Skip to main content
SpringerLink
Log in

Identification of Quantitative Trait Loci for Stem-End Chip Defect and Potato Chip Color Traits in a ‘Lenape’-Derived Full-Sib Population

  • Published:
American Journal of Potato Research Aims and scope Submit manuscript

Abstract

Chipping potatoes are bred for their ability to produce light-colored, defect-free chips. Chips with stem-end chip defect (SECD) have dark blemishes and are undesirable to consumers and chip processors. The heritability of SECD is not known and genetic loci linked to defect formation have not been identified. Chip processing varieties ‘Wauseon’ and ‘Lenape’ were crossed and tubers from parents and 191 progeny were evaluated over four years for chip color descriptors L*, a*, and b* and SECD score in January, March, and May. Broad sense heritability for SECD was 0.64 or greater at each sampling time. Genotype data were used to construct a 1282 cM linkage map. Nine quantitative trait loci (QTL) for SECD were detected, and seven overlapped QTL for chip color traits. The QTL identified are starting points for developing molecular markers that are used to select genotypes that produce light-colored chips and have resistance to SECD formation.

Resumen

Se hace mejoramiento para papas de fritura por su habilidad para producir hojuelas de color claro y libres de defectos. Las hojuelas con el defecto del extremo del tallo (SECD) tienen manchas oscuras y son indeseables para consumidores y procesadores de frituras. No se conoce la heredabilidad de SECD y no se han identificado los loci genéticos ligados a la formación del defecto. Se cruzaron las variedades para frituras Wauseon y Lenape y se evaluaron los tubérculos de los progenitores y de 191 progenies a lo largo de cuatro años para los descriptores del color de hojuelas L*, a* y b* y a la lectura de SECD en enero, marzo y mayo. La heredabilidad de amplio sentido para SECD fue de 0.64 o mayor en cada tiempo de muestreo. Se usaron los datos del genotipo para construir un mapa de ligamiento de 1282 cM. Se detectaron nueve loci de trazos cuantitativos (QTL) para SECD, y siete QTL empalmados para características de color de la hojuela. Los QTL identificados son puntos de inicio para desarrollar marcadores moleculares que se usan para seleccionar genotipos que producen hojuelas de color claro y que tienen resistencia a la formación de SECD.

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
Fig. 3

Similar content being viewed by others

References

  • Akeley, R.V., W.R. Mills, C.E. Cunningham, and J. Watts. 1968. Lenape: A new potato variety high in solids and chipping quality. American Potato Journal 45: 142–145.

    Article  Google Scholar 

  • Arnott, R. 2018. Guidelines for estimating potato production costs 2018 in Manitoba. Available at https://www.gov.mb.ca/agriculture/business-and-economics/financial-management/pubs/cop_crop_irrigatedpotato.pdf. Verified 8 May 2019.

  • Bates, D., M. Mächler, B. Bolker, and S. Walker. 2014. Fitting linear mixed-effects models using lme4. Journal of Statatistical Software 67: 1–48.

    Google Scholar 

  • Bernardo, R. 2010. Breeding for quantitative traits in plants. 2nd ed. Woodbury: Stemma Press.

    Google Scholar 

  • Bolotova, Y., and P.E. Patterson. 2009. An analysis of contracts in the Idaho processing-potato industry. Journal of Food Distribution Ressearch 40: 32–38.

    Google Scholar 

  • Bourke, P. 2014. QTL analysis in polyploids. Model testing and power calculations. Minor thesis (MSc), Wageningen University and Research Center, Wageningen, The Netherlands.

  • Burton, W.G. 1969. The sugar balance in some British potato varieties during storage. II. The effects of tuber age, previous storage temperature, and intermittent refrigeration upon low-temperature sweetening. European Potato Journal 12: 81–95.

    Article  CAS  Google Scholar 

  • Bussan, A.J., R.P. Sabba, and M.J. Drilias. 2009. Tuber maturation and potato storability : Optimizing skin set, sugars, and solids. University of Wisconsin Extension Bulletin A3884–02.

