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Exploring genetic architecture of grain yield and quality traits in a 16-way indica by japonica rice MAGIC global population

Identification of Quantitative Trait Loci (QTL) has been a challenge for complex traits due to the use of populations with narrow genetic base. Most of QTL mapping studies were carried out from crosses made within the subspecies, either indica × indica or japonica × japonica. In this study we report...

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Autores principales: Zaw, Hein, Raghavan, Chitra, Pocsedio, Arnel, Swamy, B. P. Mallikarjuna, Jubay, Mona Liza, Singh, Rakesh Kumar, Bonifacio, Justine, Mauleon, Ramil, Hernandez, Jose E., Mendioro, Merlyn S., Gregorio, Glenn B., Leung, Hei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6925145/
https://www.ncbi.nlm.nih.gov/pubmed/31862941
http://dx.doi.org/10.1038/s41598-019-55357-7
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author Zaw, Hein
Raghavan, Chitra
Pocsedio, Arnel
Swamy, B. P. Mallikarjuna
Jubay, Mona Liza
Singh, Rakesh Kumar
Bonifacio, Justine
Mauleon, Ramil
Hernandez, Jose E.
Mendioro, Merlyn S.
Gregorio, Glenn B.
Leung, Hei
author_facet Zaw, Hein
Raghavan, Chitra
Pocsedio, Arnel
Swamy, B. P. Mallikarjuna
Jubay, Mona Liza
Singh, Rakesh Kumar
Bonifacio, Justine
Mauleon, Ramil
Hernandez, Jose E.
Mendioro, Merlyn S.
Gregorio, Glenn B.
Leung, Hei
author_sort Zaw, Hein
collection PubMed
description Identification of Quantitative Trait Loci (QTL) has been a challenge for complex traits due to the use of populations with narrow genetic base. Most of QTL mapping studies were carried out from crosses made within the subspecies, either indica × indica or japonica × japonica. In this study we report advantages of using Multi-parent Advanced Generation Inter-Crosses global population, derived from a combination of eight indica and eight japonica elite parents, in QTL discovery for yield and grain quality traits. Genome-wide association study and interval mapping identified 38 and 34 QTLs whereas Bayesian networking detected 60 QTLs with 22 marker-marker associations, 32 trait-trait associations and 65 marker-trait associations. Notably, nine known QTLs/genes qPH(1)/OsGA20ox2, qDF(3)/OsMADS50, PL, QDg1, qGW-5b, grb7-2, qGL(3)/GS3, Amy6/Wx gene and OsNAS3 were consistently identified by all approaches for nine traits whereas qDF(3)/OsMADS50 was co-located for both yield and days-to-flowering traits on chromosome 3. Moreover, we identified a number of candidate QTLs in either one or two analyses but further validations will be needed. The results indicate that this new population has enabled identifications of significant QTLs and interactions for 16 traits through multiple approaches. Pyramided recombinant inbred lines provide a valuable source for integration into future breeding programs.
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spelling pubmed-69251452019-12-23 Exploring genetic architecture of grain yield and quality traits in a 16-way indica by japonica rice MAGIC global population Zaw, Hein Raghavan, Chitra Pocsedio, Arnel Swamy, B. P. Mallikarjuna Jubay, Mona Liza Singh, Rakesh Kumar Bonifacio, Justine Mauleon, Ramil Hernandez, Jose E. Mendioro, Merlyn S. Gregorio, Glenn B. Leung, Hei Sci Rep Article Identification of Quantitative Trait Loci (QTL) has been a challenge for complex traits due to the use of populations with narrow genetic base. Most of QTL mapping studies were carried out from crosses made within the subspecies, either indica × indica or japonica × japonica. In this study we report advantages of using Multi-parent Advanced Generation Inter-Crosses global population, derived from a combination of eight indica and eight japonica elite parents, in QTL discovery for yield and grain quality traits. Genome-wide association study and interval mapping identified 38 and 34 QTLs whereas Bayesian networking detected 60 QTLs with 22 marker-marker associations, 32 trait-trait associations and 65 marker-trait associations. Notably, nine known QTLs/genes qPH(1)/OsGA20ox2, qDF(3)/OsMADS50, PL, QDg1, qGW-5b, grb7-2, qGL(3)/GS3, Amy6/Wx gene and OsNAS3 were consistently identified by all approaches for nine traits whereas qDF(3)/OsMADS50 was co-located for both yield and days-to-flowering traits on chromosome 3. Moreover, we identified a number of candidate QTLs in either one or two analyses but further validations will be needed. The results indicate that this new population has enabled identifications of significant QTLs and interactions for 16 traits through multiple approaches. Pyramided recombinant inbred lines provide a valuable source for integration into future breeding programs. Nature Publishing Group UK 2019-12-20 /pmc/articles/PMC6925145/ /pubmed/31862941 http://dx.doi.org/10.1038/s41598-019-55357-7 Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Zaw, Hein
Raghavan, Chitra
Pocsedio, Arnel
Swamy, B. P. Mallikarjuna
Jubay, Mona Liza
Singh, Rakesh Kumar
Bonifacio, Justine
Mauleon, Ramil
Hernandez, Jose E.
Mendioro, Merlyn S.
Gregorio, Glenn B.
Leung, Hei
Exploring genetic architecture of grain yield and quality traits in a 16-way indica by japonica rice MAGIC global population
title Exploring genetic architecture of grain yield and quality traits in a 16-way indica by japonica rice MAGIC global population
title_full Exploring genetic architecture of grain yield and quality traits in a 16-way indica by japonica rice MAGIC global population
title_fullStr Exploring genetic architecture of grain yield and quality traits in a 16-way indica by japonica rice MAGIC global population
title_full_unstemmed Exploring genetic architecture of grain yield and quality traits in a 16-way indica by japonica rice MAGIC global population
title_short Exploring genetic architecture of grain yield and quality traits in a 16-way indica by japonica rice MAGIC global population
title_sort exploring genetic architecture of grain yield and quality traits in a 16-way indica by japonica rice magic global population
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6925145/
https://www.ncbi.nlm.nih.gov/pubmed/31862941
http://dx.doi.org/10.1038/s41598-019-55357-7
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