The molecular basis for allelic differences suggests Restorer-of-fertility 1 is a complex locus in sugar beet (Beta vulgaris L.)

Abstract Background Cytoplasmic male sterility (CMS) is a widely used trait for hybrid seed production in many crops. Sugar beet CMS is associated with a unique mitochondrial protein named preSATP6 that forms a 250-kDa complex. Restorer-of-fertility 1 (Rf1) is a nuclear gene that suppresses CMS and is, hence, one of the targets of sugar beet breeding. Rf1 has dominant, semi-dominant and recessive alleles, suggesting that it may be a multi-allelic locus; however, the molecular basis for differences in genetic action is obscure. Molecular cloning of Rf1 revealed a gene (orf20) whose protein products produced in transgenics can bind with preSATP6 to generate a novel 200-kDa complex. The complex is also detected in fertility-restored anthers concomitant with a decrease in the amount of the 250-kDa complex. Molecular diversity of the Rf1 locus involves organizational diversity of a gene cluster composed of orf20-like genes (RF-Oma1s). We examined the possibility that members of the clustered RF-Oma1 in this locus could be associated with fertility restoration. Results Six yet uncharacterized RF-Oma1s from dominant and recessive alleles were examined to determine whether they could generate the 200-kDa complex. Analyses of transgenic calli revealed that three RF-Oma1s from a dominant allele could generate the 200-kDa complex, suggesting that clustered RF-Oma1s in the dominant allele can participate in fertility restoration. None of the three copies from two recessive alleles was 200-kDa generative. The absence of this ability was confirmed by analyzing mitochondrial complexes in anthers of plants having these recessive alleles. Together with our previous data, we designed a set of PCR primers specific to the 200-kDa generative RF-Oma1s. The amount of mRNA measured by this primer set inversely correlated with the amount of the 250-kDa complex in anthers and positively correlated with the strength of the Rf1 alleles. Conclusions Fertility restoration by sugar beet Rf1 can involve multiple RF-Oma1s clustered in the locus, implying that stacking 200-kDa generative copies in the locus strengthens the efficacy, whereas the absence of 200-kDa generative copies in the locus makes the allele recessive irrespective of the copy number. We propose that sugar beet Rf1 is a complex locus.

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Selection of Nuclear Genotypes Associated with the Thermo-inducibility of Owen-type Cytoplasmic Male Sterility in Sugar Beet (Beta vulgaris L.)

10.21203/rs.3.rs-551730/v1 ◽

2021 ◽

Author(s):

Hiroaki Matsuhira ◽

Kazuyoshi Kitazaki ◽

Katsunori Matsui ◽

Keisi Kubota ◽

Yosuke Kuroda ◽

...

Keyword(s):

Sugar Beet ◽

Cytoplasmic Male Sterility ◽

Male Sterility ◽

Beta Vulgaris ◽

Parental Line ◽

Hybrid Seed Production ◽

Male Sterile ◽

Flowering Season ◽

Restorer Of Fertility ◽

The Stability

Abstract The stability of cytoplasmic male sterility expression in several genetic backgrounds was investigated in sugar beet (Beta vulgaris L.). Nine genetically heterogenous plants from old cultivars were crossed with a cytoplasmic male-sterile line to obtain 266 F1 plants. Based on marker analysis using a multiallelic DNA marker linked to restorer-of-fertility 1 (Rf1), we divided the F1 plants into 15 genotypes. We evaluated the phenotypes of the F1 plants under two environmental conditions: greenhouse rooms with or without daytime heating during the flowering season. Three phenotypic groups appeared: those consistently expressing male sterility (MS), those consistently having restored pollen fertility, and those expressing MS in a thermo-sensitive manner. All plants in the consistently male-sterile group inherited a specific Rf1 marker type named p4. We tested the potential for thermo-induced male-sterile plants to serve as seed parents for hybrid seed production, and three genotypes were selected. Open pollination by a pollen parental line with a dominant trait of red-pigmented hypocotyls and leaf veins resulted in seed setting on thermo-induced male-sterile plants, indicating that their female organs were functional. More than 99.9% of the progeny expressed the red pigmentation trait; hence, highly pure hybrids were obtained. We determined the nucleotide sequences of Rf1 from the three genotypes: one had a novel allele and two had known alleles, of which one was reported to have been selected previously as a nonrestoring allele at a single US breeding station but not at other stations in the US, or in Europe or Japan, suggesting environmental sensitivity.

