A radiation hybrid map of river buffalo &lt;i&gt;(Bubalus bubalis)&lt;/i&gt; chromosome 1 (BBU1)

Miziara, Melissa Nunes; Goldammer, Tom; Stafuzza, Nedenia Bonvino; Ianella, P.; Agarwala, Richa; Schäffer, Alejandro A.; Elliott, J.S.; Riggs, Penny K.; Womack, James E.; Amaral, M. E. J.

doi:10.1159/000109625

Cited by 15 publications

(13 citation statements)

References 39 publications

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“…A set of linked markers on the telomeric region of BBU1q showed a rearrangement when compared to the sequence from bovine chromosome 1, revealing an inversion in the region flanked by the markers rs29021684 and COPB2 (Figure 1). In the previous RH maps constructed for this buffalo chromosome (Miziara et al, 2007;Amaral et al, 2008), an inversion in the same region was also observed when compared to the bovine chromosome 1.…”

Section: Discussionmentioning

confidence: 61%

“…Its genome is organized in five pairs of bi-armed chromosomes, 19 pairs of acrocentric chromosomes, and a pair of X and Y sex chromosomes. The largest chromosome in the river buffalo karyotype, BBU1, is a sub-metacentric chromosome with reported homology between BBU1q and bovine chromosome 1 and between BBU1p and bovine chromosome 27 (Iannuzzi et al, 2003;Miziara et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

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A framework radiation hybrid map of buffalo chromosome 1 ordering scaffolds from buffalo genome sequence assembly

Stafuzza¹,

Naressi²,

Yang³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. River buffalo chromosome 1 (BBU1) is a sub-metacentric chromosome homologous to bovine chromosomes 1 and 27. In this study, we constructed a new framework radiation hybrid (RH) map from BBU1 using BBURH 5000 panel adding nine new genes (ADRB3, ATP2C1, COPB2, CRYGS, P2RY1, SLC5A3, SLC20A2, SST, and ZDHHC2) and one microsatellite (CSSM043) to the set of markers previously mapped on BBU1. 13096-13104 (2015) to sequences from bovine chromosomes 1 and 27 revealed an inversion close to the telomeric region. In addition, we ordered a set of 34 scaffolds from the buffalo genome assembly UMD_CASPUR_WB_2.0. The RH map could provide a valuable tool to order scaffolds from the buffalo genome sequence, contributing to its annotation.

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Section: Discussionmentioning

confidence: 61%

Section: Introductionmentioning

confidence: 99%

A framework radiation hybrid map of buffalo chromosome 1 ordering scaffolds from buffalo genome sequence assembly

Stafuzza¹,

Naressi²,

Yang³

et al. 2015

Genet. Mol. Res.

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“…Cytogenet Genome Res 2009;124:106-111 107 linkage maps are lacking for river buffalo and few RHmaps to single chromosomes are available for this species (Amaral et al, 2007;Strafuzza et al, 2007;Miziara et al, 2007;Iannella et al, 2008). In sheep, a linkage map is available (Maddox et al, 2001) but only a few RH-maps have been determined so far (Tetens et al, 2007;Wu et al, 2007;Drögemüller et al, 2008).…”

Section: Fish-mapping Comparison Between Bbu7 and Oar6mentioning

confidence: 99%

FISH-mapping comparison between river buffalo chromosome 7 and sheep chromosome 6: assignment of new loci and comparison with HSA4

Perucatti

Meo²,

Goldammer³

et al. 2009

Cytogenet Genome Res

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Synchronized peripheral blood lymphocytes from both river buffalo (BBU) and sheep (OAR) were treated for late incorporation of both BrdU and H-33258 to obtain R-banded preparations to be used for FISH-mapping. Ovine BAC-clones were hybridized for three days on slides pre-exposed to UV light after H-33258 staining. The following loci were mapped: GPR103 (BBU7q13, OAR6q13), TRAM1L1(OAR6q13dist), PPP3CA (BBU7q21, OAR6q15), SNCA (OAR6q17), PPARGC1A(BBU7q23, OAR6q17), UGDH (BBU7q25prox, OAR6q22prox), KDR (BBU7q27, OAR6q22), CNOT6L (BBU7q32prox, OAR6q32prox), NUP54 (BBU7q32, BBU6q32), DMP1 (BBU7q34dist-q36prox, OAR6q34dist-q36prox), QDPR (BBU7q36, OAR6q36). All loci mapped in homoeologous chromosomes and chromosome bands of the two species and their locations are in agreement with the previous RH-mapping performed on BBU7 with some difference in the distal region of BBU7. However, the present cytogenetic map better anchors the RH-map on specific river buffalo chromosome bands. In addition, eleven loci were assigned for the first time in sheep to OAR6, noticeably extending the cytogenetic map on this important chromosome which encodes caseins. Two loci (TRAM1L1 and SNCA) mapped in sheep were unmapped in river buffalo in three different FISH experiments. Comparisons between integrated cytogenetic maps of BBU7/OAR6 (and BTA6) with human chromosome 4 (HSA4) revealed complex chromosome rearrangements differentiating these chromosomes.

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“…For this study, we carried out the steps from preparing input files and computing two‐point LOD scores through to solving a restricted travelling salesman problem that assigns a cR position to each frame and placed marker in a unified instance. To compute linkage groups, we used a pairwise LOD score threshold of 7.0, which is greater than the thresholds used in previous river buffalo chromosome maps (Miziara et al. 2007; Stafuzza et al.…”

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 radiation hybrid map of river buffalo <i>(Bubalus bubalis)</i> chromosome 1 (BBU1)

Cited by 15 publications

References 39 publications

A framework radiation hybrid map of buffalo chromosome 1 ordering scaffolds from buffalo genome sequence assembly

A framework radiation hybrid map of buffalo chromosome 1 ordering scaffolds from buffalo genome sequence assembly

FISH-mapping comparison between river buffalo chromosome 7 and sheep chromosome 6: assignment of new loci and comparison with HSA4

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

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