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ARS Home » Pacific West Area » Corvallis, Oregon » Forage Seed and Cereal Research Unit » Research » Publications at this Location » Publication #383097
Research Project: Breeding, Genomics, and Integrated Pest Management to Enhance Sustainability of U.S. Hop Production and Competitiveness in Global Markets

Location: Forage Seed and Cereal Research Unit

Title: The long-read genome assembly of hop (Humulus lupulus) uncovers the pseudoautosomal region and other genomic features

Author
item PADGITT-COBB, L - Oregon State University
item KOTHEN-HILL, S - Oregon State University
item Henning, John
item HENDRIX, DAVID - Oregon State University

Submitted to: Acta Horticulturae
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/30/2021
Publication Date: 12/3/2021
Citation: Padgitt-Cobb, L.K., Kothen-Hill, S.T., Henning, J.A., Hendrix, D.A. 2021. The long-read genome assembly of hop (Humulus lupulus) uncovers the pseudoautosomal region and other genomic features. Acta Horticulturae. 1328. https://doi.org/10.17660/ActaHortic.2021.1328.1.
DOI: https://doi.org/10.17660/ActaHortic.2021.1328.1

Interpretive Summary: Hop (Humulus lupulus L. var Lupulus) is a dioecious plant, having both male and female plants, with an extensive history of cultivation and use in brewing, as a textile, and for its therapeutic properties. The genome of hop is diploid with two sex chromosomes (2n=18+XX/XY). We recently reported the first true draft genome which also reported all hop genes. Dioecious plants can contain pseudo-autosomal regions (PARs) within their X and Y chromosomes, allowing proper pairing, recombination and segregation of chromosomes in male plants during pollen formation. Previous attempts at identifying the hop PAR were challenged by fragmented incomplete genome assemblies. We report new insights about the genomic sequence and gene content of the hop PAR using new draft hop genome and a dwarf-stature linkage map. This report provides a more-comprehensive coverage of the genes and repeat sequences located in the PAR that may be involved in sex determination.

Technical Abstract: Hop (Humulus lupulus L. var Lupulus) is a dioecious plant with an extensive history of cultivation and use in brewing, as a textile, and for its therapeutic properties. The genome of hop is diploid with two sex chromosomes (2n=18+XX/XY). We recently reported our PacBio long-read assembly, which enabled assembly through repetitive regions and an improved estimate of gene and repeat content. Dioecious plants can contain pseudoautosomal regions (PARs) within their X and Y chromosomes, allowing proper segregation in male plants during meiosis. Previous attempts at identifying the hop PAR were challenged by fragmented short-read assemblies. Here we report new insights about the genomic sequence and gene content of the hop PAR using our long-read assembly and a dwarf-stature linkage map. We use the long-read assembly of the female cultivar Cascade to uncover a more-comprehensive genomic context of desirable alleles, allowing for an improved understanding of the genes and repeat sequences located in the PAR that may be involved in sex determination.