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Genetic mapping with an inbred line-derived F2 population in potato

Abstract

Key message

This is the first report of the production and use of a diploid inbred line-based F2 population for genetic mapping in potato.

Abstract

Potato (Solanum tuberosum L.) is an important global food crop, for which tetrasomic inheritance and self-incompatibility have limited both genetic discovery and breeding gains. We report here on the creation of the first diploid inbred line-derived F2 population in potato, and demonstrate its utility for genetic mapping. To create the population, the doubled monoploid potato DM1-3 was crossed as a female to M6, an S7 inbred line derived from the wild relative S. chacoense, and a single F1 plant was then self-pollinated. A genetic linkage map with 2264 single nucleotide polymorphisms was constructed and used to improve the physical anchoring of superscaffolds in the potato reference genome, which is based on DM1-3. Segregation was observed for skin and flesh color, skin and flesh pigment intensity, tuber shape, anther development, jelly end, and the presence of eye tubers instead of normal sprouts. Using the R/qtl software, we detected 10 genes, 7 of which have been previously mapped and 3 for which this is the first publication. The latter category includes tightly linked genes for the jelly end and eye tuber traits on chromosome 5. The development of recombinant inbred lines from this F2 population by single-seed descent is underway and should facilitate even better resolution of these and other loci.

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References

  • Andolfatto P, Davison D, Erezyilmaz D, Hu TT, Mast J, Sunayama-Morita T, Stern DL (2011) Multiplexed shotgun genotyping for rapid and efficient genetic mapping. Genome Res 21:610–617

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Bonierbale MW, Plaisted RL, Tanksley SD (1988) RFLP maps based on a common set of clones reveal modes of chromosomal evolution in potato and tomato. Genetics 120:1095–1103

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bradshaw JE, Hackett CA, Pande B, Waugh R, Bryan GJ (2008) QTL mapping of yield, agronomic and quality traits in tetraploid potato (Solanum tuberosum subsp. tuberosum). Theor Appl Genet 116:193–211

    Article  PubMed  Google Scholar 

  • Broman K, Wu H, Sen S, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinform 19:889–890

    CAS  Article  Google Scholar 

  • Brown C, Kim T, Ganga Z, Haynes K, De Jong D, Jahn M, Paran I, De Jong W (2006) Segregation of total carotenoid in high level potato germplasm and its relationship to beta-carotene hydroxylase polymorphism. Am J Potato Res 83:365–372

    CAS  Article  Google Scholar 

  • Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963–971

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cipar MS, Peloquin SJ, Hougas RW (1964) Variability in the expression of self-incompatibility in tuber-bearing diploid Solanum species. Am Potato J 41:155–162

    Article  Google Scholar 

  • De Jong H (1987) Inheritance of pigmented tuber flesh in cultivated diploid potatoes. Am Potato J 64:337–343

    Article  Google Scholar 

  • De Jong H (1991) Inheritance of anthocyanin pigmentation in the cultivated potato: a critical review. Am Potato J 68:585–593

    Article  Google Scholar 

  • De Jong H, Burns VJ (1993) Inheritance of tuber shape in cultivated diploid potatoes. Am Potato J 70:267–283

    Article  Google Scholar 

  • Dodds KS, Long DH (1956) The inheritance of colour in diploid potatoes II. A three-factor linkage group. J Genet 54:27–41

    Article  Google Scholar 

  • 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:e36347

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Gebhardt C, Ritter E, Debener T, Schachtschabel U, Walkemeier B, Uhrig H, Salamini F (1989) RFLP analysis and linkage mapping in Solanum tuberosum. Theor Appl Genet 78:65–75

    CAS  Article  PubMed  Google Scholar 

  • Gebhardt C, Ritter E, Barone A, Debener T, Walkemeier B, Schachtschabel U, Kaufmann H, Thompson RD, Bonierbale MW, Ganal MW, Tanksley SD, Salamini F (1991) RFLP maps of potato and their alignment with the homoeologous tomato genome. Theor Appl Genet 83:49–57

    CAS  Article  PubMed  Google Scholar 

  • Grun P, Aubertin M, Radlow M (1962) Multiple differentiation of plasmons of diploid species of Solanum. Genetics 47:1321–1333

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hackett CA, Luo ZA (2003) TetraploidMap: construction of a linkage map in autotetraploid species. J Hered 94:358–359

    CAS  Article  PubMed  Google Scholar 

  • Hackett CA, Bradshaw JE, McNicol JW (2001) Interval mapping of QTLs in autotetraploid species. Genetics 159:1819–1832

    CAS  PubMed  PubMed Central  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 Genom 12:302

