Assessment of the Insular Organization of the Wheat D Genome by Physical Mapping

普通小麦（Triticum aestivum）是由乌拉尔小麦（Triticum urartu）、斯卑尔脱山羊草（Aegilops speltoides）和山羊草（Ae. tauschii因此，小麦细胞核含有三对基因组，分别命名为AA、BB和DD。 小麦基因组的属性之一是，与模式植物拟南芥和水稻的基因组相比，它们很大。 在小的基因组中，基因被长度一致的基因间DNA分开。这已经通过对拟南芥的基因组测序直接显示。在大型基因组中，分隔基因的非编码DNA片段可能会有所不同。间接证据表明，在小麦中，可能存在基因丰富的岛（基因岛），其中基因被基因间DNA的短片段分开。推测这些基因岛被基因贫乏或基因空白的空间分隔开。 为了获得小麦D基因组中基因分布的详细图像，从Ae. tauschii（Ae. tauschii完全等同于小麦的D基因组）将被克隆到细菌人工染色体（BAC）中，并按小麦染色体中的顺序排列。这些有序的DNA片段被称为重叠群。 总共300，000个BAC克隆将通过全局指纹法表征，并基于克隆之间的指纹共享组装成重叠群。将通过指纹分析过程的自动化和基于计算机的重叠群组装来完成对大量BAC克隆的指纹分析及其组装成重叠群。将确定染色体上每个重叠群的位置，并识别相邻重叠群并连接以生成七个D-基因组染色体中的每一个的物理图谱。将数千个小麦基因的cDNA克隆放在D基因组物理图谱上，将现有的D基因组连锁和缺失图谱与其物理图谱整合，并绘制出每个D基因组染色体上基因分布的详细图片。这些cDNA克隆的核苷酸序列正在由NSF植物基因组计划资助的另一个项目中确定。 比较小麦D基因组（大基因组）、玉米基因组（中等大小基因组）和水稻基因组（小基因组）的基因组序列的物理图谱上相应基因的位置，将提供关于基因组结构变化的信息，作为禾本科基因组大小增加的函数。 小麦D基因组中insulae基因的鉴定及其定位将具有重要的实际意义，因为它将有助于基因的发现和分离，并最终对小麦基因组的最相关区域进行测序。

Common wheat, Triticum aestivum, originated by interspecific hybridization of three diploid species, Triticum urartu, Aegilops speltoides and Ae. tauschii. The wheat nucleus therefore contains three pairs of genomes, designated AA, BB, and DD, respectively. One of the attributes of wheat genomes is that they are large compared to the genomes of the model plants Arabidopsis thaliana and rice. In small genomes, genes are separated by intergenic DNA of a uniform length. This has been shown directly by sequencing the genome of Arabidopsis thaliana. In large genomes, stretches of noncoding DNA separating the genes are likely to vary. Indirect evidence suggests that in wheat, there may be gene-rich islands (gene insulae) in which genes are separated by short stretches of intergenic DNA. These gene insulae are speculated to be separated by gene-poor or gene-empty space. To obtain a detailed picture of gene distribution in the wheat D genome, DNA fragments isolated from Ae. tauschii (the genome of Ae. tauschii is completely equivalent to the D genome of wheat) will be cloned in bacterial artificial chromosomes (BACs) and ordered as they are in wheat chromosomes. These groups of ordered DNA fragments are called contigs. A total of 300,000 BAC clones will be characterized by the global fingerprinting method and assembled into contigs on the basis of fingerprint sharing among the clones. Fingerprinting of this large number of BAC clones and their assembly into contigs will be accomplished by automation of the fingerprinting process and computer-based contig assembly. The position of each contig on the chromosome will be determined and neighboring contigs identified and joined to generate the physical map of each of the seven D-genome chromosomes. Thousands of cDNA clones of wheat genes will be placed on the D-genome physical map to integrate the existing D-genome linkage and deletion maps with its physical map and to chart a detailed picture of gene distribution across each D-genome chromosome. The nucleotide sequences of these cDNA clones are being determined in another project funded by the NSF Plant Genome Program. Comparisons of the positions of corresponding genes on the physical maps of the wheat D-genome (large genome), the maize genome (medium-size genome) and the genome sequence of the rice genome (small genome) will provide information on changes in genome structure as a function of genome size increase in the grass family. The identification of gene insulae in the wheat D genome and their mapping will have great practical significance since it will facilitate gene discovery and isolation and, ultimately, the sequencing of the most relevant regions of wheat genomes.