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Identification of Rf9, a Gene Contributing to the Genetic Complexity of Fertility Restoration in Hybrid Wheat

Frontiers in Plant Science ◽

10.3389/fpls.2020.577475 ◽

2020 ◽

Vol 11 ◽

Author(s):

Fahimeh Shahinnia ◽

Manuel Geyer ◽

Annette Block ◽

Volker Mohler ◽

Lorenz Hartl

Keyword(s):

Fertility Restoration ◽

Snp Markers ◽

Genetic Maps ◽

Hybrid Seed Production ◽

Hybrid Wheat ◽

Pentatricopeptide Repeat ◽

Male Sterile ◽

Transcription Termination Factor ◽

Restorer Of Fertility ◽

Genes Encoding

Wheat (Triticum aestivum L.) is a self-pollinating crop whose hybrids offer the potential to provide a major boost in yield. Male sterility induced by the cytoplasm of Triticum timopheevii is a powerful method for hybrid seed production. Hybrids produced by this method are often partially sterile, and full fertility restoration is crucial for wheat production using hybrid cultivars. To identify the genetic loci controlling fertility restoration in wheat, we produced two cytoplasmic male-sterile (CMS) backcross (BC1) mapping populations. The restorer lines Gerek 79 and 71R1203 were used to pollinate the male-sterile winter wheat line CMS-Sperber. Seed set and numbers of sterile spikelets per spike were evaluated in 340 and 206 individuals of the populations derived from Gerek 79 and 71R1203, respectively. Genetic maps were constructed using 930 and 994 single nucleotide polymorphism (SNP) markers, spanning 2,160 and 2,328 cM over 21 linkage groups in the two populations, respectively. Twelve quantitative trait loci (QTL) controlled fertility restoration in both BC1 populations, including a novel restorer-of-fertility (Rf) locus flanked by the SNP markers IWB72413 and IWB1550 on chromosome 6AS. The locus was mapped as a qualitative trait in the BC1 Gerek 79 population and was designated Rf9. One hundred-nineteen putative candidate genes were predicted within the QTL region on chromosome 6AS. Among them were genes encoding mitochondrial transcription termination factor and pentatricopeptide repeat-containing proteins that are known to be associated with fertility restoration. This finding is a promising step to better understand the functions of genes for improving fertility restoration in hybrid wheat.

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What Does the Molecular Genetics of Different Types of Restorer-of-Fertility Genes Imply?

Plants ◽

10.3390/plants9030361 ◽

2020 ◽

Vol 9 (3) ◽

pp. 361 ◽

Cited By ~ 4

Author(s):

Tomohiko Kubo ◽

Takumi Arakawa ◽

Yujiro Honma ◽

Kazuyoshi Kitazaki

Keyword(s):

Male Sterility ◽

Rna Binding ◽

Genetic Model ◽

Mitochondrial Gene ◽

Molecular Genetic ◽

Protein A ◽

Nuclear Gene ◽

Hybrid Seed Production ◽

Pentatricopeptide Repeat ◽

Restorer Of Fertility

Cytoplasmic male sterility (CMS) is a widely used trait for hybrid seed production. Although male sterility is caused by S cytoplasm (male-sterility inducing mitochondria), the action of S cytoplasm is suppressed by restorer-of-fertility (Rf), a nuclear gene. Hence, the genetics of Rf has attained particular interest among plant breeders. The genetic model posits Rf diversity in which an Rf specifically suppresses the cognate S cytoplasm. Molecular analysis of Rf loci in plants has identified various genes; however, pentatricopeptide repeat (PPR) protein (a specific type of RNA-binding protein) is so prominent as the Rf-gene product that Rfs have been categorized into two classes, PPR and non-PPR. In contrast, several shared features between PPR- and some non-PPR Rfs are apparent, suggesting the possibility of another grouping. Our present focus is to group Rfs by molecular genetic classes other than the presence of PPRs. We propose three categories that define partially overlapping groups of Rfs: association with post-transcriptional regulation of mitochondrial gene expression, resistance gene-like copy number variation at the locus, and lack of a direct link to S-orf (a mitochondrial ORF associated with CMS). These groups appear to reflect their own evolutionary background and their mechanism of conferring S cytoplasm specificity.

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The Unstable Restorer-of-Fertility Locus in Pepper (Capsicum Annuum. L) is Delimited to a Genomic Region Containing PPR Genes

10.21203/rs.3.rs-1163811/v1 ◽

2021 ◽

Author(s):

Moo Chan Kang ◽

Hwa-Jeong Kang ◽

So-Young Jung ◽

Hae-Young Lee ◽

Min-Young Kang ◽

...

