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Differential Expression of Genes at Panicle Initiation and Grain Filling Stages Implied in Heterosis of Rice Hybrids
RNA-Seq technology was used to analyze the transcriptome of two rice hybrids, Ajay (based on wild-abortive (WA)-cytoplasm) and Rajalaxmi (based on Kalinga-cytoplasm), and their respective parents at the panicle initiation (PI) and grain filling (GF) stages. Around 293 and 302 million high quality pa...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7038112/ https://www.ncbi.nlm.nih.gov/pubmed/32041193 http://dx.doi.org/10.3390/ijms21031080 |
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author | Katara, Jawahar Lal Verma, Ram Lakhan Parida, Madhuchhanda Ngangkham, Umakanta Molla, Kutubuddin Ali Barbadikar, Kalyani Makarand Mukherjee, Mitadru C, Parameswaran Samantaray, Sanghamitra Ravi, Nageswara Rao Singh, Onkar Nath Mohapatra, Trilochan |
author_facet | Katara, Jawahar Lal Verma, Ram Lakhan Parida, Madhuchhanda Ngangkham, Umakanta Molla, Kutubuddin Ali Barbadikar, Kalyani Makarand Mukherjee, Mitadru C, Parameswaran Samantaray, Sanghamitra Ravi, Nageswara Rao Singh, Onkar Nath Mohapatra, Trilochan |
author_sort | Katara, Jawahar Lal |
collection | PubMed |
description | RNA-Seq technology was used to analyze the transcriptome of two rice hybrids, Ajay (based on wild-abortive (WA)-cytoplasm) and Rajalaxmi (based on Kalinga-cytoplasm), and their respective parents at the panicle initiation (PI) and grain filling (GF) stages. Around 293 and 302 million high quality paired-end reads of Ajay and Rajalaxmi, respectively, were generated and aligned against the Nipponbare reference genome. Transcriptome profiling of Ajay revealed 2814 and 4819 differentially expressed genes (DEGs) at the PI and GF stages, respectively, as compared to its parents. In the case of Rajalaxmi, 660 and 5264 DEGs were identified at PI and GF stages, respectively. Functionally relevant DEGs were selected for validation through qRT-PCR, which were found to be co-related with the expression patterns to RNA-seq. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated significant DEGs enriched for energy metabolism pathways, such as photosynthesis, oxidative phosphorylation, and carbon fixation, at the PI stage, while carbohydrate metabolism-related pathways, such as glycolysis and starch and sucrose metabolism, were significantly involved at the GF stage. Many genes involved in energy metabolism exhibited upregulation at the PI stage, whereas the genes involved in carbohydrate biosynthesis had higher expression at the GF stage. The majority of the DEGs were successfully mapped to know yield related rice quantitative trait loci (QTLs). A set of important transcription factors (TFs) was found to be encoded by the identified DEGs. Our results indicated that a complex interplay of several genes in different pathways contributes to higher yield and vigor in rice hybrids. |
format | Online Article Text |
id | pubmed-7038112 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-70381122020-03-10 Differential Expression of Genes at Panicle Initiation and Grain Filling Stages Implied in Heterosis of Rice Hybrids Katara, Jawahar Lal Verma, Ram Lakhan Parida, Madhuchhanda Ngangkham, Umakanta Molla, Kutubuddin Ali Barbadikar, Kalyani Makarand Mukherjee, Mitadru C, Parameswaran Samantaray, Sanghamitra Ravi, Nageswara Rao Singh, Onkar Nath Mohapatra, Trilochan Int J Mol Sci Article RNA-Seq technology was used to analyze the transcriptome of two rice hybrids, Ajay (based on wild-abortive (WA)-cytoplasm) and Rajalaxmi (based on Kalinga-cytoplasm), and their respective parents at the panicle initiation (PI) and grain filling (GF) stages. Around 293 and 302 million high quality paired-end reads of Ajay and Rajalaxmi, respectively, were generated and aligned against the Nipponbare reference genome. Transcriptome profiling of Ajay revealed 2814 and 4819 differentially expressed genes (DEGs) at the PI and GF stages, respectively, as compared to its parents. In the case of Rajalaxmi, 660 and 5264 DEGs were identified at PI and GF stages, respectively. Functionally relevant DEGs were selected for validation through qRT-PCR, which were found to be co-related with the expression patterns to RNA-seq. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated significant DEGs enriched for energy metabolism pathways, such as photosynthesis, oxidative phosphorylation, and carbon fixation, at the PI stage, while carbohydrate metabolism-related pathways, such as glycolysis and starch and sucrose metabolism, were significantly involved at the GF stage. Many genes involved in energy metabolism exhibited upregulation at the PI stage, whereas the genes involved in carbohydrate biosynthesis had higher expression at the GF stage. The majority of the DEGs were successfully mapped to know yield related rice quantitative trait loci (QTLs). A set of important transcription factors (TFs) was found to be encoded by the identified DEGs. Our results indicated that a complex interplay of several genes in different pathways contributes to higher yield and vigor in rice hybrids. MDPI 2020-02-06 /pmc/articles/PMC7038112/ /pubmed/32041193 http://dx.doi.org/10.3390/ijms21031080 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Katara, Jawahar Lal Verma, Ram Lakhan Parida, Madhuchhanda Ngangkham, Umakanta Molla, Kutubuddin Ali Barbadikar, Kalyani Makarand Mukherjee, Mitadru C, Parameswaran Samantaray, Sanghamitra Ravi, Nageswara Rao Singh, Onkar Nath Mohapatra, Trilochan Differential Expression of Genes at Panicle Initiation and Grain Filling Stages Implied in Heterosis of Rice Hybrids |
title | Differential Expression of Genes at Panicle Initiation and Grain Filling Stages Implied in Heterosis of Rice Hybrids |
title_full | Differential Expression of Genes at Panicle Initiation and Grain Filling Stages Implied in Heterosis of Rice Hybrids |
title_fullStr | Differential Expression of Genes at Panicle Initiation and Grain Filling Stages Implied in Heterosis of Rice Hybrids |
title_full_unstemmed | Differential Expression of Genes at Panicle Initiation and Grain Filling Stages Implied in Heterosis of Rice Hybrids |
title_short | Differential Expression of Genes at Panicle Initiation and Grain Filling Stages Implied in Heterosis of Rice Hybrids |
title_sort | differential expression of genes at panicle initiation and grain filling stages implied in heterosis of rice hybrids |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7038112/ https://www.ncbi.nlm.nih.gov/pubmed/32041193 http://dx.doi.org/10.3390/ijms21031080 |
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