Molecular Biology of Higher Plant Mitochondrial DNA

Fertility restoration by Ifr1 in rice with BT-type cytoplasmic male sterility is associated with a reduced level, but not processing, of atp6-orf79 co-transcribed RNA

BT-type cytoplasmic male sterility (CMS) in rice is associated with accumulation of unprocessed dicistronic RNA containing a duplicated atp6 (B-atp6) and an unusual open reading frame, orf79, encoding a cytotoxic peptide in mitochondria. The male-sterile state of BT-type CMS is stably maintained by backcrossing the plants with line Taichung 65 (T65) that has no restorer gene and is completely suppressed by the presence of the Rf1 gene through the processing of B-atp6-orf79 RNA. A variant of the T65 line, T65(T), has a weak restoration function conferred by the Ifr1 gene, which is genetically independent of the Rf1 gene. However, not much is known about the mechanism(s). In a study to examine whether the mechanism involved in fertility restoration by Ifr1 is analogous to restoration mediated by Rf1, the transcript profile of B-atp6-orf79 in male-sterile plants was compared with that in fertility restored plants obtained by crossing male-sterile plants with T65(T). The cellular level of unprocessed B-atp6-orf79 RNA was reduced in the restored plants, but no change in processing efficiency or the quantity of B-atp6-orf79 DNA was detected. These results suggest that Ifr1 restores fertility through reducing either the transcription rate of B-atp6-orf79 or the stability of its primary transcripts, a mechanism distinct from that involved in fertility restoration of BT-type CMS by Rf1.

A mitochondrial plasmid and plasmid-like RNA and DNA polymerases encoded within the mitochondrial genome of carrot (Daucus carota L.)

The mitochondrial genome of mitochondrial type (mitotype) SW3 of carrot (Daucus carota L.) encodes intact reading frames for a RNA polymerase (Rpo) and a DNA polymerase (Dpo) similar to those encoded by linear mitochondrial plasmids from plants. A BLAST search of translated nucleotide sequences in GenBank revealed previously unreported plasmid-like Rpo or Dpo sequence fragments in many plant mitochondrial DNAs. Phylogenetic analyses of the relationships between mitochondrial (mt)DNA-encoded and plasmid-encoded Rpos and Dpos from plants suggest that the mitochondrial sequences were derived from integrated plant plasmid sequences. A linear mitochondrial plasmid was detected in a different mitotype (FG21) of carrot by Southern hybridization of the Rpo and Dpo to undigested mtDNAs. Transcripts of the mtDNA-encoded Rpo and Dpo in mitotype SW3 were detected by RT-PCR.

Abundant mitochondrial genome diversity, population differentiation and convergent evolution in pines

We examined mitochondrial DNA polymorphisms via the analysis of restriction fragment length polymorphisms in three closely related species of pines from western North America: knobcone (Pinus attenuata Lemm.), Monterey (P. radiata D. Don), and bishop (P. muricata D. Don). A total of 343 trees derived from 13 populations were analyzed using 13 homologous mitochondrial gene probes amplified from three species by polymerase chain reaction. Twenty-eight distinct mitochondrial DNA haplotypes were detected and no common haplotypes were found among the species. All three species showed limited variability within populations, but strong differentiation among populations. Based on haplotype frequencies, genetic diversity within populations (HS) averaged 0.22, and population differentiation (GST and theta) exceeded 0.78. Analysis of molecular variance also revealed that >90% of the variation resided among populations. For the purposes of genetic conservation and breeding programs, species and populations could be readily distinguished by unique haplotypes, often using the combination of only a few probes. Neighbor-joining phenograms, however, strongly disagreed with those based on allozymes, chloroplast DNA, and morphological traits. Thus, despite its diagnostic haplotypes, the genome appears to evolve via the rearrangement of multiple, convergent subgenomic domains.

