Page 70 - Plant Canada 2024 Proceeding

PLANT CANADA 2024

Wednesday, July 10

Dr. Mark Allan Alexander Minow
University of Georgia

“The heritability of chromatin accessibility in
Zea mays”

Abstract: Transcription factors bind specific DNA
sequences, known as cis-regulatory elements, to
regulate the transcription of nearby genes. In
eukaryotic genomes, the accessibility of these cis-
regulatory elements is controlled by the chromatin
environment, with accessible, nucleosome-free
DNA needed for most transcription factor binding.
Cis-regulatory element accessibility changes
precede transcriptional ones, and differentially tune
gene expression in diverse cell-types. Single-cell Assay for Transposase Accessible
Chromatin sequencing (scATAC-seq) measures chromatin accessibility at a cell-type
resolved level. Here, we applied scATAC-seq to 172 diverse maize inbred genotypes to
discover how genetic diversity influences chromatin accessibility, and thus
transcriptional regulation, in seedling cell types. Using this panel, we uncovered varying
conservation of chromatin accessibility, while finding genetic variants that associate with
altered local chromatin accessibility, revealing cell type level chromatin accessibility
quantitative trait loci (caQTL). These caQTL encompass known and novel variants, and
evidence suggests these variants modify transcription factor binding which then impacts
local chromatin states. Bulk ATAC-seq was also conducted on maize F1-parent pairs to
learn more about the heritability of chromatin accessibility. Calculating narrow sense
heritability for chromatin accessibility revealed good concordance between high
heritability at a region and caQTL detection in our panel. Heritability was high for most
accessible chromatin regions but was higher in promoters or intergenic regions than
accessible genic regions. Finally, we exploited our parent-offspring pairs to find
accessible chromatin regions that had the hallmarks of trans regulation – these
candidate regions can be combined with our diversity panel to empower the detection of
trans caQTL, potentially discovering new regulatory relationships within the maize
genome.

Bio: Dr. Mark Allan Alexander Minow received his PhD in plant molecular biology and genetics
in the department of Molecular and Cellular Biology at the University of Guelph in 2020 for his
study of plant small RNA biology and the regulation of the maize floral transition. He is currently
a Postdoctoral Research Associate at the University of Georgia under the supervision of Dr.
Robert Schmitz, exploring maize biology through molecular genetics and single-cell genomics.
An avid plant lover, when not in the lab, Dr. Minow is usually found landscaping his 2.5-acre
property, nestled in the abandoned cotton terraces of rural North Georgia.

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