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

基因组工具的进步将使进化的新分析成为可能。在长寿、生长缓慢的针叶树中，如松树，基因组工具提供了一个窗口，可以了解在不适合短期实验的时间尺度上发生的过程。松树是世界上许多生态系统的重要物种，了解松树独特的遗传特征如何影响它们对环境变化的进化反应是很重要的。这对松树来说尤其重要，因为在气候变化的影响下，这种松树预计会急剧衰退。到目前为止，松树基因组的庞大和复杂限制了从基因工作中获得的见解。最近的技术进步使在松树上组装高质量的基因组成为可能。首席研究员将学习新的基因组方法，并将其与广泛的松树知识相结合。美国西南部的部落和机构将使用该项目的信息来管理松林。此外，松子是松鸦的重要食物来源，松鸦最近被提议根据《濒危物种法》被列入名单。该项目将使用种子组织的长读和短读DNA测序来组装柑橘松树的完整基因组序列。首席研究人员将接受培训，通过对测序树的多个组织、不同物种范围的树木样本以及在普通花园中受到不同生长条件影响的杂交区域的后代进行基因测序来解释基因组。这项培训将由Wegrzyn博士和她在康涅狄格大学的实验室合作提供。这项研究将研究基因组结构如何影响气候和遗传梯度的表达。该基因组将与其他松树基因组进行比较，以评估基因组的基因家族结构、拷贝数变异和其他特征。在干旱胁迫较高的地区对杂交区进行采样将有助于回答有关杂交、表达基因和基因调控在杂交区形态变异中的作用的问题。这将导致对该物种的遗传管理提出建议。这一合作将导致探索新领域的更多建议，如调查压力在诱导反转录转座子活动中的作用、由此产生的新变种以及这些新变种在松树种群进化中的命运。该奖项反映了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。

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.