La Rota Mauricio, Sorrells Mark E
Department of Plant Breeding, 252 Emerson Hall, Cornell University, Ithaca, NY 14853, USA.
Funct Integr Genomics. 2004 Mar;4(1):34-46. doi: 10.1007/s10142-003-0098-2. Epub 2004 Jan 22.
The use of DNA sequence-based comparative genomics for evolutionary studies and for transferring information from model species to related large-genome species has revolutionized molecular genetics and breeding strategies for improving those crops. Comparative sequence analysis methods can be used to cross-reference genes between species maps, enhance the resolution of comparative maps, study patterns of gene evolution, identify conserved regions of the genomes, and facilitate interspecies gene cloning. In this study, 5,780 Triticeae ESTs that have been physically mapped using wheat ( Triticum aestivum L.) deletion lines and segregating populations were compared using NCBI BLASTN to the first draft of the public rice ( Oryza sativa L.) genome sequence data from 3,280 ordered BAC/PAC clones. A rice genome view of the homoeologous wheat genome locations based on sequence analysis shows general similarity to the previously published comparative maps based on Southern analysis of RFLP. For most rice chromosomes there is a preponderance of wheat genes from one or two wheat chromosomes. The physical locations of non-conserved regions were not consistent across rice chromosomes. Some wheat ESTs with multiple wheat genome locations are associated with the non-conserved regions of similarity between rice and wheat. The inverse view, showing the relationship between the wheat deletion map and rice genomic sequence, revealed the breakdown of gene content and order at the resolution conferred by the physical chromosome deletions in the wheat genome. An average of 35% of the putative single copy genes that were mapped to the most conserved bins matched rice chromosomes other than the one that was most similar. This suggests that there has been an abundance of rearrangements, insertions, deletions, and duplications eroding the wheat-rice genome relationship that may complicate the use of rice as a model for cross-species transfer of information in non-conserved regions.
基于DNA序列的比较基因组学在进化研究以及将信息从模式物种转移到相关大基因组物种方面的应用，彻底改变了分子遗传学和改良这些作物的育种策略。比较序列分析方法可用于在物种图谱之间交叉引用基因、提高比较图谱的分辨率、研究基因进化模式、识别基因组的保守区域以及促进种间基因克隆。在本研究中，利用NCBI BLASTN将5780个已使用小麦（Triticum aestivum L.）缺失系和分离群体进行物理定位的小麦族EST与来自3280个有序BAC/PAC克隆的公共水稻（Oryza sativa L.）基因组序列数据初稿进行了比较。基于序列分析的小麦同源基因组位置的水稻基因组视图显示，与先前基于RFLP Southern分析发表的比较图谱总体相似。对于大多数水稻染色体，来自一两个小麦染色体的小麦基因占优势。非保守区域的物理位置在水稻染色体间不一致。一些在多个小麦基因组位置的小麦EST与水稻和小麦之间相似性的非保守区域相关。相反的视图，即展示小麦缺失图谱与水稻基因组序列之间关系的视图，揭示了在小麦基因组物理染色体缺失所赋予的分辨率下基因含量和顺序的破坏。平均35%定位到最保守区间的推定单拷贝基因与除最相似染色体之外的其他水稻染色体匹配。这表明存在大量的重排、插入、缺失和重复，侵蚀了小麦 - 水稻基因组关系，这可能会使在非保守区域将水稻用作跨物种信息转移模型变得复杂。
