PubMed:14968308
Annnotations
Oryza-OGER
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cloning of the rice Rf-1 gene, a restorer of BT-type cytoplasmic male sterility that encodes a mitochondria-targeting PPR protein.\nThe combination of cytoplasmic male sterility (CMS) in one parent and a restorer gene ( Rf) to restore fertility in another are indispensable for the development of hybrid varieties. We have found a rice Rf-1 gene that restores BT-type CMS by applying a positional cloning strategy. Using linkage analysis in combination with 6,104 BC(1)F(3) progeny derived from a cross between two near-isogenic lines (NILs) differing only at the Rf-1 locus, we delimited the Rf-1 gene to a 22.4-kb region in the rice genome. Duplicate open reading frames ( Rf-1A and Rf-1B) with a pentatricopeptide (PPR) motif were found in this region. Since several insertions and/or deletions were found in the regions corresponding to both the Rf-1A and Rf-1B genes in the maintainer's allele, they may have lost their function. Rf-1A protein had a mitochondria-targeting signal, whereas Rf-1B did not. The Rf-1B gene encoded a shorter polypeptide that was determined by a premature stop codon. Based on the function of the Rf-1 gene, its product is expected to target mitochondria and may process the transcript from an atp6/orf79 region in the mitochondrial genome. Since the Rf-1A gene encodes a 791-amino acid protein with a signal targeting mitochondria and has 16 repeats of the PPR motif, we concluded that Rf-1A is the Rf-1 gene. Nine duplications of Rf-1A homologs were found around the Rf-1 locus in the Nipponbare genome. However, while some of them encoded proteins with the PPR motif, they do not restore BT-type CMS based on the lack of co-segregation with the restoration phenotype. These duplicates may have played diversified roles in RNA processing and/or recombination in mitochondria during the co-evolution of these genes and the mitochondrial genome."}
pqqtest_sentence
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21k_plant_trait_mention
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OryzaGP_2021_v2
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cloning of the rice Rf-1 gene, a restorer of BT-type cytoplasmic male sterility that encodes a mitochondria-targeting PPR protein.\nThe combination of cytoplasmic male sterility (CMS) in one parent and a restorer gene ( Rf) to restore fertility in another are indispensable for the development of hybrid varieties. We have found a rice Rf-1 gene that restores BT-type CMS by applying a positional cloning strategy. Using linkage analysis in combination with 6,104 BC(1)F(3) progeny derived from a cross between two near-isogenic lines (NILs) differing only at the Rf-1 locus, we delimited the Rf-1 gene to a 22.4-kb region in the rice genome. Duplicate open reading frames ( Rf-1A and Rf-1B) with a pentatricopeptide (PPR) motif were found in this region. Since several insertions and/or deletions were found in the regions corresponding to both the Rf-1A and Rf-1B genes in the maintainer's allele, they may have lost their function. Rf-1A protein had a mitochondria-targeting signal, whereas Rf-1B did not. The Rf-1B gene encoded a shorter polypeptide that was determined by a premature stop codon. Based on the function of the Rf-1 gene, its product is expected to target mitochondria and may process the transcript from an atp6/orf79 region in the mitochondrial genome. Since the Rf-1A gene encodes a 791-amino acid protein with a signal targeting mitochondria and has 16 repeats of the PPR motif, we concluded that Rf-1A is the Rf-1 gene. Nine duplications of Rf-1A homologs were found around the Rf-1 locus in the Nipponbare genome. However, while some of them encoded proteins with the PPR motif, they do not restore BT-type CMS based on the lack of co-segregation with the restoration phenotype. These duplicates may have played diversified roles in RNA processing and/or recombination in mitochondria during the co-evolution of these genes and the mitochondrial genome."}
