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Genomic selection for quantitative adult plant stem rust resistance in wheat [Electronic Resource]

By: Rutkoski, J.E.
Contributor(s): Barbier, H [coaut.] | Jannink, J-L [coaut.] | Poland, J.A [coaut.] | Rouse, M.N [coaut.] | Sorrells, M.E [coaut.] | Huerta-Espino, J [coaut.] | Singh, R.P [coaut.] | Bhavani, S [coaut.].
Material type: materialTypeLabelArticlePublisher: 2014ISSN: 1940-3372 (Revista en electrónico); No.Subject(s): Wheat | Rusts | Nucleotide sequence | Genetic markers | Bayesian theoryOnline resources: Click here to access online In: The Plant GenomeSummary: 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 genomic selection, we characterized a set of CIMMYT germplasm at important APR loci and on a genome-wide profile using genotyping-by-sequencing. 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 lined markers (p-value = 0.12), and ordinary GBLUP (p-value = 0.15). Incorporating seedling phenotype information as fixed effects in GBLUP 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.Collection: General Book Collection
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Article CIMMYT Knowledge Center: John Woolston Library

Lic. Jose Juan Caballero Flores

 

General Book Collection Available
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Peer-review: Yes - Open Access: Yes|http://science.thomsonreuters.com/cgi-bin/jrnlst/jlresults.cgi?PC=MASTER&ISSN=1940-3372

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 genomic selection, we characterized a set of CIMMYT germplasm at important APR loci and on a genome-wide profile using genotyping-by-sequencing. 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 lined markers (p-value = 0.12), and ordinary GBLUP (p-value = 0.15). Incorporating seedling phenotype information as fixed effects in GBLUP 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.

Global Wheat Program

English

INT0610|INT2843

General Book Collection

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