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

Northern Arizona University, Flagstaff AZ

Investigators

Abstract

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.