    CAS  Article  Google Scholar 

  • Hanneman RE (1985) Self fertility in Solanum chacoense. Am Potato J 62:428–429

    Google Scholar 

  • Hanneman RE, Peloquin SJ (1981) Genetic-cytoplasmic male sterility in progeny of 4x-2x crosses in cultivated potatoes. Theor Appl Genet 59:53–55

    PubMed  Google Scholar 

  • Jansky SH, Chung YS, Kittipadukal P (2014) M6: a diploid potato inbred line for use in breeding and genetics research. J Plant Regist 8:195–199

    Article  Google Scholar 

  • Jung CS, Griffiths HM, De Jong DM, Cheng S, Bodis M, De Jong WS (2005) The potato P locus codes for flavonoid 3′,5′-hydroxylase. Theor Appl Genet 110:269–275

    CAS  Article  PubMed  Google Scholar 

  • Jung CS, Griffiths HM, De Jong DM, Cheng S, Bodis M, Kim TS, De Jong WS (2009) The potato developer (D) locus encodes an R2R3 MYB transcription factor that regulates expression of multiple anthocyanin structural genes in tuber skin. Theor Appl Genet 120:45–57

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Koopmans A (1959) Changes in sex in the flowers of the hybrid Solanum rybinii x S. chacoense. IV. Further data from reciprocal cross S. chacoense x S. rybinii. Genetica 30:384–390

    CAS  Article  PubMed  Google Scholar 

  • Li XQ, De Jong H, De Jong DM, De Jong WS (2005) Inheritance and genetic mapping of tuber eye depth in cultivated diploid potatoes. Theor Appl Genet 110:1068–1073

    CAS  Article  PubMed  Google Scholar 

  • Lindhout P, Meijer D, Schotte T, Hutten RCB, Visser RGF, van Eck HJ (2011) Towards F1 hybrid seed potato breeding. Potato Res 54:301–312

    Article  Google Scholar 

  • Liu BH (2002) Statistical genomics. CRC Press, Boca Raton

    Google Scholar 

  • Luo ZW, Zhang RM, Kearsey MJ (2004) Theoretical basis for genetic linkage analysis in autotetraploid species. Proc Natl Acad Sci USA 101:7040–7045

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Luo ZW, Zhang Z, Leach L, Zhang RM, Bradshaw JE, Kearsey MJ (2006) Constructing genetic linkage maps under a tetrasomic model. Genetics 172:2635–2645

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • M’Ribu HK, Veilleux RE (1990) Effect of genotype, explant, subculture interval and environmental conditions on regeneartion of shoots from in vitro monoploids of a diploid potato species, Solanum phureja Juz. & Buk. Plant Cell Tissue Organ Cult 23:171–179

    Google Scholar 

  • Maliepaard C, Jansen J, Van Ooijen JW (1997) Linkage analysis in a full-sib family of an outbreeding plant species: overview and consequences for applications. Genet Res 70:237–250

    Article  Google Scholar 

  • Massa AN, Manrique-Carpintero NC, Coombs JJ, Zarka DG, Boone AE, Kirk WW, Hackett CA, Bryan GJ, Douches DS (2015) Genetic linkage mapping of economically important traits in cultivated tetraploid potato (Solanum tuberosum L.) G3 (Bethesda) 5:2357–2364

  • Mather K (1936) Segregation and linkage in autotetraploids. J Genet 32:287–314

    Article  Google Scholar 

  • Pandey KK (1962) Interspecific incompatibility in Solanum species. Am J Bot 49:874–882

    Article  Google Scholar 

  • Pasare SA, Ducreux LJM, Morris WL, Campell R, Sharma SK, Roumeliotis E, Kohlen W, van der Krol S, Bramley PM, Roberts AG, Fraser PD, Taylor MA (2013) The role of the potato (Solanum tuberosum) CCD8 gene in stolon and tuber development. New Phytol 198:1108–1120

    CAS  Article  PubMed  Google Scholar 

  • Paz M, Veilleux R (1999) Infuence of culture medium and in vitro conditions on shoot regeneration in Solanum phureja monoploids and fertility of regenerated doubled monoploids. Plant Breed 118:53–57

    CAS  Article  Google Scholar 

  • Phumichai C, Mori M, Kobayashi A, Kamijima O, Hosaka K (2005) Toward the development of highly homozygous diploid potato lines using the self-compatibility controlling Sli gene. Genome 48:977–984

    CAS  Article  PubMed  Google Scholar 

  • Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–197

    Article  Google Scholar 

  • Prashar A, Hornyik C, Young V, McLean K, Sharma SK, Dale MFB, Bryan GJ (2014) Construction of a dense SNP map of a highly heterozygous diploid potato population and QTL analysis of tuber shape and eye depth. Theor Appl Genet 127:2159–2171

    Article  PubMed  Google Scholar 

  • Pushkarnath P (1942) Studies on sterility in potatoes. 1. The genetics of self- and cross-incompatibilities. Indian J Genet Plant Breed 2:11–36

