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Evaluation of Genomic Prediction for Pasmo Resistance in Flax

Pasmo (Septoria linicola) is a fungal disease causing major losses in seed yield and quality and stem fibre quality in flax. Pasmo resistance (PR) is quantitative and has low heritability. To improve PR breeding efficiency, the accuracy of genomic prediction (GP) was evaluated using a diverse worldw...

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Autores principales: He, Liqiang, Xiao, Jin, Rashid, Khalid Y., Jia, Gaofeng, Li, Pingchuan, Yao, Zhen, Wang, Xiue, Cloutier, Sylvie, You, Frank M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6359301/
https://www.ncbi.nlm.nih.gov/pubmed/30654497
http://dx.doi.org/10.3390/ijms20020359
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author He, Liqiang
Xiao, Jin
Rashid, Khalid Y.
Jia, Gaofeng
Li, Pingchuan
Yao, Zhen
Wang, Xiue
Cloutier, Sylvie
You, Frank M.
author_facet He, Liqiang
Xiao, Jin
Rashid, Khalid Y.
Jia, Gaofeng
Li, Pingchuan
Yao, Zhen
Wang, Xiue
Cloutier, Sylvie
You, Frank M.
author_sort He, Liqiang
collection PubMed
description Pasmo (Septoria linicola) is a fungal disease causing major losses in seed yield and quality and stem fibre quality in flax. Pasmo resistance (PR) is quantitative and has low heritability. To improve PR breeding efficiency, the accuracy of genomic prediction (GP) was evaluated using a diverse worldwide core collection of 370 accessions. Four marker sets, including three defined by 500, 134 and 67 previously identified quantitative trait loci (QTL) and one of 52,347 PR-correlated genome-wide single nucleotide polymorphisms, were used to build ridge regression best linear unbiased prediction (RR-BLUP) models using pasmo severity (PS) data collected from field experiments performed during five consecutive years. With five-fold random cross-validation, GP accuracy as high as 0.92 was obtained from the models using the 500 QTL when the average PS was used as the training dataset. GP accuracy increased with training population size, reaching values >0.9 with training population size greater than 185. Linear regression of the observed PS with the number of positive-effect QTL in accessions provided an alternative GP approach with an accuracy of 0.86. The results demonstrate the GP models based on marker information from all identified QTL and the 5-year PS average is highly effective for PR prediction.
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spelling pubmed-63593012019-02-06 Evaluation of Genomic Prediction for Pasmo Resistance in Flax He, Liqiang Xiao, Jin Rashid, Khalid Y. Jia, Gaofeng Li, Pingchuan Yao, Zhen Wang, Xiue Cloutier, Sylvie You, Frank M. Int J Mol Sci Article Pasmo (Septoria linicola) is a fungal disease causing major losses in seed yield and quality and stem fibre quality in flax. Pasmo resistance (PR) is quantitative and has low heritability. To improve PR breeding efficiency, the accuracy of genomic prediction (GP) was evaluated using a diverse worldwide core collection of 370 accessions. Four marker sets, including three defined by 500, 134 and 67 previously identified quantitative trait loci (QTL) and one of 52,347 PR-correlated genome-wide single nucleotide polymorphisms, were used to build ridge regression best linear unbiased prediction (RR-BLUP) models using pasmo severity (PS) data collected from field experiments performed during five consecutive years. With five-fold random cross-validation, GP accuracy as high as 0.92 was obtained from the models using the 500 QTL when the average PS was used as the training dataset. GP accuracy increased with training population size, reaching values >0.9 with training population size greater than 185. Linear regression of the observed PS with the number of positive-effect QTL in accessions provided an alternative GP approach with an accuracy of 0.86. The results demonstrate the GP models based on marker information from all identified QTL and the 5-year PS average is highly effective for PR prediction. MDPI 2019-01-16 /pmc/articles/PMC6359301/ /pubmed/30654497 http://dx.doi.org/10.3390/ijms20020359 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
He, Liqiang
Xiao, Jin
Rashid, Khalid Y.
Jia, Gaofeng
Li, Pingchuan
Yao, Zhen
Wang, Xiue
Cloutier, Sylvie
You, Frank M.
Evaluation of Genomic Prediction for Pasmo Resistance in Flax
title Evaluation of Genomic Prediction for Pasmo Resistance in Flax
title_full Evaluation of Genomic Prediction for Pasmo Resistance in Flax
title_fullStr Evaluation of Genomic Prediction for Pasmo Resistance in Flax
title_full_unstemmed Evaluation of Genomic Prediction for Pasmo Resistance in Flax
title_short Evaluation of Genomic Prediction for Pasmo Resistance in Flax
title_sort evaluation of genomic prediction for pasmo resistance in flax
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6359301/
https://www.ncbi.nlm.nih.gov/pubmed/30654497
http://dx.doi.org/10.3390/ijms20020359
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