Skip to main content
SpringerLink
Log in

Genomic markers linked to Meloidogyne chitwoodi resistance introgressed from Solanum bulbocastanum to cultivated potato and their utility in marker-assisted selection

  • Published:
Molecular Breeding Aims and scope Submit manuscript

Abstract

Meloidogyne chitwoodi is a major threat to potato production in the Pacific Northwest region of the United States. Infected tubers are rendered unmarketable; hence, growers’ profitability is adversely affected. Breeding for nematode resistance is a long-term process and phenotyping the segregating populations for nematode resistance is the most time-consuming and laborious part of the process. Using DNA-based markers closely linked to the nematode resistance trait for marker-assisted selection (MAS) could enhance breeding efficiency and accuracy. In the present study, a pool of phenotyped progenies segregating for nematode resistance and susceptibility were fingerprinted using a 21 K single-nucleotide polymorphism (SNP) array. Eight candidate SNPs located on potato Chromosome 11, segregating with the nematode resistance trait, were identified and used as landmarks for discovery of other marker types such as simple sequence repeat (SSR) and insertion–deletion (INDEL) markers. Subsequently, a total of eight SNPs, 30 SSRs, and four INDELS located on scaffold 11 of Solanum bulbocastanum were used to design primers; markers were validated in a panel of resistant and susceptible clones. Two SNPs (SB_MC1Chr11-PotVar0066518 and SB_MC1Chr11-PotVar0064140), five SSRs (SB_MC1Chr11-SSR04, SB_MC1Chr11-SSR08, SB_MC1Chr11-SSR10, SB_MC1Chr11-SSR13, and SB_MC1Chr11-SSR20), and one INDEL (SB_MC1Chr11-INDEL4) markers showed polymorphism between the resistant and susceptible clones in the test panel and in other segregating progenies. These markers are robust, highly reproducible, and easy to use for MAS of nematode-resistant potato clones to enhance the breeding program.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Austin S, Pohlman JD, Brown CR, Mojtahedi H, Santo GS, Douches DS, Helgeson JP(1993) Interspecific somatic hybridization between Solanum tuberosum L. and S. bulbocastanum Dun. as a means of transferring nematode resistance. American Potato Journal 70(6):485–95

  • Bali S, Vining K, Gleason C, Majtahedi H, Brown CR, Sathuvalli V (2019) Transcriptome profiling of resistance response to Meloidogyne chitwoodi introgressed from wild species Solanum bulbocastanum into cultivated potato. BMC Genomics 20(1):1–8

    Article  Google Scholar 

  • Bali S, Sathuvalli V, Brown C, Novy R, Ewing L, Debons J, Douches D, Coombs J, Navarre D, Whitworth J, Charlton B (2017) Genetic fingerprinting of potato varieties from the northwest potato variety development program. Am J Potato Res 1;94(1):54–63

  • Brown CR, Mojtahedi H, Santo GS (1995) Introgression of resistance to Columbia and northern root-knot nematodes from Solanum bulbocastanum into cultivated potato. Euphytica 83(1):71–78

    Article  Google Scholar 

  • Brown CR, Yang CP, Mojtahedi HA, Santo GS, Masuelli RI (1996) RFLP analysis of resistance to Columbia root-knot nematode derived from Solanum bulbocastanum in a BC 2 population. Theor Appl Genet 92(5):572–576

    Article  CAS  Google Scholar 

  • Cregan PB, Mudge J, Fickus EW, Danesh D, Denny R, Young ND (1999) Two simple sequence repeat markers to select for soybean cyst nematode resistance coditioned by the rhg1 locus. Theor Appl Genet 99(5):811–818

    Article  CAS  Google Scholar 

  • Dayteg C, Tuvesson S (2010) Automation of DNA Marker analysis for molecular breeding in crops. In Molecular techniques in crop improvement (pp. 143–161). Springer, Dordrecht

  • Felcher KJ, Coombs JJ, Massa AN, Hansey CN, Hamilton JP, Veilleux RE, Buell CR, Douches DS (2021) Integration of two diploid potato linkage maps with the potato genome sequence. PloS one 27;7(4):e36347

  • Gupta PK, Varshney RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113(3):163–185

    Article  CAS  Google Scholar 

  • Hamilton JP, Hansey CN, Whitty BR, Stoffel K, Massa AN, Van Deynze A, De Jong WS, Douches DS, Buell CR (2011) Single nucleotide polymorphism discovery in elite North American potato germplasm. BMC genomics12(1):1–2

  • Hirsch CD, Hamilton JP, Childs KL, Cepela J, Crisovan E, Vaillancourt B, Hirsch CN, Habermann M, Neal B, Buell CR (2014) Spud DB: a resource for mining sequences, genotypes, and phenotypes to accelerate potato breeding. The Plant Genome 7(1):plantgenome2013–12

  • Hussey RS (1973) A comparison of methods of collecting inocula of Meloidogyne spp., including a new technique. Plant Dis Rep 57:1025–1028

