Lab Introduction

The Brzozowski Lab studies the genetics of plant traits that mediate interactions between plants and other species. We are interested in plant traits, especially metabolites, that affect plant-pest interactions and contribute to human nutrition, and instances when these traits overlap. We integrate a variety of cutting-edge techniques - including genomics, transcriptomics and metabolomics - with field work to understand the genetic basis of these traits. We apply these findings in plant breeding for sustainable and climate-resilient regional agricultural systems.

Leveraging plant immune responses to improve resistance to pests

By investigating natural variation in plant immune responses, we develop new approaches in breeding for resistance to pests and diseases. We seek to characterize genetic variation in how plants respond to defense hormone application and to understand the implications on resistance, yield and quality traits. We currently work in oat (Avena sativa), and this work can be applied across plant species.

Computational methods:

Genome sequencing data processing, genome-wide association study, RNA sequencing data processing, gene expression analysis, gene network analyses, transcriptome-wide association study, eQTL analysis

Software:

We will use open-source software, including FastQC, Trimmomatic, TASSEL, Bowtie2, BWA, SAMtools, Bedtools, VCFtools, Hisat2, STAR, Trinity, R, R-Bioconductor, and other similar software.

Winter rye quality and genomics

Our lab collaborates with ongoing rye (Secale cereale) breeding programs at UK. We contribute genetic and genomic resources to facilitate plant breeding progress. We also conduct research on variation in plant metabolite traits that enhance quality and flavor to improve value in regional markets.

Computational methods:

Genome sequencing data processing, genome-wide association study, QTL mapping, genomic prediction, genomic selectio

Software:

We will use open-source software, including FastQC, Trimmomatic, TASSEL, Bowtie2, BWA, SAMtools, Bedtools, VCFtools, R, R-Bioconductor, and other similar software.

Winter oat breeding

Our lab is establishing a food and forage winter oat (Avena sativa) breeding program for regional production systems. We seek to improve winter hardiness as well as metabolomic quality traits, including of avenanthramides - antioxidants that contribute to health-promoting properties and disease resistance. We are building capacity for genomic selection and on-farm trialing.

Computational methods:

Genome sequencing data processing, genome-wide association study, QTL mapping, genomic prediction, genomic selection

Software:

We will use open-source software, including FastQC, Trimmomatic, TASSEL, Bowtie2, BWA, SAMtools, Bedtools, VCFtools, R, R-Bioconductor, and other similar software.

Specialty legumes

We seek to support community resiliency by developing these nourishing and accessible specialty legume varieties. We prioritize regional adaptation, especially towards organic systems, and flavor.

Computational methods:

Genome sequencing data processing, genome-wide association study, QTL mapping, genomic prediction, genomic selection

Software:

We will use open-source software, including FastQC, Trimmomatic, TASSEL, Bowtie2, BWA, SAMtools, Bedtools, VCFtools, R, R-Bioconductor, and other similar software.

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