Date of Award
2024
Document Type
Campus Access Dissertation
Degree Name
Doctor of Philosophy in Forest Molecular Genetics and Biotechnology (PhD)
Administrative Home Department
College of Forest Resources and Environmental Science
Advisor 1
Carsten Külheim
Committee Member 1
Victor Busov
Committee Member 2
Stephen Techtmann
Committee Member 3
David Kainer
Abstract
Genetic improvement of trees is essential for increasing the adaptability of trees to changing environments and biotic and abiotic stresses and for increasing the productivity and quality of forest products. For efficient tree improvement, selecting a suitable breeding method is essential. In this dissertation, I performed a meta-analysis of tree genetics improvement methods suitable for various contexts, and provided a framework for future tree genetic improvements. The results of my meta-analysis support the intelligent application of genomics and genetic engineering-based methods for the domestication, restoration, improvement, and conservation of forest trees. I conducted a comparative genome-wide association studies (GWAS) using a related species Eucalyptus grandis reference genome, an in silico generated Eucalyptus polybractea pseudo-reference and a hybrid assembled E. polybractea reference genome to answer the questions, how close a reference genome we need for accurate detection of genetic variants (single nucleotide polymorphism)? Or can we use pseudo-references or even just a related reference genome? The results of this study indicated that the high-quality genome of E. polybractea facilitated better mapping and identification of genetic variants that allowed us to identify candidate genes related to terpene production in E. polybractea. In another chapter, I performed an integrated study including mixed linear modeling, GWAS, expression quantitative trait loci (eQTL), and genetic network analysis using RNA sequencing data from six geographic regions of Australia comprising four chemotypes of E. camaldulensis for investigating the genetic architecture and transcriptomic regulation of terpene traits. I identified multiple transcription factors and their target genes including terpene synthase and stress responsive genes work together to regulate terpene production and chemotype diversity by producing specific terpenes. Overall, the studies in this dissertation provided a deep insight into trends of using tree genetic improvement methods, and how the advanced methods and technologies help in achieving the objectives of tree genetic improvement program.
Recommended Citation
Chakrabarty, Swapan, "NOVEL METHODS OF TREE IMPROVEMENT IN THE GENOMIC ERA", Campus Access Dissertation, Michigan Technological University, 2024.