Ongoing research

We are a genomics enabled lab that explores the optimization of defense using a hypothesis driven systems biology approach.

Projects in the lab are based on three central tenets:

A focus on the interaction between agriculturally important plants, their wild relatives and their biotic environments.
Investigating how dynamic factors impact these interactions on a fundamental and organismal level, integrating data from transcriptional, biochemical, and epigenetic experiments.
Discoveries in the lab will be utilized to identify cases where mis‑optimization due to breeding and domestication can be addressed and improved for the benefit of agricultural productivity and sustainability.

<p class="font_8">In recent years, it has become evident that plant defenses are controlled and optimized by the circadian clock. However, through domestication, humans have inadvertently altered the circadian rhythms of crop plants in an effort to make them more successful agriculturally. In this NIH funded research, we use tomato and other wild Solanum species as a model to assess the effects of diversity in circadian clocks on innate plant defenses.</p>

Circadian defense and domestication

In recent years, it has become evident that plant defenses are controlled and optimized by the circadian clock. However, through domestication, humans have inadvertently altered the circadian rhythms of crop plants in an effort to make them more successful agriculturally. In this NIH funded research, we use tomato and other wild Solanum species as a model to assess the effects of diversity in circadian clocks on innate plant defenses.

<p class="font_8">As part of an evolutionary strategy to optimize energy expenditure for defense, factors like plant age can impact host-pathogen interactions. Although "age-related resistance" (ARR) is observed in numerous plant pathosystems, the molecular mechanisms governing this developmental change in host resistance remain unclear. We investigate this phenomenon in tomato and its wild relatives.</p>

Ontogenic resistance in tomato

As part of an evolutionary strategy to optimize energy expenditure for defense, factors like plant age can impact host-pathogen interactions. Although "age-related resistance" (ARR) is observed in numerous plant pathosystems, the molecular mechanisms governing this developmental change in host resistance remain unclear. We investigate this phenomenon in tomato and its wild relatives.

<p class="font_8">Crop wild relatives, such as native wild apples, present a promising source of novel disease resistance genes. However, their use in breeding is hindered by long generation times and limited genomic resources. This research aims to identify and clone resistance genes from wild apples, investigate their evolutionary dynamics, and explore their role in providing resistance to key pathogens.</p>

Malus genomics & disease resistance

Crop wild relatives, such as native wild apples, present a promising source of novel disease resistance genes. However, their use in breeding is hindered by long generation times and limited genomic resources. This research aims to identify and clone resistance genes from wild apples, investigate their evolutionary dynamics, and explore their role in providing resistance to key pathogens.

<p class="font_8">Most model organisms are homozygous and inbred; however, many important out‑crossing crop and plant species are highly heterozygous. High heterozygosity can result in allele specific gene expression (ASE), in which one allele of a gene is preferentially expressed over the other. We examine how heterozygous structural variations affect ASE, and how this, in turn, impacts disease resistance.</p>

The impact of heterozygosity & structural variation on defense

Most model organisms are homozygous and inbred; however, many important out‑crossing crop and plant species are highly heterozygous. High heterozygosity can result in allele specific gene expression (ASE), in which one allele of a gene is preferentially expressed over the other. We examine how heterozygous structural variations affect ASE, and how this, in turn, impacts disease resistance.

<p class="font_8">During my PhD, I developed a successful R software package (QTLseqr; <a href="https://acsess.onlinelibrary.wiley.com/doi/full/10.3835/plantgenome2018.01.0006"><u>The Plant Genome</u></a>) to perform Bulk Segregant Analyses using high‑throughput sequencing. We will continue to develop this and other tools so improve the resolution of BSA using sequencing while ensuring tools are easy to use and accessible to researchers with different backgrounds.</p>

Computational approaches to bulk segregant analysis

During my PhD, I developed a successful R software package (QTLseqr; The Plant Genome) to perform Bulk Segregant Analyses using high‑throughput sequencing. We will continue to develop this and other tools so improve the resolution of BSA using sequencing while ensuring tools are easy to use and accessible to researchers with different backgrounds.

More soon...

Lots of other projects in the works!