  • Busse, J.S., A.E. Wiberley-Bradford, and P.C. Bethke. 2019. Transient heat stress during tuber development alters post-harvest carbohydrate composition and decreases processing quality of chipping potatoes. Journal of the Science of Food and Agriculture 99: 2579–2588.

    CAS  PubMed  Google Scholar 

  • Chen, X., F. Salamini, and C. Gebhardt. 2001. A potato molecular-function map for carbohydrate metabolism and transport. Theoretical and Applied Genetics 102: 284–295.

    Article  CAS  Google Scholar 

  • Colgan R, D. Rees, and A. Briddon. 2012. Research review: Senescent sweetening. Agriculture and Horticulture Development Board, Potato Council Report R442, Stoneleigh Park, Warwickshire, UK.

  • Curtis, K.R., and J.J. McCluskey. 2003. Contract incentives in the processed potato industry. Available at http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.200.6071&rep=rep1&type=pdf. Verified 8 May 2019.

  • D’hoop, B.B., P.L.C. Keizer, M.J. Paulo, R.G.F. Visser, F.A. van Eeuwijk, and H.J. van Eck. 2014. Identification of agronomically important QTL in tetraploid potato cultivars using a marker-trait association analysis. Theoretical and Applied Genetics 127: 731–748.

    Article  PubMed  Google Scholar 

  • Dickman, L.V. 2016. Stem end chipping defect incidence and severity in potatoes (Solanum tuberosum). Masters thesis. University of Wisconsin-Madison.

  • Douches, D.S., K. Jastrzebski, D. Maas, and R.W. Chase. 1996. Assessment of potato breeding over the past century. Crop Science 36: 1544–1552.

    Article  Google Scholar 

  • Eborn, P. E. 2019. Potato cost of production for Idaho 2018 with comparisons to 2017. Available at https://www.uidaho.edu/-/media/UIdaho-Responsive/Files/cals/programs/idaho-agbiz/publications/cost-of-potato-production-full-report-2018.pdf?la=en&hash=F6916496EE929FFFBFEDDDD215DA33B86FDC6B33. Verified 8 May 2019.

  • Fischer, M., M. Kuckenberg, R. Kastilan, J. Muth, and C. Gebhardt. 2014. Novel in vitro inhibitory functions of potato tuber proteinaceous inhibitors. Molecular Genetics and Genomics 290: 387–398.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gebhardt, C., A. Ballvora, B. Walkemeier, P. Oberhagemann, and K. Schüler. 2004. Assessing genetic potential in germplasm collections of crop plants by marker-trait association: A case study for potatoes with quantitative variation of resistance to late blight and maturity type. Molecular Breeding 13: 93–102.

    Article  CAS  Google Scholar 

  • Glaczinski, H., A. Heibges, F. Salamini, and C. Gebhardt. 2002. Members of the Kunitz-type protease inhibitor gene family of potato inhibit soluble tuber invertase in vitro. Potato Reseasrch 45: 163–176.

    Article  CAS  Google Scholar 

  • Habib, A.T., and H.D. Brown. 1957. Role of reducing sugars and amino acids in the browning of potato chips. Food Technology 11: 85–89.

    CAS  Google Scholar 

  • Hackett, C., J.E. Bradshaw, and J.W. McNicol. 2001. Interval mapping of quantitative trait loci in autotetraploid species. Genetics 159: 1819–1832.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hackett, C., K. McLean, and G.J. Bryan. 2013. Linkage analysis and QTL mapping using SNP dosage data in a tetraploid potato mapping population. PLoS One 8: 1–21.

    Google Scholar 

  • Hackett, C., J.E. Bradshaw, and G.J. Bryan. 2014. QTL mapping in autotetraploids using SNP dosage information. Theoretical and Applied Genetics 127: 1885–1904.

