Contribution of Radiation Hybrids to Genome Mapping in Domestic Animals

Faraut, Thomas; Givry, Simon de; Hitte, Christophe; Lahbib-Mansais, Y.; Morisson, Mireille; Milan, Denis; Schiex, Thomas; Servin, Bertrand; Vignal, Alain; Galibert, Francis; Yerle, Martine M.

doi:10.1159/000245904

Cited by 18 publications

(22 citation statements)

References 244 publications

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“…Only eight BAC contigs could not be uniquely oriented in this study, the largest of which was only 0.4 Mb in size. Such high resolution has been observed in many human and animal radiation hybrid maps before [21,27,29], but among plant studies reported to date only a resolution of ~0.2 Mb calculated on the number of obligate breaks for chromosome 1D of wheat [35] is close to the high resolution presented here.…”

Section: Discussionsupporting

confidence: 83%

DNA repair and crossing over favor similar chromosome regions as discovered in radiation hybrid of Triticum

et al. 2012

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BackgroundThe uneven distribution of recombination across the length of chromosomes results in inaccurate estimates of genetic to physical distances. In wheat (Triticum aestivum L.) chromosome 3B, it has been estimated that 90% of the cross over events occur in distal sub-telomeric regions representing 40% of the chromosome. Radiation hybrid (RH) mapping which does not rely on recombination is a strategy to map genomes and has been widely employed in animal species and more recently in some plants. RH maps have been proposed to provide i) higher and ii) more uniform resolution than genetic maps, and iii) to be independent of the distribution patterns observed for meiotic recombination. An in vivo RH panel was generated for mapping chromosome 3B of wheat in an attempt to provide a complete scaffold for this ~1 Gb segment of the genome and compare the resolution to previous genetic maps.ResultsA high density RH map with 541 marker loci anchored to chromosome 3B spanning a total distance of 1871.9 cR was generated. Detailed comparisons with a genetic map of similar quality confirmed that i) the overall resolution of the RH map was 10.5 fold higher and ii) six fold more uniform. A significant interaction (r = 0.879 at p = 0.01) was observed between the DNA repair mechanism and the distribution of crossing-over events. This observation could be explained by accepting the possibility that the DNA repair mechanism in somatic cells is affected by the chromatin state in a way similar to the effect that chromatin state has on recombination frequencies in gametic cells.ConclusionsThe RH data presented here support for the first time in vivo the hypothesis of non-casual interaction between recombination hot-spots and DNA repair. Further, two major hypotheses are presented on how chromatin compactness could affect the DNA repair mechanism. Since the initial RH application 37 years ago, we were able to show for the first time that the iii) third hypothesis of RH mapping might not be entirely correct.

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Section: Discussionsupporting

confidence: 83%

DNA repair and crossing over favor similar chromosome regions as discovered in radiation hybrid of Triticum

et al. 2012

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“…By taking advantage of the conservation of syntenies, optimal orders can be proposed [58,59], thus maximizing the information obtained as first proposed by Hitte et al [60,61]. Indeed in duck, a dense RH map combined with scaffold sequencing and comparison to the chicken sequence, should lead to an improved genome assembly.…”

Section: Resultsmentioning

confidence: 99%

A duck RH panel and its potential for assisting NGS genome assembly

et al. 2012

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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 BioMarkTM Integrated Fluidic Circuits (IFC) Dynamic ArrayTM 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 BioMarkTM Integrated Fluidic Circuits (IFC) Dynamic ArrayTM 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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“…However, these stocks provide limited resolution due to a large deletion size (average deletion bin is ~35 Mb) and the inability to order markers within a given bin [8]. Radiation hybrid (RH) mapping is a valuable alternative to recombination-based maps and has been adopted for scaffold assembly of numerous animal genomes [9]. …”

Section: Introductionmentioning

confidence: 99%

“…Radiation hybrid mapping, in combination with recombination mapping, has contributed enormously towards whole genome physical analysis and sequence assembly of human and animal genomes [9,17]. However, there have been relatively few examples of using RH mapping in plants, which include maize [18,19], barley ( Hordeum vulgare L.; [20]), cotton ( Gossipium hirsutum L.; [21,22]), and wheat [8,14,23-25].…”

Section: Introductionmentioning

confidence: 99%

Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor Aegilops tauschii

et al. 2012

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BackgroundDevelopment of a high quality reference sequence is a daunting task in crops like wheat with large (~17Gb), highly repetitive (>80%) and polyploid genome. To achieve complete sequence assembly of such genomes, development of a high quality physical map is a necessary first step. However, due to the lack of recombination in certain regions of the chromosomes, genetic mapping, which uses recombination frequency to map marker loci, alone is not sufficient to develop high quality marker scaffolds for a sequence ready physical map. Radiation hybrid (RH) mapping, which uses radiation induced chromosomal breaks, has proven to be a successful approach for developing marker scaffolds for sequence assembly in animal systems. Here, the development and characterization of a RH panel for the mapping of D-genome of wheat progenitor Aegilops tauschii is reported.ResultsRadiation dosages of 350 and 450 Gy were optimized for seed irradiation of a synthetic hexaploid (AABBDD) wheat with the D-genome of Ae. tauschii accession AL8/78. The surviving plants after irradiation were crossed to durum wheat (AABB), to produce pentaploid RH1s (AABBD), which allows the simultaneous mapping of the whole D-genome. A panel of 1,510 RH1 plants was obtained, of which 592 plants were generated from the mature RH1 seeds, and 918 plants were rescued through embryo culture due to poor germination (<3%) of mature RH1 seeds. This panel showed a homogenous marker loss (2.1%) after screening with SSR markers uniformly covering all the D-genome chromosomes. Different marker systems mostly detected different lines with deletions. Using markers covering known distances, the mapping resolution of this RH panel was estimated to be <140kb. Analysis of only 16 RH lines carrying deletions on chromosome 2D resulted in a physical map with cM/cR ratio of 1:5.2 and 15 distinct bins. Additionally, with this small set of lines, almost all the tested ESTs could be mapped. A set of 399 most informative RH lines with an average deletion frequency of ~10% were identified for developing high density marker scaffolds of the D-genome.ConclusionsThe RH panel reported here is the first developed for any wild ancestor of a major cultivated plant species. The results provided insight into various aspects of RH mapping in plants, including the genetically effective cell number for wheat (for the first time) and the potential implementation of this technique in other plant species. This RH panel will be an invaluable resource for mapping gene based markers, developing a complete marker scaffold for the whole genome sequence assembly, fine mapping of markers and functional characterization of genes and gene networks present on the D-genome.

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Contribution of Radiation Hybrids to Genome Mapping in Domestic Animals

Cited by 18 publications

References 244 publications

DNA repair and crossing over favor similar chromosome regions as discovered in radiation hybrid of Triticum

DNA repair and crossing over favor similar chromosome regions as discovered in radiation hybrid of Triticum

A duck RH panel and its potential for assisting NGS genome assembly

Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor Aegilops tauschii

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