The plant mitochondrial genome: homologous recombination as a mechanism for generating heterogeneity

The mitochondrial genomes of higher plants are among the largest and most complex organelle genomes described. They are generally multicircular or partly linear; in some species, extrachromosomal plasmids are present. It is proposed that inter- and intramolecular homologous recombination can account for the diversity of the observed genome organizations. The ability of mitochondria to fuse establishes a panmictic mitochondrial DNA population which is in recombinational equilibrium. It is suggested that this suppresses the base mutation rate, and unequal partitioning of the cytoplasm during cell division can lead to the rapid evolution of mitochondrial genome structure. This contrasts with the observed rates of base-sequence and genome evolution in chloroplasts. This difference can be accounted for solely by the inability of chloroplasts to fuse, thereby preventing chloroplast genome panmixis.

Recombinant mitochondrial plasmids in Neurospora composed of Varkud and a new multimeric mitochondrial plasmid

A mitochondrial plasmid, V5124, in Neurospora intermedia isolate 5124 has a deletion in its sequence relative to the highly similar Mauriceville and Varkud plasmids. These insertions in the latter plasmids are 28 bp in length and are positioned at sites that correspond to their major transcript 5' termini. The 28-bp sequence is nearly identical to a putative processing site upstream of the ND4L gene on the mitochondrial genome. The absence of this 28-bp sequence in V5124 apparently results in transcripts whose 5' termini correspond to an upstream consensus promoter sequence. Two variant forms of V5124 coexist with V5124 and have either of two similar 0.3-kb inserts positioned exactly as is the 28-bp insert in Varkud. These long inserts are chimeric, partly deriving from a newly discovered multimeric plasmid, MP. MP has significant similarity to a short region of the mitochondrial satellite plasmid VS. Another part of the 0.3-kb inserts in V5124 variants derives from the mitochondrial genome, within restriction fragment EcoRI-8. Neurospora mitochondria in many isolates can have several types of mitochondrial plasmids belonging to different homology groups. We propose that a common ancestral plasmid acquired insertions from either the mitochondrial genome or from other plasmids. The V5124 variants are the first instance of a chimeric mitochondrial plasmid in which distinct plasmids have recombined. This recombination proves that different plasmids coexist currently, or else did so at some point in their evolution, within a single mitochondrion.

Mitochondrial plasmid-like DNAs of the B1 family in the genus Oryza: sequence heterogeneity and evolution

Four kinds of circular plasmid-like DNA, designated B1, B2, B3 and B4, have been found in the mitochondria of Oryza sativa L. with an AA genome. Three novel B1-homologous mitochondrial plasmid-like DNAs, designated, M1, M2 and M3, were isolated in the present study from strains with CC and CCDD genomes in the genus Oryza. We cloned and sequenced these DNAs and found that the sequences of these molecules have wide regions of homology. B1, M2 and M3 each lack about 300 bp of a region that is present in M1 and small repeats were found at the sites of deleted sequences. Therefore, we propose the hypothesis that the B1 family differentiated from a common ancient molecule that was similar to M1 via, probably, slipped mispairing during DNA replication at several stages in the evolution in the genus Oryza.

Polymorphic distribution and molecular diversification of mitochondrial plasmid-like DNAs in the genus Oryza

Four kinds of circular plasmid-like DNA, designated B1, B2, B3 and B4, have been found in the mitochondria of rice (Oryza sativa L.). We analyzed the distribution of families of plasmid-like DNAs homologous to those of O. sativa in 40 strains of the genus Oryza with AA, BB, BBCC, CC, CCDD and EE genomes. Plasmid-like DNAs were observed only strains having AA, CC and CCDD genomes. The distribution patterns of strains with AA genome were highly polymorphic. We amplified the plasmid-like DNAs from strains with the AA genome by PCR and examined restriction fragments length polymorphisms (RFLPs). RFLPs were detected among families of plasmid-like DNA amplified from different strains. This result indicated that some mutations, such as base substitutions and the insertion or deletion of a small fragment of DNA, had occurred and had accumulated during the differentiation of strains with an AA genome.

Selective DNA amplification regulates transcript levels in plant mitochondria

Most plant mitochondrial genomes exist as subgenomic-size fragments apparently due to recombination between repetitive sequences. This leads to the possibility that independently replicating subgenomic domains could result in mitochondrial gene copy number variation. We show, through Southern-blot analysis of both restricted and intact mtDNA, that there are gene-specific copy number differences in the monocot Zea mays. Comparison of two different maize genotypes, B37(N) and B37(T), a cytoplasmic male-sterile strain, reveal fewer gene copy number differences for B37(T) than for B37(N). In contrast to maize, significant gene copy number differences are not detected in the dicot Brassica hirta. We also demonstrate that mitochondrial transcriptional rates in both species are apparently dependent on gene copy number since relative rates determined by run-on analysis are proportional to relative gene copy numbers. Thus a direct relationship exists between plant mitochondrial gene copy number and transcriptional rate.