Keyword(s):

Genetic Mapping ◽

Capsicum Annuum ◽

Fertility Restoration ◽

Dominant Gene ◽

Genomic Region ◽

Gene Isolation ◽

Hybrid Seed Production ◽

Capsicum Annuum L ◽

Restorer Of Fertility ◽

Ppr Genes

Abstract The use of cytoplasmic-genic male sterility (CGMS) systems greatly increases the efficiency of hybrid seed production. Although marker development and candidate gene isolation have been performed for the Restorer-of-fertility (Rf) gene in pepper (Capsicum annuum L.), the broad use of CGMS systems has been hampered by the instability of fertility restoration among pepper accessions, especially sweet peppers, due to the widespread presence of the Unstable Restorer-of-fertility (Rfu) locus. Therefore, to investigate the genetic factors controlling unstable fertility restoration in sweet peppers, we developed a segregation population from a cross between a male-sterile line and an Rfu-containing line to examine the inheritance of Rfu. Individuals with unstable restoration vs. sterility segregated at a 3:1 ratio, indicating that a single dominant gene controls unstable fertility restoration. Genetic mapping delimited the Rfu locus to a 479 kb genomic region on chromosome 6 flanked by two markers, which is close to but different from the previously identified Rf-containing region. The Rfu-containing region harbors a pentatricopeptide repeat (PPR) gene, along with 13 other candidate genes. In addition, this region is syntenic to the genomic region containing the largest number of Rf-like PPR genes in tomato. Therefore, the dynamic evolution of PPR genes might be responsible for both the restoration and instability of fertility in pepper. During genetic mapping, we developed various molecular markers, including one that co-segregated with Rfu. These markers showed higher accuracy for genotyping than previously developed markers, pointing to their possible use in marker-assisted breeding of sweet peppers.

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Transcriptome Analysis Implicates Involvement of Long Noncoding RNAs in Cytoplasmic Male Sterility and Fertility Restoration in Cotton

International Journal of Molecular Sciences ◽

10.3390/ijms20225530 ◽

2019 ◽

Vol 20 (22) ◽

pp. 5530

Author(s):

Bingbing Zhang ◽

Xuexian Zhang ◽

Meng Zhang ◽

Liping Guo ◽

Tingxiang Qi ◽

...

Keyword(s):

Cytoplasmic Male Sterility ◽

Male Sterility ◽

Regulatory Networks ◽

Fertility Restoration ◽

Noncoding Rnas ◽

Reduction Reaction ◽

Anther Development ◽

Long Noncoding Rnas ◽

Hybrid Seed Production ◽

Restorer Of Fertility

The cytoplasmic male sterility (CMS)/restorer-of-fertility system is an important tool to exploit heterosis during commercially hybrid seed production. The importance of long noncoding RNAs (lncRNAs) in plant development is recognized, but few analyses of lncRNAs during anther development of three-line hybrid cotton (CMS-D2 line A, maintainer line B, restorer-of-fertility line R) have been reported. Here, we performed transcriptome sequencing during anther development in three-line hybrid cotton. A total of 80,695 lncRNAs were identified, in which 43,347 and 44,739 lncRNAs were differentially expressed in A–B and A–R comparisons, respectively. These lncRNAs represent functional candidates involved in CMS and fertility restoration. GO analysis indicated that cellular hormone metabolic processes and oxidation–reduction reaction processes might be involved in CMS, and cellular component morphogenesis and small molecular biosynthetic processes might participate in fertility restoration. Additionally, 63 lncRNAs were identified as putative precursors of 35 miRNAs, and quantitative reverse transcription polymerase chain reaction (qRT-PCR) showed a similar expression pattern to RNA-seq data. Furthermore, construction of lncRNA regulatory networks indicated that several miRNA–lncRNA–mRNA networks might be involved in CMS and fertility restoration. Our findings provide systematic identification of lncRNAs during anther development and lays a solid foundation for the regulatory mechanisms and utilization in hybrid cotton breeding.

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Transcriptome analysis implicates involvement of long noncoding RNAs in cytoplasmic male sterility and fertility restoration in cotton

10.21203/rs.2.11529/v1 ◽

2019 ◽

Author(s):

Bingbing Zhang ◽

Xuexian Zhang ◽

Meng Zhang ◽

Liping Guo ◽

Tingxiang Qi ◽

...

