A century of breeding has preserved genetic variation, accumulated favorable alleles, and shaped the Rht gene portfolio in North American spring wheat

Authors: GILL, HARSIMARDEEP - University Of Minnesota; Blecha, Sarah; CONLEY, EMILY - University Of Minnesota; BRAULT, CHARLOTTE - University Of Minnesota; Fiedler, Jason; COOK, JASON - Montana State University; GLOVER, KARL - South Dakota State University; GREEN, ANDREW - South Dakota State University; Read, Andrew; ANDERSON, JAMES - University Of Minnesota

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 9/24/2025
Publication Date: 9/24/2025
Citation: Gill, H., Blecha, S.M., Conley, E., Brault, C., Fiedler, J.D., Cook, J., Glover, K., Green, A., Read, A.C., Anderson, J.A. 2025. A century of breeding has preserved genetic variation, accumulated favorable alleles, and shaped the Rht gene portfolio in North American spring wheat. bioRxiv. https://doi.org/10.1101/2025.09.22.677111.
DOI: https://doi.org/10.1101/2025.09.22.677111

Interpretive Summary: Wheat is an important US crop that is relied on for domestic food security. Hard red spring wheat, an important class of wheat, is primarily grown in the upper Midwest and Northern Great Plains. Over the past 100 years, most wheat lines being developed by public and private breeding programs were evaluated in USDA coordinated uniform regional nurseries prior to release. In recent years, material in the uniform nursery undergoes genetic testing to provide breeders valuable information about their material. However, little is known about the relatedness and gene content in cultivars included in the nursery prior to the availability of this technology, resulting in gaps in our understanding of how breeding has affected genetic variation over the history of these important breeding programs. Seed was obtained for important breeding material tested from the 1920s to the present, DNA extracted, and gene analysis was done to identify genetic variants. Early breeding efforts were found to have increased the gene pools. The semi-dwarfing genes, which resulted in breakthroughs in global wheat production, were found to be present in the breeding populations earlier than expected. These formerly rare variants are being used more by modern wheat breeders. Additional agronomically important traits such as flowering time were tracked throughout the historical collection. These data will be valuable for wheat breeders as they work to integrate the best genetics into their future wheat cultivars to maximize grain yields for US farmers growing wheat under variable environmental conditions.

Technical Abstract: Hard red spring wheat (HRSW) is an important class of wheat in North America with a rich breeding history. For continuous crop improvement, it is essential to understand how plant breeding has shaped genetic variation and influenced temporal shifts in adaptive genes, exemplified by the introduction of reduced height (Rht) genes in wheat during the Green Revolution. Despite the considerable agronomic impact of semidwarf wheat, no study has examined the regional deployment and effects of various Rht genes in the HRSW region. Here, we genotyped 1,140 HRSW lines representing a century of breeding material using a low-density SNP array and targeted KASP assays. Our analysis revealed that early breeding efforts broadened an initially narrow gene pool, that levels of genetic variation have been maintained in recent decades, and that favorable alleles, including Rht genes, have accumulated in breeding programs. We found that Rht-D1b was the prominent semi-dwarf allele present from its introduction in the 1960s until the scab epidemics of the 1990s when most breeding programs shifted to Rht-B1b. Alternative dwarf alleles Rht24 and Rht25 were found in HRSW material at low frequencies prior to the introduction of the Rht1 genes and these genes have increased in frequency over recent decades. In addition to Rht genes, we found evidence of positive selection for photoperiod sensitivity, particularly in high-latitude regions. This study provides a valuable genomic resource, and findings enhance our understanding of past breeding efforts while offering insights to guide future plant breeding strategies.