Location: Cereal Crops Improvement Research
Project Number: 3060-21000-046-041-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Jul 1, 2025
End Date: Jun 30, 2027
Objective:
Small grains are an important staple crop in the United States, providing nutritious food and feed to humans and livestock, and durable economic value to producers. To maintain competition with other crops and international markets, new varieties need to consistently yield better than before in the face of unknown future threats like new diseases, precipitation changes, and soil degradation. To continually push genetic gain and release elite varieties, small grain breeders’ germplasm enhancement programs are constantly leveraging new technologies to stay ahead. Over the last 30 years, agricultural genomics research has unlocked many discoveries that have been deployed by breeders to generate elite lines for commercial release. The USDA-ARS North Central Small Grains Genotyping Laboratory in Fargo, ND is a vital part of this process, enabling high-impact genomics research and molecular breeding throughout the US. This tight collaboration with the breeding and research stakeholders has resulted in the identification of several challenges where additional research and development is necessary to meet the challenging demands of crop improvement. To that end, the overall objective of this project is to continue our ongoing research efforts in several areas of small grains biology and directly transfer this information to breeders to inform selection decisions. These projects are directly aligned with the USDA mission and stakeholders’ priorities to support producers by increasing the performance of new elite crop varieties and the rate at which they can be released to the public. These new lines will durably yield high-quality grain in more demanding conditions and under the threat of emerging diseases – Increasing revenue for the producers and our decreasing risks on our domestic food supply.
Approach:
Sub-Objective 1a: Preliminary analysis with two biparental mapping populations with the sources PI520392 and PI383416 identified several distinct QTLs conferring resistance to different rust isolates on 2B, 4A, 5B, and 6A. Several rounds of marker-assisted backcrossing has resulted in BC3F2:3 families for screening. To identify dominance characteristics of these QTL and further fine-map the gene region, the BC3F2 parents will be genotyped with a genome-wide 90K Illumina array and the BC3F2:3 families will be screened for disease reaction scores at the Cereal Disease Laboratory in St. Paul. Additionally, the parents will be re-sequenced and high-throughput molecular marker assays will be developed to track these delimited QTL for introgression into adapted durum germplasm.
Sub-Objective 1b: Two cultivated emmer lines (PI94627 and PI94674) exhibit hyper-sensitivity and necrosis upon inoculation of the tan-spot-causing fungal isolate Ptr 1, but not to the major effector gene it excretes - ToxA. RIL populations have been derived from these parents and F5 individuals will screened against Ptr race 1 and genotyped with genome-wide markers to map new non-ToxA susceptibility loci.
Sub-Objective 2: Fusarium head blight (FHB) is a devastating disease of small grains crops and durable genetic resistance has been challenging to acquire. To fully understand how genetics can limit disease, we have generated full-genome sequences and de novo annotations of the major germplasm source. Here, we will fully characterize these genomes and develop a pan-genome of derivative lines to identify linkage blocks that are required for an adapted wheat line to maintain agronomic performance and FHB resistance. Additionally, we will use these new resources to conduct RNA-Seq on 12 lines that contain different combinations of genes to fully understand the mechanisms of resistance upon infection.
Sub-Objective 3: Oat is a small grain crop that provides numerous health benefits and molecular breeding methods of marker-assisted and genomic selection have shown promise to increase genetic gain in breeding programs. In this project, we will generate genomic selection models with ~2000 lines evaluated over six years. These will be integrated with previously identified high-effect marker-trait associations and the predicted performance metrics will be provided to the breeder. These predicted values will then be used to inform selections in the field and triage the lines that will likely never make it to release.
Sub-Objective 4: Genomic selection is a powerful molecular breeding tool to predict performance. To support prediction needs of this tool, we have developed a genotyping platform that targets approximately 3,000 markers on wheat barley and oat. To improve this platform, we will identify poor performing probes with the genotyping data from the 30,000 samples already evaluated. Using machine learning techniques trained on this previous data and the pangenomes of these crops, we will build a prediction algorithm to assist in picking new probes to replace the poor performers and fill in linkage block gaps so it better supports all the breeding programs.