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

Jann, O.; Aerts, Jan; Jones, Michelle L.; Hastings, Nicola; Law, Andy; McKay, Stephanie; Marques, Elisa; Prasad, Aparna; Yu, Jody; Moore, S. S.; Floriot, Sandrine; Mahé, Marie‐Françoise; Eggen, Andre A.; Silveri, Licia; Negrini, Riccardo; Milanesi, Elisabetta; Ajmone‐Marsan, Paolo; Valentini, Alessio; Marchitelli, Cinzia; Savarese, M. C.; Janitz, Michael; Herwig, Ralf; Hennig, Steffen; Gorni, C.; Connor, Erin E.; Sonstegard, Tad S.; Smith, Timothy P. L.; Drögemüller, Cord; Williams, J. L.

doi:10.1186/1471-2164-7-283

Cited by 27 publications

(26 citation statements)

References 40 publications

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“…They were chosen for containing spots from a bovine brain library [6], a bovine monocyte library [7] and 979 control spots (landing lights, blank, salmon sperm, housekeeping genes). As stated in the previous section, the disease is likely to be linked to the nervous system [3,4].…”

Section: Methodsmentioning

confidence: 99%

Microarray gene expression profiling of neural tissues in bovine spastic paresis

Pariset

Bongiorni

Bueno³

et al. 2013

BMC Vet Res

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BackgroundBovine Spastic Paresis (BSP) is a neuromuscular disorder which affects both male and female cattle. BSP is characterized by spastic contraction and overextension of the gastrocnemious muscle of one or both limbs and is associated with a scarce increase in body weight. This disease seems to be caused by an autosomal and recessive gene, with incomplete penetration, although no genes clearly involved with its onset have been so far identified. We employed cDNA microarrays to identify metabolic pathways affected by BSP in Romagnola cattle breed. Investigation of those pathways at the genome level can help to understand this disease.ResultsMicroarray analysis of control and affected individuals resulted in 268 differentially expressed genes. These genes were subjected to KEGG pathway functional clustering analysis, revealing that they are predominantly involved in Cell Communication, Signalling Molecules and Interaction and Signal Transduction, Diseases and Nervous System classes. Significantly enriched KEGG pathway’s classes for the differentially expressed genes were calculated; interestingly, all those significantly under-expressed in the affected samples are included in Neurodegenerative Diseases. To identify genome locations possibly harbouring gene(s) involved in the disease, the chromosome distribution of the differentially expressed genes was also investigated.ConclusionsThe cDNA microarray we used in this study contains a brain library and, even if carrying an incomplete transcriptome representation, it has proven to be a valuable tool allowing us to add useful and new information to a poorly studied disease. By using this tool, we examined nearly 15000 transcripts and analysed gene pathways affected by the disease. Particularly, our data suggest also a defective glycinergic synaptic transmission in the development of the disease and an alteration of calcium signalling proteins. We provide data to acquire knowledge of a genetic disease for which literature still presents poor results and that could be further and specifically analysed in the next future. Moreover this study, performed in livestock, may also harbour molecular information useful for understanding human diseases.

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Section: Methodsmentioning

confidence: 99%

Microarray gene expression profiling of neural tissues in bovine spastic paresis

Pariset

Bongiorni

Bueno³

et al. 2013

BMC Vet Res

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“…In both assemblies this inverted region ends at contig breakpoints and could be an assembly artefact rather than a true biological difference. We could not resolve this discrepancy using RH and linkage maps [33][34][35] because the marker density was insufficient. Alignments of the Brahman cattle X chromosome with those of the water buffalo, goat and sheep, revealed a high level of co-linearity, but with numerous break points and several inversions.…”

Section: Discussionmentioning

confidence: 99%

New Insights into Mammalian Sex Chromosome Structure and Evolution from High-quality Bovine X and Y Chromosome Sequences

