Genetics and trait associations in dual-purpose wheat production under southeastern U.S. production systems

Dual-purpose winter wheat can provide both high-quality and quantity forage and grain, but balancing these outputs requires optimization of management and genetics. A genome-wide association study (GWAS) on 182 soft red winter wheat lines was evaluated in multi-location trials in three Georgia locations over two growing seasons (2023–2025). Sixteen different traits were studied, including Zadok’s growth stage (GS), eight forage quality traits, three forage yields, and four grain yield (GY) and related traits. Significant phenotypic variation was detected for most of the traits studied. Heritability estimates ranged from low-to-moderate (0.00 to 0.33) in the combined dataset and from low-to-high (0.00 to 0.81) within individual locations. Delaying forage harvest to later GS (after 30–31) increased forage yield (~ 670-1,670 kg ha− 1 per GS) but reduced GY (~ 100–300 kg ha⁻¹ per GS). Several genotypes combined above-average forage biomass (maximum 13929.56 kg ha⁻¹) with acceptable GY. Genome-wide association analysis identified 138 marker-trait associations for GY and related traits, and 74 QTLs, including 24 major-effect loci explaining ≥ 10% phenotypic variance. Similarly, 121 QTL (including 27 major-effect) were identified for forage-quality traits, and 59 QTLs (18 major-effect) for forage yield traits. Genotypes from the Georgia and Louisiana breeding programs ranked among the highest for dual-purpose productivity. Thirteen multi-trait QTLs were identified on chromosomes 1B, 2 A, 2B, 4 A, 6B, and 7 A, with these regions associated with multiple traits, including GS, dry matter, sugar content, crude protein, plant height, regrowth height, fresh/dry forage weight, and GY. The abundance of stable QTL for GS and plant height highlights developmental timing and canopy architecture as primary determinants of dual-purpose adaptation in this germplasm. These results identified superior lines for a dual-purpose production system in wheat. Upon further validation these results provide candidate loci for studied traits for marker-assisted and genomic selection aimed at improving dual-purpose wheat performance in the U.S. southeastern region. Multi-environment GWAS identified QTLs controlling dual-purpose wheat performance. Multi-trait QTLs revealed shared genetic control of dual-purpose performance. Later growth stage (GS) increased forage biomass but penalized grain yield (GY). Stable major-effect QTLs provide targets for marker-assisted wheat improvement. Superior soft red winter wheat lines balanced forage production and GY.