Plant Molecular Biology Reporter

, Volume 33, Issue 3, pp 474–479 | Cite as

Identification and Validation of a SNP Marker Linked to the Gene HsBvm-1 for Nematode Resistance in Sugar Beet

  • Piergiorgio Stevanato
  • Daniele Trebbi
  • Lee Panella
  • Kelley Richardson
  • Chiara Broccanello
  • Linda Pakish
  • Ann L. Fenwick
  • Massimo Saccomani
Original Paper

Abstract

The beet-cyst nematode (Heterodera schachtii Schmidt) is one of the major pests of sugar beet. The identification of molecular markers associated with nematode tolerance would be helpful for developing tolerant varieties. The aim of this study was to identify single nucleotide polymorphism (SNP) markers linked to nematode tolerance from the Beta vulgaris ssp. maritima source WB242. A WB242-derived F2 population was phenotyped for host-plant nematode reaction revealing a 3:1 segregation ratio of the tolerant and susceptible phenotypes and suggesting the action of a gene designated as HsBvm-1. Bulked segregant analysis (BSA) was used. The most tolerant and susceptible individuals were pooled and subjected to restriction site associated DNA sequencing (RAD-Seq) analysis, which identified 7,241 SNPs. A subset of 384 candidate SNPs segregating between bulks were genotyped on the 20 most-tolerant and most-susceptible individuals, identifying a single marker (SNP192) showing complete association with nematode tolerance. Segregation of SNP192 confirmed the inheritance of tolerance by a single gene. This association was further validated on a set of 26 commercial tolerant and susceptible varieties, showing the presence of the SNP192 WB242-type allele only in the tolerant varieties. We identified and mapped on chromosome 5 the first nematode tolerance gene (HsBvm-1) from Beta vulgaris ssp. maritima and released information on SNP192, a linked marker valuable for high-throughput, marker-assisted breeding of nematode tolerance in sugar beet.

Keywords

HsBvm-1 Beta vulgaris ssp. maritima Biotic stresses Beet-cyst nematode WB242 genetic tolerance SNP 

Abbreviations

SNP

Single nucleotide polymorphisms

RAD-Seq

Restriction site associated DNA sequencing

BSA

Bulk segregant analysis

Supplementary material

11105_2014_763_MOESM1_ESM.doc (29 kb)
Supplementary material S1(DOC 29 kb)
11105_2014_763_MOESM2_ESM.doc (28 kb)
Supplementary material S2(DOC 27 kb)

