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QTL mapping of potato chip color and tuber traits within an autotetraploid family

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Abstract

Cultivated potato (Solanum tuberosum L.) is a highly heterozygous autotetraploid crop species, and this creates challenges for traditional line development and molecular breeding. Recent availability of a single-nucleotide polymorphism (SNP) array with 8303 features and software packages for linkage and association mapping in autotetraploid species present new opportunities for the identification of genomic regions that contribute to high-value traits in cultivated potato. A biparental tetraploid potato population was evaluated across three field seasons and storage trials in order to identify quantitative trait loci (QTL) for multiple tuber traits including fried chip color after 5.5–7.2 °C storage. Tetra-allelic dosage information was used to construct a genetic linkage map that covered 1041 cM and contained 2095 SNP markers with a median marker interval of 0.4 cM. A total of 41 QTL were identified for flower color, tuber yield, tuber number per plant, tuber weight, tuber size, and chip color after various storage regimes. Moderate effect QTL for chip color at 3 months were identified that co-localized with candidate genes vacuolar invertase (VInv), invertase inhibitor (INH2), and apoplastic invertase (Inv ap -b). A separate QTL for chip color after 6 months of storage was identified in the short arm of chromosome 2, and this locus may contribute to variation in senescent sweetening resistance. QTL for tuber weight, length, and width co-localized with a known QTL for plant maturity on chromosome 5. Genome-wide association mapping using a polyploid model detected the tuber size QTL and identified a number of candidate SNPs, but was unable to detect markers significantly associated with chip color.

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References

  • Bhaskar PB, Wu L, Busse JS et al (2010) Suppression of the vacuolar invertase gene prevents cold-induced sweetening in potato. Plant Physiol 154:939–948. doi:10.1104/pp.110.162545

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bourke PM (2014) QTL analysis in polyploids: model testing and power calculations for an autotetraploid. In: Minor thesis (MSc) plant breeding. University and Research Centre, Wageningen

    Google Scholar 

  • Bradshaw JE, Hackett CA, Pande B et al (2008) QTL mapping of yield, agronomic and quality traits in tetraploid potato (Solanum tuberosum subsp. tuberosum). Theor Appl Genet 116:193–211. doi:10.1007/s00122-007-0659-1

    Article  PubMed  Google Scholar 

  • Bradshaw JE, Pande B, Bryan GJ et al (2004) Interval mapping of quantitative trait loci for resistance to late blight [Phytophthora infestans (Mont.) de Bary], height and maturity in a tetraploid population of potato (Solanum tuberosum subsp. tuberosum). Genetics 168:983–995. doi:10.1534/genetics.104.030056

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Braun SR (2013) Quantitative trait loci analysis and breeding for resistance to common scab in potato. Ph.D. Thesis, University of Wisconsin--Madison

  • Brummell DA, Chen RKY, Harris JC et al (2011) Induction of vacuolar invertase inhibitor mRNA in potato tubers contributes to cold-induced sweetening resistance and includes spliced hybrid mRNA variants. J Exp Bot 62:3519–3534. doi:10.1093/jxb/err043

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Burton WG (1989a) Post-harvest physiology. In: The potato, 3rd edn. John Wiley & Sons, Inc., New York, pp 423–522

    Google Scholar 

  • Burton WG (1989b) Yield and content of dry matter. In: The potato, 3rd edn. John Wiley & Sons, Inc., New York, pp 84–268

    Google Scholar 

  • Cattell RB (1966) The scree test for the number of factors. Multivar Behav Res 1:245–276. doi:10.1207/s15327906mbr0102_10

    Article  CAS  Google Scholar 

  • Cochran WG, Cox GM (1992) Experimental Designs, 2nd edn. Wiley, New York

    Google Scholar 

  • Coffin RH, Yada RY, Parkin KL et al (1987) Effect of low temperature storage on sugar concentrations and chip color of certain processing potato cultivars and selections. J Food Sci 52:639–645. doi:10.1111/j.1365-2621.1987.tb06692.x