Distribution of seven homology groups of mitochondrial plasmids in Neurospora: evidence for widespread mobility between species in nature

A survey of mitochondrial DNAs from over 225 Neurospora and related fungal isolates from around the world uncovered three new homology groups of mitochondrial plasmids, two divergent subgroups of the Fiji plasmid family, and extended previous data about plasmid distribution patterns. Newly-discovered circular plasmids, Java and MB1, and the linear Moorea plasmids, were found in relatively-few isolates. A large proportion of isolates (51%) were found to have these or previously-discovered plasmids in the Varkud, kalilo, LaBelle, or Fiji families. Plasmids in most families were found in isolates worldwide and distributed nearly randomly with respect to species. As many as three types of plasmids were found in single isolates, and plasmids typically were found alone or in pairs in a random, independent pattern. The regional clustering of some plasmids was independent of species, providing a strong argument that horizontal transfer of plasmids occurs frequently in nature. Some plasmid families were much more diverse than others. The Fiji plasmids are a superfamily composed of distinct subgroups defined by degrees of cross-hybridization. Between some subgroups there were large regions of non-homology.

Restriction fragments homologous to mitochondrial plasmid-like DNAs are located within limited chromosomal regions on the rice nuclear genome

The chromosomal locations of restriction fragments of nuclear DNA that were homologous to four mitochondrial plasmid-like DNAs, namely, B1, B2, B3 and B4, were analyzed by restriction fragment length polymorphism (RFLP) analysis in cultivated rice. Nine kinds of fragments homologous to plasmidlike DNAs were analyzed for their segregation in three different F2 populations derived from intercrosses between rice subspecies; these were found to be localized in three chromosomal regions: three, one and five kinds of nuclear homologues were situated on chromosomes 1,3 and 8, respectively. Nuclear homologues on a given chromosome were tightly linked even though they were homologous to different plasmid-like DNAs. The loci of nuclear homologues found commonly in two or three cultivars were found to be highly conserved, a result that is consistent with their stable transmission. These results and those of the Southern analysis suggest the independent integration of these sequences during the varietal differentiation of rice. The concentration of loci for nuclear homologues on chromosomes 1 and 8 suggests that these sequences were integrated non-randomly into these chromosomal regions.

Plastid engineering in land plants: a conservative genome is open to change

We have developed efficient transformation protocols to modify each of the 500-10,000 plastid genome copies in a tobacco cell. The transforming DNA is introduced on the surface of microscopic tungsten particles by the biolistic process. Selection for transplastomes is by spectinomycin resistance based on expression of aminoglycoside-3"-adenyltransferase from a chimeric aadA gene in the transforming DNA. Manipulations that are now feasible include replacement of endogenous plastid genes with DNA sequences modified in vitro, targeted gene disruption, and insertion of reporter genes into the plastid genome. Alternative methods for plastid genome manipulations may be developed utilizing an extrachromosomal element which was identified during the transformation studies. Introduction of foreign genes under control of plastid gene expression elements results in duplication of endogenous regulatory sequences. A sensitive somatic assay to detect deletions via such direct repeats confirmed that these sequence duplications do not result in significant genome instability. The ability to transform plastids will facilitate the study of plastid gene regulation, and the application of genetic engineering to crop improvement.

Male-sterile chicory cybrids obtained by intergeneric protoplast fusion

Male-sterile chicory plants were obtained by fusion of chicory mesophyll protoplasts and hypocotyl protoplasts derived from male-sterile sunflower plants. The protoplasts of both species were fused by the PEG method and the products were selected manually and cultivated at very low density in a liquid medium. Three to twenty percent of the heterokaryocytes divided and evolved into microcalli, then into calli where budding could be induced. The mitochondrial genome of ten male-sterile or totally sterile plants was studied. Restriction endonuclease profiles of mitochondrial DNA and molecular hybridization with specific genes of the mitochondrial genome used as probes indicated that mitochondrial DNA rearrangement had occurred between sunflower and chicory and the intensity of the rearrangements correlated with the degree of sterility of the different plants.

