Effect of a remarkably variable genome structure on meiotic recombination in maize

知识价值。同源减数分裂重组是一个重要的过程，因为它通过重组染色体片段来创造新的基因型，否则染色体片段将作为块遗传，并通过确保染色体正确分离来促进生育。玉米是已知基因组结构最多样化的物种。在许多染色体片段中，不同的自交系只共享基因序列，而不共享周围的重复DNA。后者由转座子组成，逆转录转座子占基因组的一半以上。这种高水平的结构变异影响重组，并可能影响基因表达。本项目旨在分析这些影响。所采用的遗传系统为bz位点，对重组的研究具有独特的优势。先前的研究表明，基因组结构变异以多种方式影响玉米重组事件的频率和分布。虽然重组仅限于基因，但其分布是高度不均匀的：一些基因是热点，另一些是冷点。Helitron转座子中的基因不能重组。一个序列是否重组取决于它的c甲基化状态，转座子是高度甲基化的。反转录转座子块仅存在于一个同源物中，这是杂交中常见的情况，抑制了相邻基因的重组。与杂交无关的重组，称为基因转换，显示出强烈的极性：基因两端的bz突变转换（即重组）比中心突变更频繁。该项目将继续利用bz地区基因分析的力量。它将阐明植物基因内的重组模式，并将重组作为基因表达差异遗传分析的工具。其具体目标是：1。测试基因组结构变异（+/-基因间反转录转座子）是否影响相邻基因转换的频率和极性。2. 确定在bz5高转换端从一个同源物转移到另一个同源物（转换束）的DNA片段是否延伸到相邻基因中。3. 研究当重组dna仅在两个位点上不同时，转换链是否通常比在许多位点上不同时更短，就像通常研究的杂合子一样。4. 测量相同染色体间杂合子（即自交系）的重组和交叉干扰，并与标准玉米F1杂合子（即杂交种）的值进行对比。5. 确定两个已被充分研究的系的sh-bz区间的所有基因，并使用重组来剖析基因组结构变异对等位基因表达差异的贡献。更广泛的影响。该项目将培训一名植物遗传学研究生，并为学生提供暑期就业和培训，包括那些来自主要本科生院校的学生，这些学生与首席研究员合作。它将包括代表人数不足的群体的几名成员，并将帮助首席研究员与发展中国家的研究人员保持持续的合作。该项目与美国农业的长期改善有关，因为它研究重组，这是遗传学的基石和大多数动植物育种的基础，它利用玉米，一种优秀的模式生物和重要的经济作物。大部分拟议的工作都是基于首席研究员实验室的一项早期发现，即玉米基因组结构变异达到了前所未有的水平。该项目旨在研究它如何影响重组和基因表达。

Intellectual merit. Homologous meiotic recombination is an important process because it creates new genotypes by shuffling chromosomal segments that otherwise would be inherited as blocks and promotes fertility by ensuring that chromosomes segregate properly. Maize is the species with the most diverse genome structure known. In many chromosomal segments, different inbred lines share just the gene sequences, but none of the surrounding repetitive DNA. The latter consists of transposons, retrotransposons making up more than half of the genome. This high level of structural variation affects recombination and, possibly, gene expression. This project aims to analyze those effects. The genetic system used is the bz locus, which has unique advantages for studies of recombination. Previous work showed that genome structural variation affects the frequency and distribution of recombination events in maize in multiple ways. Although recombination is limited to genes, its distribution is highly nonuniform: some genes are hotspots and others are coldspots. Genes in Helitron transposons fail to recombine. Whether a sequence recombines or not depends on its C-methylation status and transposons are highly methylated. The presence of a retrotransposon block in only one homolog, a common situation in hybrids, inhibits recombination in adjacent genes. Recombination not associated with crossing over, called gene conversion, shows a strong polarity: bz mutations at both ends of the gene convert (i.e., recombine) more frequently than central ones. This project will continue to exploit the power of genetic analysis in the bz region. It will elucidate the pattern of recombination within a plant gene and will use recombination as a tool in the genetic analysis of gene expression differences. Its specific objectives are to: 1. Test whether genomic structural variation (+/- intergenic retrotransposons) impacts the frequency and polarity of conversion in an adjacent gene. 2. Determine if the stretch of DNA transferred from one homolog to another (conversion tract) at the bz 5 high conversion end extends into the adjacent gene. 3. Investigate whether conversion tracts are generally shorter when the recombining DNAs differ at only two sites than when they differ at many, as in the heterozygotes commonly studied. 4. Measure recombination and crossing-over interference in heterozygotes between identical chromosomes, i.e., an inbred, and contrast with values obtained from standard maize F1 heterozygotes, i.e., hybrids. 5. Define all genes in the sh-bz interval of two well studied lines and use recombinants to dissect the contribution of genomic structural variation to allelic expression differences.Broader impacts. This project will train a graduate student in plant genetics and provide summer employment and training for students, including those from a predominantly undergraduate institution with which the Principal Investigator collaborates. It will incorporate several members of underrepresented groups and will help the Principal Investigator to maintain ongoing collaborations with investigators in developing countries. The project is relevant to the long-term improvement of U.S. agriculture in that it studies recombination, a cornerstone of genetics and the basis of most plant and animal breeding, and it utilizes maize, an excellent model organism and a crop of economic importance. Much of the proposed work is based on an earlier discovery in the Principal Investigator's lab of an unprecedented level of maize genome structure variation. The project aims to study how recombination and gene expression are affected by it.