Location: Cereal Crops Improvement Research
Project Number: 3060-21000-046-014-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Apr 15, 2022
End Date: Apr 14, 2027
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
3. Generate genome assembly and genome annotations of two phenotypically contrasting lines of Aegilops sp.
4. Generate genome assembly and genome annotations of two lines of hexaploid wheat and 2 lines of oats
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. The approach described above will be used to generate genome assembly and annotation for two phenotypically contrasting lines of Aegilops sp.The approach described above will be used to generate genome assembly and annotation for two lines of hexaploid wheat and two line of oat.
