Snelling Warren M, Chiu Readman, Schein Jacqueline E, Hobbs Matthew, Abbey Colette A, Adelson David L, Aerts Jan, Bennett Gary L, Bosdet Ian E, Boussaha Mekki, Brauning Rudiger, Caetano Alexandre R, Costa Marcos M, Crawford Allan M, Dalrymple Brian P, Eggen André, Everts-van der Wind Annelie, Floriot Sandrine, Gautier Mathieu, Gill Clare A, Green Ronnie D, Holt Robert, Jann Oliver, Jones Steven Jm, Kappes Steven M, Keele John W, de Jong Pieter J, Larkin Denis M, Lewin Harris A, McEwan John C, McKay Stephanie, Marra Marco A, Mathewson Carrie A, Matukumalli Lakshmi K, Moore Stephen S, Murdoch Brenda, Nicholas Frank W, Osoegawa Kazutoyo, Roy Alice, Salih Hanni, Schibler Laurent, Schnabel Robert D, Silveri Licia, Skow Loren C, Smith Timothy Pl, Sonstegard Tad S, Taylor Jeremy F, Tellam Ross, Van Tassell Curtis P, Williams John L, Womack James E, Wye Natasja H, Yang George, Zhao Shaying
USDA, ARS, US Meat Animal Research Center, Clay Center, NE 68933, USA.
Genome Biol. 2007;8(8):R165. doi: 10.1186/gb-2007-8-8-r165.
Cattle are important agriculturally and relevant as a model organism. Previously described genetic and radiation hybrid (RH) maps of the bovine genome have been used to identify genomic regions and genes affecting specific traits. Application of these maps to identify influential genetic polymorphisms will be enhanced by integration with each other and with bacterial artificial chromosome (BAC) libraries. The BAC libraries and clone maps are essential for the hybrid clone-by-clone/whole-genome shotgun sequencing approach taken by the bovine genome sequencing project.
A bovine BAC map was constructed with HindIII restriction digest fragments of 290,797 BAC clones from animals of three different breeds. Comparative mapping of 422,522 BAC end sequences assisted with BAC map ordering and assembly. Genotypes and pedigree from two genetic maps and marker scores from three whole-genome RH panels were consolidated on a 17,254-marker composite map. Sequence similarity allowed integrating the BAC and composite maps with the bovine draft assembly (Btau3.1), establishing a comprehensive resource describing the bovine genome. Agreement between the marker and BAC maps and the draft assembly is high, although discrepancies exist. The composite and BAC maps are more similar than either is to the draft assembly.
Further refinement of the maps and greater integration into the genome assembly process may contribute to a high quality assembly. The maps provide resources to associate phenotypic variation with underlying genomic variation, and are crucial resources for understanding the biology underpinning this important ruminant species so closely associated with humans.
牛在农业上很重要，并且作为一种模式生物也具有相关性。先前描述的牛基因组遗传图谱和辐射杂种（RH）图谱已被用于识别影响特定性状的基因组区域和基因。通过相互整合以及与细菌人工染色体（BAC）文库整合，这些图谱在识别有影响力的基因多态性方面的应用将得到增强。BAC文库和克隆图谱对于牛基因组测序项目采用的逐个克隆/全基因组鸟枪法测序方法至关重要。
用来自三个不同品种动物的290,797个BAC克隆的HindIII酶切片段构建了牛BAC图谱。对422,522个BAC末端序列的比较定位有助于BAC图谱的排序和组装。来自两个遗传图谱的基因型和系谱以及来自三个全基因组RH板的标记分数被整合到一个包含17,254个标记的复合图谱上。序列相似性使得能够将BAC图谱和复合图谱与牛草图组装（Btau3.1）整合起来，建立了一个描述牛基因组的综合资源。尽管存在差异，但标记图谱、BAC图谱和草图组装之间的一致性很高。复合图谱和BAC图谱比它们与草图组装的相似性更高。
进一步完善图谱并更好地整合到基因组组装过程中可能有助于实现高质量的组装。这些图谱提供了将表型变异与潜在基因组变异相关联的资源，并且是理解与人类密切相关的这一重要反刍动物物种生物学基础的关键资源。
