Doctor of Philosophy (PhD)


Biological Sciences

Document Type



Boron toxicity is a worldwide agricultural problem that limits crop productivity and quality. However, our understanding on the genetic responses and adaption mechanisms to boron toxicity in plants is very limited. To address this gap in our knowledge, I compared boron stress-sensitive model, Arabidopsis thaliana and its stress-adapted relative Schrenkiella parvula to study how plants respond and adapt to excess boron at physiological, genomic, transcriptomic, and metabolic levels.

The overall project goal involved integration of multi-omics datasets to develop genome to phenome interpretations. To achieve this, I developed a python package, GOMCL, to facilitate the extraction of biologically meaningful information from transcriptomic data, and established an Agrobacterium-floral dip based transformation method for S. parvula to enable further functional characterization of candidate genes in this species.

Using a multi-omics framework with the tools developed, I demonstrated that excess boron induced pectin biosynthesis that facilitated boron sequestration in cell walls during excess boron stress, while the entire transcriptome shifted to a higher mean expression level. Compared to Arabidopsis, the magnitude of responses in S. parvula was much less. This was partly attributed to the greater capacity of S. parvula to maintain lower boron levels relative to A. thaliana. The transcriptomic analyses led to the identification of an understudied putative boron exporter BOR5, as the main candidate boron excluder during excess boron stress. We were able to characterize its boron exclusion function in yeast and show that SpBOR5 functioned more efficiently than any of the other closely related boron transporters in Arabidopsis and S. parvula. Besides, I showed that the S. parvula transcriptome is pre-adapted to boron toxicity, exhibiting substantial overlap with the boron-stressed transcriptome of A. thaliana.

In summary, I developed both computational tools and a transformation method to facilitate comparative genomic studies that use the extremophyte, S. parvula to study its stress adaptive mechanisms. With these tools, I investigated how excess boron can lead to cellular toxicity and how tolerant plants adapted to boron toxicity. The findings made during this investigation expands our current understanding of genetic responses underlying boron stress tolerance, while the methods developed during this project could be broadly applied in comparative genomics analyses.

Committee Chair

Dassanayake, Maheshi