Polymerase chain reaction amplified markers for bird sexing

Female birds are heterogametic (Z/W), while males are homogametic (Z/Z). PCR assays are often useful in sexing avian species, especially at hatch or in ovo. Two previously described assays are based on differences between the Z and W copy of the chicken chromodomain-helicase DNA-binding protein gene (CHD1Z and CHD1W). Applicability of these assays were tested in five other galliforms: red junglefowl, turkey, peafowl, bobwhite quail and common quail, and one waterfowl, mallard. Using primers described by Fridolfsson and Ellegren (1999), males of all galliform species studied displayed one 450-bp, Z-specific fragment, whereas females showed both CHD1Z (450-bp) and CHD1W (600-bp) fragments. Both mallard sexes yielded a single product of 600 bp. Using primers designed by Kahn and Quinn (1999), three species, red junglefowl, turkey and peafowl, displayed one Z-specific fragment (240 bp) in males and two fragments (240 and 265 bp) in females. Only a single fragment was obtained, irrespective of sex, in bobwhite quail (250 bp), common quail (275 bp) and mallard (240 bp). By screening a chicken BAC library with a CHD1W genomic fragment, two overlapping BAC inserts were obtained that, by PCR analysis, appear to contain the chicken CHD1Z gene. To date, we have been unable to identify a CHD1W-containing BAC in our library. Additional BAC analysis is underway

A comparative physical map reveals the pattern of chromosomal evolution between the turkey (Meleagris gallopavo) and chicken (Gallus gallus) genomes

<p>Abstract</p> <p>Background</p> <p>A robust bacterial artificial chromosome (BAC)-based physical map is essential for many aspects of genomics research, including an understanding of chromosome evolution, high-resolution genome mapping, marker-assisted breeding, positional cloning of genes, and quantitative trait analysis. To facilitate turkey genetics research and better understand avian genome evolution, a BAC-based integrated physical, genetic, and comparative map was developed for this important agricultural species.</p> <p>Results</p> <p>The turkey genome physical map was constructed based on 74,013 BAC fingerprints (11.9 × coverage) from two independent libraries, and it was integrated with the turkey genetic map and chicken genome sequence using over 41,400 BAC assignments identified by 3,499 overgo hybridization probes along with > 43,000 BAC end sequences. The physical-comparative map consists of 74 BAC contigs, with an average contig size of 13.6 Mb. All but four of the turkey chromosomes were spanned on this map by three or fewer contigs, with 14 chromosomes spanned by a single contig and nine chromosomes spanned by two contigs. This map predicts 20 to 27 major rearrangements distinguishing turkey and chicken chromosomes, despite up to 40 million years of separate evolution between the two species. These data elucidate the chromosomal evolutionary pattern within the <it>Phasianidae </it>that led to the modern turkey and chicken karyotypes. The predominant rearrangement mode involves intra-chromosomal inversions, and there is a clear bias for these to result in centromere locations at or near telomeres in turkey chromosomes, in comparison to interstitial centromeres in the orthologous chicken chromosomes.</p> <p>Conclusion</p> <p>The BAC-based turkey-chicken comparative map provides novel insights into the evolution of avian genomes, a framework for assembly of turkey whole genome shotgun sequencing data, and tools for enhanced genetic improvement of these important agricultural and model species.</p

A New Chicken Genome Assembly Provides Insight into Avian Genome Structure

The importance of the Gallus gallus (chicken) as a model organism and agricultural animal merits a continuation of sequence assembly improvement efforts. We present a new version of the chicken genome assembly (Gallus_gallus-5.0; GCA_000002315.3), built from combined long single molecule sequencing technology, finished BACs, and improved physical maps. In overall assembled bases, we see a gain of 183 Mb, including 16.4 Mb in placed chromosomes with a corresponding gain in the percentage of intact repeat elements characterized. Of the 1.21 Gb genome, we include three previously missing autosomes, GGA30, 31, and 33, and improve sequence contig length 10-fold over the previous Gallus_gallus-4.0. Despite the significant base representation improvements made, 138 Mb of sequence is not yet located to chromosomes. When annotated for gene content, Gallus_gallus-5.0 shows an increase of 4679 annotated genes (2768 noncoding and 1911 protein-coding) over those in Gallus_gallus-4.0. We also revisited the question of what genes are missing in the avian lineage, as assessed by the highest quality avian genome assembly to date, and found that a large fraction of the original set of missing genes are still absent in sequenced bird species. Finally, our new data support a detailed map of MHC-B, encompassing two segments: one with a highly stable gene copy number and another in which the gene copy number is highly variable. The chicken model has been a critical resource for many other fields of study, and this new reference assembly will substantially further these efforts

Comparative BAC-based mapping in the white-throated sparrow, a novel behavioral genomics model, using interspecies overgo hybridization

