Genetic Analyses and Mapping of Pink-Root Resistance in Onion

in Journal of the American Society for Horticultural Science

Pink root [PR (caused by Phoma terrestris)] is a major soil-borne disease of onion (Allium cepa) and reduces both yield and quality of bulbs. PR-resistant cultivars offer the best control option for this disease. The objectives of this study were to complete genetic analyses and mapping of PR resistances from independent sources. Segregating families were developed from different sources of PR resistance and evaluated using a seedling screen. PR severity in two segregating families from the same source of resistance mapped to one position on chromosome 4 with logarithm of odds (LOD) scores of 8.0 and 10.3, and explained 28% and 35% of the phenotypic variation, respectively. Estimates of additive and dominance effects revealed this source of PR resistance is codominantly inherited. PR resistance from a second source was assessed by percent survival in the seedling evaluation, showed codominance, and mapped to the same region on chromosome 4 at LOD 12.5 and explained 54% of the phenotypic variation. This research demonstrates that PR resistance from different sources mapped to the same chromosome region and showed similar modes of inheritance.

Contributor Notes

We thank Nancy Koval for technical assistance and Karl Broman for statistical advice. We gratefully acknowledge the support of USDA Specialty Crop Research Initiative Block Grant Wisconsin 15-06 and a Monsanto graduate student fellowship for JCM.

Names are necessary to report factually on available data; however, the U.S. Department of Agriculture (USDA) neither guarantees nor warrants the standard of the product, and the use of the name by USDA implies no approval of the product to the exclusion of others that may also be suitable.

These authors contributed equally to this research.

Corresponding author. E-mail: michael.havey@ars.usda.gov.

Article Sections

Article Figures

  • View in gallery

    Additive effects of alleles at isotig32829_1057 (A) and isotig29175_343 (B) on pink-root (PR) severity (y-axis) on a 1 (resistant) to 9 (susceptible) scale for the PR1 (A) and PR2 (B) families of onion, respectively. Allele B from the resistant parent decreased disease severity relative to allele A from the susceptible parent.

  • View in gallery

    Additive effects of alleles at marker isotig26045_1046 on percent survival of onion seedlings (y-axis) in pink root evaluations from the PR3 and PR4 families. Allele B from the resistant parent increased % survival relative to allele A from the susceptible parent.

  • View in gallery

    Genetic linkages on chromosome 4 of onion among single nucleotide polymorphisms (SNPs) across the 1.5 logarithm of odds (LOD) confidence interval (black bars) for pink-root resistance for segregating families PR1 (DehyA × B5351), PR2 (DehyA × Ski-MsMs), and the combined analysis of PR3 and PR4 (B5351 × W446) families. SNP names are shown on right (Duangjit et al., 2013) and genetic distances in centimorgans are shown on left. Genetic map was developed using an F2 family from DehyA × B5351 as reported by Damon and Havey (2014).

Article References

  • AhmedA.A.HarringtonJ.F.1974Onion seed yield as affected by pink rot disease, soil fumigation, mother bulb fertilization and bulb sizeHortScience4394396

    • Search Google Scholar
    • Export Citation
  • BlackL.ChanE.K.F.ColcolJ.F.JonesR.KramerC.XiangW.2015Disease resistance loci in onion. United States patent application 20150150155A1. Filed 28 May 2015

  • BromanK.W.BromanA.T.2016R/broman: Karl Broman's R Code. R package version 0.62-1. 28 Aug. 2018. <https://CRAN.R-project.org/package=broman>

  • BromanK.W.WuH.SenS.ChurchillG.A.2003R/qtl: QTL mapping in experimental crossesBioinformatics19889890

  • ChavesG.M.EricksonH.T.1960Pink root disease on onions in Minas Gerais, BrazilPlant Dis. Rpt.44877

  • ColemanP.M.EllerbrockL.A.1992Interaction of Phoma terrestris and soil moisture level on yield of two onion cultivars differentially susceptible to pink rootPlant Dis.7612131216

    • Search Google Scholar
    • Export Citation
  • DamonS.J.HaveyM.J.2014Quantitative trait loci controlling amounts and types of epicuticular waxes in onionJ. Amer. Soc. Hort. Sci.139597602

    • Search Google Scholar
    • Export Citation
  • DhingraO.D.SinclairJ.B.1985Basic plant pathology methods. 2nd ed. CRC Press Boca Raton FL

  • DuangjitJ.BohanecB.ChanA.P.TownC.D.HaveyM.J.2013Transcriptome sequencing to produce SNP-based genetic maps of onionTheor. Appl. Genet.12620932101

    • Search Google Scholar
    • Export Citation
  • EntwistleA.R.1990Root diseases p. 103–154. In: H.D. Rabinowitch and J.L. Brewster (eds.). Onion and allied crops. Vol II. CRC Press Boca Raton FL

