Development of genetic and genomic resources to evaluate wheat organellar genome variants and their functional implications

Authors: Liberatore, Katie; MILLER, MARISA - University Of Minnesota; Kianian, Shahryar

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/30/2017
Publication Date: 1/13/2018
Citation: Liberatore, K.L., Miller, M.E., Kianian, S. 2018. Development of genetic and genomic resources to evaluate wheat organellar genome variants and their functional implications. Plant and Animal Genome Conference [abstract]. Paper No. 31800.

Interpretive Summary: Fungal pathogens pose a major worldwide threat to grain quality and yield in cereal crops (e.g. wheat, barley, and oats). In addition to the nuclear DNA that most genetics studies and breeding programs focus on, plant cells have two types of sub-compartments (organelles) that contain their own genetic material. One organelle is called the mitochondria, which is often dubbed the "powerhouse of the cell" due to its roles in energy production. The other organelle is called the chloroplast, which is responsible for photosynthesis. Both organelles have also been shown to have roles in integrating environmental signals and stress signals. Therefore, organellar genome diversity represents a potential untapped source for improving disease resistance and additional agronomic traits in these important crop species. However, little is known about the genetic diversity of organellar genomes from diverse Triticum and Aegilops species and how organelles contribute to disease resistance and other agronomic traits. This work aims to understand the range of available diversity in wheat and related wild species and the functional roles of their organelles in disease resistance.

Technical Abstract: Organellar genome diversity represents a potential untapped source for improving agronomic traits. Due to the nature of hybridization and domestication events that led to modern cultivated wheat, organellar (mitochondria and chloroplast) genome diversity was dramatically reduced. However, wheat has the largest known collection of alloplasmic (alien cytoplasm) lines. In these lines, the cytoplasms, and therefore the organelles, of wild relatives have been mismatched with the nuclear genome of domesticated wheat through extensive backcrossing. Disruption of native nuclear-cytoplasmic interactions (NCI) impacts a number of agronomic traits including fertility, biomass, grain yield, and stress response. To understand the functional implications of organellar genome variants and genetic mechanisms underlying NCI, we generated organellar genomic resources. We developed a method to couple organellar DNA enrichment from total gDNA utilizing a pull-down approach and ultra-low input library preparations for long-read sequencing. We sequenced 20 organellar-enriched samples with PacBio, including 13 diverse wild species, T. durum, T. aestivum cv. Chinese Spring, and three alloplasmic lines. We also generated Illumina short-read sequences for >75 cultivars, wild species, and alloplasmics. Comparative analyses are investigating organellar diversity across the Triticum-Aegilops complex and how sequences change in the alloplasmic condition. In parallel, we are generating additional genetic and genomic resources in wheat and the model system Brachypodium distachyon for functional genomics studies. These resources will be useful to the broader community for furthering our understanding of the molecular mechanisms involved in NCI and their affects on plant phenotype as well as for breeding efforts to improve agronomic traits.