MCA: Genomic tools for elucidating evolutionary response to climate change in declining pine populations

MCA：阐明松树种群数量下降对气候变化的进化反应的基因组工具

• 批准号: 2322288
• 负责人: Amy Whipple
• 金额: $ 33.62万
• 依托单位: Northern Arizona University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-01 至 2026-08-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2322288&HistoricalAwards=false
• 关键词: MCA; Genomic; tools; elucidating; evolutionary

Advances in genomic tools are poised to enable novel analyses of evolution. In long-lived, slow growing conifers, such as pinyon pine, genomic tools offer a window into processes that occur over timescales that do not lend themselves to short-term experiments. Pine trees are important species to many of the world’s ecosystems and it is important to understand how their unique genetic characteristics affect their evolutionary response to environmental change. This is especially crucial for the pinyon pine, Pinus edulis, which is expected to decline precipitously under climate change. The large size and complexity of pine genomes have limited the insights gained from genetic work to date. Recent technological advances make the assembly of a good quality genome in a pine tree feasible. The lead researcher will learn new genomic methods and merge that with extensive knowledge of pinyon pines. Tribes and agencies in the southwestern US will use information from this project to manage pinyon woodlands. Additionally, pinyon pine seeds are a critical food source for the pinyon jay which has recently been proposed for listing under the Endangered Species Act. This project will use long and short read DNA sequencing of seed tissue to assemble a complete genome sequence for Pinus edulis. The lead researcher will be trained to interpret the genome using sequencing of genes from multiple tissues of the sequenced tree, a sample of trees from across the species range, and offspring from a hybrid zone subjected to variable growing conditions in common gardens. This training will be provided by a collaboration with Dr. Wegrzyn and her laboratory at the University of Connecticut. The research will examine how genome structure affects expression across climate and genetic gradients. The genome will be compared to other pine genomes to assess gene family structure, copy number variation, and other characteristics of the genome. Sampling of a hybrid zone in a location with high drought stress will help answer questions about the role of hybridization, expressed genes, and gene regulation in morphological variability in a hybrid zone. This will lead to recommendations for the genetic management of the species. This collaboration will lead to additional proposals exploring novel areas such as investigating the role of stress in inducing retrotransposon activity, the resulting new variants, and the fate of those new variants in evolving pine populations.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.

基因组工具的进步被中毒以实现新的进化分析。在长期增长的会议（例如Pinyon Pine）中，基因组工具为过程提供了一个窗口，这些过程在时间尺度上不适合短期实验。松树对世界许多生态系统都是重要的物种，重要的是要了解它们的独特遗传特征如何影响其对环境变化的进化反应。这对于Pinyon Pine Pinus Edulis尤其重要，预计在气候变化下会精确下降。迄今为止，松树基因组的大尺寸和复杂性限制了从遗传工作中获得的见解。最近的技术进步使得在松树中的一棵优质基因组的组装可行。首席研究人员将学习新的基因组方法，并将其与对Pinyon Pines的广泛了解合并。美国西南部的部落和机构将使用该项目中的信息来管理Pinyon Woodlands。此外，Pinyon Pine种子是Pinyon Jay的关键食物来源，最近提出了根据《濒危物种法》列出的。该项目将使用种子组织的长而短读的DNA测序，以组装Pinus Edulis的完整基因组序列。首席研究人员将接受培训，可以使用测序树的多个时机的基因测序解释基因组，从物种范围跨种类的树木样本，以及来自杂种区的后代，在普通花园中受到可变生长条件的影响。这项培训将由Wegrzyn博士及其在康涅狄格大学的实验室合作提供。该研究将研究基因组结构如何影响气候和遗传梯度之间的表达。将将基因组与其他PINE基因组进行比较，以评估基因组的基因家族结构，拷贝数变异和基因组的其他特征。在具有高干旱应力的位置中对杂种区的采样将有助于回答有关杂交，表达基因和基因调节在杂交区中形态变异性中的作用的问题。这将导致该物种遗传管理的建议。这项合作将导致探索新领域的其他建议，例如调查压力在诱导的返回跨座子活动中的作用，由此产生的新变体，以及这些新变体在不断发展的松树种群中的命运。这奖反映了NSF的法规使命，并通过评估基金会的知识绩效和广泛的范围来诚实地通过评估来诚实地进行评估。