  • GoldmanI.L.1996A list of germplasm releases from the University of Wisconsin onion breeding program, 1957-1993HortScience31878879

  • GomezK.A.GomezA.A.1984Statistical procedures for agricultural research. Wiley New York NY

  • GorenzA.M.LarsonR.H.WalkerJ.C.1949Factors affecting pathogenicity of pink root fungus of onionsJ. Agr. Res.78118

  • HartzT.K.BogleC.R.BenderD.A.AvilaF.A.1989Control of pink root disease in onion using solarization and fumigationJ. Amer. Soc. Hort. Sci.114587590

    • Search Google Scholar
    • Export Citation
  • JonesH.A.PerryB.A.1956Inheritance of resistance to pink root in the onionJ. Hered.473334

  • KatanJ.1980Solar pasteurization of soils for disease control: Status and prospectsPlant Dis.64450454

  • KlingnerA.Pontis-VidelaR.E.1961Pink root disease of onions in Mendoza, ArgentinaPlant Dis. Rpt.45235

  • LacyM.L.RobertsD.L.1982Yields of onion cultivars in Midwestern organic soils infested with Fusarium oxysporum f. sp. cepae and Pyrenochaeta terrestrisPlant Dis.6610031006

    • Search Google Scholar
    • Export Citation
  • LeeC.J.LeeJ.T.MoonJ.S.HaL.I.KimH.D.KimW.CheonM.G.2007Effects of solar heating for control of pink root and other soil-borne diseases of onionsPlant Pathol.23295299

    • Search Google Scholar
    • Export Citation
  • LevyD.GornikA.1981Tolerance of onions (Allium cepa L.) to the pink root disease caused by Pyrenochaeta terrestrisPhytoparasitica95157

  • MarzuJ.C.2015Genetic analyses of resistances to Fusarium basal rot and pink root in onion. PhD Diss. Univ. Wisconsin Madison

  • NetzerD.RabinowitchH.D.WeintalC.H.1985Greenhouse technique to evaluate onion resistance to pink rootEuphytica34385391

  • NicholsC.G.1963Determination of the inheritance of resistance in the onion Allium cepa L. to the pink root fungus Pyrenochaeta terrestris. PhD Diss. Univ. Wisconsin Madison

  • NicholsC.G.LarsonR.H.GabelmanW.H.1960Relative pink root resistance of commercial onion hybrids and varietiesProc. Amer. Soc. Hortic. Sci.76468469

    • Search Google Scholar
    • Export Citation
  • NicholsC.G.GabelmanW.H.LarsonR.H.WalkerJ.C.1965The expression and inheritance of resistance to pink root in onion seedlingsPhytopathology55752756

    • Search Google Scholar
    • Export Citation
  • PerryB.A.JonesH.A.1955Performance of short-day pink-root-resistant varieties of onions in southern TexasJ. Amer. Soc. Hort. Sci.66350353

    • Search Google Scholar
    • Export Citation
  • PerryB.A.DavisE.W.JonesH.A.1964Establishment of a pink root nurseryEcon. Bot.187779

  • PflegerF.L.VaughanE.K.1972Pyrenochaeta terrestris as a naturally occurring component of the soil in OregonPlant Dis. Rep.56180182

  • PorterI.J.MerrimanP.R.KeaneP.J.1989Integrated control of pink root (Pyrenochaeta terrestris) of onions by dazomet and soil solarizationAustral. J. Agr. Res.40861869

    • Search Google Scholar
    • Export Citation
  • R Core Team2013R: A language and environment for statistical computing. 28 Aug. 2018. <http://www.R-project.org/>

  • R Studio Team2016R Studio: Integrated development for R. R Studio Boston MA

  • RabinowitchH.D.KatanJ.RotemI.1981The response of onions to solar heating, agricultural practices and pink-root diseaseScientia Hort.15331340

    • Search Google Scholar
    • Export Citation
  • StraleyE.2018QTL analyses of Fusarium basal rot and pink root resistance in onion. MS Thesis. Univ. Wisconsin Madison

  • SummerD.R.1995Pink root p. 12–13. In: H.F. Schwartz and S.K. Mohan (eds.). Compendium of onion and garlic diseases. APS Press St. Paul MN

  • TabenhausJ.J.1917Pink root, a new disease of onions in TexasPhytopathology7217(abstr.)

  • TabenhausJ.J.MallyF.W.1921Pink root disease of onions and its control in Texas. Texas Agr. Exp. Sta. Bul. 273

  • Van OoijenJ.W.2006JoinMap®4 Software for the calculation of genetic linkage maps in experimental populations. Kyazma Wageningen Neth

Article Information

Google Scholar

Related Content

Article Metrics

All Time Past Year Past 30 Days
Abstract Views 133 133 10
Full Text Views 58 58 3
PDF Downloads 20 20 2