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Utilization of variation to understand Camelina sativa genome evolution

dc.contributor.advisorParkin, Isobel
dc.contributor.advisorBett, Kirstin
dc.contributor.committeeMemberBeattie, Aaron
dc.contributor.committeeMemberHegedus, Dwayne
dc.contributor.committeeMemberLinks, Matthew
dc.contributor.committeeMemberWarkentin, Tom
dc.creatorChaudhary, Raju
dc.creator.orcid0000-0001-5370-6945 2021
dc.description.abstractCamelina sativa is an oilseed crop gaining interest for its oil content, protein content, and potential as a new oilseed for human consumption. The main disadvantages of this crop are its smaller seed size and lower total yield compared to other commercial oilseed crops; however, breeding efforts has been progressing to improve yield traits. A low level of genetic diversity and limited breeding efforts have been identified as impediments in C. sativa crop improvement. This study was designed to improve access to genetic diversity in C. sativa by developing genetic tools and identifying genetic mechanisms to accelerate C. sativa breeding. The objectives of this study were: to explore the genetic diversity in available Camelina germplasm using Genotyping-by-Sequencing (GBS), with a focus on close relatives of C. sativa and a collection from Ukraine and Russia; to develop segregating generations through intra- and interspecific hybridization; and to complete whole genome transcriptome analysis to observe gene expression patterns across subgenomes in hexaploid species of Camelina. Genetic markers in this study were developed using GBS, whereas whole transcriptome analysis was performed for subgenome dominance analysis. The genetic diversity study with 193 genotypes identified two subpopulations in C. sativa, where C. microcarpa was found to be a close relative of this species. Winter C. sativa species, such as C. sativa ssp. pilosa and C. alyssum, formed a separate clade and were closely-associated with C. microcarpa. Principal coordinate and phylogenetic analysis differentiated the genotypes based on species and subpopulations. Mapping of reads to the reference genome identified C. neglecta as a progenitor species for the first subgenome of C. sativa. Likewise, a tetraploid was identified that encompassed the first and second subgenomes, and a novel C. microcarpa species differing from C. sativa in terms of genome structure was also identified. Flow cytometry analysis and chromosome count validated the read mapping and confirmed that the novel C. microcarpa possessed 19 chromosomes (n, haploid number) with a different third subgenome not present in C. sativa. The inter- and intraspecific hybridizations enabled genetic linkage maps to be developed, where a common C. sativa genotype was hybridized with other related species. A mapping study identified four quantitative trait loci (QTL) associated with winter behaviour in C. sativa. The winter trait mapped to one locus on chromosome 8 (subgenome 1) in C. sativa ssp. pilosa, to two loci in C. alyssum on chromosomes 13 (subgenome 2) and 20 (subgenome 3), and to one locus on chromosome 13 (subgenome 2) in C. microcarpa. All of the QTL represented homologous segments in the C. sativa reference genome and were proximate to a major flowering gene, Flowering Locus C (FLC). Differential gene expression analysis between the parents at the early seedling stage suggested FLC could be a candidate gene responsible for vernalization responses in winter C. sativa populations. In addition, interspecific hybridization identified a homoeologous recombination (HeR) event between subgenome 1 of C. sativa with subgenome 3 of C. microcarpa (n = 19), and a number of anueploids were identified, as expected. The nature of HeR could create challenges for the success of conventional breeding activities in Camelina species, as recombination could occur between any subgenomes due to the undifferentiated nature of the subgenomes. However, variation in morphology, such as leaf characteristics, days to flowering and fertility suggested a huge potential for increasing genetic variability in C. sativa by use of distantly-related Camelina species. Subgenome dominance has evolutionary significance and can play an important role in improving phenotypic diversity. Subgenome dominance analysis suggested the third subgenome was dominant in the case of Camelina species with n = 20, whereas the second subgenome was dominant for Camelina species with n = 19 and was correlated with the age of divergence of the subgenomes from C. neglecta. Overall, the results provided insight into the subgenome structure and a first step towards identifying the mechanism of a stepwise whole genome duplication process in polyploid C. sativa, which would be instrumental in developing genetic tools for Camelina breeding activities.
dc.subjectCamelina sativa, interspecific hybridization, genetic diversity, evolution, subgenome dominance
dc.titleUtilization of variation to understand Camelina sativa genome evolution
local.embargo.terms2022-01-28 Sciences Sciences of Saskatchewan of Philosophy (Ph.D.)


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