Differential RNA Editing of Mitochondrial Genes in WA-Cytoplasmic Based Male Sterile Line Pusa 6A, and Its Maintainer and Restorer Lines

doi:10.1016/j.rsci.2019.08.002

Abstract

Abstract:

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.

Key words: cleaved amplified polymorphism sequence, cytoplasmic male sterility, hybrid rice, RNA editing, mitochondrial gene, wild abortive, nucleotide

Ngangkham Umakanta, Kumar Parida Swarup, Kumar Singh Ashok, Mohapatra Trilochan. Differential RNA Editing of Mitochondrial Genes in WA-Cytoplasmic Based Male Sterile Line Pusa 6A, and Its Maintainer and Restorer Lines[J]. Rice Science, 2019, 26(5): 282-289.

Figures/Tables 3

References 38

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Gene	Biological function	Forward primer (5′-3′)	Reverse primer (5′-3′)	Amplicon size (bp)
18SrRNA	Ribosomal subunit	GTGTTGCTGAGACATGCGCC	ATATGGCGCAAGACGATTCC	749
atp6	Subunit of ATPase	ATGGGTTTGAATCAGAGAGA	ATTCAATTATGAAATTACTC	999
atp9	Subunit of ATPase	GGTGTGGTGTTCAGTCTACC	GGGCCTCGTATCTCTATTTG	406
cobII	Apocytochrome B	AAGGAACCAACGATTCTCTC	CGGTCGAAAACTTGAACTAC	1 001
coxI	Cytochrome C oxidase subunit	TATTACCAGCCATTCTGGAG	CTACGAAGAAACGACGAATC	1 008
coxIII	Cytochrome C oxidase subunit	GGAGAGGGCATGATAAAGAC	AAATAGTGGAGGGTGCTTG	810
nadI	Subunit of NADH dehydrogenase	ATACACCAGGGCAACTAATG	AGGGAGTAGGGTGAGTAAGC	790
rps3	Ribosomal subunit	AAACCCTCTCTAAGGTGGAG	AGATAGTCACCCATCACACG	1 002

Gene	Biological function	Forward primer (5′-3′)	Reverse primer (5′-3′)	Amplicon size (bp)
18SrRNA	Ribosomal subunit	GTGTTGCTGAGACATGCGCC	ATATGGCGCAAGACGATTCC	749
atp6	Subunit of ATPase	ATGGGTTTGAATCAGAGAGA	ATTCAATTATGAAATTACTC	999
atp9	Subunit of ATPase	GGTGTGGTGTTCAGTCTACC	GGGCCTCGTATCTCTATTTG	406
cobII	Apocytochrome B	AAGGAACCAACGATTCTCTC	CGGTCGAAAACTTGAACTAC	1 001
coxI	Cytochrome C oxidase subunit	TATTACCAGCCATTCTGGAG	CTACGAAGAAACGACGAATC	1 008
coxIII	Cytochrome C oxidase subunit	GGAGAGGGCATGATAAAGAC	AAATAGTGGAGGGTGCTTG	810
nadI	Subunit of NADH dehydrogenase	ATACACCAGGGCAACTAATG	AGGGAGTAGGGTGAGTAAGC	790
rps3	Ribosomal subunit	AAACCCTCTCTAAGGTGGAG	AGATAGTCACCCATCACACG	1 002