    Article  Google Scholar 

  • Colgan R, Rees D (2012) Research review: senescent sweetening. Agriculture and Horticulture Development Board. Natural Resources Institute, Stoneleigh Park, UK

    Google Scholar 

  • Collins A, Milbourne D, Ramsay L et al (1999) QTL for field resistance to late blight in potato are strongly correlated with maturity and vigour. Mol Breed 5:387–398. doi:10.1023/A:1009601427062

    Article  CAS  Google Scholar 

  • D’hoop BB, Keizer PLC, Paulo MJ et al (2014) Identification of agronomically important QTL in tetraploid potato cultivars using a marker–trait association analysis. Theor Appl Genet 127:731–748. doi:10.1007/s00122-013-2254-y

    Article  PubMed  Google Scholar 

  • Danan S, Veyrieras J-B, Lefebvre V (2011) Construction of a potato consensus map and QTL meta-analysis offer new insights into the genetic architecture of late blight resistance and plant maturity traits. BMC Plant Biol 11:16. doi:10.1186/1471-2229-11-16

    Article  PubMed  PubMed Central  Google Scholar 

  • Douches D, Hirsch CN, Manrique-Carpintero NC, et al. (2014) The contribution of the solanaceae coordinated agricultural project to potato breeding. Potato Res 1–10. doi: 10.1007/s11540–014-9267-z

  • Douches DS, Freyre R (1994) Identification of genetic factors influencing chip color in diploid potato (solanum spp.). Am Potato J 71:581–590. doi:10.1007/BF02851523

    Article  Google Scholar 

  • Endelman JB (2011) Ridge regression and other kernels for genomic selection with R package rrBLUP. Plant Genome J 4:250. doi:10.3835/plantgenome2011.08.0024

    Article  Google Scholar 

  • Fischer M, Kuckenberg M, Kastilan R et al (2015) Novel in vitro inhibitory functions of potato tuber proteinaceous inhibitors. Mol Gen Genomics 290:387–398. doi:10.1007/s00438-014-0906-5

    Article  CAS  Google Scholar 

  • Gebhardt C, Ballvora A, Walkemeier B et al (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. Mol Breed 13:93–102. doi:10.1023/B:MOLB.0000012878.89855.df

    Article  CAS  Google Scholar 

  • Gebhardt C, Menendez C, Chen X et al (2005) Genomic approaches for the improvement of tuber quality traits in potato. International Society for Horticulture Science In Proc of the Meetings of the Physiol Section of the European Assoc for Potato Res 684:85–91

    CAS  Google Scholar 

  • Gebhardt C, Urbany C, Stich B (2014) Dissection of potato complex traits by linkage and association genetics as basis for developing molecular diagnostics in breeding programs. In: Genomics of plant genetic resources. pp 47–85

  • Glaczinski H, Heibges A, Salamini F, Gebhardt C (2002) Members of the Kunitz-type protease inhibitor gene family of potato inhibit soluble tuber invertase in vitro. Potato Res 45:163–176. doi:10.1007/BF02736112

    Article  CAS  Google Scholar 

  • Hackett CA, Bradshaw JE, Bryan GJ (2014) QTL mapping in autotetraploids using SNP dosage information. Theor Appl Genet 127:1885–1904. doi:10.1007/s00122-014-2347-2

    Article  PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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:e63939. doi:10.1371/journal.pone.0063939

    Article  PubMed  PubMed Central  Google Scholar 

  • Hackett CA, Milne I, Bradshaw JE, Luo Z (2007) TetraploidMap for windows: linkage map construction and QTL mapping in autotetraploid species. J Hered 98:727–729. doi:10.1093/jhered/esm086

    Article  CAS  PubMed  Google Scholar 

  • Hamilton JP, Hansey CN, Whitty BR et al (2011) Single nucleotide polymorphism discovery in elite north american potato germplasm. BMC Genomics 12:302. doi:10.1186/1471-2164-12-302