    Google Scholar 

  • R Development Core Team (2014) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna

    Google Scholar 

  • Rabiner LR (1989) A tutorial on hidden Markov models and selected applications in speech recognition. Proc IEEE 77:257–286

    Article  Google Scholar 

  • Salaman RN (1910) The inheritance of colour and other characters in the potato. J Genet 1:7–46

    Article  Google Scholar 

  • Sharma SK, Bolser D, de Boer J, Sønderkaer M, Amoros W, Carboni MF, D’Ambrosio JM, de la Cruz G, Di Genova A, Douches DS, Eguiluz M, Guo X, Guzman F, Hackett CA, Hamilton JP, Li G, Li Y, Lozano R, Maass A, Marshall D, Martinez D, McLean K, Mejía N, Milne L, Munive S, Nagy I, Ponce O, Ramirez M, Simon R, Thomson SJ, Torres Y, Waugh R, Zhang Z, Huang S, Visser RGF, Bachem CWB, Sagredo B, Feingold SE, Orjeda G, Veilleux RE, Bonierbale M, Jacobs JME, Milbourne D, Martin DMA, Bryan GJ (2013) Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps. G3 (Bethesda) 3:2031–2047

  • Sowokinos JR, Shock CC, Stieber TD, Eldredge EP (2000) Compositional and enzymatic changes associated with the sugar-end defect in Russet Burbank potatoes. Am J Potato Res 77:47–56

    CAS  Article  Google Scholar 

  • Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: JOINMAP. Plant J 3:739–744

    CAS  Article  Google Scholar 

  • Thompson AL, Love SL, Sowokinos JR, Thornton MK, Shock CC (2008) Review of the sugar end disorder in potato (Solanum tuberosum, L.). Am J Potato Res 85:375–386

    Article  Google Scholar 

  • van Eck HJ, Jacobs JME, Stam P, Ton J, Stiekema WJ, Jacobsen E (1994) Multiple alleles for tuber shape in diploid potato detected by qualitative and quantitative genetic analysis using RFLPs. Genetics 137:303–309

    PubMed  Google Scholar 

  • van Os H, Stam P, Visser RGF, van Eck HJ (2005) RECORD: a novel method for ordering loci on a genetic linkage map. Theor Appl Genet 112:30–40

    CAS  Article  PubMed  Google Scholar 

  • van Os H, Andrzejewski S, Bakker E, Barrena I, Bryan GJ, Caromel B, Ghareeb B, Isidore E, De Jong W, van Koert P, Lefebvre V, Milbourne D, Ritter E, van der Voort J, Rousselle-Bourgeois F, van Vliet J, Waugh R, Visser RGF, Bakker J, van Eck HJ (2006) Construction of a 10,000-marker ultradense genetic recombination map of potato: Providing a framework for accelerated gene isolation and a genomewide physical map. Genetics 173:1075–1087

    Article  PubMed  PubMed Central  Google Scholar 

  • Waldie T, McCulloch H, Leyser O (2014) Strigolactones and the control of plant development: lessons from shoot branching. Plant J 79:607–622

    CAS  Article  PubMed  Google Scholar 

  • Xie W, Feng Q, Yu H, Huang X, Zhao Q, Xing Y, Yu S, Han B, Zhang Q (2010) Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Proc Natl Acad Sci USA 107:10578–10583

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Zhang Y, Jung CS, De Jong WS (2009a) Genetic analysis of pigmented tuber flesh in potato. Theor Appl Genet 119:143–150

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Zhang Y, Cheng S, De Jong D, Griffiths H, Halitschke R, De Jong W (2009b) The potato R locus codes for dihydroflavonol 4-reductase. Theor Appl Genet 119:931–937

    CAS  Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

The authors acknowledge the contributions made by David Douches (Michigan State University), who provided SNP data; Grace Christensen, who extracted DNA for SNP genotyping; Andy Hamernik, who was responsible for the greenhouse and field trials; and Xiaoxi Liu (Ohio State University), who scored tuber shape in 2014. This project was supported by USDA NIFA 2014-67013-22434.

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Correspondence to Shelley H. Jansky.

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The authors declare they have no conflict of interest.

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Communicated by H. J. van Eck.

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Endelman, J.B., Jansky, S.H. Genetic mapping with an inbred line-derived F2 population in potato. Theor Appl Genet 129, 935–943 (2016). https://doi.org/10.1007/s00122-016-2673-7

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  • DOI: https://doi.org/10.1007/s00122-016-2673-7

Keywords

  • Flesh Color
  • Binary Trait
  • Carotenoid Cleavage Dioxygenase
  • Yellow Flesh
  • Potato Genome Sequencing Consortium