与家牛比较的第一代河水牛全基因组RH图谱。
A first generation whole genome RH map of the river buffalo with comparison to domestic cattle.
作者信息
Amaral M Elisabete J, Grant Jason R, Riggs Penny K, Stafuzza Nedenia B, Filho Edson A Rodrigues, Goldammer Tom, Weikard Rosemarie, Brunner Ronald M, Kochan Kelli J, Greco Anthony J, Jeong Jooha, Cai Zhipeng, Lin Guohui, Prasad Aparna, Kumar Satish, Saradhi G Pardha, Mathew Boby, Kumar M Aravind, Miziara Melissa N, Mariani Paola, Caetano Alexandre R, Galvão Stephan R, Tantia Madhu S, Vijh Ramesh K, Mishra Bina, Kumar S T Bharani, Pelai Vanderlei A, Santana Andre M, Fornitano Larissa C, Jones Brittany C, Tonhati Humberto, Moore Stephen, Stothard Paul, Womack James E
机构信息
Department of Biologia, UNESP - São Paulo State University, IBILCE, SP, Brazil.
出版信息
BMC Genomics. 2008 Dec 24;9:631. doi: 10.1186/1471-2164-9-631.
BACKGROUND
The recently constructed river buffalo whole-genome radiation hybrid panel (BBURH5000) has already been used to generate preliminary radiation hybrid (RH) maps for several chromosomes, and buffalo-bovine comparative chromosome maps have been constructed. Here, we present the first-generation whole genome RH map (WG-RH) of the river buffalo generated from cattle-derived markers. The RH maps aligned to bovine genome sequence assembly Btau_4.0, providing valuable comparative mapping information for both species.
RESULTS
A total of 3990 markers were typed on the BBURH5000 panel, of which 3072 were cattle derived SNPs. The remaining 918 were classified as cattle sequence tagged site (STS), including coding genes, ESTs, and microsatellites. Average retention frequency per chromosome was 27.3% calculated with 3093 scorable markers distributed in 43 linkage groups covering all autosomes (24) and the X chromosomes at a LOD >or= 8. The estimated total length of the WG-RH map is 36,933 cR5000. Fewer than 15% of the markers (472) could not be placed within any linkage group at a LOD score >or= 8. Linkage group order for each chromosome was determined by incorporation of markers previously assigned by FISH and by alignment with the bovine genome sequence assembly (Btau_4.0).
CONCLUSION
We obtained radiation hybrid chromosome maps for the entire river buffalo genome based on cattle-derived markers. The alignments of our RH maps to the current bovine genome sequence assembly (Btau_4.0) indicate regions of possible rearrangements between the chromosomes of both species. The river buffalo represents an important agricultural species whose genetic improvement has lagged behind other species due to limited prior genomic characterization. We present the first-generation RH map which provides a more extensive resource for positional candidate cloning of genes associated with complex traits and also for large-scale physical mapping of the river buffalo genome.
背景
最近构建的河水牛全基因组辐射杂种细胞系（BBURH5000）已被用于生成几条染色体的初步辐射杂种（RH）图谱，并且已经构建了水牛-牛比较染色体图谱。在此，我们展示了由牛源标记生成的第一代河水牛全基因组RH图谱（WG-RH）。这些RH图谱与牛基因组序列组装Btau_4.0对齐，为两个物种提供了有价值的比较图谱信息。
结果
在BBURH5000细胞系上共分型了3990个标记，其中3072个是牛源单核苷酸多态性（SNP）。其余918个被分类为牛序列标签位点（STS），包括编码基因、EST和微卫星。使用分布在43个连锁群中的3093个可评分标记计算，每个染色体的平均保留频率为27.3%，这些连锁群覆盖了所有常染色体（24条）和X染色体，LOD≥8。估计WG-RH图谱的总长度为36,933 cR5000。在LOD得分≥8时，少于15%的标记（472个）无法定位到任何连锁群中。通过纳入先前通过荧光原位杂交（FISH）分配的标记并与牛基因组序列组装（Btau_4.0）对齐，确定了每个染色体的连锁群顺序。
结论
我们基于牛源标记获得了整个河水牛基因组的辐射杂种染色体图谱。我们的RH图谱与当前牛基因组序列组装（Btau_4.0）的比对表明了两个物种染色体之间可能发生重排的区域。河水牛是一种重要的农业物种，由于先前有限的基因组特征描述，其遗传改良落后于其他物种。我们展示了第一代RH图谱，它为与复杂性状相关基因的定位候选克隆以及河水牛基因组的大规模物理图谱绘制提供了更广泛的资源。
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