Linkage map construction and QTL analysis for internal heat necrosis in autotetraploid potato

  • Mitchell J. Schumann
  • Zhao-Bang Zeng
  • Mark E. Clough
  • G. Craig Yencho
Original Article
  • 75 Downloads

Abstract

Key message

A tetraploid potato population was mapped for internal heat necrosis (IHN) using the Infinium®8303 potato SNP array, and QTL for IHN were identified on chromosomes 1, 5, 9 and 12 that explained 28.21% of the variation for incidence and 25.3% of the variation for severity. This research represents a significant step forward in our understanding of IHN, and sets the stage for future research focused on testing the utility of these markers in additional breeding populations.

Abstract

Internal heat necrosis (IHN) is a significant non-pathogenic disorder of potato tubers and previous studies have identified AFLP markers linked to IHN susceptibility in the tetraploid, B2721 potato mapping population. B2721 consists of an IHN susceptible×resistant cross: Atlantic×B1829-5. We developed a next-generation SNP-based linkage map of this cross using the Infinium® 8303 SNP array and conducted additional QTL analyses of IHN susceptibility in the B2721 population. Using SNP dosage sensitive markers, linkage maps for both parents were simultaneously analyzed. The linkage map contained 3427 SNPs and totaled 1397.68 cM. QTL were detected for IHN on chromosomes 1, 5, 9, and 12 using LOD permutation thresholds and colocation of high LOD scores across multiple years. Genetic effects were modeled for each putative QTL. Markers associated with a QTL were regressed in models of effects for IHN incidence and severity for all years. In the full model, the SNP markers were shown to have significant effects for IHN (p < 0.0001), and explained 28.21% of the variation for incidence and 25.3% of the variation for severity. We were able to utilize SNP dosage information to identify and model the effects of putative QTL, and identify SNP loci associated with IHN resistance that need to be confirmed. This research represents a significant step forward in our understanding of IHN, and sets the stage for future research focused on testing the utility of these markers in additional breeding populations.

Abbreviations

IHN

Internal heat necrosis

SNP

Single-nucleotide polymorphism

QTL

Quantitative trait loci

MAS

Marker-assisted selection

Supplementary material

122_2017_2941_MOESM1_ESM.docx (151 kb)
Supplementary material 1 (DOCX 151 kb)
122_2017_2941_MOESM2_ESM.docx (127 kb)
Supplementary material 2 (DOCX 126 kb)
122_2017_2941_MOESM3_ESM.docx (68 kb)
Supplementary material 3 (DOCX 67 kb)
122_2017_2941_MOESM4_ESM.docx (41 kb)
Supplementary material 4 (DOCX 41 kb)
122_2017_2941_MOESM5_ESM.docx (116 kb)
Supplementary material 5 (DOCX 116 kb)
122_2017_2941_MOESM6_ESM.docx (40 kb)
Supplementary material 6 (DOCX 40 kb)
122_2017_2941_MOESM7_ESM.docx (88 kb)
Supplementary material 7 (DOCX 88 kb)
122_2017_2941_MOESM8_ESM.docx (41 kb)
Supplementary material 8 (DOCX 41 kb)

