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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...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2018
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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. |
format | Online Article Text |
id | pubmed-6010284 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
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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