ArticleBMC genomics2012
A duck RH panel and its potential for assisting NGS genome assembly.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Review
- Dinosaurs: Comparative Cytogenomics of Their Reptile Cousins and Avian Descendants.Animals : an open access journal from MDPI · 2022Review
- Fourth Report on Chicken Genes and Chromosomes 2022.Cytogenetic and genome research · 2022Review
- Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication.Nature communications · 2021Article
- Article
- A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals.GigaScience · 2021Article
- Time lapse: A glimpse into prehistoric genomics.European journal of medical genetics · 2020Review
- Genome-wide association study reveals novel loci associated with body size and carcass yields in Pekin ducks.BMC genomics · 2019Article
- Genome-Wide Association Study of Growth and Feeding Traits in Pekin Ducks.Frontiers in genetics · 2019Article
- An intercross population study reveals genes associated with body size and plumage color in ducks.Nature communications · 2018Article
- Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs.Nature communications · 2018Article
- Construction of two whole genome radiation hybrid panels for dromedary (Camelus dromedarius): 5000Scientific reports · 2018Article
- Characterization of Duck (Frontiers in genetics · 2018Article
- De novo transcriptome analysis shows differential expression of genes in salivary glands of edible bird's nest producing swiftlets.BMC genomics · 2017Article
- Discovering All Transcriptome Single-Nucleotide Polymorphisms and Scanning for Selection Signatures in Ducks (Anas platyrhynchos).Evolutionary bioinformatics online · 2015Article
- Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor.BMC genomics · 2014Article
- Mapping and genotypic analysis of the NK-lysin gene in chicken.Genetics, selection, evolution : GSE · 2014Article
- Novel tools for characterising inter and intra chromosomal rearrangements in avian microchromosomes.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2014Article
- All chromosomes great and small: 10 years on.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2014Article
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10 authors.
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Abstract
backgroundOwing to the low cost of the high throughput Next Generation Sequencing (NGS) technology, more and more species have been and will be sequenced. However, de novo assemblies of large eukaryotic genomes thus produced are composed of a large number of contigs and scaffolds of medium to small size, having no chromosomal assignment. Radiation hybrid (RH) mapping is a powerful tool for building whole genome maps and has been used for several animal species, to help assign sequence scaffolds to chromosomes and determining their order.
resultsWe report here a duck whole genome RH panel obtained by fusing female duck embryonic fibroblasts irradiated at a dose of 6,000 rads, with HPRT-deficient Wg3hCl2 hamster cells. The ninety best hybrids, having an average retention of 23.6% of the duck genome, were selected for the final panel. To allow the genotyping of large numbers of markers, as required for whole genome mapping, without having to cultivate the hybrid clones on a large scale, three different methods involving Whole Genome Amplification (WGA) and/or scaling down PCR volumes by using the Fluidigm BioMark(TM) Integrated Fluidic Circuits (IFC) Dynamic Array(TM) for genotyping were tested. RH maps of APL12 and APL22 were built, allowing the detection of intrachromosomal rearrangements when compared to chicken. Finally, the panel proved useful for checking the assembly of sequence scaffolds and for mapping EST located on one of the smallest microchromosomes.
conclusionThe Fluidigm BioMark(TM) Integrated Fluidic Circuits (IFC) Dynamic Array(TM) genotyping by quantitative PCR provides a rapid and cost-effective method for building RH linkage groups. Although the vast majority of genotyped markers exhibited a picture coherent with their associated scaffolds, a few of them were discordant, pinpointing potential assembly errors. Comparative mapping with chicken chromosomes GGA21 and GGA11 allowed the detection of the first chromosome rearrangements on microchromosomes between duck and chicken. As in chicken, the smallest duck microchromosomes appear missing in the assembly and more EST data will be needed for mapping them. Altogether, this underlines the added value of RH mapping to improve genome assemblies.
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