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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Cereal Crops Research » Research » Research Project #441937

Research Project: Sequencing and Assembly of Cereal Wild Relatives’ Genomes

Location: Cereal Crops Research

Project Number: 3060-21000-038-049-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Apr 15, 2022
End Date: Apr 14, 2023

Objective:
The objective of this research project is to develop platinum standard chromosome-scale genome assembly of Aegilops umbellulata. The subobjectives include: 1. Generate genome assembly of one line of Ae. umbellulata 2. Generate genome annotations of Ae. umbellulate

Approach:
Cereals yield is significantly impacted by biotic and abiotic stresses. We are currently investigating wheat and wheat wild relatives to identify novel stress tolerance traits. Under this project, genomics and bioinformatics approaches will be utilized to support our efforts in characterizing and understanding stress tolerance responses in a diploid wild relative of wheat, Ae. umbellulata. A reference quality genome of an Ae. umbellulata genotype will be developed to facilitate the identification of genes involved in biotic and abiotic stress tolerance. For sub-objective 1, DNA/RNA sequencing will be conducted by PacBio long-read sequencing technology followed by assembly of reads into contigs using Canu2. In addition, Hi-C sequencing will be performed for scaffolding of contigs into pseudomolecules. Under sub-objective 2, the assembled genome will be annotated to identify coding-regions (genes) and downstream comparative genomics. Plant tissue will be collected from multiple developmental stages (4-6) for mRNA extraction. Extracted mRNA samples will be pooled for full-length cDNA sequencing using PacBio Iso-Seq technology. Iso-Seq data will be analyzed to annotate the assembled genome.