Association mapping for hop cone chemistry and morphology identifies natural beneficial allele stacks

Authors: CLARE, SHAUN - Washington State University; SCHMUKER, PETER - Washington State University; Altendorf, Kayla

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/10/2026
Publication Date: 4/28/2026
Citation: Clare, S.J., Schmuker, P., Altendorf, K.R. 2026. Association mapping for hop cone chemistry and morphology identifies natural beneficial allele stacks. The Plant Genome. https://doi.org/10.1002/tpg2.70238.
DOI: https://doi.org/10.1002/tpg2.70238

Interpretive Summary: Hop is a key ingredient in beer as they provide bittering, aromatics, and flavor. The regions of the hop genome that control these attributes such as a-acids, ß-acids, total oil content, as well as the shape and size of the cones from which these compounds are derived, have not been thoroughly investigated, thereby limiting the use of highly efficient genomics-assisted breeding methods. This study identifies regions within the hop genome that are associated with increases in alpha acids, beta acids, total oil content, and improved cone shape and size for increased harvestability. These findings demonstrate the use of higher-throughput methods for measuring cone chemistry using near infrared resonance (NIR) and cone morphology using image analysis. The results provide insight into the genetic control of important traits and demonstrate the potential for the use of genomics assisted breeding in hop to increase the efficiency of cultivar development.

Technical Abstract: Efforts are underway to increase the efficiency and precision of selection hop (Humulus lupulus L.) breeding using genomics. Little is known, however, about the genetic control of important traits like a-acid and ß-acid content, oil content, and cone morphological characteristics, all of which play an important role in determining the utility and harvestability of a hop and are targets of selection. In this study, we utilized association mapping with a collection of 529 female hop plants evaluated in Prosser, Washington, United States in 2023 and 2024, SNP data derived from genotyping-by-sequencing with 20,861 markers, and phenotype data generated from near infrared resonance (NIR) and image analyses of hop cones. A total of 49 significant marker trait associations were detected across five traits with 43 unique loci. High correlation estimates between wet lab and NIR data (R = 0.54-0.94), high broad sense heritability estimates (H2 = 0.32-0.71), and logical associated candidate genes nearby significant markers illustrate the validity of the methods used in detecting meaningful associations. Furthermore, existing germplasm in our study containing increasing stacks of favorable alleles showed improvement in all traits, demonstrating the potential for utilizing the markers identified herein in a genomic prediction pipeline to improve hop germplasm for key end-use traits.