Poster

Muhammad Massub Tehseen ¹, Charlotte Brault ², Emily J. Conley ², Andrew C. Read ^2,3, Harsimardeep S. Gill ², Andrew J. Green ¹, Karl D. Glover ⁴, Jason P. Cook ⁵, Ruth Dill-Macky ⁶, James A. Anderson ², Xuehui Li ¹, and Jason D. Fiedler ⁷
1. North Dakota State University, Department of Plant Sciences, Fargo, ND
2. University of Minnesota, Department of Agronomy and Plant Genetics, St. Paul, MN
3. USDA-ARS, Plant Science Research Unit, St. Paul, MN
4. South Dakota State University, Agronomy, Horticulture, and Plant Science Department, Brookings, SD
5. Montana State University, Plant Sciences and Plant Pathology Department, Bozeman, MT
6. University of Minnesota, Department of Plant Pathology, St. Paul, MN
7. USDA-ARS, Cereal Crops Improvement Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND
Corresponding Author: Jason D. Fiedler, jason.fiedler@usda.gov

Tehseen, Muhammad Massub

muhammad.tehseen@ndsu.edu

Fusarium head blight (FHB) remains the most economically damaging disease of hard red spring wheat in the Northern Great Plains, yet how three decades of resistance breeding have reshaped the underlying genome has not been characterized at the haplotype level. We assembled 33 years (1992–2024) of multi-environment FHB data from the USDA-ARS Uniform Regional Nursery (URN) and Uniform Regional Scab Nursery (URSN), comprising 943 lines, 9,649 observations, and 279 location-year environments. Per-line adjusted means from a mixed model were obtained for disease index (DIS), visually scabby kernels (VSK), and deoxynivalenol (DON). Genotypes of 699 lines from the USDA-SoyWheOatBar-3K array (2,318 SNPs) were partitioned into 1,631 linkage disequilibrium-based haplotype blocks, genome-wide RR-BLUP marker effects were summed within blocks to produce local genomic estimated breeding values (local GEBVs), and resistance haplotype frequencies were tracked across four breeding eras. Thirty-five blocks were validated for association with FHB traits (FDR < 0.05). Of these, 12 showed significant positive selection, six showed purifying selection, and 17 were neutral; none reached fixation. The strongest responses occurred at b00266 on chromosome 2A (53.7% to 88.7%), b00559 on 3B (7.4% to 47.5%), which overlaps Fhb1/TaHRC, and b00654 on 3D (62.1% to 92.6%). Eleven of the 12 positive and all six purifying signals remained significant when entry year was modeled as a continuous predictor. Mean absolute frequency change at validated blocks (0.134) was more than twice that at 200 non-associated control blocks (0.061; permutation p < 0.0001), indicating selection rather than drift. Per-era validation identified three associations stable across breeding eras: b00559 and b01209 (6A) for DIS, and b00562 (3B) for DON. Single-marker GWAS detected ten Bonferroni-significant associations for DIS and VSK and none for DON, yet 34 of the 35 validated blocks contained no SNP reaching even the suggestive threshold. The top 20 blocks per trait jointly explained 12.0% (DIS), 18.5% (VSK), and 14.2% (DON) of phenotypic variance, of which GWAS missed 96–100%. Expected heterozygosity at the validated blocks remained stable (0.438–0.454 across eras) while mean resistance allele frequency rose from 0.479 to 0.549, showing that breeders enriched resistance alleles without eroding local diversity. These results indicate that FHB resistance gains in Northern Plains wheat rest on a polygenic architecture largely invisible to single-marker analysis, and that substantial standing variation remains for continued selection, particularly at loci where resistance alleles are still at low frequency.

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