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.

速生白杨（Populus spp.）正在加紧开发传统森林产品和生物能源。白杨杂交种由于其上级生长比纯种更好而在人工林中占绝大多数。然而，与杂交作物相比，树木的未驯化性质使得预测其杂交种的表现更具挑战性。了解杂交基因组和环境中的变异如何导致理想（和不理想）的性状，有可能使白杨育种计划显着受益。在这个项目中，两个广泛的白杨品种之间的自然杂交-黑棉白杨和香脂白杨-用于表征，预测和测试杂交如何转化为经济和生态意义的复杂适应性性状。此外，与国际树木社区ArbNet的公民科学合作将协调在北美建立20个共同花园实验（迷你花园）。这些实验都将种植相同的一组不同的白杨基因型，已经有他们的全基因组测序。该项目将与ArbNet合作开发一个中学课程，重点是来自不同环境的白杨的性状如何变化。该课程将包括动手收集数据，跨站点的数据合成，并说明适应和遗传变异的原则。学生将接触到对不同环境的生物反应、实验设计和假设检验。在每个参与的大学，项目团队还将为下一代科学家提供跨学科的培训，涵盖田间生态学、基因组学和计算生物学。天然杨树杂交区提供了一个“活的实验室”，在这个实验室里，自然选择测试杂交的基因组和表型结果的历史由来已久。该项目将在复制的杨树杂交区进行采样，以捕获基因组x基因组x环境相互作用的历史，沿着环境梯度，并将该采样与全基因组重测序和计算方法结合起来，以解决以下问题：（i）基因组和景观中的渐渗是如何排列的？(ii)哪些基因组区域控制杂种适应性，它们的环境驱动因素是什么？(iii)适应性基因渗入能用控制杂交重现吗？将结合广泛的短读和长读基因组重测序来表征杂交区的基因组变异。然后，该团队将使用混合物映射将基因组祖先与气候梯度和适应性表型联系起来，预测一系列田间试验地点的杂交表现，并评估环境和空间在解释杂交模式方面的贡献。最后，该项目将使用杨树属物种之间的控制杂交来测试杂交结果的可重复性，评估被鉴定为参与杂交优势/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的基因组学图片，并增强我们对基因渗入和环境适应性之间关系的理解。该奖项反映了NSF的法定使命，并通过使用基金会的智力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