Keyword(s):

Cytoplasmic Male Sterility ◽

Male Sterility ◽

Molecular Mechanisms ◽

Fertility Restoration ◽

Noncoding Rnas ◽

Anther Development ◽

Long Noncoding Rnas ◽

Pcr Analysis ◽

Hybrid Seed Production ◽

Restorer Of Fertility

Abstract Background Hybrid cotton has greatly contributed to global increase in cotton productivity. The cytoplasmic male sterility (CMS)/restorer-of-fertility system is an important tool to exploit heterosis because it is convenient for commercial hybrid seed production. The importance of long noncoding RNAs (lncRNAs) in plant development is recognized, few analyses of lncRNAs during anther development of three-line hybrid cotton (CMS-D2 line A, maintainer line B, restorer-of-fertility line R) have been reported. Results Here, we performed transcriptome sequencing during anther development in Upland cotton carrying cytoplasmic male sterile Gossypium harknessii (D2) cytoplasm. Totally 80,695 lncRNAs were identified, in which 43,347 and 44,739 lncRNAs were differentially expressed in A–B and A–R comparisons, respectively. These lncRNAs represent functional candidates involved in CMS and fertility restoration. Gene ontology enrichment analysis indicated that cellular hormone metabolic processes and oxidation–reduction reaction processes might be involved in CMS, and cellular component morphogenesis and small molecular biosynthetic processes might participate in fertility restoration. Analysis of the putative relationship between lncRNAs and miRNAs revealed that 63 lncRNAs were identified as putative precursors of 35 miRNAs, and qRT-PCR analysis showed a similar expression pattern to that of RNA-sequencing data. Furthermore, construction of lncRNA regulatory networks indicated that several miRNA–lncRNA–mRNA networks might be involved in CMS and fertility restoration. Conclusion Our findings provide systematic identification of lncRNAs during anther development and lays a solid foundation for future investigation of the regulatory molecular mechanisms and utilization in breeding of hybrid cotton.

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Mutations in nuclear gene cyt-4 of Neurospora crassa result in pleiotropic defects in processing and splicing of mitochondrial RNAs.

Genetics ◽

10.1093/genetics/123.1.97 ◽

1989 ◽

Vol 123 (1) ◽

pp. 97-108 ◽

Cited By ~ 1

Author(s):

K F Dobinson ◽

M Henderson ◽

R L Kelley ◽

R A Collins ◽

A M Lambowitz

Keyword(s):

Neurospora Crassa ◽

Mitochondrial Protein ◽

Nuclear Gene ◽

Northern Hybridization ◽

Rrna Gene ◽

Mitochondrial Rna ◽

Group I Introns ◽

Group I ◽

Processing Pathways ◽

Aberrant Rna

Abstract The nuclear cyt-4 mutants of Neurospora crassa have been shown previously to be defective in splicing the group I intron in the mitochondrial large rRNA gene and in 3' end synthesis of the mitochondrial large rRNA. Here, Northern hybridization experiments show that the cyt-4-1 mutant has alterations in a number of mitochondrial RNA processing pathways, including those for cob, coI, coII and ATPase 6 mRNAs, as well as mitochondrial tRNAs. Defects in these pathways include inhibition of 5' and 3' end processing, accumulation of aberrant RNA species, and inhibition of splicing of both group I introns in the cob gene. The various defects in mitochondrial RNA synthesis in the cyt-4-1 mutant cannot be accounted for by deficiency of mitochondrial protein synthesis or energy metabolism, and they suggest that the cyt-4-1 mutant is defective in a component or components required for processing and/or turnover of a number of different mitochondrial RNAs. Defective splicing of the mitochondrial large rRNA intron in the cyt-4-1 mutant may be a secondary effect of failure to synthesize pre-rRNAs having the correct 3' end. However, a similar explanation cannot be invoked to account for defective splicing of the cob pre-mRNA introns, and the cyt-4-1 mutation may directly affect splicing of these introns.

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Cosegregation of Single Genes Associated with Fertility Restoration and Transcript Processing of Sorghum Mitochondrial orf107 and urf209

Genetics ◽

10.1093/genetics/150.1.383 ◽

1998 ◽

Vol 150 (1) ◽

pp. 383-391 ◽

Cited By ~ 1

Author(s):

Hoang V Tang ◽

Ruying Chang ◽

Daryl R Pring

Keyword(s):