Different CMS sources found in Beta vulgaris ssp maritima: mitochondrial variability in wild populations revealed by a rapid screening procedure

Mitochondrial DNA (mtDNA) variation in natural Beta maritima populations has been characterized by way of Southern blot hybridizations of total DNA using non-radioactive probes and chemiluminescent detection. It was found that the previously described N ("normal") mitochondrial type could be subdivided into three subtypes. A new mitochondrial genotype (type R) was distinguished in addition to the previously described type S. Both are male-sterile cytoplasms and can produce a. segregation of sexual phenotypes in their progenies depending on the nuclear background. The populations contained at least two to four different mitochondrial genotypes.

Interaction of the mitochondrial S-Pcf locus for cytoplasmic male sterility in Petunia with multiple fertility-restoration genes in somatic hybrid plants

The Cytoplasmic Male Sterility (CMS)-associated region in Petunia, the S-Pcf locus, was defined by the analysis of recombinant mitochondrial genomes of somatic hybrid plants resulting from a fusion of protoplasts from CMS and fertile lines. The presence of the S-Pcf locus was shown to correlate with the CMS trait in stable somatic hybrids and in other CMS Petunia lines. A small population of unstable, sterile somatic hybrids was also generated in this fusion, most of which underwent cytoplasmic segregation in subsequent generations. Stable revertants of such sterile somatic hybrids were shown to lose the S-Pcf locus. In this paper we present a molecular and genetic analysis of unstable progenies of an unstable, sterile somatic hybrid plant derived from the same fusion experiment. Both male-sterile and fertile progenies of this somatic hybrid plant have shown continuous segregation of fertile and male-sterile progenies. All segregants in this line contained, and transcribed, the S-Pcf locus. Genetic analysis indicated the presence of various levels of multiple nuclear fertility-restoration genes in this group of progenies. These findings consolidate the association between the S-Pcf locus and the CMS trait in Petunia. It also shows that the restoration of fertility by the multiple nuclear gene system does not affect the transcription of the S-Pcf locus and that the presence of an intact S-Pcf locus is necessary in order to maintain the potential sterility in the cytoplasm.

Genetic and physical maps and a clone bank of mitochondrial DNA from rice

Mitochondrial DNA (mtDNA) was isolated from young green leaves of rice plants. DNA fragments were cloned into lambda DNA, and clones that hybridized to mitochondrial genes from other plants were selected. Distal restriction fragments of these clones were used as probes for the selection of overlapping clones. A genetic map was finally created from the library by "walking" along the genome. The mitochondrial genome consists of five basic circles, with each circle sharing homologous sequences with one or two other circles. A master circle was constructed from the results of recombination across repeated sequences, and its size was estimated to be 492 kb. A physical map and a bank of overlapping clones were also constructed.

Organelle DNA polymorphism in apple cultivars and rootstocks

Restriction fragment length polymorphisms (RFLPs) have been used to detect chloroplast (cp) and mitochondrial (mt) DNA variation among 18 apple cultivars and three rootstocks. The distribution of RFLP patterns allowed the assignment of these genotypes into three groups of cytoplasmic relatedness. Our results also demonstrate maternal inheritance of cp- and mtDNAs in apple. Thus, the organelle DNA assay provides a convenient and reliable method to assess cytoplasmic diversity within the apple germ-plasm collection and to trace the maternal lineages involved in the evolution of apple.

Two potential Petunia hybrida mitochondrial DNA replication origins show structural and in vitro functional homology with the animal mitochondrial DNA heavy and light strand replication origins

Four Petunia hybrida mitochondrial (mt) DNA fragments have been isolated, sequenced, localized on the physical map and analyzed for their ability to initiate specific DNA synthesis. When all four mtDNA fragments were tested as templates in an in vitro DNA synthesizing lysate system, developed from purified P. hybrida mitochondria, specific initiation of DNA synthesis could only be observed starting within two fragments, oriA and oriB. When DNA synthesis incubations were performed with DNA templates consisting of both the A and B origins in the same plasmid in complementary strands, DNA synthesis first initiates in the A-origin, proceeds in the direction of the B-origin after which replication is also initiated in the B-origin. Based on these observations, a replication model for the P. hybrida mitochondrial genome is presented.