    Article  PubMed  Google Scholar 

  • Hamilton, J.P., C.N. Hansey, B.R. Whitty, K. Stoffel, A.N. Massa, A. Van Deynze, W.S. De Jong, D.S. Douches, and C.R. Buell. 2011. Single nucleotide polymorphism discovery in elite north American potato germplasm. BMC Genomics 12: 302–313.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Henderson, C.R. 1974. General flexibility of linear model techniques for sire evaluation. Journal of Dairy Science 57: 963–972.

    Article  Google Scholar 

  • Hirsch, C.N., C.D. Hirsch, K. Felcher, J. Coombs, D. Zarka, A. Van Deynze, W. De Jong, R.E. Veilleux, S. Jansky, P. Bethke, D.S. Douches, and C.R. Buell. 2013. Retrospective view of north American potato (Solanum tuberosum L.) breeding in the 20th and 21st centuries. G3 Genes, Genomes, Genetics 3: 1003–1013.

    Google Scholar 

  • Holland, J.B., W.E. Nyquist, and C.T. Cervantes-Martinez. 2003. Estimating and interpreting heritability for plant breeding: An update. Plant Breeding Reviews 22: 9–112.

    Google Scholar 

  • Kossmann, J., U. Sonnewald, and L. Willmitzer. 1994. Reduction of the chloroplastic fructose-l,6- bisphosphatase in transgenic potato plants impairs photosynthesis and plant growth. Plant Journal 6: 637–650.

    Article  CAS  Google Scholar 

  • LaFramboise, T. 2009. Single nucleotide polymorphism arrays: A decade of biological, computational and technological advances. Nucleic Acids Research 37: 4181–4193.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li, L., Strahwald, J., Hofferbert, H.-R., Lübeck, J., Tacke, E., Junghans, H., Wunder J. and Gebhardt, C. 2005. DNA variation at the invertase locus invGE/GF is associated with tuber quality traits in populations of potato breeding clones. Genetics, 170(2), 813–821.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li, L., E. Tacke, H.-R. Hofferbert, J. Lübeck, J. Strahwald, A.M. Draffehn, B. Walkemeier, and C. Gebhardt. 2013. Validation of candidate gene markers for marker-assisted selection of potato cultivars with improved tuber quality. Theoretical and Applied Genetics 126: 1039–1052.

    Article  CAS  PubMed  Google Scholar 

  • Lin, C.S., and G. Poushinsky. 1985. A modified augmented design (type 2) for rectangular plots. Canadian Journal of Plant Science 65: 743–749.

    Article  Google Scholar 

  • Love, S., J. Pavek, A. Thompson-Johns, and W. Bohl. 1998. Breeding progress for potato chip quality in north American cultivars. American Journal of Potato Research 75: 27–36.

    Article  Google Scholar 

  • Lulai, E.C., and P.H. Orr. 1979. Influence of potato specific gravity on yield and oil content of chips. American Potato Journal. 56: 379–390.

    Article  Google Scholar 

  • Luo, Z.W., C. Hackett, J.E. Bradshaw, J.W. McNicol, and D. Milbourne. 2001. Construction of a genetic linkage map in tetraploid species using molecular markers. Genetics 157: 1369–1385.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Massa, A.N., N.C. Manrique-Carpintero, J.J. Coombs, D.G. Zarka, A.E. Boone, W.W. Kirk, C.A. Hackett, G.J. Bryan, and D.S. Douches. 2015. Genetic linkage mapping of economically important traits in cultivated tetraploid potato (Solanum tuberosum L.). G3 Genes, Genomes, Genetics 5: 2357–2364.

    Google Scholar 

  • Menendez, C.M., E. Ritter, R. Schafer-Pregl, B. Walkeneier, A. Kalde, F. Salamini, and C. Gebhardt. 2002. Cold-sweetening in diploid potato : Mapping QTL and candidate genes. Genetics 162: 1423–1434.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Milbourne, D., J.E. Bradshaw, and C. Hackett. 2009. Molecular mapping and breeding in polyploid crop plants. In Principles and practices of plant genomics 2, ed. Chittaranjan Kole and Albert G. Abbott, 355–394. Boca Raton: CRC Press.