OryzaGP_2022
{"project":"OryzaGP_2022","denotations":[{"id":"T1","span":{"begin":34,"end":35},"obj":"http://identifiers.org/oryzabase.gene/11216"},{"id":"T2","span":{"begin":349,"end":350},"obj":"http://identifiers.org/oryzabase.gene/11216"},{"id":"T3","span":{"begin":477,"end":478},"obj":"http://identifiers.org/oryzabase.gene/11216"},{"id":"T4","span":{"begin":577,"end":578},"obj":"http://identifiers.org/oryzabase.gene/11216"},{"id":"T5","span":{"begin":606,"end":607},"obj":"http://identifiers.org/oryzabase.gene/11216"},{"id":"T6","span":{"begin":1143,"end":1144},"obj":"http://identifiers.org/oryzabase.gene/11216"},{"id":"T7","span":{"begin":1446,"end":1447},"obj":"http://identifiers.org/oryzabase.gene/11216"},{"id":"T8","span":{"begin":1515,"end":1516},"obj":"http://identifiers.org/oryzabase.gene/11216"}],"text":"Positional cloning of the rice Rf-1 gene, a restorer of BT-type cytoplasmic male sterility that encodes a mitochondria-targeting PPR protein.\nThe combination of cytoplasmic male sterility (CMS) in one parent and a restorer gene ( Rf) to restore fertility in another are indispensable for the development of hybrid varieties. We have found a rice Rf-1 gene that restores BT-type CMS by applying a positional cloning strategy. Using linkage analysis in combination with 6,104 BC(1)F(3) progeny derived from a cross between two near-isogenic lines (NILs) differing only at the Rf-1 locus, we delimited the Rf-1 gene to a 22.4-kb region in the rice genome. Duplicate open reading frames ( Rf-1A and Rf-1B) with a pentatricopeptide (PPR) motif were found in this region. Since several insertions and/or deletions were found in the regions corresponding to both the Rf-1A and Rf-1B genes in the maintainer's allele, they may have lost their function. Rf-1A protein had a mitochondria-targeting signal, whereas Rf-1B did not. The Rf-1B gene encoded a shorter polypeptide that was determined by a premature stop codon. Based on the function of the Rf-1 gene, its product is expected to target mitochondria and may process the transcript from an atp6/orf79 region in the mitochondrial genome. Since the Rf-1A gene encodes a 791-amino acid protein with a signal targeting mitochondria and has 16 repeats of the PPR motif, we concluded that Rf-1A is the Rf-1 gene. Nine duplications of Rf-1A homologs were found around the Rf-1 locus in the Nipponbare genome. However, while some of them encoded proteins with the PPR motif, they do not restore BT-type CMS based on the lack of co-segregation with the restoration phenotype. These duplicates may have played diversified roles in RNA processing and/or recombination in mitochondria during the co-evolution of these genes and the mitochondrial genome."}
OryzaGP_2021_FLAIR
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OryzaGP_2021
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"M_21","span":{"begin":1294,"end":1299},"obj":"hunflair:NA:Gene"},{"id":"M_22","span":{"begin":1430,"end":1435},"obj":"hunflair:NA:Gene"},{"id":"M_23","span":{"begin":1475,"end":1480},"obj":"hunflair:NA:Gene"},{"id":"M_24","span":{"begin":1237,"end":1241},"obj":"hunflair:NA:Gene"},{"id":"M_25","span":{"begin":189,"end":192},"obj":"hunflair:NA:Disease"},{"id":"M_26","span":{"begin":378,"end":381},"obj":"hunflair:NA:Disease"},{"id":"M_27","span":{"begin":1642,"end":1645},"obj":"hunflair:NA:Disease"},{"id":"M_28","span":{"begin":695,"end":700},"obj":"hunflair:NA:Gene"},{"id":"M_29","span":{"begin":870,"end":875},"obj":"hunflair:NA:Gene"},{"id":"M_30","span":{"begin":1004,"end":1009},"obj":"hunflair:NA:Gene"},{"id":"M_31","span":{"begin":1023,"end":1028},"obj":"hunflair:NA:Gene"}],"text":"Positional cloning of the rice Rf-1 gene, a restorer of BT-type cytoplasmic male sterility that encodes a mitochondria-targeting PPR protein.