A molecular characterization of Eastern Canada winter wheats for agronomic, quality, and disease resistance traits using KASP and STS markers

Abstract

Winter wheat ( Triticum aestivum L.) in Eastern Canada is under increasing pressure from stresses associated with climate change. Breeding programs must increase efficiency to keep pace with these changes, and marker‐assisted selection (MAS) remains an efficient tool to retain or introgress favorable alleles of key traits and improve their genetic gains. The present study characterized the Eastern Canadian Winter Wheat Genomic Selection (EWGS) panel of 352 varieties and breeding lines from four public winter wheat breeding programs in Ontario and Québec. The EWGS panel was genotyped using 21 Kompetitive Allele‐Specific polymerase chain reaction markers and one sequence‐tagged site marker linked to key agronomic, disease resistance, and end‐use quality traits. Results revealed a genetic foundation for environmental adaptation, with high allele frequencies for frost tolerance ( Fr‐A2 ), vernalization ( Vrn‐A1 ), and grain hardness (soft or relatively soft Pinb‐B2a , Pina‐D1a ). Allele frequencies for traits such as plant height ( Rht‐B1 , Rht‐D1 , and Rht‐8 ) and gluten strength ( Glu‐A1 and Glu‐D1 ) varied significantly among breeding programs. Favorable disease resistance alleles for Fhb1 , Fhb2 , Sr2 , and Lr34 were rare, indicating distinct selection histories and opportunities for germplasm exchange. While Eastern Canadian public wheat breeders have made considerable progress in integrating superior traits into their respective programs, much could still be gained through germplasm sharing, and MAS remains a viable tool to track the integration of new alleles into existing genetic pools.