Analysis of nuclear sequences homologous to the B4 plasmid-like DNA of rice mitochondria; evidence for sequence transfer from mitochondria to nuclei

Nuclear sequences homologous to the plasmid-like DNA, B4, were analyzed in the Japonica rice variety, Fujiminori. Homologous sequences existed at several positions in the nuclear genome, but each contained only a portion of the B4 sequence. It was impossible to reconstruct the entire sequence of B4 even by collating all the homologous sequences. Overlaps between some of the B4 sequences present in the nuclear genome resulted in parts of the sequence being represented more than once. These features indicate that nuclear sequences homologous to B4 are not the origin of B4 and that they have been transferred from mitochondria and integrated into the nuclear genome. Five other foreign sequences originating in the chloroplast or mitochondrial genome were found within 1 kb of the B4-homologous sequences. Structural analysis is consistent with the hypothesis that the DNA sequences were transferred via RNA.

Sequence analysis of a mitochondrial DNA fragment isolated from cultured cells of carrot cytoplasmic male-sterile strain

2.0 kb Hind III fragment isolated from cytoplasmic male-sterile carrot mitochondria, designated PKT5, was hybridized to ORF13 which is the coding region of a unique polypeptide in maize CMS (Dewey et al., 1986). Sequence analysis indicated that PKT5 is consisted of 3 domains. Domain 1 was identical to the 5'-flanking region of atp6 in maize CMS-TURF2H3 sequence (Dewey et al., 1986). Domain 2 contained a novel ORF encoding 72 amino acids, which was extremely homologous to the amino-terminal 67 amino acids of the unique ORF13 in maize CMS. Domain 3 except an amino acid change (Ile87 = ATT for Asn87 = AAT), was identical to ORF25 polypeptide in maize CMS. Connective sequences of these 3 domains were also highly homologous to the maize CMS-TURF2H3 sequence. Out of 7 recombination points in maize CMS-TURF2H3 sequence, at least 4 points were conserved in PKT5 sequence.

Linkage analysis of the nuclear homologues of mitochondrial plasmid-like DNAs in rice

A genetical study on the nucleotide sequences of the nuclear DNAs which share homology with rice mitochondrial plasmid-like DNAs, B1, B2, B3 and B4 was carried out. Restriction fragments of the nuclear DNAs hybridized with these plasmid-like DNAs showed polymorphisms in their length between Indica and Japonica rice cultivars. The hybridized signals found specifically in Indica or Japonica cultivars segregated in the F2 population derived from a cross between these two subspecies. The observed ratio of the nuclear homologues in the F2 population demonstrated that they were transmitted according to the Mendelian inheritance. The co-segregation of homologues was examined and the linkage was detected between the B1-nuclear homologue of Japonica and the B4-nuclear homologue of Indica, and also between the nuclear homologues of B2 and B3 of Indica. The linkage between the B1-nuclear homologue of Japonica and the B4-nuclear homologue of Indica was conserved in the different rice cultivars.

Complex determination of male sterility in Thymus vulgaris L.: genetic and molecular analysis

Nucleocytoplasmic determination of male sterility in Thymus vulgaris L. has been assumed in all papers attempting to explain the remarkably high frequencies of male steriles found in natural populations of this species. This paper provides strong evidence that both nuclear and cytoplasmic genes are involved in the determination of male sterility of this species, giving a complex inheritance. Interpopulation and intrapopulation crosses have shown that the ratio of females versus hermaphrodites among offsprings varied widely from 1∶0 to 1∶1. Furthermore, interpopulation crosses consistently yielded a higher frequency of females than intrapopulation crosses. Nucleocytoplasmic inheritance was demonstrated by an absence of male fertiles in backcrosses and asymmetrical segregation in reciprocal crosses. Molecular analysis of the mitochondrial DNA of some of the parents used in crosses suggested the involvement of different cytoplasms in the inheritance of male steriliy.

