RESEARCH-PGR: Genomic architecture of porous species boundaries: implications for climatic adaptation and hybrid breeding

研究-PGR：多孔物种边界的基因组结构：对气候适应和杂交育种的影响

• 批准号: 1856450
• 负责人: Jason Holliday
• 金额: $ 250万
• 依托单位: Virginia Polytechnic Institute and State University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-06-01 至 2025-05-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1856450&HistoricalAwards=false
• 关键词: RESEARCH; PGR; Genomic; architecture; porous

Fast-growing poplar trees (Populus spp.) are under intense development for conventional forest products and bioenergy. Poplar hybrids comprise the vast majority of trees in operational plantations due to their superior growth when compared to pure species. However, compared with hybrid crop plants, the undomesticated nature of trees makes predicting performance of their hybrids more challenging. Understanding how variation in hybrid genomes and in the environment lead to desirable (and undesirable) traits has the potential to benefit poplar breeding programs significantly. In this project, natural hybrids between two wide-ranging poplar species - black cottonwood and balsam poplar - are used to characterize, predict, and test how hybridization translates into complex adaptive traits of economic and ecological significance. In addition, a citizen science collaboration with ArbNet, an international community of arboreta, will coordinate establishment of 20 common garden experiments (mini gardens) across North America. These experiments will all be planted with the same set of different poplar genotypes that have had their full genomes sequenced. The project will work with ArbNet to develop a middle school curriculum focused on how traits vary in poplar trees originating from diverse environments. This curriculum will include hands-on collection of data, synthesis of data across sites and illustrating the principles of adaptation and genetic variation. Students will be exposed to biological responses to different environments, experimental design, and hypothesis testing. At each participating university, the project team will also provide interdisciplinary training to the next generation of scientists, spanning field ecology, genomics, and computational biology.Natural Populus hybrid zones provide a 'living laboratory' in which there has been a long history of natural selection testing the genomic and phenotypic outcomes of hybridization. This project will sample across replicated Populus hybrid zones to capture the history of Genome x Genome x Environment interactions along environmental gradients, and couple this sampling with genome-wide re-sequencing and computational approaches to address the following questions: (i) How is introgression arrayed across the genome and landscape? (ii) What genomic regions control hybrid fitness and what are their environmental drivers? (iii) Can adaptive introgression be recapitulated using controlled crosses? Extensive short and long-read genome resequencing will be combined to characterize genomic variation across the hybrid zones. The team will then use admixture mapping to associate genomic ancestry with climate gradients and adaptive phenotypes, predict hybrid performance across a range of field test sites, and evaluate the contributions of environment and space in explaining patterns of hybridization. Finally, the project will test the repeatability of hybrid outcomes using controlled crosses among Populus species, assessing the predictive value of loci identified as being involved in hybrid vigor/heterosis, and the role of allele-specific expression in generating hybrid phenotypes. This project will provide the most comprehensive picture to date of the genomics of hybridization and heterosis in a tree species and enhance our understanding of the relationship between introgression and fitness across environments.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.

快速生长的杨树（Populus spp.）作为常规林产品和生物能源正在得到大力开发。与纯种相比，杂交杨树在经营人工林中占绝大多数，因为它们的生长性能优越。然而，与杂交作物相比，树木的未驯化特性使得预测其杂交作物的表现更具挑战性。了解杂交基因组和环境的变化如何导致理想（和不理想）的性状，有可能使杨树育种计划显著受益。在这个项目中，两种分布广泛的杨树物种——黑棉杨和苦杨——之间的自然杂交被用来表征、预测和测试杂交如何转化为具有经济和生态意义的复杂适应性性状。此外，一个与国际植物园ArbNet的公民科学合作项目将协调在北美建立20个普通花园实验（迷你花园）。这些实验都将种植同一组不同基因型的杨树，这些基因型已经完成了完整的基因组测序。该项目将与ArbNet合作，开发一套中学课程，重点介绍来自不同环境的杨树的特征如何变化。本课程将包括动手收集数据，跨站点的数据综合和说明适应和遗传变异的原则。学生将接触到不同环境下的生物反应、实验设计和假设检验。在每一所参与的大学，项目团队还将为下一代科学家提供跨学科的培训，涵盖领域生态学、基因组学和计算生物学。自然杨树杂交区提供了一个“活的实验室”，在那里有很长的自然选择历史，测试杂交的基因组和表型结果。该项目将在复制的杨树杂交带进行采样，以捕捉基因组x基因组x环境沿环境梯度相互作用的历史，并将此采样与全基因组重测序和计算方法相结合，以解决以下问题：(i)基因渗入如何在基因组和景观中排列？（ii）哪些基因组区域控制杂交适合度，它们的环境驱动因素是什么？（iii）能否利用控制杂交重现适应性基因渗入？广泛的短读和长读基因组重测序将结合在一起，以表征杂交区域的基因组变异。然后，该团队将使用混合图谱将基因组祖先与气候梯度和适应性表型联系起来，预测在一系列现场试验点的杂交表现，并评估环境和空间在解释杂交模式方面的贡献。最后，该项目将通过在杨树物种之间进行对照杂交来测试杂交结果的可重复性，评估被确定为参与杂交活力/杂种优势的位点的预测价值，以及等位基因特异性表达在产生杂交表型中的作用。该项目将提供迄今为止最全面的树种杂交和杂种优势基因组图谱，并增强我们对环境中遗传渗入和适应性之间关系的理解。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。

项目成果

GWAS on the Attack by Aspen Borer Saperda calcarata on Black Cottonwood Trees Reveals a Response Mechanism Involving Secondary Metabolism and Independence of Tree Architecture

• DOI: 10.3390/f14061129
• 发表时间: 2023-05
• 期刊: Forests
• 影响因子: 2.9
• 作者: S. Sepúlveda;D. Neale;J. Holliday;Randi A. Famula;O. Fiehn;B. Stanton;Fernando P. Guerra