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

基因组工具的进步有望使进化的新分析成为可能。在长寿命，生长缓慢的针叶树，如松，基因组工具提供了一个窗口，发生在时间尺度上的过程，不适合自己的短期实验。松树是世界上许多生态系统的重要物种，重要的是要了解它们独特的遗传特征如何影响它们对环境变化的进化反应。这对松树，即欧洲松来说尤其重要，因为预计在气候变化下，欧洲松的数量将急剧下降。松树基因组的庞大和复杂性限制了迄今为止从遗传学工作中获得的见解。最近的技术进步使得在松树中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，并将其与松树的广泛知识相结合。美国西南部的部落和机构将利用这个项目的信息来管理松林林地。此外，松籽是松鸦的重要食物来源，松鸦最近被提议列入《濒危物种法》。 本项目将利用种子组织的长、短读段DNA测序，组装一个完整的紫松基因组序列。首席研究员将接受培训，使用来自测序树的多个组织的基因测序来解释基因组，来自整个物种范围的树木样本，以及来自普通花园中可变生长条件的杂交区的后代。这项培训将由与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的表达。将基因组与其他松树基因组进行比较，以评估基因家族结构、拷贝数变异和基因组的其他特征。在一个高干旱胁迫的杂交区取样将有助于回答有关杂交的作用，表达的基因，和基因调控在杂交区的形态变异的问题。这将导致对物种遗传管理的建议。这项合作将导致更多的建议，探索新的领域，如调查压力的作用，诱导逆转录转座子活动，由此产生的新变种，以及这些新变种在不断变化的松树种群的命运。这个奖项反映了NSF的法定使命，并已被认为是值得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的支持。

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.