RFLP analysis of nuclear DNAs homologous with mitochondrial plasmid-like DNAs in cultivated rice

B1 and B2 are small, circular, mitochondrial plasmid-like DNAs found in male-sterile cytoplasm (cms-Bo) of rice. In this study, nuclear sequences homologous to these DNAs were investigated among a number of rice cultivars. Several copies of nuclear B1-and B2-homologous sequences were detected in all examined cultivars, regardless of the presence or absence of the B1 and B2 DNAs in mitochondria, indicating that the existence of the B1- and B2-homologous sequences in the rice nuclear genome was widespread. A restriction fragment length polymorphism (RFLP) was detected for both sequences, and we propose that these DNAs could be useful RFLP markers for the rice nuclear genome. To analyze these nuclear homologues genetically, segregation analysis of the RFLP was carried out in the F2 progenies of an Indica-Japonica rice hybrid. Of the B1 homologues, there were two nonallelic fragments, one specific to the Indica parent and the other to the Japonica. These results indicate that the B1 and B2 homologues were dispersed in the nuclear genome. The integration of B1-homologous DNA into the nuclear DNA may have occurred independently after sexual isolation of the Indica and Japonica rice varietal groups, or a intranuclear transposition of these sequences took place during the process of rice differentiation into the varietal groups.

Red algal plasmids

Five of 21 red algal genera were found to contain circular dsDNA plasmids, typically of two or more sizes per species. Clones of the two plasmids (GL4.4 and GL3.5 kbp), characterizing all isolates of Gracilariopsis lemaneiformis, do not cross-hybridize with each other, with the nuclear, plastid or mitochondrial genomes of G. lemaneiformis, or with any DNA genomes of the other red algae examined. Clones of both plasmids hybridized with discrete bands on Northern blots of total RNA and poly(A)+ RNA. Sequencing of the G. lemaneiformis 3.5 kbp plasmid revealed two potential open reading frames which, when used to probe Northern blots, confirmed the presence of specific transcripts. These autonomously replicating plasmids are present in high copy number per cell and in constant proportion to each other. Their constancy suggests a function of significance to the species. Red algal plasmids may provide useful vectors for transforming economically important red algal species.

A chimeric gene containing the 5' portion of atp6 is associated with cytoplasmic male-sterility of rice

Three ATPase subunit 6 (atp6) genes of rice mitochondria were isolated, one from normal and two from cms-Bo male-sterile cytoplasms, in order to determine whether the extra atp6 gene in cms-Bo rice plays a role in cytoplasmic male-sterility (CMS). The nucleotide sequences of all three genes were determined and analysis showed a chimeric atp6 gene (urf-rmc) as well as a normal atp6 gene in cms-Bo cytoplasm, but only the normal atp6 gene in normal cytoplasm. The urf-rmc gene is completely homologous to the normal atp6 gene from at least position -426 in the 5' flanking region to position +511 downstream from the initiation codon ATG: however, the following downstream sequence shows no homology with the normal rice atp6 gene, or any other reported sequence. Introduction of the restorer of fertility gene altered transcription of the urf-rmc gene but not the atp6 gene, indicating participation of the chimeric gene in the expression of CMS. Southern blot analysis showed that the urf-rmc gene was generated by an intramolecular recombination event in mitochondrial DNA, and the homologous recombination point between the atp6 gene and the opposite ancestral sequence was identified as 5'-TTCCCTC-3'.

Nuclear genotype affects mitochondrial genome organization of CMS-S maize

A WF9 strain of maize with the RD subtype of the S male-sterile cytoplasm (CMS-S) was converted to the inbred M825 nuclear background by recurrent backcrossing. The organization of the mitochondrial genomes of the F1 and succeeding backcross progenies was analyzed and compared with the progenitor RD-WF9 using probes derived from the S1 and S2 mitochondrial episomes, and probes containing the genes for cytochrome c oxidase subunit I (coxI), cytochrome c oxidase subunit II (coxII) and apocytochrome b (cob). Changes in mitochondrial DNA (mtDNA) organization were observed for S1-, S2-, and coxI-homologous sequences that involve loss of homologous restriction enzyme fragments present in the RD-WF9 progenitor. With the coxI probe, the loss of certain fragments was accompanied by the appearance of a fragment not detectable in the progenitor. The changes observed indicate the effect of the nuclear genome on the differential replication of specific mitochondrial subgenomic entities.

