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, 2028
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 1: To fine map rust resistance QTL from durum wheat lines PI 520392, PI 383416, and PI 192711, backcross populations have been developed with the help of markers that target the resistance gene region. Previously, screening of BC3F2:3 families showed dominant inheritance of the resistance gene(s). With high-density genotyping and sequencing of the parents, we will expand the BC3F3 lines with heterozygous calls in the QTL region to further identify recombinants. Coupled with a 2nd round of progeny screening with synonymous local rust isolates and at the Cereal Disease Laboratory in St. Paul, we will further decrease the QTL interval – setting up introgression work into adapted durum germplasm.
Sub-Objective 2: We have generated full genome sequences of local FHB resistant lines and identified haplotype blocks in ~30 durum and wheat lines that show differential FHB response. Out of these, 16 lines were chosen to undergo transcriptomic investigation over three years in the greenhouse (along with field screening for two years) This data will be combined with haplotype and epigenetic analysis to determine causal haplotype blocks and/or methylation signals that influence resistant gene expression in response to fungal infection. We will validate these important genes with qPCR on tissue samples taken during FHB infection at the end of 2025.
Sub-Objective 3: Oat is an important cereal grain with many health benefits. To assist in the development of elite oat varieties, we have developed a large(~1000 lines) inter-cross population with parents that differ in many traits including agronomic performance, milling traits and end-use quality. This population will be evaluated in the field for the first time in 2026. This information will be coupled with high-density genotyping information and association mapping will be conducted to identify genomic regions that influence these traits. This information will then be converted into predictive molecular assays available for the breeding program to use to assist in selections and accelerate genetic gain.
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.