Identification of agronomically important QTL in tetraploid potato cultivars using a marker–trait association analysis
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Nineteen tuber quality traits in potato were phenotyped in 205 cultivars and 299 breeder clones. Association analysis using 3364 AFLP loci and 653 SSR-alleles identified QTL for these traits.
Two association mapping panels were analysed for marker–trait associations to identify quantitative trait loci (QTL). The first panel comprised 205 historical and contemporary tetraploid potato cultivars that were phenotyped in field trials at two locations with two replicates (the academic panel). The second panel consisted of 299 potato cultivars and included recent breeds obtained from five Dutch potato breeding companies and reference cultivars (the industrial panel). Phenotypic data for the second panel were collected during subsequent clonal selection generations at the individual breeding companies. QTL were identified for 19 agro-morphological and quality traits. Two association mapping models were used: a baseline model without, and a more advanced model with correction for population structure and genetic relatedness. Correction for population structure and genetic relatedness was performed with a kinship matrix estimated from marker information. The detected QTL partly not only confirmed previous studies, e.g. for tuber shape and frying colour, but also new QTL were found like for after baking darkening and enzymatic browning. Pleiotropic effects could be discerned for several QTL.
KeywordsQuantitative Trait Locus Association Mapping Phenotypic Analysis Flesh Colour Trait Association
We thank Agrico Research B. V. (Bant, Netherlands), Averis Seeds B. V. (Valthermond, Netherlands), C. Meijer B. V. (Rilland, Netherlands), HZPC Holland B. V. (Metslawier, Netherlands) and KWS Potato B. V. (Emmeloord, Netherlands) for providing tuber material, sharing phenotypic data and for their help in the academic trial. We acknowledge the genebanks Agriculture and Agri-Food (Canada), Arche Noah (Austria), IPK Gatersleben (Germany), INRA (France), SASA (Scotland), Teagasc (Ireland) and USDA-ARS (USA) for providing scarce heirloom potato cultivars. This study was financed as project P8 and PP2 by the Centre for BioSystems Genomics (CBSG), which is part of the Netherlands Genomics Initiative, Netherlands Organization for Scientific Research for financing this study. Fred van Eeuwijk and Paul Keizer worked wholly and João Paulo partially on this paper within the context of the CBSG projects BB9 and BB12.
Conflict of interest
The authors declare that they have no conflict of interest.
- Bradshaw JE, Pande B, Bryan GJ, Hackett CA, McLean K 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 168:983–995PubMedCrossRefGoogle Scholar
- Breseghello F, Sorrells ME (2006a) Association analysis as a strategy for improvement of quantitative traits in plants. CropSci 46:1323–1330Google Scholar
- Fischer M, Schreiber L, Colby T, Kuckenberg M, Tacke E, Hofferbert H-R, Schmidt J, Gebhardt C (2013) Novel candidate genes influencing natural variation in potato tuber cold sweetening identified by comparative proteomics and association mapping. BMC Plant Biol 13(1):113PubMedCentralPubMedCrossRefGoogle Scholar
- Gebhardt C, Ballvora A, Walkemeier B, Oberhagemann P, Schuler K (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 13:93–102CrossRefGoogle Scholar
- Gebhardt C, Menendez CM, Chen X, Li L, Schäfer-Pregl R et al (2005) Genomic approaches for the improvement of tuber quality traits in potato. Acta Hortic 684:85–92Google Scholar
- Jannink JL, Walsh B (2002) Association mapping in plant populations. In: Kang MS (ed) Quantitative genetics, genomics and plant breeding, chap 5. CABI, UK, pp 59–68 Google Scholar
- Kloosterman B, Abelenda JA, del Mar Carretero Gomez M, Oortwijn M, de Boer JM, Kowitwanich K, Horvath BM, van Eck HJ, Smaczniak C, Prat S, Visser RGF, Bachem CWB (2013) Naturally occurring allele diversity allows potato cultivation in northern latitudes. Nature 495(7440):246–250PubMedCrossRefGoogle Scholar
- Lindhout P, Meijer D, Schotte T, Hutten RCB, Visser RGF, van Eck HJ (2011) Towards F1 hybrid seed potato breeding. Potato Res 54(4):301–312Google Scholar
- Lu H, Redus MA, Coburn JR, Rutger JN, McCouch SR et al (2005) Population structure and breeding patterns of 145 US rice cultivars based on SSR marker analysis. CropSci 45:66–76Google Scholar
- Montgomery DC, Peck EA, Vining GG (2001) Introduction to linear regression analysis. John Wiley & Sons Inc., New York, p 641Google Scholar
- Thomas WTB, Powell W, Waugh R, Chalmers KJ, Barua UM, Jack P, Lea V, Forster BP, Swanston JS, Ellis RP, Hanson PR, Lance RCM (1995) Detection of quantitative trait loci for agronomic, yield, grain and disease characters in spring barley (Hordeum vulgare L.). Theor Appl Genet 91:1037–1047PubMedGoogle Scholar
- Urbany C, Stich B, Schmidt L, Simon L, Berding H, Junghans H, Niehoff K-H, Braun A, Tacke E, Hofferbert H-R, Lübeck J, Strahwald J, Gebhardt C (2011) Association genetics in Solanum tuberosum provides new insights into potato tuber bruising and enzymatic tissue discoloration. BMC Genom 12:7CrossRefGoogle Scholar
- Verbeke G, Molenberghs G (2000) Mixed models for longitudinal data. Springer, Berlin, p 568Google Scholar