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Genomics of the hop pseudo-autosomal regions

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Abstract

Hop is one of the few dioecious plants with dimorphic sex chromosomes. Because the entire Cannabaceae family is dioecious, hop and other members of this family are thought to have a relatively older sex chromosomal system than other plant species. Hop cones are only produced in female hops with or without fertilization. This has lead to most genomic research being directed toward female plants. The work we present provides genomic resources surrounding male plants. We have produced a draft genome for the male hop line USDA 21422M using a novel genome assembly method. In addition, we identified a 1.3 Mb set of scaffolds, which appear to be the male specific region based upon specificity with male hop accessions. This set includes a smaller high confidence total length 18 Kb set of scaffolds, which are supported by over 500 individuals, including the USDA world collection of hop varieties and two mapping populations, with genotyping by sequencing. We also have identified a portion of the Teamaker × 21422M linkage map to be associated with the pseudo-autosomal region (PAR). Within the genomic scaffolds, we identified a set of genes that are sex-linked and likely located in the PAR.

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Authors and Affiliations

  1. Electrical Engineering and Computer Science, Oregon State University, Corvallis, USA

    S. T. Hill & D. Hendrix

  2. Biochemistry and Biophysics, Oregon State University, Corvallis, USA

    D. Hendrix

  3. Roy Farms Inc, Moxie, WA, USA

    J. Coggins

  4. Botany and Plant Pathology, Oregon State University, Corvallis, USA

    A. Liston

  5. USDA-ARS-Forage Seed & Cereal Research, Corvallis, OR, 97331, USA

    J. A. Henning

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  1. S. T. Hill
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  2. J. Coggins
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  3. A. Liston
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  4. D. Hendrix
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  5. J. A. Henning
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Correspondence to J. A. Henning.

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D. Hendrix and J. A. Henning are co-investigators.

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Hill, S.T., Coggins, J., Liston, A. et al. Genomics of the hop pseudo-autosomal regions. Euphytica 209, 171–179 (2016). https://doi.org/10.1007/s10681-016-1655-9

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  • DOI: https://doi.org/10.1007/s10681-016-1655-9

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