Liu

Low

Tearle

et al. 2019

Preprint

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Background Mammalian X chromosomes are mainly euchromatic with a similar size and structure among species whereas Y chromosomes are smaller, have undergone substantial evolutionary changes and accumulated male specific genes and genes involved in sex determination. The PAR is conserved on the X and Y and pair during meiosis. The structure, evolution and function of mammalian sex chromosomes is still poorly understood because few species have high quality sex chromosome assemblies. Results Here we report the first bovine sex chromosome assemblies that include the complete pseudoautosomal region (PAR) spanning 6.84 Mb and three Y chromosome X-degenerate (X-d) regions. We show that the ruminant PAR comprises 31 genes and is similar to the PAR of pig and dog but extends further than those of human and horse. Differences in the pseudoautosomal boundaries are consistent with evolutionary divergence times. Conclusions A bovidae-specific expansion of members of the lipocalin gene family in the PAR may reflect immune-modulation and anti-inflammatory responses that contribute to parasite resistance in ruminants. Comparison of the X-d regions of Y chromosomes across species reveal five conserved X-Y gametologs, which are global regulators of gene activity, and may have a fundamental role in mammalian sexual dimorphism.

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“…2000, 2003) includes a total of 28 markers (seven genes and 21 microsatellites) assigned by FISH. In contrast, the cattle X chromosome map contains 176 markers ordered by RH technology (Jann et al. 2006).…”

Section: Cattle‐derived Markers From Btax Mapped With the Bburh5000 mentioning

confidence: 99%

“…1) were distributed in two linkage groups: LG1, spanning 125.6 cR with eight markers (one gene, one ESTs and six microsatellites) and LG2, spanning 366.3 cR with 25 markers (nine genes, three ESTs and 13 microsatellites). Six markers from LG1 on the BBUX map can be placed on bovine sequence assembly build 3.1, but their order is shuffled between the two maps, and another pair of markers ( BMS2227 and BL1098 ) is inverted when BBUX is compared to the BTAX RH map (Jann et al. 2006).…”

Section: Cattle‐derived Markers From Btax Mapped With the Bburh5000 mentioning

confidence: 99%

First radiation hybrid map of the river buffalo X chromosome (BBUX) and comparison with BTAX

et al. 2008

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We report the first radiation hybrid map of the river buffalo X chromosome generated from a recently constructed river buffalo (Bubalus bubalis) whole-genome radiation hybrid panel (BBURH(5000)). This map contains a total of 33 cattle-derived markers, including 10 genes, four ESTs and 19 microsatellites. The markers are distributed in two linkage groups: LG1 contains eight markers spanning 125.6 cR, and LG2 contains 25 markers spanning 366.3 cR. LG1 contains six markers in common with bovine sequence assembly build 3.1. With the exception of BMS2152, the order of these markers on our BBUX map is shuffled when compared to the cow X chromosome (Bos taurus; BTAX). From LG2, two markers (AMELX and BL22) map to a more distal portion of BTAX compared to BBUX. In addition, two pairs of LG2 markers exhibit inversions compared to BTAX (ILSTS017 and ATRX; XBM38 and PPEF1). Alternatively, when compared to the most recent bovine RH map (Bov-Gen 3000rads), BL1098 and BMS2227 from LG1 as well as PLS3 and BMS1820 from LG2 showed inverted positions on the BBUX map. These discrepancies in buffalo and cattle maps may reflect evolutionary divergence of the chromosomes or mapping errors in one of the two species. Although the set of mapped markers does not cover the entire X chromosome, this map is a starting point for the construction of a high-resolution map, which is necessary for characterization of small rearrangements that might have occurred between the Bubalus bubalis and Bos taurus X chromosomes.

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

Cited by 27 publications

References 40 publications

Microarray gene expression profiling of neural tissues in bovine spastic paresis

Microarray gene expression profiling of neural tissues in bovine spastic paresis

New Insights into Mammalian Sex Chromosome Structure and Evolution from High-quality Bovine X and Y Chromosome Sequences

First radiation hybrid map of the river buffalo X chromosome (BBUX) and comparison with BTAX

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