    Google Scholar 

  • Da Maia LC, Palmieri DA, De Souza VQ, Kopp MM, de Carvalho FI, Costa de Oliveira A (2008) SSR locator: tool for simple sequence repeat discovery integrated with primer design and PCR simulation. Int j plant genomics

  • Mojtahedi H, Brown CR, Santo GS (1995) Characterization of resistance in a somatic hybrid of Solanum bulbocastanum and S. tuberosum, to Meloidogyne chitwoodi. J Nematol 27(1):86

  • Mojtahedi H, Santo GS, Wilson JH (1998) Host tests to differentiate Meloidogyne chitwoodi races 1 and 2 and M. hapla. J Nematol 20(3):468

  • NASS-USDA (2020) https://www.nass.usda.gov/Statistics_by_State/Washington/Publications/Potatoes/2020/PT09_1.pdf

  • Nybom H (1991) Applications of DNA fingerprinting in plant breeding. In DNA fingerprinting: approaches and applications, pp 294–311 Birkhäuser Basel

  • Pham GM, Hamilton JP, Wood JC, Burke JT, Zhao H, Vaillancourt B, Ou S, Jiang J, Buell CR (2020) Construction of a chromosome-scale long-read reference genome assembly for potato. Gigascience 9(9):giaa100

  • Presting GG, Smith OP, Brown CR (1995) Resistance to potato leafroll virus in potato plants transformed with the coat protein gene or with vector control constructs. Phytopathol 85(4):436–442

    Article  CAS  Google Scholar 

  • Santo GS, O'bannon JH, Finley AM, Golden AM (1980) Occurrence and host range of a new root-knot nematode (Meloidogyne chitwoodi) in the Pacific Northwest. Plant Dis 64(10):951-2

  • Smith HM, Smith BP, Morales NB, Moskwa S, Clingeleffer PR, Thomas MR (2018) SNP markers tightly linked to root knot nematode resistance in grapevine (Vitis cinerea) identified by a genotyping-by-sequencing approach followed by Sequenom MassARRAY validation. PLoS One 20;13(2):e0193121

  • The Potato genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475 (doi:https://doi.org/10.1038/nature10158)

  • Williamson VM, Ho JY, Wu FF, Miller N, Kaloshian I (1994) A PCR-based marker tightly linked to the nematode resistance gene, Mi, in tomato. Theor Appl Genet 87(7):757–763

    Article  CAS  Google Scholar 

  • Zhang LH, Mojtahedi H, Kuang H, Baker B, Brown CR (2007) Marker-assisted selection of Columbia root-knot nematode resistance introgressed from Solanum bulbocastanum. Crop Sci 47(5):2021–2026

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors would like to thank Aguilar Moises for technical help.

Funding

Funding for this work is provided by the Northwest Potato Research Consortium and the USDA-ARS state partnership award.

Author information

Authors and Affiliations

  1. Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston-97838, OR, USA

    Sapinder Bali & Vidyasagar Sathuvalli

  2. Department of Plant Pathology, Washington State University, Pullman-99164, WA, USA

    Sapinder Bali

  3. Temperate Tree Fruit and Vegetable Research Unit, USDA-Agricultural Research Service, Prosser-99350, WA, USA

    Charles Brown, Hassan Majtahedi, Launa Cimrhakl & Rich Quick

  4. Department of Crop and Soil Sciences, Oregon State University, Corvallis-97331, OR, USA

    Solomon Yilma

  5. Department of Botany and Plant Pathology, Oregon State University, Corvallis-97333, OR, USA

    Russell E. Ingham

Authors
  1. Sapinder Bali
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Charles Brown
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hassan Majtahedi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Solomon Yilma
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Russell E. Ingham
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Launa Cimrhakl
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Rich Quick
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Vidyasagar Sathuvalli
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

SB and VS designed the research. SB performed all the experiments including genotyping, data analysis, marker validation, progeny screening, and manuscript preparation. VS conceptualized the project, secured the funding, and supervised and reviewed the manuscript. SY, LC, RQ, CB, HM, and RI helped in breeding and phenotyping of the progenies.

Corresponding author

Correspondence to Vidyasagar Sathuvalli.

Ethics declarations

Ethics approval and consent to participate

Not applicable.

Consent for publication

All authors (except CB and HM, who are now deceased) have approved the manuscript for publication.

Availability of data and material

All data generated or analyzed in this study are included in the published article and supplementary files.

Conflicts of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Charles Brown and Hassan Majtahedi have retired and passed away.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (XLSX 1181 KB)

Supplementary file2 (XLSX 13 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Bali, S., Brown, C., Majtahedi, H. et al. Genomic markers linked to Meloidogyne chitwoodi resistance introgressed from Solanum bulbocastanum to cultivated potato and their utility in marker-assisted selection. Mol Breeding 42, 12 (2022). https://doi.org/10.1007/s11032-022-01285-w

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s11032-022-01285-w

Keywords

Search

Navigation