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jansen RC (1992) A general mixture model for mapping quantitative trait loci by using molecular markers. Theor Appl Genet 85:252–260. doi:10.1007/BF00222867

    CAS  PubMed  Google Scholar 

  • Li L, Paulo M-J, Strahwald J et al (2008) Natural DNA variation at candidate loci is associated with potato chip color, tuber starch content, yield and starch yield. Theor Appl Genet 116:1167–1181. doi:10.1007/s00122-008-0746-y

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li L, Strahwald J, Hofferbert H-R et al (2005) DNA variation at the invertase locus invGE/GF is associated with tuber quality traits in populations of potato breeding clones. Genetics 170:813–821. doi:10.1534/genetics.104.040006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lin C-S, Poushinsky G (1985) A modified augmented design (type 2) for rectangular plots. Can J Plant Sci 65:743–749. doi:10.4141/cjps85-094

    Article  Google Scholar 

  • Lindqvist-Kreuze H, Gastelo M, Perez W et al (2014) Phenotypic stability and genome-wide association study of late blight resistance in potato genotypes adapted to the tropical highlands. Phytopathology 104:624–633. doi:10.1094/PHYTO-10-13-0270-R

    Article  PubMed  Google Scholar 

  • Liu X, Lin Y, Liu J et al (2013) StInvInh2 as an inhibitor of StvacINV1 regulates the cold-induced sweetening of potato tubers by specifically capping vacuolar invertase activity. Plant Biotechnol J 11:640–647. doi:10.1111/pbi.12054

    Article  CAS  PubMed  Google Scholar 

  • Love SL, Pavek JJ, Thompson-Johns A, Bohl W (1998) Breeding progress for potato chip quality in north American cultivars. Am J Potato Res 75:27–36. doi:10.1007/BF02883514

    Article  Google Scholar 

  • Luo ZW, Hackett CA, Bradshaw JE et al (2001) Construction of a genetic linkage map in tetraploid species using molecular markers. Genetics 157:1369–1385

    CAS  PubMed  PubMed Central  Google Scholar 

  • Matsuura-Endo C, Kobayashi A, Noda T et al (2004) Changes in sugar content and activity of vacuolar acid invertase during low-temperature storage of potato tubers from six Japanese cultivars. J Plant Res 117:131–137. doi:10.1007/s10265-003-0137-z

    Article  CAS  PubMed  Google Scholar 

  • McCord PH, Sosinski BR, Haynes KG et al (2011a) QTL mapping of internal heat necrosis in tetraploid potato. Theor Appl Genet 122:129–142. doi:10.1007/s00122-010-1429-z

    Article  CAS  PubMed  Google Scholar 

  • McCord PH, Sosinski BR, Haynes KG et al (2011b) Linkage mapping and QTL analysis of agronomic traits in tetraploid potato (Solanum tuberosum subsp. tuberosum). Crop Sci 51:771–785. doi:10.2135/cropsci2010.02.0108

    Article  CAS  Google Scholar 

  • Menéndez CM, Ritter E, Schäfer-Pregl R et al (2002) Cold sweetening in diploid potato: mapping quantitative trait loci and candidate genes. Genetics 162:1423–1434

    PubMed  PubMed Central  Google Scholar 

  • Muktar MS (2014) Using comparative transcript profiling and association mapping to detect QTLs and diagnostic SNP markers for maturity corrected resistance to Phytophthora infestans in potato (Solanum tuberosum L.). Ph.D. Thesis, Universität zu Köln

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

    Article  CAS  PubMed  Google Scholar 

  • Ou Y, Song B, Liu X et al (2013) Profiling of StvacINV1 expression in relation to acid invertase activity and sugar accumulation in potato cold-stored tubers. Potato Res 56:157–165. doi:10.1007/s11540-013-9237-x

    Article  CAS  Google Scholar 

  • Pressey R (1969) Role of invertase in the accumulation of sugars in cold-stored potatoes. Am Potato J 46:291–297. doi:10.1007/BF02877144

