INVESTIGATORS: Luca Comai (PI), Andrew Groover, Isabelle Henry
INSTITUTIONS: University of California Davis, US Forest Service
PROJECT SUMMARY: Interspecific hybridization is the most effective method for producing poplar clones for commercial applications, including biomass production. Previous research has shown that commercial F1 hybrids frequently exhibit dosage variation, i.e. variation in the number of pieces or entire chromosomes, and that these variants can have transgressive phenotypes desirable for biomass production. Poplar is an excellent system for studying and exploiting gene dosage because germplasm is propagated vegetatively for research and production, and advanced genome-enabled tools can be directly employed on the actual feedstock. In the previous funding cycle, we have produced and characterized a population of interspecific hybrids carrying insertions and deletions, which together, tile the entire genome with dosage variation. In this proposal, we will complete the development of this unique resource for the research community and use the germplasm to investigate the role of gene dosage in poplar hybrid performance, and to identify chromosomal regions and genes that contribute to poplar bioenergy traits. Our specific objectives are as follows:
Create and maintain a resource for poplar feedstock functional genomics: We will use next-generation sequencing and bioinformatics pipelines already developed in the previous funding period to catalog dosage variation in ~500 additional and already available P. deltoides x P. nigra F1 individuals and identify the smallest set of lines with the highest information content. We will make germplasm and sequence data available to the research community without IP restrictions.
Investigate the phenotypic effects of dosage change: We will use field trials to characterize variation for traits central to sustainable production of biomass with optimal feedstock properties. We will document correlations between trait values and copy number along each chromosome to associate particular traits with chromosomal regions.
Exploit the indel germplasm for functional genomics: First at genome resolution, then more in depth on specific indel regions, we will describe and analyze dosage-dependent regulation, identify gene modules and candidate genes that influence traits of interest.
Outputs will include a population of interspecific hybrid of poplar carrying well defined dosage variation that spans the majority of the poplar genome at least once, and extensively characterized trait measurements. Additionally, we will identify specific regulatory or functional gene modules underlying phenotypes of interest. Finally, because our dosage variants were produced in a hybrid type that is of interest to the poplar industry, it is possible that our germplasm collection already includes new cultivars directly usable for bioenergy applications. Importantly, the approaches we describe here can be generalized to other poplar hybrid combinations and to germplasm development for other vegetatively-propagated species. Our efforts will add new, useful and unique tools that have both functional and practical applications for poplar breeding and is widely applicable to other biomass crops such as switchgrass, alfalfa, willow, and Miscanthus.
Name: Comai, Luca