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QTL examination of a bi-parental mapping population segregating for “short-stature” in hop (Humulus lupulus L.)

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Abstract

Increased labor costs and reduced labor pools for hop production necessitate the development of strategies that improve efficiency and automation of hop production. One solution for reducing labor inputs is the use of “short-trellis” hop varieties. Unfortunately, little information exists on the genetic control of this trait in hop, and there are no known molecular markers available for selection. This preliminary study was enacted to identify QTLs associated with expression of short-stature growth phenotype using SNPs identified within genome-assembled scaffolds. A bi-parental mapping population of 87 offspring was obtained from the cross, “Pioneer × 25/95/15”. Genotyping-by-sequencing was performed on parents and offspring. SNPs were identified using TASSEL v3.0 with either ‘Teamaker’ reference genome or ‘Shinsuwase’ genome. The genetic map derived from ‘Teamaker’ SNPs was far superior and was used for all further analysis. QTL analysis identified eight QTLs linked to short stature with five showing strong statistical association based upon three different statistical analyses. All eight QTLs were found on linkage group one. Evaluation of scaffolds containing SNP markers located at or surrounding QTL regions (±1 cM) identified 67 putative genes—several of which are known structural genes. A genome-wide scan of SNP markers identified an additional marker found on a scaffold containing a putative gene (Aspartyl protease family protein) known to induce dwarf characteristics in other species. Further validation of significantly associated markers on different populations is necessary prior to implementation in marker-assisted selection.

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Acknowledgements

We wish to thank Ms. Jamie Coggins, former Oregon State University student and now employee of Roy Farms Inc, Moxie, WA, for extracting DNA and preparing it for submission for sequencing as well as cataloging all samples associated with this study.

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Authors and Affiliations

  1. USDA-ARS-FSCRU, 3450 SW Campus Way, Corvallis, OR, 97331, USA

    J. Henning

  2. School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, 97331, USA

    S. Hill & D. Hendrix

  3. Wye Hops Ltd., Upper Harbledown, Canterbury, CT2 9AR, UK

    P. Darby

  4. Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR, 97331, USA

    D. Hendrix

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  1. J. Henning
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  2. S. Hill
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  3. P. Darby
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  4. D. Hendrix
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Correspondence to J. Henning.

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Henning, J., Hill, S., Darby, P. et al. QTL examination of a bi-parental mapping population segregating for “short-stature” in hop (Humulus lupulus L.). Euphytica 213, 77 (2017). https://doi.org/10.1007/s10681-017-1848-x

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  • DOI: https://doi.org/10.1007/s10681-017-1848-x

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