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，在正常生长过程中会出现类似的变种，称为运动。这些新的变种可能具有巨大的经济价值，但人们对这些现象的原因、性质和进化意义知之甚少。这个项目将研究马铃薯中的这些变化。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。预计会产生两方面的社会影响。首先，这个项目将解决一个很大程度上被忽视的潜在变异来源，可能会影响主要的经济物种。第二，该项目有几项外联活动，有两个目标：1)使代表性不足社区的年轻学生熟悉科学研究和职业；2)培训高级学生和专业人员，使他们掌握适用于植物育种的基因组方法。这些目标将通过在外展期刊上发表、提供国际研讨会和制作学习视频来实现。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，不稳定虽然往往是有害的，但也可以以破坏性较小和潜在的适应性较小的方式重塑基因组，例如通过导致杂合性的变化或丢失，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选择和人工选择中的作用，并为预测、识别和适当地利用这些变化提供信息。这项工作将集中在同源四倍体马铃薯基因组上，其中我们记录了组织培养再生马铃薯中广泛的基因组变化，从非整倍体到Indels，极端重排，但也有与同源DNA修复一致的杂合性更细微的变化。对马铃薯的变异分析表明，基因组的不稳定性因环境而异，在正常生长过程中可能会发生这种情况。其具体目的是：i)描述与马铃薯体细胞无性系变异相关的分子模式。通过检查由此产生的重排，将检验关于潜在机制的假说，例如dsDNA断裂的同源修复与非同源修复，ii)研究与马铃薯克隆分化相关的分子模式。对无性系繁殖的马铃薯进行基因组分析，将检验体细胞同源重组导致变异的假设，以及(Iii)研究dsDNA断裂与杂合性丧失的关系。这一目标将利用诱导和自发杂合性丢失模型来测试dsDNA断裂修复的可能机制，如有丝分裂交叉和断裂诱导重组。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势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.