Creating and utilizing genomic and genetic resources for Camelina sativa to advance understanding of genetic systems regulating agronomic traits

Abstract

Camelina (Camelina sativa L. Crantz) has shown promise as a bioenergy oilseed crop and for translational plant biology research. To support future research and breeding programs new tools for genomic analysis and refinement of previous genetic analysis were needed. This dissertation presents a chromosome-level genome of the widely used variety Suneson. The genome presented is ~652 Mb long across 20 chromosome length subassemblies, and an additional ~90 Mb contained in 1601 scaffolds of 10Kb or longer. Two genome annotations are presented, one with 121,345 gene models and another with 170,151 gene models. The genome was masked across 46% of its length. This manuscript also presents the genomic analysis of whole genome sequencing data of two populations using genome-wide association studies and quantitative trait analysis. The diversity panel was grown in four locations to account for environmental effects. Almost 400 marker-trait associations were found from the diversity panel, 118 of which were related to oil content or fatty acid content. Quantitative trait analysis of a recombinant inbred line population revealed over 300 marker-trait associations, many of which are pleiotropic, yielding multiple potential candidate genome regions for future analysis. To support the search for candidate genes the pangenome alignment analyzer was written to make use of expanding pan-genomic resources. This tool aids in this search by comparing the pan- genomic gene sequences to search for variation linked to the quantitative trait locus.