Open AccessGenomic Selection for Quantitative Adult Plant Stem Rust Resistance in Wheat
Author(s) -
Rutkoski Jessica E.,
Poland Jesse A.,
Singh Ravi P.,
HuertaEspino Julio,
Bhavani Sridhar,
Barbier Hugues,
Rouse Matthew N.,
Jannink JeanLuc,
Sorrells Mark E.
Publication year - 2014
Publication title -
the plant genome
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.403
H-Index - 41
ISSN - 1940-3372
DOI - 10.3835/plantgenome2014.02.0006
Subject(s) - best linear unbiased prediction , biology , germplasm , stem rust , selection (genetic algorithm) , puccinia , plant breeding , genetics , agronomy , botany , gene , machine learning , computer science , mildew
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 Cπ (BCπ). 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.