High-rate spontaneous reversion to cytoplasmic male sterility in sugar beet: a characterization of the mitochondrial genomes

Among the fertile sugar beet lines with nuclear sterility maintenance genes, rf, in a homozygous recessive state, sublines capable of reverting spontaneously at a high rate to sterility were identified. Of 24 related fertile sublines studied, 6 were found to spontaneously revert to sterility with a frequency of about 19%. Genetic analysis confirmed the cytoplasmic nature of spontaneously arising sterility. Reversion to sterility in these sublines was accompanied by alterations in the mitochondrial genome structure: loss of the autonomously replicating minicircle c (1.3 kb) and changes in the restriction patterns of high-molecular-weight mitochondrial DNA (mtDNA). Southern hybridixation analysis with cloned minicircle c as a probe revealed no integration of this DNA molecule into the main mitochondrial and nuclear genomes of the revertants. Comparative BamHI and EcoRI restriction analysis of the mtDNA from the sterile revertants and fertile parental subline showed that the spontaneous reversion is accompanied by extensive genomic rearrangement. Southern blot analysis with cloned α-subunit of F1-ATPase (atpA) and cytochrome c oxidase subunit II (COX II) genes as probes indicated that the changes in mtDNA accompanying spontaneous reversion to sterility involved these regions. The mitochondrial genomes of the spontaneous revertants and the sterile analogue were shown to be identical.

Protoplast-fusion-derived Solanum cybrids: application and phylogenetic limitations

We established interspecific Solanum cybrids in order to study the intrageneric nuclear-organelle compatibility and the introgression of advantageous plasmone-coded breeding traits into potato. Cybridization was performed by the donor-recipient protoplast-fusion procedure. We found that the plastomes of S. chacoense, S. brevidens, and S. etuberosum could be transferred into the cybrids having S. tuberosum nuclear genomes; chondriome components were likewise transferred from the former species into these cybrids. The combination with S. chacoense as organelle donor and potato as recipient resulted in green fertile plants with potato morphology. By using S. etuberosum as an organelle donor and potato as recipient, male-sterile cybrid plants, most of them having pigmentation abnormalities, were obtained. The combination of S. brevidens with potato resulted in palegreen (almost albino) regenerants. The latter albino plantlets had both the chloroplast DNA and the mitochondrial DNA of the donor (S. brevidens) and did not survive the transfer into the greenhouse. An immediately applicative result of this study is the de novo establishment of male-sterile plants in a potato cultivar. Such plants should be useful as seed parents in the production of hybrid, true-potato seeds.

Evolution of plant mitochondrial genomes via substoichiometric intermediates

Comparison of the modern fertile maize mitochondrial genome (N) with an ancestral maize mitochondrial genome (RU) reveals a 12 kb duplication (containing the atpA gene) in the modern genome that is absent from the ancestor. Cloning, mapping, and sequencing of the relevant portions of the ancestral genome shows that this duplication probably arose via a three-stage recombination process involving substoichiometric intermediates. Comparison with analogous observations on yeast mitochondrial genomes suggests that this three-stage model of genome reorganization can be generally applied to plant mitochondrial genomes to explain both deletions and the creation of novel repeats, common features of plant mitochondrial genome evolution.

Alloplasmic male sterility in AD allotetraploid Gossypium hirsutum upon replacement of its resident A cytoplasm with that of D species G. harknessii

Alloplasmic male sterile (cms) and restoration-of-fertility (Rf) lines of the AD allotetraploid Gossypium hirsutum were earlier derived from the presumed introgression of the cytoplasm of the D species G. harknessii. To confirm that this happened and address its significance, cytoplasms of the maternal progenitor, backcross intermediates, derived breeding lines, related A, D, and F species, and a synthetic AD tetraploid were examined by agarose and polyacrylamide gel electrophoresis of 140 restriction enzyme fragments of chloroplast DNA. Length mutations of 10-50 nucleotides predominate over site loss/gain mutations. Chloroplast DNA is maternally inherited and that of G. harknessii has been maintained in the cms lines for at least 13 successive generations without detectable alteration. Chloroplast DNA divergence is consistent with current nuclear genome classification and shows that the A progenitor was the maternal parent of the AD tetraploids. As predicted from incompatability models of cms, the degree of male sterility in alloplasmic Gossypium tetraploids is correlated with the extent of evolutionary divergence of their cytoplasms. It is suggested that the A genome in the AD tetraploids dominates those nuclear-cytoplasm interactions reflected by male fertility.

