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。）在传统的森林产品和生物能源方面正在强烈开发。与纯种相比，杨树杂种构成了营业种植园的绝大多数树木。但是，与杂种作物植物相比，树木的未种植性质使预测其杂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（和不希望的）特征有可能使杨树育种计划受益。在这个项目中，使用两个广泛的杨树之间的天然杂种 - 黑棉木和香脂杨树 - 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自适应特征。此外，与Arboreta国际社会Arbnet进行的公民科学合作将协调北美的20个常见花园实验（迷你花园）的建立。这些实验将使用与已进行完整基因组测序的相同的不同杨树基因型进行种植。该项目将与Arbnet合作，开发一门中学课程，重点介绍了源自不同环境的杨树树木的特征如何变化。该课程将包括动手收集数据，跨站点的数据合成以及说明适应性和遗传变异的原理。学生将接触到对不同环境，实验设计和假设检验的生物学反应。在每所参与大学中，项目团队还将为下一代科学家提供跨学科培训，跨越现场生态学，基因组学和计算生物学。自然的人口混合区提供了一个“活实验室”，其中有悠久的自然选择测试测试基因组和表型型卫生型卫生型的历史。该项目将在重复的人口混合区域进行采样，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，并将此抽样与全基因组的重新序列和计算方法进行融入以下问题：（i）在基因组和景观中如何渗入insogression阵列？ （ii）哪些基因组区域控制混合健身，它们的环境驱动因素是什么？ （iii）可以使用受控杂交概括自适应的渗入吗？将合并大量的短而长读的基因组，以表征整个杂种区域的基因组变异。然后，团队将使用混合图将基因组血统与气候梯度和自适应表型相关联，预测一系列现场测试地点的混合性能，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Populus物种中的受控十字架测试杂种结局的可重复性，评估所鉴定的基因座的预测价值与杂交活力/异因而涉及的基因座，以及等位基因特异性表达在产生杂交表型中的作用。该项目将为树种中杂交和杂种基因组的迄今为止提供最全面的了解，并增强我们对跨环境中渗入和适应性之间关系的理解。该奖项反映了NSF的法定任务，并被视为值得通过基金会的知识分子和更广泛影响的评估来审查审查标准来通过评估来获得支持。

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