Miscellaneous (sugars and sweets, pickled and salted food items). Three pictorial FBDGs were then designed: a plate, a pyramid, and a rectangle. Thus, three posters were prepared by the working teams and revised by a group of experts, followed by a preliminary evaluation. The final step will be field testing of the three revised, modified designs by the public and experts and their final evaluation.
Nutrient Profiles – A Suitable Means of Nutrition Information
Authors: Erbersdobler Helmut F.
Published: July 2007

For several years, nutrient profiling has been discussed as a regulatory instrument for health claims made on foods. The aims of the European Commission are mainly to protect consumers from misleading and even dangerous information and to ban advertisements for foods and menus for children if they are not healthy. Generally, nutrient profiling will be established on the basis of contents of different nutrients and substances like fat, saturated fat, trans fatty acids, salt/sodium and sugars ‘whose excessive intakes in the overall diet are not recommended and those such as poly- and monounsaturated fats, available carbohydrates other than sugars, vitamins, minerals, protein and fiber’. In the present paper, 4 out of >20 proposals will be discussed: the US requirement for health claims (FDA Code), the ‘a little a lot’ system from the UK, the ‘tripartite classification’ model of the Netherlands and the FSA scoring system from the UK. At present, several details remain uncertain, e.g. the reference basis (100 g, serving size or 100 kcal, respectively), moreover the use of thresholds or a scoring system. The evaluation may be ‘across the board’ versus in categories, respectively. In all cases, exceptions will be necessary.
Hemostatic Alterations in Liver Disease: A Review on Pathophysiology, Clinical Consequences, and Treatment
Authors: Lisman Ton , Leebeek Frank W.G.
Published: July 2007

In most patients with acute or chronic liver failure, extensive changes in all pathways contributing to hemostasis are found. These hemostatic alterations concern both pro- and antihemostatic pathways, and therefore the net result of the hemostatic dysbalance is unclear. Although it is generally believed that patients with liver disease have a hemostasis-related bleeding tendency, this concept is challenged in recent literature. Although the bleeding problems in patients with liver disease are obvious, the clinically most relevant bleeding episodes, i.e., bleeding from ruptured varices or ulcers, are due to vascular abnormalities and portal hypertension, and not to an abnormal hemostatic system. Moreover, patients with liver disease sometimes experience thrombosis of the portal vein or hepatic artery, which is in part attributed to hypercoagulation. In addition, a substantial part of the patients with liver disease undergoing liver transplantation can nowadays undergo this major surgical procedure, which involves significant hemostatic challenges, without transfusion of blood products. Therefore, the recent debate on the presence of a major hemostatic defect in patients with liver disease seems justified. This paper will review the hemostatic changes that occur in acute and chronic liver failure, and will review hemostasis testing and reversal of coagulopathy in these patients.
Use of Topical Hemostatic Agents during Liver Resection
Authors: Berrevoet Frederik , de Hemptinne Bernard
Published: July 2007

Despite all recent developments in surgical techniques during liver surgery, blood loss is still one of the main causes for postoperative morbidity and mortality. Other complications include bile leakage and fluid accumulation intraperitoneally. Fibrin sealants are able not only to enhance clot formation and wound healing but possibly work as a sealing device for postoperative leakage and fistula formation. In this overview the underlying mechanisms for these agents are discussed and several clinical data concerning liver surgery will be reported.
Prevention of Biliary Leakage after Partial Liver Resection Using Topical Hemostatic Agents
Authors: Erdogan Deha , Busch Olivier R.C. , Gouma Dirk J. , van Gulik Thomas M.
Published: July 2007

Liver resection is widely accepted as the only potentially curative treatment in malignant or benign hepatobiliary lesions. Although not frequent, biliary leakage is a postoperative complication which may have considerable consequences. The field of topical hemostatic agents is rapidly developing, with various products currently available. This article reviews the risk factors associated with biliary leakage and the methods used for testing or prevention of biliary leakage. A literature search was performed using key words related to experimental and clinical studies dealing with biliary leakage. Experimental studies assessed the potential biliostatic effect of different topical hemostatic agents after bile duct reconstruction. Clinical series show biliary leakage rates up to 12%. There is no evidence that flushing of the bile duct system after resection reduces the incidence of biliary leakage. Further controlled studies are needed to clarify the preventive effect of topical hemostatic agents on biliary leakage after liver resection.