ArticleBMC genomics2006
A second generation radiation hybrid map to aid the assembly of the bovine genome sequence.
Article in BMC genomics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- A linkage disequilibrium-based approach to position unmapped SNPs in crop species.BMC genomics · 2021Article
- New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes.BMC genomics · 2019Article
- Construction of two whole genome radiation hybrid panels for dromedary (Camelus dromedarius): 5000Scientific reports · 2018Article
- A clone-free, single molecule map of the domestic cow (Bos taurus) genome.BMC genomics · 2015Article
- Microarray gene expression profiling of neural tissues in bovine spastic paresis.BMC veterinary research · 2013Article
- Assignment of chromosomal locations for unassigned SNPs/scaffolds based on pair-wise linkage disequilibrium estimates.BMC bioinformatics · 2010Article
- Article
- Novel transcripts discovered by mining genomic DNA from defined regions of bovine chromosome 6.BMC genomics · 2009Article
- A second generation genetic map for rainbow trout (Oncorhynchus mykiss).BMC genetics · 2008Article
- A high-resolution radiation hybrid map of rhesus macaque chromosome 5 identifies rearrangements in the genome assembly.Genomics · 2008Article
- A 4,103 marker integrated physical and comparative map of the horse genome.Cytogenetic and genome research · 2008Article
- High resolution radiation hybrid maps of bovine chromosomes 19 and 29: comparison with the bovine genome sequence assembly.BMC genomics · 2007Article
- A high resolution radiation hybrid map of bovine chromosome 14 identifies scaffold rearrangement in the latest bovine assembly.BMC genomics · 2007Article
- Generation of an improved cytogenetic and comparative map of Bos taurus chromosome BTA27.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2007Article
- A physical map of the bovine genome.Genome biology · 2007Article
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Authors and funding
29 authors.
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Abstract
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 6x 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 6x 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 6x sequence assembly. This suggests that the bovine sequence assembly could be significantly improved by incorporating additional independent mapping information.
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