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

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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.

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Abbreviations

IHN:

Internal heat necrosis

SNP:

Single-nucleotide polymorphism

QTL:

Quantitative trait loci

MAS:

Marker-assisted selection

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Acknowledgements

This paper was submitted as part of an MS research project. We would like to thank all the staff at the North Carolina Department of Agriculture and Consumer Services Tidewater Research Station, Plymouth, NC for their hard work and dedication to quality research in aiding with the field aspect of this study. We would like to thank the Michigan State University Potato Breeding and Genetics Program for their assistance with the Illumina Infinium® 8303 potato array. We would like to thank Dr. Christine Hackett for her assistance with TetraploidMap. We would like to thank USDA-ARS and USDA-NIFA for project funding. We would also like to thank Pioneer and Monsanto for providing graduate student fellowships to support the student who worked on this project. Funding was provided by Agricultural Research Service (Grant Nos. 58-1245-3-307, 2014-34141-22266), National Institute of Food and Agriculture (Grant No. 2013-34141-21392), and Monsanto Plant Breeding Fellowship.

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Authors and Affiliations

  1. Department of Horticultural Science, North Carolina State University, 214A Kilgore Hall, Box 7609, Raleigh, NC, 27695-7609, USA

    Mitchell J. Schumann & G. Craig Yencho

  2. Bioinformatics Research Center, North Carolina State University, 1 Lampe Drive, Box 7566, Raleigh, NC, 27695-7566, USA

    Zhao-Bang Zeng

  3. Department of Horticultural Science, North Carolina State University - Vernon James Research and Extension Center, 207 Research Station Road, Plymouth, NC, 27962-9526, USA

    Mark E. Clough

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  1. Mitchell J. Schumann
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  2. Zhao-Bang Zeng
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  3. Mark E. Clough
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  4. G. Craig Yencho
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Correspondence to G. Craig Yencho.

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The authors declare that they have no conflict of interest.

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Communicated by Herman J. van Eck.

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Schumann, M.J., Zeng, ZB., Clough, M.E. et al. Linkage map construction and QTL analysis for internal heat necrosis in autotetraploid potato. Theor Appl Genet 130, 2045–2056 (2017). https://doi.org/10.1007/s00122-017-2941-1

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