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Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima

BACKGROUND: African rice, Oryza glaberrima, is an invaluable resource for rice cultivation and for the improvement of biotic and abiotic resistance properties. Since its domestication in the inner Niger delta ca. 2500 years BP, African rice has colonized a variety of ecologically and climatically di...

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Autores principales: Cubry, Philippe, Pidon, Hélène, Ta, Kim Nhung, Tranchant-Dubreuil, Christine, Thuillet, Anne-Céline, Holzinger, Maria, Adam, Hélène, Kam, Honoré, Chrestin, Harold, Ghesquière, Alain, François, Olivier, Sabot, François, Vigouroux, Yves, Albar, Laurence, Jouannic, Stefan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer US 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7494698/
https://www.ncbi.nlm.nih.gov/pubmed/32936396
http://dx.doi.org/10.1186/s12284-020-00424-1
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author Cubry, Philippe
Pidon, Hélène
Ta, Kim Nhung
Tranchant-Dubreuil, Christine
Thuillet, Anne-Céline
Holzinger, Maria
Adam, Hélène
Kam, Honoré
Chrestin, Harold
Ghesquière, Alain
François, Olivier
Sabot, François
Vigouroux, Yves
Albar, Laurence
Jouannic, Stefan
author_facet Cubry, Philippe
Pidon, Hélène
Ta, Kim Nhung
Tranchant-Dubreuil, Christine
Thuillet, Anne-Céline
Holzinger, Maria
Adam, Hélène
Kam, Honoré
Chrestin, Harold
Ghesquière, Alain
François, Olivier
Sabot, François
Vigouroux, Yves
Albar, Laurence
Jouannic, Stefan
author_sort Cubry, Philippe
collection PubMed
description BACKGROUND: African rice, Oryza glaberrima, is an invaluable resource for rice cultivation and for the improvement of biotic and abiotic resistance properties. Since its domestication in the inner Niger delta ca. 2500 years BP, African rice has colonized a variety of ecologically and climatically diverse regions. However, little is known about the genetic basis of quantitative traits and adaptive variation of agricultural interest for this species. RESULTS: Using a reference set of 163 fully re-sequenced accessions, we report the results of a Genome Wide Association Study carried out for African rice. We investigated a diverse panel of traits, including flowering date, panicle architecture and resistance to Rice yellow mottle virus. For this, we devised a pipeline using complementary statistical association methods. First, using flowering time as a target trait, we found several association peaks, one of which co-localised with a well described gene in the Asian rice flowering pathway, OsGi, and identified new genomic regions that would deserve more study. Then we applied our pipeline to panicle- and resistance-related traits, highlighting some interesting genomic regions and candidate genes. Lastly, using a high-resolution climate database, we performed an association analysis based on climatic variables, searching for genomic regions that might be involved in adaptation to climatic variations. CONCLUSION: Our results collectively provide insights into the extent to which adaptive variation is governed by sequence diversity within the O. glaberrima genome, paving the way for in-depth studies of the genetic basis of traits of interest that might be useful to the rice breeding community.
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spelling pubmed-74946982020-09-28 Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima Cubry, Philippe Pidon, Hélène Ta, Kim Nhung Tranchant-Dubreuil, Christine Thuillet, Anne-Céline Holzinger, Maria Adam, Hélène Kam, Honoré Chrestin, Harold Ghesquière, Alain François, Olivier Sabot, François Vigouroux, Yves Albar, Laurence Jouannic, Stefan Rice (N Y) Original Article BACKGROUND: African rice, Oryza glaberrima, is an invaluable resource for rice cultivation and for the improvement of biotic and abiotic resistance properties. Since its domestication in the inner Niger delta ca. 2500 years BP, African rice has colonized a variety of ecologically and climatically diverse regions. However, little is known about the genetic basis of quantitative traits and adaptive variation of agricultural interest for this species. RESULTS: Using a reference set of 163 fully re-sequenced accessions, we report the results of a Genome Wide Association Study carried out for African rice. We investigated a diverse panel of traits, including flowering date, panicle architecture and resistance to Rice yellow mottle virus. For this, we devised a pipeline using complementary statistical association methods. First, using flowering time as a target trait, we found several association peaks, one of which co-localised with a well described gene in the Asian rice flowering pathway, OsGi, and identified new genomic regions that would deserve more study. Then we applied our pipeline to panicle- and resistance-related traits, highlighting some interesting genomic regions and candidate genes. Lastly, using a high-resolution climate database, we performed an association analysis based on climatic variables, searching for genomic regions that might be involved in adaptation to climatic variations. CONCLUSION: Our results collectively provide insights into the extent to which adaptive variation is governed by sequence diversity within the O. glaberrima genome, paving the way for in-depth studies of the genetic basis of traits of interest that might be useful to the rice breeding community. Springer US 2020-09-16 /pmc/articles/PMC7494698/ /pubmed/32936396 http://dx.doi.org/10.1186/s12284-020-00424-1 Text en © The Author(s) 2020 Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Original Article
Cubry, Philippe
Pidon, Hélène
Ta, Kim Nhung
Tranchant-Dubreuil, Christine
Thuillet, Anne-Céline
Holzinger, Maria
Adam, Hélène
Kam, Honoré
Chrestin, Harold
Ghesquière, Alain
François, Olivier
Sabot, François
Vigouroux, Yves
Albar, Laurence
Jouannic, Stefan
Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima
title Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima
title_full Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima
title_fullStr Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima
title_full_unstemmed Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima
title_short Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima
title_sort genome wide association study pinpoints key agronomic qtls in african rice oryza glaberrima
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7494698/
https://www.ncbi.nlm.nih.gov/pubmed/32936396
http://dx.doi.org/10.1186/s12284-020-00424-1
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