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ARS Home » Plains Area » Manhattan, Kansas » Center for Grain and Animal Health Research » Hard Winter Wheat Genetics Research » Research » Publications at this Location » Publication #343772
Title: A comparison between genotyping-by-sequencing and array-based scoring of SNPs for genomic prediction accuracy in winter wheat

Author
item EL-BASYONI, IBRAHIM - Damanhour University
item LORENZ, AARON - University Of Minnesota
item Guttieri, Mary
item FRELS, KATHERINE - University Of Minnesota
item BAENZIGER, P. STEPHEN - University Of Nebraska
item POLAND, JESSE - Kansas State University
item AKHUNOV, EDUARD - Kansas State University

Submitted to: Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/17/2018
Publication Date: 2/21/2018
Citation: El-Basyoni, I., Lorenz, A.J., Guttieri, M.J., Frels, K., Baenziger, P., Poland, J., Akhunov, E. 2018. A comparison between genotyping-by-sequencing and array-based scoring of SNPs for genomic prediction accuracy in winter wheat. Plant Science. 270:123-130. https://doi.org/10.1016/j.plantsci.2018.02.019.
DOI: https://doi.org/10.1016/j.plantsci.2018.02.019

Interpretive Summary: One goal of modern wheat breeding is to predict the field performance of wheat experimental lines without field plot testing, which is costly and limits the number of offspring of a cross of two parents that can be tested. Genomic selection is an approach that uses the genetic relationship among wheat lines and an incomplete set of field testing data in order to predict the performance of all of the lines that were fingerprinted. This approach requires data for a very large number of distinctive DNA markers. The question addressed by this study is whether two techniques for collecting these DNA sequence differences are equally effective. One technique, genotyping array technology, tests for a specific, predetermined set of DNA sequences. The other technique, Genotyping-by-Sequencing (GBS), identifies differences between lines based on DNA sequencing information that is not predetermined. Both methods have strengths and weaknesses. A set of 299 winter wheats were characterized for plant height, flowering time, time to maturation, and grain yield. The conclusion of the analysis was that the two methods of collecting DNA sequence difference, genotyping array technology, and genotyping by sequencing, were similarly effective in predicting the wheat performance.

Technical Abstract: The utilization of DNA molecular markers in plant breeding to maximize selection response via marker assisted selection (MAS) and genomic selection (GS) has the potential to revolutionize plant breeding. A key factor affecting GS applicability is the choice of molecular marker platform. Genotypying-by-sequencing scored SNPs (GBS-scored SNPs) provides large number of markers, albeit with high rates of missing data. While array scored SNPs are of high quality, but often the cost per sample is substantially higher. The objectives of the this study were 1) compare GBS-scored SNPs and array scored SNPs in terms of appropriateness for genomic selection; and 2) compare estimates of genomic kinship and population structure calculated using the two marker platforms. A diversity panel consisting of 299 hard winter wheat (Triticum aestivum L) accessions that was part of a TCAP (Triticeae Coordinated Agricultural Project) multi-year, multi-environments association mapping study was used. The panel was phenotyped in Ithaca, eastern 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 and array scored SNPs are equivalent for genomic prediction application; and identifying same genetic patterns in the panel in which 90% of the lines were classified to common genetic groups across the two marker platforms. Overall we concluded that GBS-scored SNPs has the potential to be the marker platform of choice for genetic diversity and genomic selection in winter wheat.