RESEARCH-PGR: Variants and Recombinants without Meiosis

在组织培养过程中，植物基因组经常发生意想不到的变化，导致植物具有不同的特征，称为体细胞无性系变异。在较低的频率下，在正常生长过程中出现类似的称为运动的变异。这些新的变异可能具有巨大的经济价值，但对这些现象的原因、性质和进化意义所知相对较少。本项目将调查马铃薯的这些变化。适合分析这些基因组变化的方法将适用于其他作物，并将提供给科学和植物育种界。预计将产生两方面的社会影响。首先，该项目将解决一个很大程度上被忽视的潜在变异来源，可能影响主要经济物种。其次，该项目需要若干外展活动，有两个目标：1)让代表性不足社区的年轻学生熟悉科学研究和职业；2)培养适用于植物育种的基因组方法的高级学生和专业人员。这些目标将通过在外联期刊上发表文章、举办国际讲习班和制作学习录象带来实现。该项目的长期目标是了解基因组不稳定和重组的机制和结果。核心假设是，不稳定性虽然通常是有害的，但也可以以破坏性较小且具有潜在适应性的方式重塑基因组，例如通过引起杂合性的改变或丧失，以及剂量变化。阐明这些变化的原因、机制和后果将有助于阐明它们在自然和人工选择中的作用，并为预测、识别和（如果适当的话）利用这些变化提供信息。这项工作将集中在马铃薯的同源四倍体基因组上，我们已经在组织培养再生马铃薯中记录了广泛的基因组变化，从非整倍体到缺失，极端重排，以及与同源DNA修复一致的杂合性的更微妙的变化。对马铃薯变异的分析表明，基因组不稳定性随环境的变化而变化，在正常生长过程中也可能发生。具体目的是：1)表征与马铃薯体细胞无性系变异相关的分子模式。通过检查产生的重排，对潜在机制的假设，如同源与非同源修复的dsDNA断裂，将被测试。ii)研究与马铃薯克隆分化相关的分子模式。对马铃薯无性系繁殖的基因组分析将验证体细胞同源重组导致变异的假设，iii)研究dsDNA断裂与杂合性丧失的关系。该目标将利用诱导和自发的杂合性缺失模型来测试dsDNA断裂修复的可能机制，如有丝分裂交叉和断裂诱导重组。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

During tissue culture, plant genomes undergo frequent unexpected changes resulting in plants with different characteristics, called somaclonal variants. At lower frequency, similar variants called sports arise during normal growth. These new variants can have great economic value, but relatively little is known of the causes, nature and evolutionary significance of these phenomena. This project will investigate these changes in potato. The methods suitable to analyze these genomic changes will be applicable to other crops, and will be made available to the scientific and plant breeding community. Societal impact is expected along two lines. First, this project will address a largely ignored potential source of variation likely to affect leading economic species. Second, the project entails several outreach activities, with two objectives: 1) Familiarize young students in underrepresented communities with science studies and careers and 2) Train advanced students and professionals in genomic approaches applicable to plant breeding. These objectives will be achieved through a combination of publishing in outreach journals, provision of international workshops, and production of learning videos.The long term goal of this project is to understand the mechanisms and outcomes of genome instability and restructuring. The central hypothesis is that instability, while often deleterious, can also reshape the genome in ways that are less disruptive and potentially adaptive, such as by causing change or loss of heterozygosity, and dosage variation. Elucidating the causes, mechanisms, and consequences of these changes will help clarify their role in natural and artificial selection, and inform prediction, identification and, if appropriate, exploitation of these changes. The work will focus on the autotetraploid potato genome, in which we have documented extensive genomic changes in tissue culture regenerated potatoes, ranging from aneuploidy to indels, extreme rearrangements, but also more subtle changes in heterozygosity consistent with homologous DNA repair. Analysis of variation in potato suggests that genome instability varies according to environment and that it can occur during normal growth. The specific aims are to: i) Characterize the molecular patterns associated with somaclonal variation in potato. By examining resulting rearrangements, hypotheses on potential mechanisms, such as homologous vs. nonhomologous repair of dsDNA breaks, will be tested, ii) Study molecular patterns associated with differentiation of potato clones. Genomic analysis of clonally propagated potato will test the hypothesis that somatic homologous recombination results in variation and, iii) Investigate relation of dsDNA breaks to loss of heterozygosity. This objective will leverage induced and spontaneous loss of heterozygosity models to test possible mechanisms of dsDNA break repair, such as mitotic crossover and break-induced recombination.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.