Author ORCID Identifier
Semester
Spring
Date of Graduation
2023
Document Type
Dissertation
Degree Type
PhD
College
Eberly College of Arts and Sciences
Department
Biology
Committee Chair
Stephen P. DiFazio
Committee Member
Vagner A. Benedito
Committee Member
Gancho T. Slavov
Committee Member
Jennifer Hawkins
Committee Member
Craig F. Barrett
Abstract
Dissecting the genetic architecture of a highly complex trait can be a challenging task and insight into the mechanistic role of these genetic elements do not always follow. Association genetics and quantitative trait loci (QTL) mapping techniques are used to identify key genetic elements associated with complex traits. However, in order to characterize the mechanistic role of the interaction among these genetic elements that results in ultimate trait features, it may be helpful to peer into intermediate molecular phenotypes such as gene expression.
In this dissertation work we have genetically mapped complex traits related to biomass and wood chemistry in P. trichocarpa (black cottonwood), as they represent key adaptive traits for this species and are key commercially traits related to biomass recalcitrance in view of its potential as a bioenergy feedstock. Since, formation of wood involves the interaction of many biological pathways related to managing internal resources as well as reacting to biotic and abiotic stress, we have characterized the transcriptome of the xylem to glean its major features and interacting molecular pathways involved. Tree improvement towards modified wood chemistry is under considerable inertia due to lack of clear evidence on trade-offs related to biomass and stress tolerance. This work characterized the extent of genetic control and genetic correlations among these traits that may provide breeders a perspective of what they can expect when using standing genetic variation to improve biomass recalcitrance.
We leveraged a large multiparent controlled cross of P. trichocarpa to construct multiple genetic linkage maps, since accurate and dense maps are the cornerstone of successfully mapping traits that we examined in this study. We produced fine-scale recombination rate estimates and characterized its variation within the species and the P. trichocarpagenome. The maps produced and fine-scale recombination rates estimated here will be highly valued for future efforts to accelerate domestication of this species, as well as future studies that investigate broader questions such as evolutionary history, perennial development related to phenology, vegetative propagation, and dioecy that cannot be studied using conventional plant model systems such as Arabidopsis, rice, or maize. The genes or genomic regions we identified in this study together with the transcriptomic data we analyzed will compose an integral part of genomic selection and multi-omic predictive models that we aim to develop for this species
Recommended Citation
Abeyratne, Chanaka R., "Leveraging a multiparent cross of Populus trichocarpa to characterize recombination rates and dissect the genetic architecture of wood chemistry" (2023). Graduate Theses, Dissertations, and Problem Reports. 11921.
https://researchrepository.wvu.edu/etd/11921
Supplementary data tables
Included in
Bioinformatics Commons, Computational Biology Commons, Genetics Commons, Genomics Commons, Integrative Biology Commons, Other Genetics and Genomics Commons
Comments
The dissertation has a companion Microsoft Excel file named 'chapters_2_3_4_Supplementary_tables.xlsx' that contains all the supplementary tables