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.）正在大力开发传统林产品和生物能源。杨树杂交种占运营种植园中的绝大多数树木，因为与纯种相比，它们的生长速度更快。然而，与杂交作物相比，树木的未驯化性质使得预测其杂交品种的性能更具挑战性。了解杂交基因组和环境中的变异如何导致理想（和不良）性状有可能使杨树育种计划受益匪浅。在该项目中，利用两种广泛的杨树品种——黑三叶杨和香脂杨——之间的自然杂交来表征、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特征。此外，与 Arboreta 国际社区 ArbNet 的公民科学合作将协调在北美建立 20 个公共花园实验（迷你花园）。这些实验将全部种植相同的一组不同基因型的杨树，这些杨树的完整基因组已被测序。该项目将与 ArbNet 合作开发中学课程，重点关注来自不同环境的杨树的性状变化。该课程将包括动手收集数据、跨站点数据综合以及说明适应和遗传变异的原理。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。在每所参与的大学，项目团队还将为下一代科学家提供跨学科培训，涵盖野外生态学、基因组学和计算生物学。天然杨树杂交区提供了一个“活实验室”，在这个实验室中，自然选择测试杂交的基因组和表型结果有着悠久的历史。该项目将对复制的杨树杂交区进行采样，以捕获基因组 x 基因组 x 环境沿环境梯度相互作用的历史，并将该采样与全基因组重新测序和计算方法结合起来，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混合适应性以及它们的环境驱动因素是什么？ (iii) 可以使用受控杂交来重现适应性基因渗入吗？广泛的短读长和长读长基因组重测序将被结合起来，以表征跨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，预测一系列现场测试地点的杂交表现，并评估环境和空间在解释杂交模式中的贡献。最后，该项目将使用杨属物种之间的受控杂交来测试杂交结果的可重复性，评估被确定为参与杂交优势/杂种优势的基因座的预测价值，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学图景，并增强我们对跨环境渗入和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