A Comparative Genomics Investigation of Unprecedented Haplotype Variability in Maize

玉米可能是所有作物物种中最多样化的。玉米内部巨大遗传多样性最显著的实际后果是杂种优势现象。亲缘关系较远的品种往往会产生高度健壮的F1杂交品种，这种杂交品种被种植在整个玉米带。然而，杂种活力的分子基础尚不清楚。然而，对近交系间等位基因区域的分析表明，同一区间内的等位基因序列和基因含量存在差异。因此，有一种假说认为，杂种优势可以用两个自交系中不同但又互补的基因集来解释。为了研究这种正负型变化的发生程度，我们将对玉米的12个自交系、小种和近缘种中两个基因密集的基因组区域bz和fie2-orp2的基因组组织进行研究。将构建12个大小分离的NotI BAC文库，并从每个文库中分离bz和fi2个克隆并测序。因此，将产生1mb的DNA序列并存储在中央序列库中。多态性的分布将根据杂种优势群体之间的差异和近交在基因组重排中的潜在作用进行研究。BAC数据将用群体遗传方法进行分析，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。具体可交付成果如下：从12个访问中特定于bz和fi2 -orp2区域的BAC库2。1 Mb序列数据存入GenBank和maizeGDB3。所选区域基因存在/缺失及多态性特征分析特定区域的多组分重组率分析

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