Application of AFLP® technology to radiation hybrid mapping

Gorni, C.; Williams, J. L.; Heuven, H.C.M.; Negrini, Riccardo; Valentini, Alessio; Eijk, Michiel J. T. van; Waddington, David; Zevenbergen, M.J.; Ajmone‐Marsan, Paolo; Peleman, J.

doi:10.1023/b:chro.0000021912.22552.ff

Cited by 10 publications

(7 citation statements)

References 18 publications

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“…An error rate of 2% in the 81 common markers was found for 162 Italian samples genotyped in duplicate, which is considered typical for AFLP‐based population genetic studies (Bonin et al. 2004; Gorni et al. 2004).…”

Section: Resultsmentioning

confidence: 89%

Differentiation of European cattle by AFLP fingerprinting

et al. 2007

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The Neolithic introduction of domestic cattle into Europe was followed by differential adaptation, selection, migration and genetic isolation, leading ultimately to the emergence of specialized breeds. We have studied the differentiation of European cattle by amplified fragment length polymorphism (AFLP) fingerprinting. Combining AFLP data sets from two laboratories yielded 81 biallelic polymorphic markers scored in 19-22 individual animals from 51 breeds. Model-based clustering differentiated Podolian cattle as well as French and Alpine breeds from other European cattle. AFLP genetic distances correlated well with microsatellite-based genetic distances calculated for the same breeds. However, the AFLP data emphasized the divergence of taurine and indicine cattle relative to the variation among European breeds and indicated an Eastern influence on Italian and Hungarian Podolian breeds. This probably reflects import from the East after the original introduction of domestic cattle into Europe. Our data suggest that Italian cattle breeds are relatively diverse at the DNA sequence level.

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Section: Resultsmentioning

confidence: 89%

Differentiation of European cattle by AFLP fingerprinting

et al. 2007

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“…2735 markers were added to those on the first-generation RH map of Williams et al . [ 7 ], of which 2473 are newly mapped loci and 262 are previously reported AFLP markers [ 26 ], giving a final total of 3966 markers (Table 1 ). The majority of the new markers, 1999, are within genes, 1072 are microsatellite loci, 262 AFLP markers, 376 BAC end sequences and 257 are from ESTs sequences that do not show convincing similarity to the annotated bovine sequence.…”

Section: Resultsmentioning

confidence: 99%

“…2473 marker loci were successfully typed on the 94 cell lines of a 3000-rad bovine/hamster RH panel as described by Williams et al [ 7 ]. Vectors of 262 AFLP markers [ 26 ] were added to the dataset. Resulting vectors for the 3966 marker loci used (including 1231 previously mapped loci [ 7 ]) are available in the Additional File 4 for download.…”

Section: Methodsmentioning

confidence: 99%

A second generation radiation hybrid map to aid the assembly of the bovine genome sequence

et al. 2006

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BackgroundSeveral approaches can be used to determine the order of loci on chromosomes and hence develop maps of the genome. However, all mapping approaches are prone to errors either arising from technical deficiencies or lack of statistical support to distinguish between alternative orders of loci. The accuracy of the genome maps could be improved, in principle, if information from different sources was combined to produce integrated maps. The publicly available bovine genomic sequence assembly with 6× coverage (Btau_2.0) is based on whole genome shotgun sequence data and limited mapping data however, it is recognised that this assembly is a draft that contains errors. Correcting the sequence assembly requires extensive additional mapping information to improve the reliability of the ordering of sequence scaffolds on chromosomes. The radiation hybrid (RH) map described here has been contributed to the international sequencing project to aid this process.ResultsAn RH map for the 30 bovine chromosomes is presented. The map was built using the Roslin 3000-rad RH panel (BovGen RH map) and contains 3966 markers including 2473 new loci in addition to 262 amplified fragment-length polymorphisms (AFLP) and 1231 markers previously published with the first generation RH map. Sequences of the mapped loci were aligned with published bovine genome maps to identify inconsistencies. In addition to differences in the order of loci, several cases were observed where the chromosomal assignment of loci differed between maps. All the chromosome maps were aligned with the current 6× bovine assembly (Btau_2.0) and 2898 loci were unambiguously located in the bovine sequence. The order of loci on the RH map for BTA 5, 7, 16, 22, 25 and 29 differed substantially from the assembled bovine sequence. From the 2898 loci unambiguously identified in the bovine sequence assembly, 131 mapped to different chromosomes in the BovGen RH map.ConclusionAlignment of the BovGen RH map with other published RH and genetic maps showed higher consistency in marker order and chromosome assignment than with the current 6× sequence assembly. This suggests that the bovine sequence assembly could be significantly improved by incorporating additional independent mapping information.

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“…Although not widely used, the amplified fragmentlength polymorphism (AFLP) technique was shown to enable the mapping of a large number of markers and the rapid construction of RH maps, particularly in minor species for which extensive genome information is not available [Gorni et al, 2004;Ajmone Marsan et al, 2008].…”

Section: Selecting and Genotyping Markersmentioning

confidence: 99%

Contribution of Radiation Hybrids to Genome Mapping in Domestic Animals

Faraut

Givry²,

Hitte³

et al. 2009

Cytogenet Genome Res

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Radiation hybrid mapping has emerged in the end of the 1990s as a successful and complementary approach to map genomes, essentially because of its ability to bridge the gaps between genetic and clone-based physical maps, but also using comparative mapping approaches, between ‘gene-rich’ and ‘gene-poor’ maps. Since its early development in human, radiation hybrid mapping played a pivotal role in the process of mapping animal genomes, especially mammalian ones. We review here all the different steps involved in radiation hybrid mapping from the constitution of panels to the construction of maps. A description of its contribution to whole genome maps with a special emphasis on domestic animals will also be presented. Finally, current applications of radiation hybrid mapping in the context of whole genome assemblies will be described.

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Application of AFLP® technology to radiation hybrid mapping

Cited by 10 publications

References 18 publications

Differentiation of European cattle by AFLP fingerprinting

Differentiation of European cattle by AFLP fingerprinting

A second generation radiation hybrid map to aid the assembly of the bovine genome sequence

Contribution of Radiation Hybrids to Genome Mapping in Domestic Animals

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