Abstract

Chenopodium is a diverse genus of nutritionally and ecologically important species in the Amaranthaceae family. This thesis investigates two outstanding questions in the genus: how Chenopodium quinoa responds transcriptionally to nutrient deficiency and how Australian Chenopodium species are related through their subgenomic ancestry and evolutionary history. First, we characterized transcriptomic responses of C. quinoa to deficiencies of twelve essential macro- and micronutrients across leaf and root tissues using RNA sequencing. Leaves showed the strongest responses under nitrogen, potassium, magnesium, and zinc deficiency, while roots responded more evenly across conditions. Recurring responses included suppression of photosynthesis, remodeling of translational machinery, reactive oxygen species scavenging, stress signaling, ion transport, and nutrient recycling, alongside nutrient-specific signatures such as endoplasmic reticulum stress under manganese deficiency and riboflavin biosynthesis as a putative iron-acquisition response in roots. Boron, calcium, and molybdenum produced limited signatures at this timepoint, whereas genes shared across all deficiencies in roots suggested a conserved stress response involving ubiquitin-mediated protein degradation and mRNA turnover. Second, we investigated genome evolution within Australian Chenopodium by generating a chromosome-level assembly of the halophytic tetraploid Chenopodium trigonon using PacBio HiFi and Hi-C sequencing. The 830.9 Mb assembly achieved a scaffold N50 of 45.9 Mb and 99.2% BUSCO completeness. Synteny and orthology analyses revealed C. trigonon as an allotetraploid composed of an A subgenome and a previously undescribed lineage designated the I subgenome, with LTR retrotransposon accumulation identified as a major driver of genome size variation. Read-mapping analyses of the octoploid C. baccatum indicated predominant A and I ancestry, suggesting an ancestral A-I combination underlies Australian Chenopodium diversification. Together, these studies provide new insights into nutrient stress adaptation and genome evolution in Chenopodium and establish genomic resources that will support future research on nutrient use efficiency, environmental adaptation, and polyploid genome evolution across this agronomically important genus.

Degree

MS

College and Department

Life Sciences; Plant and Wildlife Sciences

Rights

https://lib.byu.edu/about/copyright/

Date Submitted

2026-07-17

Document Type

Thesis

Keywords

Chenopodium quinoa, LTR retrotransposons, nutrient deficiency, polyploid evolution, RNA-seq, subgenome divergence, transcriptomics

Language

english

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