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.

速生杨树(Pillius spp.)正在紧锣密鼓地开发常规森林产品和生物能源。与纯树种相比，杨树杂交种的生长优势使其构成了人工林中绝大多数的树木。然而，与杂交作物相比，树木的未驯化性质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中的变异是如何导致理想的(和不理想的)性状的，这对杨树育种计划有很大的帮助。在这个项目中，两个广泛的杨树物种-黑杨和苦瓜杨之间的天然杂交被用来描述、预测和测试杂交是如何转化为具有经济和生态意义的复杂适应性状的。此外，与木本植物国际社区ArbNet的公民科学合作将协调在北美各地建立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杨树基因型，并对它们的全基因组进行了测序。该项目将与ArbNet合作开发一门中学课程，重点关注来自不同环境的杨树的特征如何变化。本课程将包括数据的实际收集、跨地点数据的合成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的培训，涉及领域生态学、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已经有了很长的历史。这个项目将在复制的杨树杂交区中采样，以捕捉基因组x基因组x环境沿环境梯度的相互作用的历史，并将这种采样与全基因组范围的重新测序和计算方法结合起来，以解决以下问题：(I)导入是如何在基因组和景观中排列的？(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)是否可以使用受控杂交来重现适应性渐渗？广泛的短读和长读基因组重测序将结合在一起，以表征杂交区的基因组变异。然后，该团队将使用混合作图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，该项目将使用杨树物种间的受控杂交来测试杂交结果的可重复性，评估与杂交优势/杂种优势有关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。这个项目将提供到目前为止最全面的关于树种杂交和杂种优势的基因组学图景，并加强我们对渗透和跨环境适应之间关系的理解。这个奖项反映了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。

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