RESEARCH-PGR: The Cytonuclear Dimension of Allopolyploidy

基因组学时代的关键认识之一是，所有植物，包括我们的主要农作物，都有基因组复制的历史，其中细胞内的DNA含量翻了一番(多倍体)。尽管近年来关于基因组加倍的后果已经有了很多了解，但关于基因组复制如何有助于植物生物学和作物生产力的许多基本问题仍然存在。基因组复制的一个重要方面是现在加倍的核基因组如何与植物细胞中发现的其他基因组间隔相互作用，如线粒体和叶绿体。计划中的研究将调查基因组复制这一未被探索的方面，并暗示在基因组加倍事件之后，在生长、繁殖和产量中发挥关键作用的细胞能量学是如何改变的。这项研究将使用各种重要的作物系统和最先进的基因组学技术。项目资源、数据和人员将用于扩大外展和教育项目，包括一个关于基因组学的国际研讨会系列，以及为高中教师提供身临其境的实践研究和课程开发体验的长期努力。该项目将在研究和服务学习方面为参与者创造各种教育和职业阶段的培训机会。综上所述，这项研究旨在提供对基因组相互作用和作物生物学的基本见解，并扩大对植物生物学研究的参与。同源多倍体事件包括来自两个不同谱系的基因组同时合并，以及核基因组含量加倍。由于细胞质基因组通常只从一个(母体)亲本那里遗传，异源多倍化预计会对核质基因组的相对拷贝数(即化学计量比)产生复杂的影响，还会产生新的、“未经测试的”核质基因对。计划中的研究将揭示基因组反应的光谱，以缓解异源多倍体对细胞核相互作用的破坏效应，并促进杂交/多倍体谱系的成功建立。生物信息学分析将测试细胞器靶向核基因中预测的补偿反应，这些基因解决了父源核亚基因组和母源细胞质基因组之间不适应的相互作用，包括：(1)母系偏向的基因转换；(2)父系亚组中序列进化的选择压力改变；(3)父系偏向的伪基因化和基因丢失；以及(4)父系同源基因的优先下调。通过利用600个来自棉花异源多倍体的重新测序的基因组，拟议的研究将扩展到群体基因组水平，以检测这些影响。最后，核质基因组与细胞质基因组的相对拷贝数以及在核、线粒体和质体中的相对表达水平将被精确量化，以区分对化学计量失衡的多种假想反应。总而言之，这些分析将对细胞核相互作用是否以及如何有助于多倍体作物的形成和进化提供强有力的测试。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。

One of the key realizations of the genomics era is that all plants, including our major crop plants, have histories of genome duplication in which the DNA content inside cells is doubled (polyploidy). Although much has been learned about the consequences of genome doubling in recent years, many fundamental questions remain regarding how genome duplication contributes to plant biology and crop productivity. An important dimension of genome duplication is how the now-doubled nuclear genome interacts with other genomic compartments found within the plant cell, such as the mitochondria and plastids. The planned research will investigate this underexplored aspect of genome duplications, with implications for how cellular energetics, which play a key role in growth, reproduction, and yield, are altered in the wake of genome doubling events. The research will use a diverse panel of important crop systems and state-of-the-art genomics techniques. Project resources, data, and personnel will be used to expand outreach and education programs, including an international workshop series on genomics and a long-term effort to provide high school teachers with an immersive experience in hands-on research and curricular development. The project will create training opportunities for participants across the full range of educational and career stages in both research and service-learning. In sum, this research aims to provide fundamental insights into genome interactions and crop biology and broaden participation in plant biological research.Allopolyploidy events entail the simultaneous merger of genomes from two divergent lineages combined with the doubling of nuclear genome content. Because cytoplasmic genomes are typically inherited from only a single (maternal) parent, allopolyploidization is expected to have complex effects on the relative copy number (i.e., stoichiometry) of nuclear and cytoplasmic genomes, and also create novel, "untested" pairings of nuclear and cytoplasmic genotypes. The planned research will reveal the spectrum of genomic responses that alleviate the disruptive effects of allopolyploidy on cytonuclear interactions and facilitate the successful establishment of hybrid/polyploid lineages. Bioinformatic analyses will test for predicted compensatory responses in organelle-targeted nuclear genes that resolve maladapted interactions between the paternally derived nuclear subgenome and maternally derived cytoplasmic genomes, including: (1) maternally biased gene conversion; (2) altered selection pressures on sequence evolution in the paternal subgenome; (3) paternally biased pseudogenization and gene loss; and (4) preferential down-regulation of paternal homoeologs. By taking advantage of 600 re-sequenced genomes from cotton allopolyploids, the proposed research will be extended to the population-genomic level to detect these effects "in action". Finally, the relative copy number of nuclear vs. cytoplasmic genomes and the relative expression levels in the nucleus, mitochondria, and plastids will be precisely quantified to differentiate among multiple hypothesized responses to stoichiometric imbalance. Together, these analyses will provide a powerful test of whether and how cytonuclear interactions contribute to the formation and evolution of polyploid crops.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.