Fertility Restoration ◽

Mitochondrial Gene ◽

Pollen Viability ◽

Single Gene ◽

Dominant Gene ◽

Nuclear Gene ◽

Male Sterile ◽

Reading Frame ◽

Transcript Processing ◽

Backcross Populations

Abstract Defective nuclear-cytoplasmic interactions leading to aberrant microgametogenesis in sorghum carrying the IS1112C male-sterile cytoplasm occur very late in pollen maturation. Amelioration of this condition, the restoration of pollen viability, involves a novel two-gene gametophytic system, wherein genes designated Rf3 and Rf4 are required for viability of individual gametes. Rf3 is tightly linked to, or represents, a single gene that regulates a transcript processing activity that cleaves transcriptsof orf107, a chimeric mitochondrial open reading frame specific to IS1112C. The mitochondrial gene urf 209 is also subject to nucleus-specific enhanced transcript processing, 5′ to the gene, conferred by a single dominant gene designated Mmt1. Examinations of transcript patterns in F2 and two backcross populations indicated cosegregation of the augmented orf107 and urf209 processing activities in IS1112C. Several sorghum lines that do not restore fertility or confer orf107 transcript processing do exhibit urf209 transcript processing, indicating that the activities are distinguishable. We conclude that the nuclear gene(s) conferring enhanced orf107 and urf209 processing activities are tightly linked in IS1112C. Alternatively, the similarity in apparent regulatory action of the genes may indicate allelic differences wherein the IS1112C Rf3 allele may differ from alleles of maintainer lines by the capability to regulate both orf107 and urf209 processing activities.

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Yeast CBP1 mRNA 3' end formation is regulated during the induction of mitochondrial function

Molecular and Cellular Biology ◽

10.1128/mcb.11.2.813-821.1991 ◽

1991 ◽

Vol 11 (2) ◽

pp. 813-821

Author(s):

S A Mayer ◽

C L Dieckmann

Keyword(s):

Mitochondrial Function ◽

Developmental Stages ◽

Single Gene ◽

Mitochondrial Protein ◽

Nuclear Gene ◽

State Level ◽

Yeast Cells ◽

Cdna Clones ◽

Coding Sequence ◽

Polyadenylation Sites

Alternative mRNA processing is one mechanism for generating two or more polypeptides from a single gene. While many mammalian genes contain multiple mRNA 3' cleavage and polyadenylation signals that change the coding sequence of the mature mRNA when used at different developmental stages or in different tissues, only one yeast gene has been identified with this capacity. The Saccharomyces cerevisiae nuclear gene CPB1 encodes a mitochondrial protein that is required for cytochrome b mRNA stability. This 66-kDa protein is encoded by a 2.2-kb mRNA transcribed from CPB1. Previously we showed that a second 1.2-kb transcript is initiated at the CBP1 promoter but has a 3' end near the middle of the coding sequence. Furthermore, it was shown that the ratio of the steady-state level of 2.2-kb CBP1 message to 1.2-kb message decreases 10-fold during the induction of mitochondrial function, while the combined levels of both messages remain constant. Having proposed that regulation of 3' end formation dictates the amount of each CBP1 transcript, we now show that a 146-bp fragment from the middle of CBP1 is sufficient to direct carbon source-regulated production of two transcripts when inserted into the yeast URA3 gene. This fragment contains seven polyadenylation sites for the wild-type 1.2-kb mRNA, as mapped by sequence analysis of CBP1 cDNA clones. Deletion mutations upstream of the polyadenylation sites abolished formation of the 1.2-kb transcript, whereas deletion of three of the sites only led to a reduction in abundance of the 1.2-kb mRNA. Our results indicate that regulation of the abundance of both CBP1 transcripts is controlled by elements in a short segment of the gene that directs 3' end formation of the 1.2-kb transcript, a unique case in yeast cells.

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Unstable mitochondrial DNA in natural-death nuclear mutants of Neurospora crassa

Molecular and Cellular Biology ◽

10.1128/mcb.9.10.4259-4264.1989 ◽

1989 ◽

Vol 9 (10) ◽

pp. 4259-4264

Author(s):

B L Seidel-Rogol ◽

J King ◽

H Bertrand

Keyword(s):

Neurospora Crassa ◽

Mitochondrial Protein ◽

Nuclear Gene ◽

Recessive Mutation ◽

Natural Death ◽

Mitochondrial Ribosomes ◽

Large Deletions ◽

Group I ◽

Mitochondrial Functions ◽

Mitochondrial Chromosome

The natural-death mutant of Neurospora crassa has an accelerated senescence phenotype caused by a recessive mutation, nd, in a nuclear gene that is located in linkage group I. An examination of mitochondrial functions, however, revealed that the mutant has phenotypic and molecular defects similar to those commonly associated with maternally transmitted fungal senescence syndromes, including (i) deficiencies in cytochromes aa3 and b; (ii) a deficit in small subunits of mitochondrial ribosomes, and hence defective mitochondrial protein synthesis; and (iii) accumulation of gross rearrangements, including large deletions, in the mitochondrial chromosome of vegetatively propagated cells. These traits indicate that the nd+ allele codes for a function that is essential for stable maintenance of the mitochondrial chromosome, possibly a protein involved in replication, repair, or recombination.

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