A Comparative Genomics Investigation of Unprecedented Haplotype Variability in Maize

玉米可能是所有农作物品种中最多样化的。玉米内部巨大的遗传多样性最重要的实际后果是杂交优势现象。远缘系往往产生活力很强的F1杂交种，这些杂交种种植在整个玉米带上。然而，杂交优势的分子基础尚不清楚。然而，对自交系之间的等位基因区域的分析表明，相同的区间在序列和基因含量上是不同的。因此，可以假设杂交优势可以由两个自交系中不同但互补的基因组来解释。为了研究这种正-负型变化的发生程度，将对12个玉米自交系、小种和近亲的两个基因密集基因组区域Bz和fie2-orp2的基因组组织进行研究。将构建12个大小不同的Noti BAC文库，并从每个文库中分离BZ和fie2克隆并进行测序。因此，将产生1Mb的DNA序列并存储在中央序列储存库中。多态的分布将根据杂种群体之间的差异和近亲交配在基因组重排中的潜在作用进行检查。BAC数据将用群体遗传学方法进行分析，以对比基因之间的进化历史，并检查连锁不平衡和重组之间的关系。具体成果如下：1.12个材料中BZ和fie2-orp2区域的BAC文库。1Mb序列数据保存在GenBank和maizeGDB3中。所选区域的基因存在/缺失和多态的特征4。特定地区多个种质间的重组率分析

Maize is probably the most diverse of all crop species. The most significant practical consequence of the huge genetic diversity within maize is the phenomenon of hybrid vigor (heterosis). Distantly related lines tend to produce highly vigorous F1 hybrids, which are planted across the entire Corn Belt. Yet, the molecular basis of hybrid vigor is not understood. However, analysis of allelic regions between inbreds has indicated that the same interval differs in sequence and gene content. Therefore, it has been hypothesized that hybrid vigor could be explained on the basis of different, yet complementing, gene sets in the two inbreds. To investigate the extent of occurrence of such plus-minus type changes, the genomic organization of two gene-dense genomic regions, bz and fie2-orp2, will be investigated in a group of 12 inbred lines, races, and relatives of maize. Twelve size-fractionated, NotI BAC libraries will be constructed and bz and fie2 clones will be isolated and sequenced from each library. Thus, 1 Mb of DNA sequence will be generated and deposited in central sequence repositories. The distribution of polymorphism will be examined with respect to differences among heterotic groups and to the potential role of inbreeding in genome rearrangement. BAC data will be analyzed with population genetic methods to contrast evolutionary histories between genes and examine the relationship between linkage disequilibrium and recombination.Specific deliverables are:1. BAC libraries specific to the bz and fie2-orp2 regions from 12 accessions2. 1 Mb sequence data deposited in GenBank and maizeGDB3. Characterization of gene presence/absence and polymorphisms in the selected regions4. Analysis of recombination rates across multiple accessions for the specific regions