References

  1. Barchi L, Lanteri S, Portis E, Acquadro A, Valè G, Toppino L, Rotino GL (2011) Identification of SNP and SSR markers in eggplant using RAD tag sequencing. BMC Genomics 12:304CrossRefPubMedCentralPubMedGoogle Scholar
  2. Biancardi E, Lewellen RT, De Biaggi M, Erichsen AW, Stevanato P (2002) The origin of rhizomania resistance in sugar beet. Euphytica 127:383–397CrossRefGoogle Scholar
  3. Biancardi E, McGrath JM, Panella LW, Lewellen RT, Stevanato P (2010) Sugar beet. In: Bradshaw J (ed) Handbook of plant breeding, vol 4, Tuber and Root Crops. Springer, New York, pp 173–219Google Scholar
  4. Biancardi E, Panella LW, Lewellen RT (2012) Beta maritima: the origin of beets Springer-Verlag New York Inc., pp 293Google Scholar
  5. Brandes A, Jung C, Wricke G (1987) Nematode resistance derived from wild beet and its meiotic stability in sugar beet. Plant Breed 99:56–64CrossRefGoogle Scholar
  6. Cai D, Kleine M, Kifle S, Harloff HJ, Sandal NN, Marcker KA, Klein-Lankhorst RM, Salentijn EM, Lange W, Stiekema WJ, Wyss U, Grundler FM, Jung C (1997) Positional cloning of a gene for nematode resistance in sugar beet. Science 275:832–834CrossRefPubMedGoogle Scholar
  7. Chutimanitsakun Y, Nipper RW, Cuesta-Marcos A, Cistué L, Corey A, Filichkina T, Johnson EA, Hayes PM (2011) Construction and application for QTL analysis of a restriction site associated DNA (RAD) linkage map in barley. BMC Genomics 12:4CrossRefPubMedCentralPubMedGoogle Scholar
  8. Conover WJ (1980) Practical non-parametric statistics. Wiley, New York, p 592Google Scholar
  9. Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12:499–510CrossRefPubMedGoogle Scholar
  10. Jung C, Cai D, Kleine M (1998) Engineering nematode resistance in crop species. Trends Plant Sci 3:266–271CrossRefGoogle Scholar
  11. Kleine M, Voss H, Cai D, Jung C (1998) Evaluation of nematode-resistant sugar beet (Beta vulgaris L.) lines by molecular analysis. Theor Appl Gen 97:896–904CrossRefGoogle Scholar
  12. McCarter JP (2008) Molecular approaches toward resistance to plant-parasitic nematodes. In: Plant cell monographs. Springer, Berlin, pp 1–29Google Scholar
  13. Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88:9828–9832CrossRefPubMedCentralPubMedGoogle Scholar
  14. Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res 17:240–248CrossRefPubMedCentralPubMedGoogle Scholar
  15. Panella L, Lewellen RT (2007) Broadening the genetic base of sugar beet: introgression from wild relatives. Euphytica 154:383–400CrossRefGoogle Scholar
  16. Pegadaraju V, Nipper R, Hulke B, Qi L, Schultz Q (2013) De novo sequencing of sunflower genome for SNP discovery using RAD (Restriction site Associated DNA) approach. BMC Genomics 14:556CrossRefPubMedCentralPubMedGoogle Scholar
  17. Pelsy F, Merdinoglu D (1996) Identification and mapping of random amplified polymorphic DNA markers linked to a rhizomania resistance gene in sugar beet (Beta vulgaris L.) by bulked segregant analysis. Plant Breed 115:371–377CrossRefGoogle Scholar
  18. Stevanato P, Trebbi D, Saccomani M (2010) Root traits and yield in sugar beet: identification of AFLP markers associated with root elongation rate. Euphytica 173:289–298CrossRefGoogle Scholar
  19. Stevanato P, Broccanello C, Biscarini F, Del Corvo M, Panella L, Gaurav S, Stella A, Concheri G (2013) First application of QuantStudio platform for high throughput SNP marker assessment in sugar beet. Plant Mol Biol Rep. doi:10.1007/s11105-013-0685-x Google Scholar
  20. Taguchi K, Okazaki K, Takahashi H, Kubo T, Mikami T (2010) Molecular mapping of a gene conferring resistance to Aphanomyces root rot (black root) in sugar beet (Beta vulgaris L.). Euphytica 173:409–418CrossRefGoogle Scholar
  21. Thurau T, Ye W, Menkhaus J, Knecht K, Tang G, Cai D (2010) Plant nematode control. Sugar Tech 12:229–237CrossRefGoogle Scholar
  22. Touzet P, Hueber N, Burkholz A, Barnes S, Cuguen J (2004) Genetic analysis of male fertility restoration in wild cytoplasmic male sterility G of beet. Theor Appl Genet 109:240–247CrossRefPubMedGoogle Scholar
  23. Van Ooijen JW (2011) Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species. Gen Res 93:343–349CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Piergiorgio Stevanato
    • 1
  • Daniele Trebbi
    • 1
  • Lee Panella
    • 2
  • Kelley Richardson
    • 3
  • Chiara Broccanello
    • 1
  • Linda Pakish
    • 3
  • Ann L. Fenwick
    • 4
  • Massimo Saccomani
    • 1
  1. 1.DAFNAE, Dipartimento di Agronomia Animali Alimenti Risorse Naturali e AmbienteUniversità degli Studi di PadovaLegnaroItaly
  2. 2.USDA-ARS, NPA, Sugarbeet Research UnitCrops Research LaboratoryFort CollinsUSA
  3. 3.USDA-ARSCrop Improvement and Protection Research UnitSalinasUSA
  4. 4.Beet Sugar Development FoundationCrops Research LaboratoryFort CollinsUSA

Personalised recommendations