CAREER: Integrating Whole-Genome Association Mapping and Landscape Genomics to Understand Climatic Adaptation in Populus

01 Feb 2011 31 Jan 2017

Jason Holliday (PI)


Endodormancy is a hallmark of woody perennial plants of the temperate and boreal regions that enables above ground meristems to survive the freezing and dehydration stresses of winter. This project takes a population genomics approach to dissect the genomic basis for endodormancy transitions and cold hardiness in Populus. A recently developed technology for genome complexity reduction will be used to pursue this goal on a genome-wide scale, and collaboration with groups working in related poplar species will facilitate comparative analysis of adaptation. Sequence capture technology will be employed to retrieve exons and upstream regulatory sequences for all expressed genes in Populus trichocarpa (black cottonwood), and captured targets will be sequenced in a large black cottonwood mapping population that spans most of the species range. Genotype-phenotype associations will be sought with three phenotypic traits, namely, timing of budset, timing of budflush, and cold hardiness. Associations will also be sought with climate variables that represent the principle selective constraint related to these traits. Positive associations will be validated in a separate cohort of poplar clones, and using data provided by collaborators, the extent of overlap in adaptive loci in both Populus tremuloides (trembling aspen) and Populus deltoides (eastern cottonwood) will be determined. A web-based bioinformatic resource will be developed to disseminate sequence data, SNP data, and SNP associations. This work will provide by far the most comprehensive picture to date of the genomic basis for local adaptation to climate in a tree species. In addition to answering long standing questions in evolutionary ecology about the genomic architecture of adaptation, this work will provide a link to practical breeding applications that can exploit naturally occurring ecologically-relevant genetic variation for tree improvement in a changing climate.

Forest tree populations are well adapted to their local environments at present, but climate change is substantially altering adaptive landscapes, and is expected to lead to widespread maladaptation of tree populations to their seasonal temperature regimes. Adapting management strategies to account for these changes depends crucially on an understanding of the genomic architecture of adaptive traits. By integrating molecular biology, bioinformatics, and population genomics, this project will substantially advance this goal, while providing interdisciplinary education and training at various levels (undergraduate, graduate and postdoctoral). Research personnel associated with this project will develop investigative field workshops for students and landowners in collaboration with Virginia's Link to Education about Forestry (LEAF) program. Field trials will be used to host these outdoor LEAF learning workshops, through which landowners, practitioners, and local students will explore the relationship between climatic adaptation and seed sources, as well as the potential impacts of climate change on forest productivity. In addition, publicaly available web-based modules complimentary to the field experiences workshop will be developed. Sequence data will be deposited at GenBank, dbSNP at NCBI, and genotype-phenotype data at Data Dryad (www.datadryad.org).