Pedigree Reconstruction with Genome-Wide Markers in Potato

Jeffrey B. Endelman; Cari A. Schmitz Carley; David S. Douches; Joseph J. Coombs; Benoit Bizimungu; Walter S. De Jong; Kathleen G. Haynes; David G. Holm; J. Creighton Miller; Richard G. Novy; Jiwan P. Palta; David L. Parish; Gregory A. Porter; Vidyasagar R. Sathuvalli; Asunta L. Thompson; G. Craig Yencho

doi:10.1007/s12230-016-9556-y

Pedigree Reconstruction with Genome-Wide Markers in Potato

Jeffrey B. Endelman, Cari A. Schmitz Carley, David S. Douches, Joseph J. Coombs, Benoit Bizimungu, Walter S. De Jong, Kathleen G. Haynes, David G. Holm, J. Creighton Miller, Richard G. Novy, Jiwan P. Palta, David L. Parish, Gregory A. Porter, Vidyasagar R. Sathuvalli, Asunta L. Thompson, G. Craig Yencho

Horticultural Science

Research output: Contribution to journal › Article › peer-review

13 Scopus citations

Abstract

Reliable pedigree information facilitates a scientific approach to breeding, but errors can be introduced in many stages of a breeding program. Our objective was to use single nucleotide polymorphisms (SNPs) to check the pedigree records of elite North American potato germplasm. A population of 719 tetraploids was genotyped with an Infinium SNP array, yielding 5063 high-quality markers. Based on pedigree records, the dataset contained 198 parent-offspring trios, of which 182 were consistent with the marker data. For 13 of the 16 trios with a pedigree error, the true parent was identified in the population. By comparing the additive relationship matrix calculated from pedigree with the genetic distance calculated from markers, an additional 24 pedigree modifications were proposed, including the paternity of several varieties developed with bulk pollen. To ensure accurate pedigree records are published in the future, we recommend that new varieties be SNP genotyped and checked against this dataset.

Original language	English (US)
Pages (from-to)	184-190
Number of pages	7
Journal	American Journal of Potato Research
Volume	94
Issue number	2
DOIs	https://doi.org/10.1007/s12230-016-9556-y
State	Published - Apr 1 2017

Bibliographical note

Funding Information:
Financial support for this research was provided by Potatoes USA (formerly the U.S. Potato Board), state potato industry boards, the National Chip and Fry Processing Trial consortia, and USDA-NIFA-Hatch Project Number 1002731. The authors thank Felix Navarro and Horia Groza for contributing pedigree records.

Publisher Copyright:
© 2017, The Potato Association of America.

Keywords

Pedigrees
SNPs
Solanum tuberosum

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10.1007/s12230-016-9556-y

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Endelman, J. B., Schmitz Carley, C. A., Douches, D. S., Coombs, J. J., Bizimungu, B., De Jong, W. S., Haynes, K. G., Holm, D. G., Miller, J. C., Novy, R. G., Palta, J. P., Parish, D. L., Porter, G. A., Sathuvalli, V. R., Thompson, A. L., & Yencho, G. C. (2017). Pedigree Reconstruction with Genome-Wide Markers in Potato. American Journal of Potato Research, 94(2), 184-190. https://doi.org/10.1007/s12230-016-9556-y

Endelman, JB, Schmitz Carley, CA, Douches, DS, Coombs, JJ, Bizimungu, B, De Jong, WS, Haynes, KG, Holm, DG, Miller, JC, Novy, RG, Palta, JP, Parish, DL, Porter, GA, Sathuvalli, VR, Thompson, AL & Yencho, GC 2017, 'Pedigree Reconstruction with Genome-Wide Markers in Potato', American Journal of Potato Research, vol. 94, no. 2, pp. 184-190. https://doi.org/10.1007/s12230-016-9556-y

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abstract = "Reliable pedigree information facilitates a scientific approach to breeding, but errors can be introduced in many stages of a breeding program. Our objective was to use single nucleotide polymorphisms (SNPs) to check the pedigree records of elite North American potato germplasm. A population of 719 tetraploids was genotyped with an Infinium SNP array, yielding 5063 high-quality markers. Based on pedigree records, the dataset contained 198 parent-offspring trios, of which 182 were consistent with the marker data. For 13 of the 16 trios with a pedigree error, the true parent was identified in the population. By comparing the additive relationship matrix calculated from pedigree with the genetic distance calculated from markers, an additional 24 pedigree modifications were proposed, including the paternity of several varieties developed with bulk pollen. To ensure accurate pedigree records are published in the future, we recommend that new varieties be SNP genotyped and checked against this dataset.",

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N1 - Funding Information: Financial support for this research was provided by Potatoes USA (formerly the U.S. Potato Board), state potato industry boards, the National Chip and Fry Processing Trial consortia, and USDA-NIFA-Hatch Project Number 1002731. The authors thank Felix Navarro and Horia Groza for contributing pedigree records. Publisher Copyright: © 2017, The Potato Association of America.

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N2 - Reliable pedigree information facilitates a scientific approach to breeding, but errors can be introduced in many stages of a breeding program. Our objective was to use single nucleotide polymorphisms (SNPs) to check the pedigree records of elite North American potato germplasm. A population of 719 tetraploids was genotyped with an Infinium SNP array, yielding 5063 high-quality markers. Based on pedigree records, the dataset contained 198 parent-offspring trios, of which 182 were consistent with the marker data. For 13 of the 16 trios with a pedigree error, the true parent was identified in the population. By comparing the additive relationship matrix calculated from pedigree with the genetic distance calculated from markers, an additional 24 pedigree modifications were proposed, including the paternity of several varieties developed with bulk pollen. To ensure accurate pedigree records are published in the future, we recommend that new varieties be SNP genotyped and checked against this dataset.

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Pedigree Reconstruction with Genome-Wide Markers in Potato

Abstract

Bibliographical note

Keywords

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