Evolutionary history and rhizosphere microbial community composition in domesticated hops (Humulus lupulus L.)

Authors: MCELWEE-ADAME, ALEXANDRA - San Diego State University; ESPLIN -STOUT, RAYA - San Diego State University; MUGOYA, TREVOR - San Diego State University; VOURLITIS, GEORGE - California State University; Henning, John; AFRAM, KAYSER - San Diego State University; AHMADI JESHVAGHANE, MARYAM - San Diego State University; BINGHAM, NATHAN - San Diego State University; DOCKTER, ALEXIS - San Diego State University; ESLAVA, JACOB - San Diego State University; GIOVANNI, GIL - San Diego State University; MERGENS, JOSHUA - San Diego State University; MOHAMED, AMRAN - San Diego State University; SETHURAMAN, ARUN - San Diego State University; NGUYEN, TRAM - San Diego State University; NOOR, FATUM - San Diego State University; SALCEDO, NATHAN - San Diego State University

Submitted to: Molecular Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/31/2025
Publication Date: 4/24/2025
Citation: Mcelwee-Adame, A., Esplin -Stout, R., Mugoya, T., Vourlitis, G., Henning, J.A., Afram, K., Ahmadi Jeshvaghane, M., Bingham, N., Dockter, A., Eslava, J., Giovanni, G., Mergens, J., Mohamed, A., Sethuraman, A., Nguyen, T., Noor, F., Salcedo, N. 2025. Evolutionary history and rhizosphere microbial community composition in domesticated hops (Humulus lupulus L.). Molecular Ecology. https://doi.org/10.1111/mec.17769.
DOI: https://doi.org/10.1111/mec.17769

Interpretive Summary: Humulus lupulus L., commonly known as hops, is a perennial crop grown worldwide and is well known for its pharmacological, commercial, and most importantly brewing applications. For hundreds of years, hops have undergone intense artificial selection with over 250 cultivated varieties being developed worldwide. However, little is known about their evolutionary history and the variability in their associated rhizospheric microbial communities. Using plant measurements, genetic data, and soil characteristic data, this study aims to explore the global population structure and domestication history of 98 hops cultivars. Contrary to previous studies, our study revealed that worldwide hop cultivars cluster into four primary subpopulations; Central European, English, and American ancestry as previously reported, and one new group, the Nobles, revealing further substructure amongst Central European cultivars. Modeling the evolutionary history of domesticated hops reveals an early divergence of the common ancestors of modern US cultivars around 2800 ybp, and more recent divergences with gene flow across English, Central European, and Noble cultivars, reconciled with key events in human history and migrations.

Technical Abstract: Humulus lupulus L., commonly known as hops, is a perennial crop grown worldwide and is well known for its pharmacological, commercial, and most importantly brewing applications. For hundreds of years, hops have undergone intense artificial selection with over 250 cultivated varieties being developed worldwide, all displaying differences in key characteristics such as bitter acid concentrations, flavor and aroma profiles, changes in photoperiod, growth, and pathogen/pest resistances. However, little is known about their evolutionary history and the variability in their associated rhizospheric microbial communities. Coupling phenotypic, genomic, and soil metagenomic data, our study aims to explore the global population structure and domestication history of 98 hops cultivars. Additionally, we assessed differences in growth rates, rates of viral infection, usage of dissolvable nitrogen, and soil microbial communities compositions between US and non-US based cultivars. Contrary to previous studies, our study revealed that worldwide hop cultivars cluster into four primary subpopulations; Central European, English, and American ancestry as previously reported, and one new group, the Nobles, revealing further substructure amongst Central European cultivars. Modeling the evolutionary history of domesticated hops reveals an early divergence of the common ancestors of modern US cultivars around 2800 ybp, and more recent divergences with gene flow across English, Central European, and Noble cultivars, reconciled with key events in human history and migrations.