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Molecular Breeding

, 38:83 | Cite as

Characterization of aphid resistance loci in black raspberry (Rubus occidentalis L.)

  • Jill M. Bushakra
  • Michael Dossett
  • Katherine A. Carter
  • Kelly J. Vining
  • Jana C. Lee
  • Douglas W. Bryant
  • Robert VanBuren
  • Jungmin Lee
  • Todd C. Mockler
  • Chad E. Finn
  • Nahla V. Bassil
Article
  • 94 Downloads

Abstract

Viruses vectored by the aphid Amphorophora agathonica cause decline in black raspberry plant health resulting in a shortened life and poor fruit quality of the infected plantings. New aphid resistant cultivars could increase the longevity of plantings providing growers and processors with consistent fruit production. Recent exploration of the native range of black raspberry identified three sources of aphid resistance: Ag4 from Ontario (ON), Canada, Ag5 from Maine (ME), and a third source from Michigan (MI) with no formal designation. The objectives of this study were to assess segregation of these three sources of aphid resistance in populations with single and combined sources and develop markers that can identify each source of resistance. A genetic linkage map constructed for ORUS 4305 placed the ON aphid resistance locus on Rubus linkage group (RLG) 6. Segregation ratios in populations with single and combined sources, and linkage mapping in two populations (ORUS 4304 and ORUS 4812) segregating for the Ag5 and MI sources, respectively, indicated that these three sources of resistance are each conferred by single dominant genes/alleles that are linked on RLG6. Confirmation of marker association in 16 validation populations identified four markers that could be used to predict resistance; however, none could distinguish between the ON and MI sources. These four markers may be useful for screening populations to enrich the field-planted progeny for aphid resistance. Fine mapping of the resistance loci is needed to develop functional markers at each of the resistance loci to enable pyramiding and durable aphid resistance.

Keywords

Aphid resistance Linkage mapping Necrosis virus Virus vector Association analysis 

Notes

Acknowledgements

Thanks to Mary Peterson, Melissa Clark, Jessica Cesar, Victoria Skillman, Amanda Lake, Adam Cave, and Kathleen Knight at USDA-ARS Horticultural Crops Research Unit for care and maintenance of the aphid colonies and help with phenotyping and to summer interns Jamie Willard, Sabrina Teo, and Sarabeth Pearce-Smith for screening scaffold SSR primers.

Funding sources

The authors thank the Washington Red Raspberry Commission, the Oregon Raspberry and Blackberry Commission, the North American Raspberry and Blackberry Growers Association, the USDA-ARS, and the Northwest Center for Small Fruit Research for providing matching funds or other support. This work was funded by the USDA-National Institute of Food and Agriculture (NIFA) Specialty Crop Research Initiative (SCRI) USDA-ARS CRIS 2072-21000-044-00D, 2072-21000-047-00D and 2072-21220-002-00D. Mention of trade names or commercial products in this publication is solely for the purpose of providing scientific information and does not imply recommendation or endorsement by the US Department of Agriculture.

Author contributions

JMB is the project coordinator who performed marker screening, designed primers, scored all markers, constructed the genetic linkage maps, phenotyped aphid resistance on population ORUS 4812 and additional aphid populations, and wrote the manuscript.

MD developed the mapping population, designed primers, performed the initial aphid screening, phenotyped aphid resistance in the mapping populations ORUS 4304 and ORUS 4305, and assisted with segregation interpretation and manuscript writing. MD is the primary drafter of the funded NIFA SCRI grant.

KAC extracted DNA, ran and prepared all markers for analysis, performed preliminary analysis, and provided technical assistance.

KJV performed the association analysis and assisted with bioinformatic analyses.

DWB developed a custom pipeline for bioinformatic analyses and performed GBS SNP calling.

DWB and RVB performed bioinformatic analyses, BLAST analyses, and linkage mapping.

JCL provided the aphid colonies and technical support.

JL is the PD (project director) on NIFA SCRI grant (project main funding) and contributed to manuscript writing.

TCM is the PI on NIFA SCRI grant (project main funding) and contributed computational resources and bioinformatics analysis.

CEF is the project director on NIFA SCRI grant (project main funding), helped assemble and phenotype the germplasm, develop the mapping population, and contributed to manuscript writing. CEF is the primary advisor for the phenotyping portion of the NIFA SCRI grant.

NVB is the project director on NIFA SCRI grant (project main funding), helped develop and test molecular markers, and contributed to manuscript writing. NVB is the primary advisor for the genomics portion of the NIFA SCRI grant.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

11032_2018_839_MOESM1_ESM.docx (2 mb)
ESM 1 (DOCX 2070 kb)
11032_2018_839_MOESM2_ESM.docx (59 kb)
ESM 2 (DOCX 59 kb)

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Copyright information

© This is a U.S. government work and its text is not subject to copyright protection in the United States; however, its text may be subject to foreign copyright protection 2018

Authors and Affiliations

  • Jill M. Bushakra
    • 1
  • Michael Dossett
    • 2
  • Katherine A. Carter
    • 1
  • Kelly J. Vining
    • 3
  • Jana C. Lee
    • 4
  • Douglas W. Bryant
    • 5
  • Robert VanBuren
    • 5
    • 6
  • Jungmin Lee
    • 7
  • Todd C. Mockler
    • 5
  • Chad E. Finn
    • 4
  • Nahla V. Bassil
    • 1
  1. 1.USDA-ARS National Clonal Germplasm RepositoryCorvallisUSA
  2. 2.BC Berry Cultivar Development Inc. (in partnership with Agriculture and Agri-Food Canada)Pacific Agri-Food Research CentreAgassizCanada
  3. 3.Department of Horticulture, Agriculture and Life ScienceOregon State UniversityCorvallisUSA
  4. 4.USDA-ARS Horticultural Crops Research UnitCorvallisUSA
  5. 5.The Donald Danforth Plant Science CenterSt. LouisUSA
  6. 6.Department of HorticultureMichigan State UniversityEast LansingUSA
  7. 7.USDA-ARS Horticultural Crops Research Unit worksiteParmaUSA

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