First report on chicken genes and chromosomes 2000

Improvement of the comparative map of chicken chromosome 13

A comparative map was made of chicken chromosome 13 (GGA13) with a part of human chromosome 5 (HSA5). Microsatellite markers specific for GGA13 were used to screen the Wageningen chicken bacterial artificial chromosome (BAC) library. Selected BAC clones were end sequenced and 57 sequence tag site (STS) markers were designed for contig building. In total, 204 BAC clones were identified which resulted in a coverage of about 20% of GGA13. Identification of genes was performed by a bi-directional approach. The first approach starting with sequencing mapped chicken BAC subclones, where sequences were used to identify orthologous genes in human and mouse by a basic local alignment search tool (BLAST) database search. The second approach started with the identification of chicken orthologues of human genes in the HSA5q23-35 region. The chicken orthologous genes were subsequently mapped by fluorescent in situ hybridisation (FISH) and/or single neucleotide polymorphism typing. The total number of genes mapped on GGA13 is increased from 14 to a total of 20 genes. Genes mapped on GGA13 have their orthologues on HSA5q23-5q35 in human and on Mmu11, Mmu13 and Mmu18 in mouse.

Non-random radial arrangements of interphase chromosome territories: evolutionary considerations and functional implications

In the nucleus of animal and plant cells individual chromosomes maintain a compartmentalized structure. Chromosome territories (CTs), as these structures were named by Theodor Boveri, are essential components of the higher-order chromatin architecture. Recent studies in mammals and non-mammalian vertebrates indicate that the radial position of a given CT (or segments thereof) is correlated with its size, its gene-density and its replication timing. As a representative case, chicken cell nuclei show highly consistent radial chromatin arrangements: gene-rich, early replicating microchromosomes are clustered within the nuclear interior, while gene-poor, later replicating macrochromosomes are preferentially located at the nuclear periphery. In humans, chromosomes 18 and 19 (HSA18 and 19) territories that are of similar size show a distinctly different position in the cell nuclei of lymphocytes and lymphoblastoid cells: the gene-rich and early replicating HSA19 CTs are typically found close to the nuclear center, while the gene-poor and later replicating HSA18 CTs are preferentially located at the nuclear periphery. Recent comparative maps between human and chicken chromosomes revealed that the chicken macrochromosomes 2 and Z contain the genes homologous to HSA18, while the genes on HSA19 are located onto the chicken microchromosomes. These data lend tentative support to the hypothesis that differences in the radial nuclear positions of gene-rich, early replicating and gene-poor, later replicating chromatin have been evolutionarily conserved during a period of more than 300 million years irrespective of the evolution of highly divergent karyotypes between humans and chicken.

A comparative map of chicken chromosome 24 and human chromosome 11

To improve the physical and comparative map of chicken chromosome 24 (GGA24; former linkage group E49C20W21) bacterial artificial chromosome (BAC) contigs were constructed around loci previously mapped on this chromosome by linkage analysis. The BAC clones were used for both sample sequencing and BAC end sequencing. Sequence tagged site (STS) markers derived from the BAC end sequences were used for chromosome walking. In total 191 BAC clones were isolated, covering almost 30% of GGA24, and 76 STS were developed (65 STS derived from BAC end sequences and 11 STS derived within genes). The partial sequences of the chicken BAC clones were compared with sequences present in the EMBL/GenBank databases, and revealed matches to 19 genes, expressed sequence tags (ESTs) and genomic clones located on human chromosome 11q22-q24 and mouse chromosome 9. Furthermore, 11 chicken orthologues of human genes located on HSA11q22-q24 were directly mapped within BAC contigs of GGA24. These results provide a better alignment of GGA24 with the corresponding regions in human and mouse and identify several intrachromosomal rearrangements between chicken and mammals.

Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates

We demonstrate that the nuclear topological arrangement of chromosome territories (CTs) has been conserved during primate evolution over a period of about 30 million years. Recent evidence shows that the positioning of chromatin in human lymphocyte nuclei is correlated with gene density. For example, human chromosome 19 territories, which contain mainly gene-dense and early replicating chromatin, are located toward the nuclear center, whereas chromosome 18 territories, which consist mainly of gene-poor and later replicating chromatin, is located close to the nuclear border. In this study, we subjected seven different primate species to comparative analysis of the radial distribution pattern of human chromosome 18- and 19-homologous chromatin by three-dimensional fluorescence in situ hybridization. Our data demonstrate that gene-density-correlated radial chromatin arrangements were conserved during higher-primate genome evolution, irrespective of the major karyotypic rearrangements that occurred in different phylogenetic lineages. The evolutionarily conserved positioning of homologous chromosomes or chromosome segments in related species supports evidence for a functionally relevant higher-order chromatin arrangement that is correlated with gene-density.

Sympathetic control of the cardiovascular response to acute hypoxemia in the chick embryo

In response to an acute hypoxemic insult, the mammalian fetus shows a redistribution of the cardiac output in favor of the heart and brain. Peripheral vasoconstriction contributes to this response and is partly mediated by the release of catecholamines. Two mechanisms of catecholamine release in the fetus are reported: 1) neurogenic sympathetic stimulation and 2) a nonneurogenic mechanism via a direct effect of hypoxemia on chromaffin tissues. In the present study, the effects of sympathetic blockade on plasma catecholamine release and cardiac output distribution in response to acute hypoxemia were studied in the chick embryo at different stages of incubation. Only at the end of the incubation period, sympathetic blockade markedly attenuated the increase in plasma catecholamine concentrations and resulted in a greater fraction of the cardiac output distributed to the carcass. However, these effects did not prevent a significant increase in cardiac output to the brain and heart during acute hypoxemia. These data imply that in the chick embryo the contribution of neurogenic mechanisms to the catecholaminergic response to acute hypoxemia becomes greater by the end of the incubation period.

Absence of Z-chromosome inactivation for five genes in male chickens

In order to examine if Z-chromosome inactivation, which is analogous to X-chromosome inactivation in mammals, takes place in male birds having ZZ sex chromosomes, five Z-linked genes of chickens which are expressed in both sexes in certain tissues were selected: i.e. genes for growth hormone receptor, nicotinic acetylcholine receptor beta3, aldolase B, beta1,4-galactosyltransferase I, and iron-responsive element-binding protein (also known as cytosolic aconitase). Antisense or sense riboprobe was prepared from an intronic sequence of each gene and subjected to fluorescence in situ hybridization to nascent transcripts of each gene in a nucleus. Each antisense riboprobe hyridized to two spots of nascent RNA which corresponded to its gene loci on the two Z chromosomes in a majority of nuclei in a tissue of the male. The efficiency of detection of two spots per nucleus was comparable to that for the glyceraldehyde-3-phosphate dehydrogenase gene, an autosomal housekeeping gene. These results suggest strongly that Z-chromosome inactivation, i.e. virtual silence of transcription at one of the alleles, does not take place for these five Z-linked genes in male chickens.

Localization of the muscular dystrophy AM locus using a chicken linkage map constructed with the Kobe University resource family

A chicken linkage map, constructed with the Kobe University (KU) resource family, was used to locate the genetic locus for muscular dystrophy of abnormal muscle type (AM). The KU resource family is a backcross pedigree with 55 offspring produced from the mating of a White Leghorn F-line (WL-F) male and a hybrid female produced from a cross between the WL-F male and a female of the Fayoumi OPN line who was homozygous for the AM gene. In total, 872 loci were genotyped on the pedigree; 749 (86%) were informative and mapped to 38 linkage groups. These informative loci included 649 AFLPs, 93 MS, three functional genes, the AM locus, sex phenotype, and two red blood cell loci. The remaining 123 markers were unlinked. Nineteen of the 38 KU linkage groups were assigned to macrochromosomes 1-8 and 11 microchromosomes including chromosome W, while 19 linkage groups were unassigned. The total map was 3569 cM in length, with an average marker interval of 4.8 cM. The AM locus was mapped 130 cM from the distal end of chromosome 2q.

