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

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 α-and β-acids contents, 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, WA USA in 2023 and 2024, single nucleotide polymorphism data derived from genotyping-by-sequencing with 20,861 markers, and phenotype data generated from near-infrared (NIR) spectroscopy 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 near-infrared spectroscopy data (R = 0.54-0.94), high broad-sense heritability estimates (H² = 0.32-0.71), and logical associated candidate genes 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.