Differential RNA Editing of Mitochondrial Genes in WA-Cytoplasmic Based Male Sterile Line Pusa 6A, and Its Maintainer and Restorer Lines
RNA editing changes the nucleotides at the transcript level of mitochondrial genes which results in synthesis of functional proteins. This study was designed to find the editing sites which could be implicated in male fertility restoration and to develop editing based markers for differentiation of...
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doaj-70f0fed53e1146a7b37d18fa3b33f5422020-11-24T22:11:48ZengElsevierRice Science1672-63082019-09-01265282289Differential RNA Editing of Mitochondrial Genes in WA-Cytoplasmic Based Male Sterile Line Pusa 6A, and Its Maintainer and Restorer LinesUmakanta Ngangkham0Swarup Kumar Parida1Ashok Kumar Singh2Trilochan Mohapatra3National Research Centre on Plant Biotechnology, New Delhi 110012, India; Indian Council of Agricultural Research-Research Complex for North East Hill Region, Indian Council of Agricultural Research, Umiam 793103, IndiaNational Research Centre on Plant Biotechnology, New Delhi 110012, India; National Institute of Plant Genome Research, New Delhi 110067, IndiaDivision of Genetics, Indian Agricultural Research Institute, New Delhi 110012, IndiaNational Research Centre on Plant Biotechnology, New Delhi 110012, India; Indian Council of Agricultural Research, New Delhi 110001, India; Corresponding author.RNA editing changes the nucleotides at the transcript level of mitochondrial genes which results in synthesis of functional proteins. This study was designed to find the editing sites which could be implicated in male fertility restoration and to develop editing based markers for differentiation of cytoplasmic male sterility and maintainer lines from each other. DNA and RNA from young panicles were isolated from three-line system of hybrid rice PRH10, wild abortive (WA) cytoplasm based male sterile (A line Pusa 6A), maintainer (B line Pusa 6B) and restorer (R line PRR78) lines. Pusa 6A and PRR78 having the same WA cytoplasm are allo-nuclear and iso-cytpolasmic lines. The genomic and cDNA amplicons for eight mitochondrial genes (18SrRNA, atp6, atp9, cobII, coxI, coxIII, nadI and rps3) were sequenced and compared. Differences in genomic and cDNA sequences were considered as editing. Two hundred and thirty editing sites having base substitution or insertion/deletion were identified with the highest in 18SrRNA (5.74%) and the lowest in coxI (0.60%). The highest editing sites were observed in fertile maintainer Pusa 6B followed by PRR78 and Pusa 6A, of which random five editing sites in five different rice mitochondrial transcripts namely atp9, cobII, coxIII, rps3 and 18SrRNA were chosen and validated through cleaved amplified polymorphism sequence (CAPS) analysis and found to be partially edited in four genes. The identical editing sites of different mitochondrial genes from maintainer and restorer lines might reflect their possible contribution to fertility restoration of sterile WA cytoplasm. Keywords: Cleaved amplified polymorphism sequence, Cytoplasmic male sterility, Hybrid rice, RNA editing, Mitochondrial gene, Wild abortive, Nucleotidehttp://www.sciencedirect.com/science/article/pii/S1672630819300605 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Umakanta Ngangkham Swarup Kumar Parida Ashok Kumar Singh Trilochan Mohapatra |
spellingShingle |
Umakanta Ngangkham Swarup Kumar Parida Ashok Kumar Singh Trilochan Mohapatra Differential RNA Editing of Mitochondrial Genes in WA-Cytoplasmic Based Male Sterile Line Pusa 6A, and Its Maintainer and Restorer Lines Rice Science |
author_facet |
Umakanta Ngangkham Swarup Kumar Parida Ashok Kumar Singh Trilochan Mohapatra |
author_sort |
Umakanta Ngangkham |
title |
Differential RNA Editing of Mitochondrial Genes in WA-Cytoplasmic Based Male Sterile Line Pusa 6A, and Its Maintainer and Restorer Lines |
title_short |
Differential RNA Editing of Mitochondrial Genes in WA-Cytoplasmic Based Male Sterile Line Pusa 6A, and Its Maintainer and Restorer Lines |
title_full |
Differential RNA Editing of Mitochondrial Genes in WA-Cytoplasmic Based Male Sterile Line Pusa 6A, and Its Maintainer and Restorer Lines |
title_fullStr |
Differential RNA Editing of Mitochondrial Genes in WA-Cytoplasmic Based Male Sterile Line Pusa 6A, and Its Maintainer and Restorer Lines |
title_full_unstemmed |
Differential RNA Editing of Mitochondrial Genes in WA-Cytoplasmic Based Male Sterile Line Pusa 6A, and Its Maintainer and Restorer Lines |
title_sort |
differential rna editing of mitochondrial genes in wa-cytoplasmic based male sterile line pusa 6a, and its maintainer and restorer lines |
publisher |
Elsevier |
series |
Rice Science |
issn |
1672-6308 |
publishDate |
2019-09-01 |
description |
RNA editing changes the nucleotides at the transcript level of mitochondrial genes which results in synthesis of functional proteins. This study was designed to find the editing sites which could be implicated in male fertility restoration and to develop editing based markers for differentiation of cytoplasmic male sterility and maintainer lines from each other. DNA and RNA from young panicles were isolated from three-line system of hybrid rice PRH10, wild abortive (WA) cytoplasm based male sterile (A line Pusa 6A), maintainer (B line Pusa 6B) and restorer (R line PRR78) lines. Pusa 6A and PRR78 having the same WA cytoplasm are allo-nuclear and iso-cytpolasmic lines. The genomic and cDNA amplicons for eight mitochondrial genes (18SrRNA, atp6, atp9, cobII, coxI, coxIII, nadI and rps3) were sequenced and compared. Differences in genomic and cDNA sequences were considered as editing. Two hundred and thirty editing sites having base substitution or insertion/deletion were identified with the highest in 18SrRNA (5.74%) and the lowest in coxI (0.60%). The highest editing sites were observed in fertile maintainer Pusa 6B followed by PRR78 and Pusa 6A, of which random five editing sites in five different rice mitochondrial transcripts namely atp9, cobII, coxIII, rps3 and 18SrRNA were chosen and validated through cleaved amplified polymorphism sequence (CAPS) analysis and found to be partially edited in four genes. The identical editing sites of different mitochondrial genes from maintainer and restorer lines might reflect their possible contribution to fertility restoration of sterile WA cytoplasm. Keywords: Cleaved amplified polymorphism sequence, Cytoplasmic male sterility, Hybrid rice, RNA editing, Mitochondrial gene, Wild abortive, Nucleotide |
url |
http://www.sciencedirect.com/science/article/pii/S1672630819300605 |
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