From chicken coops to genome maps: generating phenotype from the molecular blueprint

The tools of molecular and cellular biology can be used to precisely describe traits in terms of a sequence of nucleic acids when their molecular and cellular bases are well understood. The entire genome of elite production birds, however, cannot be written as a series of A's, T's, C's, and G's because the interaction between alleles at the same and different loci is too large and there is likely to be many genotypes that encode the same production trait phenotype. A first draft of the genetic map of the chicken is anticipated within the next few years, but a complete molecular description of the genome of birds with elite production characteristics is not anticipated in the near future. Quantitative genetics will remain the cornerstone of breeding programs for production traits. Novel sequences encoding traits such as enhanced nutritional capability (e.g., expression of phytase) and resistance to specific diseases could be introduced into lines of chickens using the tools of molecular and cellular biology. Cloning could be used by the poultry industry to disperse highly desirable genotypes without the need for grandparent and parent flocks for multiplication.

A strategy to identify positional candidate genes conferring Marek's disease resistance by integrating DNA microarrays and genetic mapping

Marker-assisted selection (MAS) to enhance genetic resistance to Marek's disease (MD), a herpesvirus-induced T cell cancer in chicken, is an attractive alternative to augment control with vaccines. Our earlier studies indicate that there are many quantitative trait loci (QTL) containing one or more genes that confer genetic resistance to MD. Unfortunately, it is difficult to sufficiently resolve these QTL to identify the causative gene and generate tightly linked markers. One possible solution is to identify positional candidate genes by virtue of gene expression differences between MD resistant and susceptible chicken using deoxyribonucleic acid (DNA) microarrays followed by genetic mapping of the differentially-expressed genes. In this preliminary study, we show that DNA microarrays containing approximately 1200 genes or expressed sequence tags (ESTs) are able to reproducibly detect differences in gene expression between the inbred ADOL lines 63 (MD resistant) and 72 (MD susceptible) of uninfected and Marek's disease virus (MDV)-infected peripheral blood lymphocytes. Microarray data were validated by quantitative polymerase chain reaction (PCR) and found to be consistent with previous literature on gene induction or immune response. Integration of the microarrays with genetic mapping data was achieved with a sample of 15 genes. Twelve of these genes had mapped human orthologues. Seven genes were located on the chicken linkage map as predicted by the human-chicken comparative map, while two other genes defined a new conserved syntenic group. More importantly, one of the genes with differential expression is known to confer genetic resistance to MD while another gene is a prime positional candidate for a QTL.

Development of 112 unique expressed sequence tags from chicken liver using an arbitrarily primed reverse transcriptase-polymerase chain reaction and single strand conformation gel purification method

In order to provide information on chicken genome expression, expressed sequence tags (ESTs) were developed from chicken liver RNAs using a method based on arbitrarily primed reverse transcription-polymerase chain reaction (RT-PCR) of total RNAs. The method is similar to differential display, using one base anchored oligo-d(T) reverse-primers and 20-mer arbitrary forward-primers. A purification step by single strand conformation gel electrophoresis was added before sequencing. With a ratio of 112 unique sequences out of 155, we found this method to be highly effective when compared with EST production with randomly selected clones from non-subtracted, non-normalized libraries. A large proportion of the ESTs sequenced correspond to genes involved in transcriptional and post-transcriptional events. Cytogenetic mapping was performed for a subset of ESTs and four regions of conserved synteny between chicken and human were confirmed.

Structure and chromosomal localization of chicken CD5

CD5 is a transmembrane glycoprotein on all T cells and on a subpopulation of B cells. Based on the analysis of chicken CD5-cDNA we have previously shown that the structure of the CD5 protein is conserved between species. Here we report the isolation and chromosomal mapping of the chicken CD5 gene. The gene spans 3.4 kb and is extremely compact with a high GC-nucleotide content. There are 10 exons and the introns are spliced out similarly to those in the human CD5 gene. Each of the three extracellular scavenger receptor cysteine-rich (SRCR) domains is encoded as an exon of its own, as is the proline-rich hinge region that separates the first two membrane-distal SRCR domains. The fluorescence in situ hybridization (FISH) technique was used to map the gene to chromosome five. This is the first report describing the organization of the CD5 gene from a nonmammalian species.