重叠群物理图谱的构建及其应用

Construction and Application of Large-insert Clones-based Physical Map

人类对各种生物的基因组结构和功能的研究都需要确定DNA序列在染色体上的位置。与遗传图相比,物理图反映了基因或DNA标记之间在染色体上的真实距离。依其作图方法分为三类,即限制性酶切图谱、重叠群图谱和DNA序列图谱。重叠群物理图是将获得的大片段克隆,如YAC、BAC克隆,依其在染色体上的真实顺序排列而成,主要应用于基因组测序、重要基因的图位克隆、靶分子标记开发及比较基因组学研究等,特别是为那些由于缺乏合适的作图群体而不能建立遗传图的物种提供了一个重要的从事基因组学研究的平台。本文综述了近年来重叠群物理图构建研究的主要进展,比较分析了不同重叠群物理图谱构建方法的特点,提出了改进物理作图质量的建议,认为应根据基因组不同区域的特点,综合特异性探针的杂交、PCR筛选、酶切指纹分析、BAC克隆STC延伸、BAC末端测序等多种方法才能完成重叠群的构建。此外,物理图的构建还应努力整合各种基因组的资源和数据,如遗传连锁图、分子细胞遗传图、DNA序列图、EST数据等,这将有助于提高其在基因组学研究中的使用价值及应用范围。文章最后对重叠群物理图的发展趋势进行了展望。

The locations of DNA sequences in chromosomes need to be identified for the study of genome structure and function. Compare to genetic maps, physical maps reflect the real distance among genes/DNA markers in chromosomes, which are classified into three types according to mapping methods, i.e. restriction endonuclease map, contig map, and DNA sequence map. A contig is a chromosome map showing the locations of those regions of a chromosome where contiguous large-insert clones overlap. It is essential for genome sequencing, position cloning of agronomically important genes, comparative genome analysis, target DNA marker development etc., and provides an important genomics research platform even for those species for which development of genetic maps is impossible owing to the absence of appropriate mapping populations. This review summarized recent progress on the construction of genome contig maps. On the basis of comparative analysis of the major physical mapping methods and the structures of different regions of chromosomes, it was concluded that a combination of two or more strategies, such as overgo hybridization, restriction fingerprint analysis, mapped DNA marked-based chromosome landing, BAC clone ends sequencing, and sequence-tagged connectors （STC） approach etc., will greatly facilitate genome physical mapping. Moreover, various genome resources and data should be integrated into contig maps including genetic maps, molecular cytogenetic maps, genome sequencing data, expressed sequence tags （ESTs） etc.. The integrated genome maps will contribute to the more extensive application and enhanced utility of themselves in genome research. The current application and future prospects ofcontig maps are also discussed.