Genome-wide association mapping of resistance to Fusarium head blight and deoxynivalenol accumulation and haplotype analysis in a diverse barley collection

Authors: PAGE, RAE - Syngenta; Sallam, Ahmad; SZINYEI, TAMAS - University Of Minnesota; MATNY, OADI - University Of Minnesota; WODAREK, JOSEPH - University Of Minnesota; STEFFENSON, BRIAN - University Of Minnesota

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/22/2025
Publication Date: 8/15/2025
Citation: Page, R., Sallam, A.H., Szinyei, T., Matny, O., Wodarek, J., Steffenson, B.J. 2025. Genome-wide association mapping of resistance to Fusarium head blight and deoxynivalenol accumulation and haplotype analysis in a diverse barley collection. Crop Science. 65(4). Article e70119. https://doi.org/10.1002/csc2.70119.
DOI: https://doi.org/10.1002/csc2.70119

Interpretive Summary: Genome-wide association mapping study (GWAS) is an efficient approach for identifying quantitative trait loci (QTL) because of the richness of allelic diversity in GWAS panels. A panel of 234 spring barley accessions was assembled to include a diverse mix of land races, older cultivars, and modern breeding lines. This panel was evaluated for Fusarium head blight (FHB) in disease nurseries in St. Paul and Crookston, Minnesota. FHB disease severity, deoxynivalenol (DON) accumulation, heading date and plant height were assessed in this barley panel in a total of 11 environments. This panel was genotyped with the 50k Illumina Infinium iSelect genotyping array, and after maker filtering 25,589 markers with Morex v3 positions were used in the genetic analysis. Linkage disequilibrium was assessed between markers, and GWAS was performed on the four traits. A total of 26 marker trait associations (MTAs) were identified for each of FHB severity and DON accumulation. Haplotype analysis was performed to identify the most favorable haplotype alleles and the individuals carrying those alleles for all MTAs. The haplotype pattern at resistance QTL was used to identify accessions that complement each other to improve resistance. Eight two-rowed barley accessions were selected as parents for a multi-parent advanced generation inter-cross (MAGIC) population to combine resistance alleles.

Technical Abstract: Fusarium head blight (FHB) is an economically damaging fungal disease of barley. Improving host resistance to FHB and the resultant accumulation of mycotoxins produced by Fusarium graminearum, such as deoxynivalenol (DON), is one of the most effective approaches for disease control and reduction of economic losses. Unfortunately, breeding for resistance to FHB in barley is difficult, due to the highly quantitative nature of the trait. Numerous mapping studies have identified many quantitative trait loci (QTL) for resistance to FHB and DON accumulation in barley; however, most contribute only small effects or are coincident with undesirable agro-morphological traits (e.g. heading date and plant height). Genome-wide association mapping (GWAS) panels have the potential to capture more QTL than bi-parental mapping populations, as they are comprised of diverse individuals which may possess different genes/alleles for the traits of interest, rather than just those originating from two parents. A diverse panel of 234 barley accessions was assembled, evaluated in multi-year and multi-environment field trials, and genotyped to identify QTL controlling FHB severity and DON concentration in grain. Multiple FHB (24) and DON (20) QTL were detected, some of which were notably independent of QTL influencing heading date, plant height, and row type. These significant QTL were used to generate multi-marker haplotypes in relevant genomic regions. Haplotype-trait associations were then tested, and haplotype diversity of the panel was explored. Haplotype patterns at resistance QTL were used to assess which accessions would best complement one another for use in breeding for resistance.