    Google Scholar 

  • Nei, M. 1972. Genetic distance between populations - part 3: Wahlund’s principle as related to genetic distance and an application. American Naturalist 106: 283–292.

    Article  Google Scholar 

  • Nettleton, D., and R.W. Doerge. 2000. Accounting for variability in the use of permutation testing to detect quantitative trait loci. Biometrics 56: 52–58.

    Article  CAS  PubMed  Google Scholar 

  • R Core Team. 2014. R: A language and environment for statistical computing. R Found. Stat. Comput. Vienna, Austria (January): Available at https://www.r-project.org/.

  • Rabiner, L.R. 1989. A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE 77: 257–286.

    Article  Google Scholar 

  • Rak, K. 2015. Breeding and molecular genetics for the improvement of cold storage potato chip quality. Ph.D. thesis, University of Wisconsin-Madison.

  • Robinson, G.K. 1991. That BLUP is a good thing: The estimation of random effects. Statistical Science 6: 15–32.

    Google Scholar 

  • Scanlon, M.G., R. Roller, G. Mazza, and M.K. Pritchard. 1994. Computerized video image analysis to quantify color of potato chips. American Potato Journal 71: 717–733.

    Article  Google Scholar 

  • Schreiber, L., A.C. Nader-Nieto, E.M. Schonhals, B. Walkemeier, and C. Gebhardt. 2014. SNPs in genes functional in starch-sugar interconversion associate with natural variation of tuber starch and sugar content of potato (Solanum tuberosum L.). G3 Genes, Genomes, Genetics 4: 1797–1811.

    CAS  Google Scholar 

  • Schwarz, G. 1978. Estimating the dimension of a model. Annals of Statistics 6: 461–464.

    Article  Google Scholar 

  • Shallenberger, R., O. Smith, and R. Treadway. 1959. Food color changes - role of the sugars in the browning reaction in potato chips. Journal of Agricultural Food Chememistry 7: 274–277.

    Article  CAS  Google Scholar 

  • Sharma, S.K., D. Bolser, J. de Boer, M. Sønderkær, W. Amoros, M.F. Carboni, J.M. D’Ambrosio, G. de la Cruz, A. Di Genova, D.S. Douches, M. Eguiluz, X. Guo, F. Guzman, C. Hackett, J.P. Hamilton, G. Li, Y. Li, R. Lozano, A. Maass, D. Marshall, D. Martinez, K. McLean, N. Mejía, L. Milne, S. Munive, I. Nagy, O. Ponce, M. Ramirez, R. Simon, S.J. Thomson, Y. Torres, R. Waugh, Z. Zhang, S. Huang, R.G.F. Visser, C.W.B. Bachem, B. Sagredo, S.E. Feingold, G. Orjeda, R.E. Veilleux, M. Bonierbale, J.M.E. Jacobs, D. Milbourne, D.M.A. Martin, and G.J. Bryan. 2013. Construction of reference chromosome-scale pseudomolecules for potato: Integrating the potato genome with genetic and physical maps. G3 Genes, Genomes, Genetics 3: 2031–2047.

    Google Scholar 

  • Simko, I. 2004. One potato, two potato: Haplotype association mapping in autotetraploids. Trends in Plant Science 9: 441–448.

    Article  CAS  PubMed  Google Scholar 

  • Sowokinos, J.R. 2001. Biochemical and molecular control of cold-induced sweetening in potatoes. American Journal of Potato Research 78: 221–236.

    Article  CAS  Google Scholar 

  • Stam, P. 1993. Construction of integrated genetic linkage maps by means of a new computer package: Join map. The Plant Journal. 3: 739–744.

    Article  CAS  Google Scholar 

  • Sweetlove, L.J., and S.A. Hill. 2000. Source metabolism dominates the control of source to sink carbon flux in tuberizing potato plants throughout the diurnal cycle and under a range of environmental conditions. Plant, Cell and Environment 23: 523–529.

    Article  CAS  Google Scholar 

  • Sweetman, M.D. 1930. Color of potato chips as influenced by storage temperatures of the tubers and other factors. Journal of Agricultural Research 41: 479–490.

