Genomic selection for quantitative adult plant stem rust resistance in wheat

Jessica E. Rutkoski, Jesse A. Poland, Ravi P. Singh, Julio Huerta-Espino, Sridhar Bhavani, Hugues Barbier, Matthew N. Rouse, Jean Luc Jannink, Mark E. Sorrells

Research output: Contribution to journalArticle

Abstract

Quantitative adult plant resistance (APR) to stem rust (Puccinia graminis f. sp. tritici) is an important breeding target in wheat (Triticum aestivum L.) and a potential target for genomic selection (GS). To evaluate the relative importance of known APR loci in applying GS, we characterized a set of CIMMYT germplasm at important APR loci and on a genome-wide profile using genotyping-by-sequencing (GBS). Using this germplasm, we describe the genetic architecture and evaluate prediction models for APR using data from the international Ug99 stem rust screening nurseries. Prediction models incorporating markers linked to important APR loci and seedling phenotype scores as fixed effects were evaluated along with the classic prediction models: Multiple linear regression (MLR), Genomic best linear unbiased prediction (G-BLUP), Bayesian Lasso (BL), and Bayes Cp (BCp). We found the Sr2 region to play an important role in APR in this germplasm. A model using Sr2 linked markers as fixed effects in G-BLUP was more accurate than MLR with Sr2 linked markers (p-value = 0.12), and ordinary G-BLUP (p-value = 0.15). Incorporating seedling phenotype information as fixed effects in G-BLUP did not consistently increase accuracy. Overall, levels of prediction accuracy found in this study indicate that GS can be effectively applied to improve stem rust APR in this germplasm, and if genotypes at Sr2 linked markers are available, modeling these genotypes as fixed effects could lead to better predictions.

Original languageEnglish (US)
JournalPlant Genome
Volume7
Issue number3
DOIs
StatePublished - Nov 1 2014
Externally publishedYes

Fingerprint

Plant Stems
stem rust
mature plants
marker-assisted selection
Triticum
wheat
prediction
germplasm
genomics
Seedlings
Linear Models
Genotype
loci
Phenotype
Bayes Theorem
Nurseries
Puccinia graminis
phenotype
seedlings
Breeding

ASJC Scopus subject areas

  • Genetics
  • Agronomy and Crop Science
  • Plant Science

Cite this

Rutkoski, J. E., Poland, J. A., Singh, R. P., Huerta-Espino, J., Bhavani, S., Barbier, H., ... Sorrells, M. E. (2014). Genomic selection for quantitative adult plant stem rust resistance in wheat. Plant Genome, 7(3). https://doi.org/10.3835/plantgenome2014.02.0006

Genomic selection for quantitative adult plant stem rust resistance in wheat. / Rutkoski, Jessica E.; Poland, Jesse A.; Singh, Ravi P.; Huerta-Espino, Julio; Bhavani, Sridhar; Barbier, Hugues; Rouse, Matthew N.; Jannink, Jean Luc; Sorrells, Mark E.

In: Plant Genome, Vol. 7, No. 3, 01.11.2014.

Research output: Contribution to journalArticle

Rutkoski, JE, Poland, JA, Singh, RP, Huerta-Espino, J, Bhavani, S, Barbier, H, Rouse, MN, Jannink, JL & Sorrells, ME 2014, 'Genomic selection for quantitative adult plant stem rust resistance in wheat', Plant Genome, vol. 7, no. 3. https://doi.org/10.3835/plantgenome2014.02.0006
Rutkoski, Jessica E. ; Poland, Jesse A. ; Singh, Ravi P. ; Huerta-Espino, Julio ; Bhavani, Sridhar ; Barbier, Hugues ; Rouse, Matthew N. ; Jannink, Jean Luc ; Sorrells, Mark E. / Genomic selection for quantitative adult plant stem rust resistance in wheat. In: Plant Genome. 2014 ; Vol. 7, No. 3.
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