References

  1. Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963–971PubMedPubMedCentralGoogle Scholar
  2. De Jong W, Leister D, Gebhardt C, Baulcombe DC (1997) A potato hypersensitive resistance gene against potato virus × maps to a resistance gene cluster on chromosome 5. Theor Appl Genet 95:246–252CrossRefGoogle Scholar
  3. Felcher KJ, Coombs JJ, Massa AN, Hansey CN, Hamilton JP, Veilleux RE, Buell CR, Douches DS (2012) Integration of two diploid potato linkage maps with the potato genome sequence. PLoS One 7:e36347CrossRefPubMedPubMedCentralGoogle Scholar
  4. Hackett CA, Milne I, Bradshaw JE, Luo Z (2007) TetraploidMap for windows: linkage map construction and QTL mapping in autotetraploid species. J Hered 98:727–729CrossRefPubMedGoogle Scholar
  5. Hackett CA, McLean K, Bryan GJ (2013) Linkage analysis and QTL mapping using SNP dosage data in a tetraploid potato mapping population. PLoS One 8:e63939CrossRefPubMedPubMedCentralGoogle Scholar
  6. Hackett CA, Bradshaw JE, Bryan GJ (2014) QTL mapping in autotetraploids using SNP dosage information. Theor Appl Genet 127:1885–1904CrossRefPubMedPubMedCentralGoogle Scholar
  7. 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 Genomics 12:302CrossRefPubMedPubMedCentralGoogle Scholar
  8. Henninger MR, Sterrett SB, Haynes KG (2000) Broad-sense heritability and stability of internal heat necrosis and specific gravity in tetraploid potatoes. Crop Sci 40:977–984CrossRefGoogle Scholar
  9. 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. Plant Genome 7:1CrossRefGoogle Scholar
  10. IPCC (2014) Mitigation of climate change. Contribution of working group iii to the fifth assessment report of the intergovernmental panel on climate change. Cambridge, United Kingdom and New York, USAGoogle Scholar
  11. Iritani WM, Weller LD, Knowles NR (1984) Factors influencing incidence of internal brown spot in Russet Burbank potatoes. Am J Potato Res 61:335–343CrossRefGoogle Scholar
  12. Kloosterman B, Prat S, Visser R, Bachem C, Abelenda J, Gomez M, Oortwijn M, de Boer J, Kowitwanich K, Horvath B, van Eck H, Smaczniak C (2013) Naturally occurring allele diversity allows potato cultivation in northern latitudes. Nature 495:246–250CrossRefPubMedGoogle Scholar
  13. Levy D, Veilleux RE (2007) Adaptation of potato to high temperatures and salinity—a review. Am J Potato Res 84:487–506CrossRefGoogle Scholar
  14. McCord PH (2009) Genetic, Genomic, and transgenic approaches to understand internal heat necrosis in potato. Ph.D. diss., North Carolina State University, RaleighGoogle Scholar
  15. McCord PH, Sosinski BR, Haynes KG, Clough ME, Yencho GC (2011a) QTL mapping of internal heat necrosis in tetraploid potato. Theor Appl Genet 122:129–142CrossRefPubMedGoogle Scholar
  16. McCord PH, Sosinski BR, Haynes KG, Clough ME, Yencho GC (2011b) Linkage mapping and QTL analysis of agronomic traits in tetraploid potato (Solanum tuberosum subsp. tuberosum). Crop Sci 51:771–785CrossRefGoogle Scholar
  17. Nettleton D, Doerge RW (2000) Accounting for variability in the use of permutation testing to detect quantitative trait loci. Biometrics 56:52–58CrossRefPubMedGoogle Scholar
  18. Preedy KF, Hackett CA (2016) A rapid marker ordering approach for high-density genetic linkage maps in experimental autotetraploid populations using multidimensional scaling. Theor Appl Genet 129:2117–2132CrossRefPubMedGoogle Scholar
  19. Schumann MJ (2015) QTL mapping in tetraploid potatoes for horticultural and nutritional traits. M.S. thesis., North Carolina State UniversityGoogle Scholar
  20. Schwarz G (1978) Estimating the dimension of a model. Ann Stat 6:461–464CrossRefGoogle Scholar
  21. Sterrett SB, Henninger MR (1991) Influence of calcium on internal heat necrosis of Atlantic potato. Am J Potato Res 68:467–477CrossRefGoogle Scholar
  22. Sterrett S, Wilson G (1990) Internal heat necrosis in ‘Atlantic’: a survey of the disorder. Veg Grow News 44:2–4Google Scholar
  23. Vandenberg JH, Ewing EE, Plaisted RL, McMurry S, Bonierbale MW (1996) QTL analysis of potato tuberization. Theor Appl Genet 93:307–316CrossRefGoogle Scholar
  24. Voorrips RE, Gort G, Vosman B (2011) Genotype calling in tetraploid species from bi-allelic marker data using mixture models. BMC Bioinform 12:172CrossRefGoogle Scholar
  25. Webb RE, Wilson DR, Shumaker JR, Graves B, Henninger MR, Watts J, Frank JA, Murphy HJ (1978) Atlantic: a new potato variety with high solids, good processing quality, and resistance to pests. Am J Potato Res 55:141–145CrossRefGoogle Scholar
  26. Xu X, Wang J, Orjeda G, Guzman F, Torres M, Lozano R, Ponce O, Martinez D, De la Cruz G, Chakrabarti SK, Patil VU, Pan S, Skryabin KG, Kuznetsov BB, Ravin NV, Kolganova TV, Beletsky AV, Mardanov AV, Di Genova A, Bolser DM, Martin DMA, Li G, Cheng S, Yang Y, Kuang H, Hu Q, Xiong X, Bishop GJ, Sagredo B, Mejía N, Zagorski W, Gromadka R, Gawor J, Zhang B, Szczesny P, Huang S, Zhang Z, Liang C, He J, Li Y, He Y, Xu J, Zhang Y, Xie B, Mu D, Du Y, Qu D, Bonierbale M, Ghislain M, Herrera MR, Giuliano G, Pietrella M, Perrotta G, Facella P, O’Brien K, Ni P, Feingold SE, Barreiro LE, Massa GA, Diambra L, Whitty BR, Vaillancourt B, Lin H, Massa AN, Geoffroy M, Lundback S, Zhang G, DellaPenna D, Buell CR, Sharma SK, Marshall DF, Waugh R, Bryan GJ, Destefanis M, Nagy I, Milbourne D, Thomson SJ, Yang S, Fiers M, Jacobs JE, Nielsen KL, Sønderkær M, Iovene M, Torres GA, Jiang J, Veilleux RE, Bachem CB, De Boer J, Li R, Borm T, Kloosterman B, Van Eck H, Datema E, Hekkert BL, Goverse A, Ham Van, Roeland CJ, Visser RF, Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–195CrossRefPubMedGoogle Scholar
  27. Yencho GC, McCord PH, Haynes KG, Sterrett SBR (2008) Internal heat necrosis of potato—a review. Am J Potato Res 85:69–76CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  1. 1.Department of Horticultural ScienceNorth Carolina State UniversityRaleighUSA
  2. 2.Bioinformatics Research CenterNorth Carolina State UniversityRaleighUSA
  3. 3.Department of Horticultural ScienceNorth Carolina State University - Vernon James Research and Extension CenterPlymouthUSA

Personalised recommendations