    Google Scholar 

  • Tkalčič, M., and J.F. Tasič. 2003. Colour spaces - Perceptual, historical and applicational background. IEEE Reg. 8 EUROCON 2003 Computation as a Tool - Proc. A: 304–308.

  • USDA ERS. 2018. Vegetable and Pulses Yearbook, March 2018, USDA, Economic Research Service. Available at https://usda.library.cornell.edu/concern/publications/d791sg170?locale=en. Verified 8 May 2019.

  • Van Berloo, R., R.C.B. Hutten, H.J. Van Eck, and R.G.F. Visser. 2007. An online potato pedigree database resource. Potato Research 50: 45–57.

    Article  Google Scholar 

  • Voorrips, R.E., G. Gort, and B. Vosman. 2011. Genotype calling in tetraploid species from bi-allelic marker data using mixture models. BMC Bioinformatics 12: 172.

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang, Y., A.J. Bussan, and P.C. Bethke. 2012. Stem-end defect in chipping potatoes (Solanum tuberosum L.) as influenced by mild environmental stresses. American Journal of Potato Research 89: 392–399.

    Article  Google Scholar 

  • Wang, Y., P.C. Bethke, M.J. Drilias, W.G. Schmitt, and A.J. Bussan. 2015. A multi-year survey of stem-end chip defect in chipping potatoes (Solanum tuberosum L.). American Journal of Potato Research 92: 79–90.

    Article  Google Scholar 

  • Wiberley-Bradford, A.E., and P.C. Bethke. 2018. Suppression of the vacuolar invertase gene delays senescent sweetening in chipping potatoes. Journal of the Science of Food and Agriculture. 98: 354–360.

    Article  CAS  PubMed  Google Scholar 

  • Zheng, C., R.E. Voorrips, J. Jansen, C.A. Hackett, J. Ho, and M.C.A.M. Bink. 2016. Probabilistic multilocus haplotype reconstruction in outcrossing tetraploids. Genetics 203: 119–131.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zitnak, A., and G.R. Johnston. 1970. Glycoalkaloid content of B5141-6 potatoes. American Potato Journal 47: 256–260.

    Article  CAS  Google Scholar 

  • Zorilla Cisneros, C. 2013. Understanding the genetics of potato tuber calcium and its implications in breeding for improved quality. Ph. D. Thesis, University of Wisconsin-Madion. Available at https://search.library.wisc.edu/catalog/9910177870902121.

Download references

Acknowledgements

The authors are grateful to Dr. James Busse for assistance with sample collection and processing. Assistance from the staff at the Hancock Research Station and Hancock Storage Research Facility was greatly appreciated. USDA-NIFA-SCRI Grant No. 2011-51181-30629 (Improved Breeding and Variety Evaluation Methods to Reduce Acrylamide Content and Increase Quality in Processed Potato Products) and the Wisconsin Potato and Vegetable Growers Association Chip Committee provided financial support for this project.

Author information

Author notes

  1. Curtis M. Frederick

    Present address: Sterman Masser Potato Farms, 2 Fearnot Road, P.O. Box 210, Sacramento, PA, 17968, USA

Authors and Affiliations

  1. Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI, 53706, USA

    Curtis M. Frederick

  2. USDA Agricultural Research Service, Vegetable Crops Research Unit, 1575 Linden Drive, Madison, WI, 53706, USA

    Paul C. Bethke

Authors
  1. Curtis M. Frederick
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Paul C. Bethke
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Paul C. Bethke.

Ethics declarations

Disclaimers

The authors claim no competing interests.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Frederick, C.M., Bethke, P.C. Identification of Quantitative Trait Loci for Stem-End Chip Defect and Potato Chip Color Traits in a ‘Lenape’-Derived Full-Sib Population. Am. J. Potato Res. 96, 564–577 (2019). https://doi.org/10.1007/s12230-019-09746-3

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12230-019-09746-3

Keywords

Search

Navigation