Characterization of aphid resistance loci in black raspberry (Rubus occidentalis L.)
- 138 Downloads
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.
KeywordsAphid resistance Linkage mapping Necrosis virus Virus vector Association analysis
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.
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.
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.
- Bassil, NV, Gilmore, Hummer KE, Dossett M, Mockler T, Filichkin S, Peterson M, Finn CE, Lee J, Fernandez G, Perkins-Veazie P, Weber C, Agunga R, Rhodes E, Scheerens JC, Lewers K, Graham J, Fernández-Fernández F, and Yun SJ (2014) Genetic and developing genomic resources in black raspberry. Acta Hortic (ISHS) 1048:19–24Google Scholar
- Bassil NV, Davis TM, Zhang H, Ficklin S, Mittmann M, Webster T, Mahoney L, Wood D, Alperin ES, Rosyara UR, Koehorst-vanc Putten H, Monfort A, Sargent DJ, Amaya I, Denoyes B, Bianco L, van Dijk T, Pirani A, Iezzoni A, Main D, Peace C, Yang Y, Whitaker V, Verma S, Bellon L, Brew F, Herrera R, van de Weg E (2015) Development and preliminary evaluation of a 90K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria ×ananassa. BMC Genomics 16:30. https://doi.org/10.1186/s12864-015-1310-1 CrossRefGoogle Scholar
- Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics btu170Google Scholar
- Bradish CM (2016) Studies of linkage mapping, trait heritability, anstern black and red raspberry. North Carolina State University. PhD Thesis at http://www.lib.ncsu.edu/resolver/1840.20/33395
- Bus VGM, Chagné D, Bassett HCM, Bowatte D, Calenge F, Celton JM, Durel CE, Malone MT, Patocchi A, Ranatunga AC, Rikkerink EHA, Tustin DS, Zhou J, Gardiner SE (2008) Genome mapping of three major resistance genes to woolly apple aphid (Eriosoma lanigerum Hausm.). Tree Genet Genomes 4:223–236. https://doi.org/10.1007/s11295-007-0103-3 CrossRefGoogle Scholar
- Bushakra JM, Stephens MJ, Atmadjaja AN, Lewers KS, Symonds VV, Udall JA, Chagné D, Buck EJ, Gardiner SE (2012) Construction of black (Rubus occidentalis) and red (R. idaeus) raspberry linkage maps and their comparison to the genomes of strawberry, apple, and peach. Theor Appl Genet 125:311–327. https://doi.org/10.1007/s00122-012-1835-5 CrossRefPubMedGoogle Scholar
- Bushakra JM, Bryant DW, Dossett M, Vining KJ, VanBuren R, Gilmore BS, Lee J, Mockler TC, Finn CE, Bassil NV (2015) A genetic linkage map of black raspberry (Rubus occidentalis) and the mapping of Ag 4 conferring resistance to the aphid Amphorophora agathonica. Theor Appl Genet 128:1631–1646. https://doi.org/10.1007/s00122-015-2541-x CrossRefPubMedPubMedCentralGoogle Scholar
- Daubeny HA (1966) Inheritance of immunity in the red raspberry to the North American strain of the aphid Amphorophora rubi Kltb. Proc Natl Acad Sci 88:346–351Google Scholar
- Daubeny HA, Stary D (1982) Identification of resistance to Amphorophora agathonica in the native North American red raspberry. J Amer Soc Hortic Sci 107:593–597Google Scholar
- Dossett M, Finn CE (2010) Identification of resistance to the large raspberry aphid in black raspberry. J Amer Soc Hortic Sci 135:438–444Google Scholar
- Dossett M, Kempler C (2012) Biotypic diversity and resistance to the raspberry aphid Amphorophora agathonica in Pacific Northwestern North America. J Amer Soc Hortic Sci 137:445–451Google Scholar
