Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat
Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat
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DOI：
10.1073/pnas.0509473102
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发表时间：
2005-12-27
影响因子：
11.1
通讯作者：
Bennetzen, JL
中科院分区：
文献类型：
--
作者：
Devos, KM;Ma, JX;Bennetzen, JL
目前关于小麦基因组组成的观点是，基因被划分为基因富集区和基因贫乏区。这个模型可以通过分析随机选择的细菌人工染色体(BAC)克隆的基因内容进行测试，然后将这些BAC放置到物理和遗传地图上。对于完全由重复元素组成的BAC来说，地图本地化可能很困难。因此，我们开发了一种使用重复连接来生成唯一标记的技术。从六倍体小麦品种中国春中随机选取4个BAC克隆进行4-6倍冗余度测序。大约50%的BAC序列对应于以前发现的重复序列，主要是LTR-逆转录转座子，而其余大部分DNA由未知来源或功能的序列组成。平均基因含量为1%，尽管每个BAC包含一个或两个已鉴定的基因。重复边界被放大，并用于将每个克隆定位到染色体臂上。根据小麦-水稻的比较知识推断，四个BAC克隆中有三个来自小麦基因组的“基因丰富”区域。然而，由于这些BAC只携带一个基因(两个BAC)或两个基因(一个BAC)，预测的基因密度约为每75kb 1个基因，大大低于先前估计的小麦基因丰富区的基因密度(每5-20kb一个基因)。对随机选择的小麦BAC克隆的分析表明，基因在小麦中的分布比以前认为的更均匀，并证实了大规模随机BAC测序来确定小麦基因组组织的必要性。
The current view of wheat genome composition is that genes are compartmentalized into gene-rich and gene-poor regions. This model can be tested by analyzing randomly selected bacterial artificial chromosome (BAC) clones for gene content, followed by placement of these BACs onto physical and genetic maps. Map localization could be difficult for BACs that consist entirely of repeated elements. We therefore developed a technique where repeat junctions are used to generate unique markers. Four BAC clones from hexaploid wheat variety Chinese Spring were randomly selected and sequenced at 4- to 6-fold redundancy. About 50% of the BAC sequences corresponded to previously identified repeats, mainly LTR-retrotransposons, whereas most of the remaining DNA consisted of sequences with unknown origin or function. The average gene content was < 1%, although each BAC contained one or two identified genes. Repeat boundaries were amplified and used to map each clone to a chromosome arm. Extrapolation from wheat-rice comparative knowledge suggests that three of the four BAC clones originate from "gene-rich" regions of the wheat genome. Nevertheless, because these BACs carry only a single gene (two BACs) or two genes (one BAC), the predicted gene density is approximate to 1 gene per 75 kb, which is considerably lower than previously estimated gene densities (one gene per 5-20 kb) for gene-rich regions in wheat. This analysis of randomly selected wheat BAC clones suggests that genes are more evenly distributed in wheat than previously believed and substantiates the need for large-scale random BAC sequencing to determine wheat genome organization.