\nThe combination of cytoplasmic male sterility (CMS) in one parent and a restorer gene ( Rf) to restore fertility in another are indispensable for the development of hybrid varieties. We have found a rice Rf-1 gene that restores BT-type CMS by applying a positional cloning strategy. Using linkage analysis in combination with 6,104 BC(1)F(3) progeny derived from a cross between two near-isogenic lines (NILs) differing only at the Rf-1 locus, we delimited the Rf-1 gene to a 22.4-kb region in the rice genome. Duplicate open reading frames ( Rf-1A and Rf-1B) with a pentatricopeptide (PPR) motif were found in this region. Since several insertions and/or deletions were found in the regions corresponding to both the Rf-1A and Rf-1B genes in the maintainer's allele, they may have lost their function. Rf-1A protein had a mitochondria-targeting signal, whereas Rf-1B did not. The Rf-1B gene encoded a shorter polypeptide that was determined by a premature stop codon. Based on the function of the Rf-1 gene, its product is expected to target mitochondria and may process the transcript from an atp6/orf79 region in the mitochondrial genome. Since the Rf-1A gene encodes a 791-amino acid protein with a signal targeting mitochondria and has 16 repeats of the PPR motif, we concluded that Rf-1A is the Rf-1 gene. Nine duplications of Rf-1A homologs were found around the Rf-1 locus in the Nipponbare genome. However, while some of them encoded proteins with the PPR motif, they do not restore BT-type CMS based on the lack of co-segregation with the restoration phenotype. These duplicates may have played diversified roles in RNA processing and/or recombination in mitochondria during the co-evolution of these genes and the mitochondrial genome."}
PubmedHPO
{"project":"PubmedHPO","denotations":[{"id":"T1","span":{"begin":1262,"end":1275},"obj":"HP_0001427"},{"id":"T2","span":{"begin":1459,"end":1471},"obj":"HP_0009609"},{"id":"T3","span":{"begin":1720,"end":1730},"obj":"HP_0009609"},{"id":"T4","span":{"begin":1867,"end":1880},"obj":"HP_0001427"}],"text":"Positional cloning of the rice Rf-1 gene, a restorer of BT-type cytoplasmic male sterility that encodes a mitochondria-targeting PPR protein.\nThe combination of cytoplasmic male sterility (CMS) in one parent and a restorer gene ( Rf) to restore fertility in another are indispensable for the development of hybrid varieties. We have found a rice Rf-1 gene that restores BT-type CMS by applying a positional cloning strategy. Using linkage analysis in combination with 6,104 BC(1)F(3) progeny derived from a cross between two near-isogenic lines (NILs) differing only at the Rf-1 locus, we delimited the Rf-1 gene to a 22.4-kb region in the rice genome. Duplicate open reading frames ( Rf-1A and Rf-1B) with a pentatricopeptide (PPR) motif were found in this region. Since several insertions and/or deletions were found in the regions corresponding to both the Rf-1A and Rf-1B genes in the maintainer's allele, they may have lost their function. Rf-1A protein had a mitochondria-targeting signal, whereas Rf-1B did not. The Rf-1B gene encoded a shorter polypeptide that was determined by a premature stop codon. Based on the function of the Rf-1 gene, its product is expected to target mitochondria and may process the transcript from an atp6/orf79 region in the mitochondrial genome. Since the Rf-1A gene encodes a 791-amino acid protein with a signal targeting mitochondria and has 16 repeats of the PPR motif, we concluded that Rf-1A is the Rf-1 gene. Nine duplications of Rf-1A homologs were found around the Rf-1 locus in the Nipponbare genome. However, while some of them encoded proteins with the PPR motif, they do not restore BT-type CMS based on the lack of co-segregation with the restoration phenotype. These duplicates may have played diversified roles in RNA processing and/or recombination in mitochondria during the co-evolution of these genes and the mitochondrial genome."}