- Dossett M, Kempler C (2016) Breeding raspberries for aphid resistance in British Columbia: progress and challenges. In: Acta Hortic (ISHS). Internatl Soc Hortic Sci (ISHS), Leuven, Belgium, pp 115–120. https://doi.org/10.17660/ActaHortic.2016.1133.17
- Gilmore BS, Bassil NV, Hummer KE (2011) DNA extraction protocols from dormant buds of twelve woody plant genera. J Amer Pomol Soc 65:201–207Google Scholar
- Haskell G (1960) Biometrical characters and selection in cultivated raspberry. Euphytica 9:17–34Google Scholar
- Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079. https://doi.org/10.1093/bioinformatics/btp352 CrossRefPubMedPubMedCentralGoogle Scholar
- Mace TA, King SA, Ameen Z, Elnaggar O, Young G, Riedl KM, Schwartz SJ, Clinton SK, Knobloch TJ, Weghorst CM, Lesinski GB (2014) Bioactive compounds or metabolites from black raspberries modulate T lymphocyte proliferation, myeloid cell differentiation and Jak/STAT signaling. Cancer Immunol Immunother 63:889–900. https://doi.org/10.1007/s00262-014-1564-5 CrossRefPubMedPubMedCentralGoogle Scholar
- MacFarlane SA, Tzanetakis IE, Halgren AB, Martin RR (2017) Raspberry mosaic virus. In: Martin RR, Ellis MA, Williamson B, Williams RN (eds) Compendium of raspberry and blackberry diseases and pests, 2nd edn. APS Press, St. Paul, pp 75–78Google Scholar
- Ourecky DK (1975) Brambles. In: Janick J, Moore JN (eds) Advances in fruit breeding. Purdue University Press, West Lafayette, pp 98–129Google Scholar
- Pagliarani G, Dapena E, Miñarro M, Denancé C, Lespinasse Y, Rat-Morris E, Troggio M, Durel CE, Tartarini S (2016) Fine mapping of the rosy apple aphid resistance locus Dp-fl on linkage group 8 of the apple cultivar ‘Florina’. Tree Genet Genomes 12:1–12. https://doi.org/10.1007/s11295-016-1015-x CrossRefGoogle Scholar
- Preacher KJ (2001) Calculation for the chi-square test: an interactive calculation tool for chi-square tests of goodness of fit and independence. http://quantpsy.org
- Rodrigo KA, Rawal Y, Renner RJ, Schwartz SJ, Tian Q, Larsen PE, Mallery SR (2006) Suppression of the tumorigenic phenotype in human oral squamous cell carcinoma cells by an ethanol extract derived from freeze-dried black raspberries. Nutr Cancer 54:58–68. https://doi.org/10.1207/s15327914nc5401_7 CrossRefPubMedPubMedCentralGoogle Scholar
- Salinas NR, Zurn JD, Mathey M, Mookerjee S, Denoyes B, Perrotte J, Potier A, Finn CE, Hancock JF, Stewart P, Bassil NV (2017) Validation of molecular markers associated with perpetual flowering in octoploid Fragaria germplasm. Mol Breed 37:70. https://doi.org/10.1007/s11032-017-0672-2 CrossRefGoogle Scholar
- Sargent D, Fernández-Fernández F, Rys A, Knight V, Simpson D, Tobutt K (2007) Mapping of A 1 conferring resistance to the aphid Amphorophora idaei and dw (dwarfing habit) in red raspberry (Rubus idaeus L.) using AFLP and microsatellite markers. BMC Plant Biol 7:15CrossRefPubMedPubMedCentralGoogle Scholar
- Van Ooijen JW (2006) JoinMap® 4, Software for the calculation of genetic linkage maps in experimental populations. Kyazma B.V, WageningenGoogle Scholar
- Weber CA (2003) Genetic diversity in black raspberry detected by RAPD markers. HortSci 38:269–272Google Scholar
- Winter JD (1929) A preliminary account of the raspberry aphids. U Minnesota Agricult Exp Station Tech Bull 61:1–30Google Scholar