BACKGROUND The genomics era has produced an arsenal of resources from sequenced organisms allowing researchers to target species that do not have comparable mapping and sequence information. These new "non-model" organisms offer unique opportunities to examine environmental effects on genomic patterns and processes. Here we use comparative mapping as a first step in characterizing the genome organization of a novel animal model, the white-throated sparrow (Zonotrichia albicollis), which occurs as white or tan morphs that exhibit alternative behaviors and physiology. Morph is determined by the presence or absence of a complex chromosomal rearrangement. This species is an ideal model for behavioral genomics because the association between genotype and phenotype is absolute, making it possible to identify the genomic bases of phenotypic variation. FINDINGS We initiated a genomic study in this species by characterizing the white-throated sparrow BAC library via filter hybridization with overgo probes designed for the chicken, turkey, and zebra finch. Cross-species hybridization resulted in 640 positive sparrow BACs assigned to 77 chicken loci across almost all macro-and microchromosomes, with a focus on the chromosomes associated with morph. Out of 216 overgos, 36% of the probes hybridized successfully, with an average number of 3.0 positive sparrow BACs per overgo. CONCLUSIONS These data will be utilized for determining chromosomal architecture and for fine-scale mapping of candidate genes associated with phenotypic differences. Our research confirms the utility of interspecies hybridization for developing comparative maps in other non-model organisms

Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis

The combined application of next-generation sequencing platforms has provided an economical approach to unlocking the potential of the turkey genome

Erratum: Corrigendum: Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

International Chicken Genome Sequencing Consortium. The Original Article was published on 09 December 2004. Nature432, 695–716 (2004). In Table 5 of this Article, the last four values listed in the ‘Copy number’ column were incorrect. These should be: LTR elements, 30,000; DNA transposons, 20,000; simple repeats, 140,000; and satellites, 4,000. These errors do not affect any of the conclusions in our paper. Additional information. The online version of the original article can be found at 10.1038/nature0315

Cross-species overgo hybridization and comparative physical mapping within avian genomes

The chicken genome sequence facilitates comparative genomics within other avian species. We performed cross-species hybridizations using overgo probes designed from chicken genomic and zebra finch expressed sequence tags (ESTs) to turkey and zebra finch BAC libraries. As a result, 3772 turkey BACs were assigned to 336 markers or genes, and 1662 zebra finch BACs were assigned to 164 genes. As expected, cross-hybridization was more successful with overgos within coding sequences than within untranslated region, intron or flanking sequences and between chicken and turkey, when compared with chicken-zebra finch or zebra finch-turkey cross-hybridization. These data contribute to the comparative alignment of avian genome maps using a 'one sequence, multiple genomes' strategy

The chicken genome: from maps to sequence

The chicken has long served as a model organism with which to study principles of genetics, virology, development, immunology, and other basic biological processes. The chicken is also a prime model species in which to study complex quantitative trait loci. The chicken genome provides an intermediate comparison to human between those of mouse and fugu. Although avian genomes are only about 40% the size of those of mammals, and despite a separation of about 300 million years from their last common ancestor, local gene order and arrangement can be surprisingly well-conserved between the chicken and human genomes. The chicken genetic map is about 4000 cM, with 2000+ molecular markers mapped using three major reference families. Both bacterial artificial chromosome (BAC) and small insert sequencing libraries have been constructed from DNA of a single female inbred Red Jungle Fowl, the nearest wild relative of domestic chickens. BAC fingerprint analyses and alignments of BACs to the pre-existing linkage map have generated a BAC contig physical map of the genome. This is the platform on which the Washington University Genome Sequencing Center has assembled a 6.6X draft sequence of the chicken. We have contributed to the assembly process by mapping markers/genes to BACs and contigs using overgo hybridization. We've assigned over 6000 BACs to over 600 markers across almost all chicken chromosomes and linkage groups. Overgo hybridization provides a cost-effective, high throughput method for integration of physical maps, sequences and linkage maps for many species, including other avians. Supported, in part, by the USDA/CSREES (Project numbers: 99-35205-8566 and 2001-52100-11225

Development of a physical and comparative map of the turkey genome

The recent release of the draft chicken genome sequence provides new opportunities for comparative analysis of other avian genomes, for example, that of the turkey, another major agricultural animal species. A BAC contig physical map of the turkey (or other avian) genome, aligned with the chicken sequence, would provide a valuable resource — a one sequence, two (or more) genomes strategy. Furthermore, such a comparative map would aid in the analysis and application of the chicken sequence itself. A turkey BAC library (11X genome coverage) was previously constructed at the Children’s Hospital of Oakland Research Institute (http://bacpac.chori.org). We performed an initial test to see if chicken sequence-based probes could be used in combination with this BAC library, despite the 25-50 million years of separate evolution of the turkey and chicken genomes. We screened the turkey BAC library with a set of 210 pre-existing chicken overgo probes used previously in constructing the chicken BAC contig physical map. As a result, over 2,000 turkey BACs were identified as containing 176 chicken genes or markers located across much of the chicken genome. As expected, overgos designed from chicken coding exons were most often successful (93%), but even overgos from UTRs, introns and gene flanking regions were surprisingly effective (73-75%). Overgo hybridization probes based on the chicken genome sequence provide a cost-effective, high throughput method that, along with end sequence analysis of turkey BACs, could rapidly generate a physical and comparative BAC contig map for the turkey and/or other avian species