    Article  CAS  Google Scholar 

  • Qiagen (2012) DNeasy Plant Handbook

  • R Development Core Team (2011) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria

    Google Scholar 

  • Rabiner L (1989) A tutorial on hidden Markov models and selected applications in speech recognition. Proc IEEE 77:257–286. doi:10.1109/5.18626

    Article  Google Scholar 

  • Rak K, Palta JP (2015) Influence of mating structure on agronomic performance, chip fry color, and genetic distance among biparental tetraploid families. Amer J Potato Res 92:518–535

    Article  Google Scholar 

  • Rosyara UR (2015) Genome-wide association studies for autopolyploids - potato. Poster-- Plant and Animal Genome Conference XXV, San Diego, CA

    Google Scholar 

  • Schönhals EM (2014) Identifying novel diagnostic SNP markers for potato (Solanum tuberosum L.) tuber starch and yield by association mapping. Ph.D. Thesis, Universität zu Köln

  • Schwarz G (1978) Estimating the dimension of a model. Ann Stat 6:461–464. doi:10.1214/aos/1176344136

    Article  Google Scholar 

  • Sharma SK, Bolser D, de Boer J et al (2013) Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps. G3 GenesGenomesGenetics 3:2031–2047. doi:10.1534/g3.113.007153

    Article  Google Scholar 

  • Sowokinos JR, Orr PH, Knoper JA, Varns JL (1987) Influence of potato storage and handling stress on sugars, chip quality and integrity of the starch (amyloplast) membrane. Am Potato J 64:213–226. doi:10.1007/BF02853559

    Article  Google Scholar 

  • Staaf J, Vallon-Christersson J, Lindgren D et al (2008) Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios. BMC Bioinformatics 9:409. doi:10.1186/1471-2105-9-409

    Article  PubMed  PubMed Central  Google Scholar 

  • Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: join map. Plant J 3:739–744. doi:10.1111/j.1365-313X.1993.00739.x

    Article  CAS  Google Scholar 

  • USDA Economic Research Service (2014) Vegetables and pulses data: Potatoes. http://www.ers.usda.gov/topics/crops/vegetables-pulses/potatoes.aspx. Accessed 9 Feb 2015

  • Van Os H, Andrzejewski S, Bakker E et al (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. doi:10.1534/genetics.106.055871

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wiberley-Bradford AE, Busse JS, Jiang J, Bethke PC (2014) Sugar metabolism, chip color, invertase activity, and gene expression during long-term cold storage of potato (Solanum tuberosum) tubers from wild-type and vacuolar invertase silencing lines of Katahdin. BMC Res Notes 7:801. doi:10.1186/1756-0500-7-801

    Article  PubMed  PubMed Central  Google Scholar 

  • Yu J, Pressoir G, Briggs WH et al (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203–208. doi:10.1038/ng1702

    Article  CAS  PubMed  Google Scholar 

  • Zhu X, Richael C, Chamberlain P et al (2014) Vacuolar invertase gene silencing in potato (Solanum tuberosum L.) improves processing quality by decreasing the frequency of sugar-end defects. PLoS One 9:e93381. doi:10.1371/journal.pone.0093381

    Article  PubMed  PubMed Central  Google Scholar 

  • Zorrilla C (2013) Understanding the genetics of potato tuber calcium and its implications in breeding for improved quality. Ph.D. Thesis, University of Wisconsin--Madison

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Authors and Affiliations

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

    Kyle Rak, Paul C. Bethke & Jiwan P. Palta

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

    Paul C. Bethke

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  1. Kyle Rak
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  2. Paul C. Bethke
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Correspondence to Jiwan P. Palta.

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Rak, K., Bethke, P.C. & Palta, J.P. QTL mapping of potato chip color and tuber traits within an autotetraploid family. Mol Breeding 37, 15 (2017). https://doi.org/10.1007/s11032-017-0619-7

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