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Transcriptome analysis of near-isogenic line provides novel insights into genes associated with panicle traits regulation in rice

Panicle traits in rice impact yield and quality. The OsGRF4 gene encodes a growth-regulating factor controlling panicle traits, and was recently cloned. Gene expression profiling analysis can be used to study the molecular mechanisms underlying OsGRF4 regulation. Use of near-isogenic lines (NILs) re...

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Autores principales: Zhang, Wuhan, Sun, Pingyong, He, Qiang, Shu, Fu, Deng, Huafeng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6010284/
https://www.ncbi.nlm.nih.gov/pubmed/29924832
http://dx.doi.org/10.1371/journal.pone.0199077
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author Zhang, Wuhan
Sun, Pingyong
He, Qiang
Shu, Fu
Deng, Huafeng
author_facet Zhang, Wuhan
Sun, Pingyong
He, Qiang
Shu, Fu
Deng, Huafeng
author_sort Zhang, Wuhan
collection PubMed
description Panicle traits in rice impact yield and quality. The OsGRF4 gene encodes a growth-regulating factor controlling panicle traits, and was recently cloned. Gene expression profiling analysis can be used to study the molecular mechanisms underlying OsGRF4 regulation. Use of near-isogenic lines (NILs) reduces genetic background noise in omics studies. We compared transcriptome profiling of 7 cm long young panicles of NIL-Osgrf4 and NIL-OsGRF4 using RNAs sequence analyses. Eighty differentially expressed genes (DEGs) were identified. Our target gene OsGRF4 was up-regulated in NIL-OsGRF4 plants, which is consistent with a previous qPCR analysis. Hierarchical cluster analysis showed OsGRF4 is tightly clustered with the up-regulated DEG LOC_Os02g47320. Gene Ontology (GO) and KEGG analysis suggested that DEGs were primarily involved in somatic embryogenesis and chitinase activity. Two up-regulated DEGs, LOC_Os04g41680 and LOC_Os04g41620, were significantly enriched in the top 8 GO terms, and were over_represented in term of seed development, and may play key roles in grain shape regulation. The transcription factor Osmyb1 also exhibited differential expression between NILs, and may be is an important regulator of panicle traits. By searching reported functions of DEGs and by co-localization with previous identified quantitative trait loci (QTL), we determined that the pleiotropic gene OsGRF4 may also be involve in abiotic stress resistance. This study provides new candidates genes for further understanding the molecular mechanisms underlying rice panicle trait regulation.
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spelling pubmed-60102842018-07-06 Transcriptome analysis of near-isogenic line provides novel insights into genes associated with panicle traits regulation in rice Zhang, Wuhan Sun, Pingyong He, Qiang Shu, Fu Deng, Huafeng PLoS One Research Article Panicle traits in rice impact yield and quality. The OsGRF4 gene encodes a growth-regulating factor controlling panicle traits, and was recently cloned. Gene expression profiling analysis can be used to study the molecular mechanisms underlying OsGRF4 regulation. Use of near-isogenic lines (NILs) reduces genetic background noise in omics studies. We compared transcriptome profiling of 7 cm long young panicles of NIL-Osgrf4 and NIL-OsGRF4 using RNAs sequence analyses. Eighty differentially expressed genes (DEGs) were identified. Our target gene OsGRF4 was up-regulated in NIL-OsGRF4 plants, which is consistent with a previous qPCR analysis. Hierarchical cluster analysis showed OsGRF4 is tightly clustered with the up-regulated DEG LOC_Os02g47320. Gene Ontology (GO) and KEGG analysis suggested that DEGs were primarily involved in somatic embryogenesis and chitinase activity. Two up-regulated DEGs, LOC_Os04g41680 and LOC_Os04g41620, were significantly enriched in the top 8 GO terms, and were over_represented in term of seed development, and may play key roles in grain shape regulation. The transcription factor Osmyb1 also exhibited differential expression between NILs, and may be is an important regulator of panicle traits. By searching reported functions of DEGs and by co-localization with previous identified quantitative trait loci (QTL), we determined that the pleiotropic gene OsGRF4 may also be involve in abiotic stress resistance. This study provides new candidates genes for further understanding the molecular mechanisms underlying rice panicle trait regulation. Public Library of Science 2018-06-20 /pmc/articles/PMC6010284/ /pubmed/29924832 http://dx.doi.org/10.1371/journal.pone.0199077 Text en © 2018 Zhang 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 (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Zhang, Wuhan
Sun, Pingyong
He, Qiang
Shu, Fu
Deng, Huafeng
Transcriptome analysis of near-isogenic line provides novel insights into genes associated with panicle traits regulation in rice
title Transcriptome analysis of near-isogenic line provides novel insights into genes associated with panicle traits regulation in rice
title_full Transcriptome analysis of near-isogenic line provides novel insights into genes associated with panicle traits regulation in rice
title_fullStr Transcriptome analysis of near-isogenic line provides novel insights into genes associated with panicle traits regulation in rice
title_full_unstemmed Transcriptome analysis of near-isogenic line provides novel insights into genes associated with panicle traits regulation in rice
title_short Transcriptome analysis of near-isogenic line provides novel insights into genes associated with panicle traits regulation in rice
title_sort transcriptome analysis of near-isogenic line provides novel insights into genes associated with panicle traits regulation in rice
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6010284/
https://www.ncbi.nlm.nih.gov/pubmed/29924832
http://dx.doi.org/10.1371/journal.pone.0199077
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