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Identification of agronomically important QTL in tetraploid potato cultivars using a marker–trait association analysis

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Abstract

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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.

Abstract

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.

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Acknowledgments

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.

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Authors and Affiliations

  1. Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands

    Björn B. D’hoop, M. João Paulo, Richard G. F. Visser & Herman J. van Eck

  2. Graduate School of Experimental Plant Sciences, Wageningen, The Netherlands

    Björn B. D’hoop, Richard G. F. Visser & Herman J. van Eck

  3. Centre for BioSystems Genomics (CBSG), Wageningen, The Netherlands

    Björn B. D’hoop, M. João Paulo, Richard G. F. Visser, Fred A. van Eeuwijk & Herman J. van Eck

  4. Biometris, Wageningen University and Research Centre, Wageningen, The Netherlands

    Paul L. C. Keizer, M. João Paulo & Fred A. van Eeuwijk

Authors
  1. Björn B. D’hoop
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  2. Paul L. C. Keizer
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  3. M. João Paulo
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  4. Richard G. F. Visser
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  5. Fred A. van Eeuwijk
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  6. Herman J. van Eck
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Correspondence to Herman J. van Eck.

Additional information

Communicated by C. Gebhardt.

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122_2013_2254_MOESM1_ESM.xls

Table S1. Marker–trait associations detected with the academic panel and 720 mapped AFLPs. In the left part, the associations identified with the baseline model are listed and to the right the ones found with the advanced model. The observed significance “-10logp”, the chromosome, the map position in cM and the marker name are presented as well. (XLS 44 kb)

122_2013_2254_MOESM2_ESM.xls

Table S2. Marker–trait associations detected with the industrial panel and 720 mapped AFLPs. In the left part, the associations identified with the baseline model are listed, and to the right the ones found with the advanced model. The observed significance “-10logp”, the chromosome, the map position in cM and the marker name are presented as well. (XLS 72 kb)

122_2013_2254_MOESM3_ESM.xls

Table S3. Marker–trait associations detected with the academic panel and the comprehensive set. In the left part, the associations identified with the baseline model are listed, and to the right the ones found with the advanced model. The observed significance “- 10logp”, the marker number and the marker name are presented as well. (XLS 80 kb)

122_2013_2254_MOESM4_ESM.xls

Table S4. Marker–trait associations detected with the industrial panel and the comprehensive set. In the left part, the associations identified with the baseline model are listed, and to the right the ones found with the advanced model. The observed significance “- 10logp”, the marker number and the marker name are presented as well. (XLS 227 kb)

Table S5. Marker–trait associations found with 53 microsatellites. (DOCX 13 kb)

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D’hoop, B.B., Keizer, P.L.C., Paulo, M.J. et al. Identification of agronomically important QTL in tetraploid potato cultivars using a marker–trait association analysis. Theor Appl Genet 127, 731–748 (2014). https://doi.org/10.1007/s00122-013-2254-y

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