A comparison between genotyping-by-sequencing and array-based scoring of SNPs for genomic prediction accuracy in winter wheat

Ibrahim S. Elbasyoni, A. J. Lorenz, M. Guttieri, K. Frels, P. S. Baenziger, J. Poland, E. Akhunov

Research output: Contribution to journalArticlepeer-review

37 Scopus citations


The utilization of DNA molecular markers in plant breeding to maximize selection response via marker-assisted selection (MAS) and genomic selection (GS) has revolutionized plant breeding. A key factor affecting GS applicability is the choice of molecular marker platform. Genotyping-by-sequencing scored SNPs (GBS-scored SNPs) provides a large number of markers, albeit with high rates of missing data. Array scored SNPs are of high quality, but the cost per sample is substantially higher. The objectives of this study were 1) compare GBS-scored SNPs, and array scored SNPs for genomic selection applications, and 2) compare estimates of genomic kinship and population structure calculated using the two marker platforms. SNPs were compared in a diversity panel consisting of 299 hard winter wheat (Triticum aestivum L.) accessions that were part of a multi-year, multi-environments association mapping study. The panel was phenotyped in Ithaca, Nebraska for heading date, plant height, days to physiological maturity and grain yield in 2012 and 2013. The panel was genotyped using GBS-scored SNPs, and array scored SNPs. Results indicate that GBS-scored SNPs is comparable to or better than Array-scored SNPs for genomic prediction application. Both platforms identified the same genetic patterns in the panel where 90% of the lines were classified to common genetic groups. Overall, we concluded that GBS-scored SNPs have the potential to be the marker platform of choice for genetic diversity and genomic selection in winter wheat.

Original languageEnglish (US)
Pages (from-to)123-130
Number of pages8
JournalPlant Science
StatePublished - May 2018

Bibliographical note

Funding Information:
The authors would like to thank the USDA-ARS and Kansas Wheat Alliance for supporting the GBS-scored SNPs genotyping. This research partially supported by USDA-NIFA Triticeae-CAP grant ( 2011-68002-30029 ). The authors would like also to thank Holland Computing Center (University of Nebraska-Lincoln) for using their supercomputer resources in the current publication.

Publisher Copyright:
© 2018 Elsevier B.V.


  • Genomic selection
  • Genotyping by sequencing
  • Single nucleotide polymorphism
  • Wheat


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