Location: Plant Science Research
Project Number: 6070-22000-019-024-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Sep 17, 2025
End Date: Sep 16, 2027
Objective:
This agreement supports and expands research to utilize crop genetic diversity through DNA sequencing and AI approaches to characterize resistance genes in crops (wheat, beets, and citrus) and their wild relatives, including genes for resistance to citrus HLB and wheat blast. The goal of this work is the increase characterization and efficient utilization of material in the ARS National Plant Germplasm System by developing a database of R gene content of selected accessions. A further goal is developing datasets on shared gene features associated with resistance to major fungal, bacterial, phytoplasma, virus or oomycete pathogens across species.
Approach:
Approach 1: Available data sets from resistance gene sequencing (RenSeq) in various crop species, along with other data from the literature, will be utilized to identify structural signatures of genes associated with resistance to various plant pathogens. Cooperator has experience with these datasets. Kits to capture R-genes based on conserved sequences from other species will be developed and used to preferentially amplify R genes from accessions of wheat, beet and citrus at the population level. We will attempt a novel approach of long read sequencing to capture full length R gene sequences. This will require that cooperators adjust and test existing protocols, particularly for preparing samples for sequencing from large numbers of accessions. Cooperator will use available expertise and liquid handling resources to develop libraries that are sent out for sequence analysis. The resulting DNA sequence data will contribute to a catalog for R-genes available in these accessions.
Approach 2: We will add information on R-genes in wheat through targeted sequencing of accessions of hexaploid T. aestivum, as well as accessions of the A-genome diploid wheat (known as einkorn wheat). Analysis of diversity based on molecular markers, along with phenotypic information about pest resistance, will be used to select accessions. Whole genome sequencing libraries will be prepared by cooperators and sent for sequencing using long read and short read technologies. The DNA sequencing data will be analyzed in conjunction with pan-genomes of hexaploid and diploid wheat developed collaboratively by ARS and cooperator. New variants in genes across the genome will be identified. This database of variants allows allele mining of R-genes available in this diverse set of cultivated and wild wheat accessions. Some accession of einkorn wheat possess high levels of resistance to multiple diseases, including (but not limited to) Fusarium head blight, wheat blast, powdery mildew, leaf rust, stem rust, and stripe rust.