Assignment of five polymorphic ovine microsatellites to bovine syntenic groups

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

BACKGROUND

Several 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.

RESULTS

An 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.

CONCLUSION

Alignment 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.

Gene mapping in the river buffalo (Bubalus bubalis L.): five syntenic groups

SUMMARY

Forty-five somatic buffalo-hamster hybrid clones were analysed for the presence or absence of PCR products of 10 primers. Five syntenic groups were identified: CGA-D9S1; CD18-D1S4; OXT-PRNP; LDLR-D7S3; BSPN-D14S2. These same syntenic groups were reported to be syntenic in cattle and were assigned to U2 (BTA 9), U10 (BTA 1), U11 (BTA 13), U22 (BTA 7), and U24 (BTA 14), respectively. Based on chromosomal homology between cattle and river buffalo chromosomes, these syntenic groups are expected to be assigned to buffalo chromosomes BBU 10, BBU 1q, BBU 14, BBU 9, and BBU 15, respectively. ZUSAMMENFASSUNG: Genkartierung beim Flußbüffel (Bubalis bubalis L.): Fünf Syntäniegruppen Fünfundvierzig somatische Büffel-Hamster Hygrid Klone wurden bezüglich An-oder Abwesenheit von PCR Produkten von 10 primern analysiert. Es wurden 5 Syntäniegruppen identifiziert: CGA-D9S1; CD18-D1S4; OXT-PRNP; LDLR-D7S3; BSPN-D14S2. Dieselben Syntäniegruppen wurden in Rindern gfunden und zugeordnet zu U2(BTA 9), U10(BTA 1), U11(BTA 13), U22(BTA 7) und U24(BTA 14). Auf grund chromosomaler Homolgie zwischen beiden Arten sollten die Syntäniegruppen auf den Büffelchromosomen BBU 10, BBU 1q, BBU 14, BBU 9, und BBU 15 liegen.

An integrated genetic and physical map of the bovine X chromosome

Genotypic data for 56 microsatellites (ms) generated from maternal full sib families nested within paternal half sib pedigrees were used to construct a linkage map of the bovine X Chromosome (Chr) (BTX) that spans 150 cM (ave. interval 2.7 cM). The linkage map contains 36 previously unlinked ms; seven generated from a BTXp library. Genotypic data from these 36 ms was merged into an existing linkage map to more than double the number of informative BTX markers. A male specific linkage map of the pseudoautosomal region was also constructed from five ms at the distal end of BTXq. Four informative probes physically assigned by fluorescence in situ hybridization defined the extent of coverage, confirmed the position of the pseudoautosomal region on the q-arm, and identified a 4.1-cM marker interval containing the centromere of BTX.

Thirteen loci physically assigned to sheep chromosome 2 by cell hybrid analysis and in situ hybridization

Sheep x hamster cell hybrids containing sheep metacentric Chromosome (Chr) 2 were produced by fusing blood leukocytes from normal sheep with hamster auxotrophic Ade F-minus mutants. Cell clones that were isocitrate dehydrogenase 1 (IDH1) positive were cytogenetically characterized, confirming that they contained sheep Chr 2. The following loci were newly assigned by Southern hybridization to sheep Chr 2: lipoprotein lipase (LPL), glycoprotein-4-beta galactosyltransferase 2 (GGTB2), neurofilament light polypeptide (68 kDa; NEFL), surfactant-associated protein 2 (SFTP2), lymphocyte-specific protein tyrosine kinase (LCK), and nebulin (NEB). These new assignments and the in situ localization of gelsolin (GSN) to sheep Chr 2pter-p24 are consistent with the predicted homology of cattle Chr 8 (U18) with sheep Chr 2p, and of cattle Chr 2 (U17) with sheep 2q. In addition, the assignment by cell hybrid analysis of loci previously mapped to Chr 2 in sheep, viz., cholinergic receptor, nicotinic, delta polypeptide (CHRND), collagen type III alpha 1 (COL3A1), fibronectin 1 (FN1), isocitrate dehydrogenase (IDH1), and villin 1 (VIL1), confirmed the localization of sheep syntenic group U11 to this chromosome. By nutritional selection and complementation of the hamster auxotrophic Ade F mutation, the multifunctional enzyme locus phosphoribosylaminoimidazolecarboxamide formyltransferase (AICAR transformylase)/IMP cyclohydrolase (inosinicase) (provisionally given the symbol PRACFT) has also been newly assigned to sheep Chr 2. This report significantly extends the number of loci physically mapped to sheep Chr 2 and confirms its close homology with cattle Chrs 2 and 8.