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Interacted QTL Mapping in Partial NCII Design Provides Evidences for Breeding by Design

The utilization of heterosis in rice, maize and rapeseed has revolutionized crop production. Although elite hybrid cultivars are mainly derived from the F(1) crosses between two groups of parents, named NCII mating design, little has been known about the methodology of how interacted effects influen...

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Autores principales: Bu, Su Hong, Xinwang, Zhao, Yi, Can, Wen, Jia, Jinxing, Tu, Zhang, Yuan Ming
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4379165/
https://www.ncbi.nlm.nih.gov/pubmed/25822501
http://dx.doi.org/10.1371/journal.pone.0121034
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author Bu, Su Hong
Xinwang, Zhao
Yi, Can
Wen, Jia
Jinxing, Tu
Zhang, Yuan Ming
author_facet Bu, Su Hong
Xinwang, Zhao
Yi, Can
Wen, Jia
Jinxing, Tu
Zhang, Yuan Ming
author_sort Bu, Su Hong
collection PubMed
description The utilization of heterosis in rice, maize and rapeseed has revolutionized crop production. Although elite hybrid cultivars are mainly derived from the F(1) crosses between two groups of parents, named NCII mating design, little has been known about the methodology of how interacted effects influence quantitative trait performance in the population. To bridge genetic analysis with hybrid breeding, here we integrated an interacted QTL mapping approach with breeding by design in partial NCII mating design. All the potential main and interacted effects were included in one full model. If the number of the effects is huge, bulked segregant analysis were used to test which effects were associated with the trait. All the selected effects were further shrunk by empirical Bayesian, so significant effects could be identified. A series of Monte Carlo simulations was performed to validate the new method. Furthermore, all the significant effects were used to calculate genotypic values of all the missing F(1) hybrids, and all these F(1) phenotypic or genotypic values were used to predict elite parents and parental combinations. Finally, the new method was adopted to dissect the genetic foundation of oil content in 441 rapeseed parents and 284 F(1) hybrids. As a result, 8 main-effect QTL and 37 interacted QTL were found and used to predict 10 elite restorer lines, 10 elite sterile lines and 10 elite parental crosses. Similar results across various methods and in previous studies and a high correlation coefficient (0.76) between the predicted and observed phenotypes validated the proposed method in this study.
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spelling pubmed-43791652015-04-09 Interacted QTL Mapping in Partial NCII Design Provides Evidences for Breeding by Design Bu, Su Hong Xinwang, Zhao Yi, Can Wen, Jia Jinxing, Tu Zhang, Yuan Ming PLoS One Research Article The utilization of heterosis in rice, maize and rapeseed has revolutionized crop production. Although elite hybrid cultivars are mainly derived from the F(1) crosses between two groups of parents, named NCII mating design, little has been known about the methodology of how interacted effects influence quantitative trait performance in the population. To bridge genetic analysis with hybrid breeding, here we integrated an interacted QTL mapping approach with breeding by design in partial NCII mating design. All the potential main and interacted effects were included in one full model. If the number of the effects is huge, bulked segregant analysis were used to test which effects were associated with the trait. All the selected effects were further shrunk by empirical Bayesian, so significant effects could be identified. A series of Monte Carlo simulations was performed to validate the new method. Furthermore, all the significant effects were used to calculate genotypic values of all the missing F(1) hybrids, and all these F(1) phenotypic or genotypic values were used to predict elite parents and parental combinations. Finally, the new method was adopted to dissect the genetic foundation of oil content in 441 rapeseed parents and 284 F(1) hybrids. As a result, 8 main-effect QTL and 37 interacted QTL were found and used to predict 10 elite restorer lines, 10 elite sterile lines and 10 elite parental crosses. Similar results across various methods and in previous studies and a high correlation coefficient (0.76) between the predicted and observed phenotypes validated the proposed method in this study. Public Library of Science 2015-03-30 /pmc/articles/PMC4379165/ /pubmed/25822501 http://dx.doi.org/10.1371/journal.pone.0121034 Text en © 2015 Bu et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Bu, Su Hong
Xinwang, Zhao
Yi, Can
Wen, Jia
Jinxing, Tu
Zhang, Yuan Ming
Interacted QTL Mapping in Partial NCII Design Provides Evidences for Breeding by Design
title Interacted QTL Mapping in Partial NCII Design Provides Evidences for Breeding by Design
title_full Interacted QTL Mapping in Partial NCII Design Provides Evidences for Breeding by Design
title_fullStr Interacted QTL Mapping in Partial NCII Design Provides Evidences for Breeding by Design
title_full_unstemmed Interacted QTL Mapping in Partial NCII Design Provides Evidences for Breeding by Design
title_short Interacted QTL Mapping in Partial NCII Design Provides Evidences for Breeding by Design
title_sort interacted qtl mapping in partial ncii design provides evidences for breeding by design
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4379165/
https://www.ncbi.nlm.nih.gov/pubmed/25822501
http://dx.doi.org/10.1371/journal.pone.0121034
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