DNA polymorphism in Allium cepa cytoplasms and its implications concerning the origin of onions

Mitochondrial and chloroplast DNA was isolated from fertile and cytoplasmic male sterile cultivars of cultivated onions. Restriction fragment length polymorphism led to the distinction between cytoplasms S and M. Mitochondrial DNA patterns from S cytoplasms appeared dentical and characterized mostly male sterile lines. An open-pollinated variety was found to bear this cytoplasm and thought to be the origin of S types. Mitochondrial DNA patterns from M cytoplasms were subdivided into four types, M1 and M2 corresponding to normal N cytoplasm, M3 and M4 probably corresponding to T cytoplasms. S and M cytoplasms were also distinguished by chloroplast DNA restriction patterns. Our results confirm previous genetic distinction between S, N and T cytoplasms.

Nucleotide sequence and molecular characterization of plasmid-like DNAs from mitochondria of cytoplasmic male-sterile rice

Two plasmid-like DNAs, B2 and B3, were isolated from mitochondria of the cytoplasmic male-sterile rice, A-58 CMS. Molecular clones having their complete sequences were constructed and used as probes of mitochondrial and nuclear genomes by Southern hybridization. No evidence was found that integrated copies of either one exist in the main mitochondrial genome, but sequences homologous to both were present in the nuclear genome. The complete nucleotide sequences of B2 and B3 were established and compared to those of rice B1 and B4 and to the 1.9- and the 1.4-kbp plasmid-like DNAs of maize. Many of the sequences were common to both plant species.

Properties and nucleotide sequence of a mitochondrial plasmid from sunflower

The 1.413 circular supercoiled mitochondrial DNA plasmid P1 from a fertile sunflower line was sequenced, and a series of 160 bp tandemly repeated sequences was observed. The P1 plasmid was detected in both fertile and cytoplasmic male-sterile (CMS) lines, but in different quantities. Two other circular plasmids, P2 and P3, each 1.8 kbp in length, were shown to share common sequences with P1. The mitochondrial plasmid P1 detected homologous sequences in the nuclear DNA of sunflower, but not in chloroplast DNA nor in main band mitochondrial DNA. RNA molecules of about 680 and 550 nucleotides were detected that were complementary to mt plasmid P1.

Minicircle variation in Beta mitochondrial DNA

Mitochondrial DNAs from nine male fertile and eight cytoplasmic male sterile (cms) accessions of wild and cultivated Beta beets were investigated for the presence of low molecular weight DNA molecules. Five different supercoiled DNA molecules were detected, varying in size from 1.33 to 1.63 kb. Southern hybridizations revealed multimeric forms and sequence homologies between the minicircles. The occurrence of the different minicircles among the 17 accessions was investigated by agarose gel electrophoresis and Southern hybridization using minicircle specific probes. The 1.33 and 1.63 kb minicircles were found in most accessions, the other three minicircles were found in one or two of the wild Beta beet accessions. The presence of a low number of small, more or less homologous, minicircles in all investigated plants makes these molecules a general characteristic of Beta mtDNA. No association is found between the presence or absence of specific minicircles and the expression of male sterility. Neither does the distribution of the different minicircles in Beta beets indicate any essential biological role of these minicircles.

A NADH dehydrogenase subunit gene is co-transcribed with the abnormal Petunia mitochondrial gene associated with cytoplasmic male sterility

DNA sequence analysis 3' to the Petunia S-pcf coding region has resulted in the identification of an open reading frame similar to mammalian mitochondrial genes for subunit 3 of the NADH dehydrogenase complex (nad3). Both the abnormal fused gene S-pcf and S-nad3 fall within the mitochondrial DNA region previously shown to be associated with cytoplasmic male sterility (CMS). The S-nad3 sequence, co-transcribed with S-pcf, is present in only one copy within the Petunia CMS genome. A homologous transcribed sequence from the mitochondrial genome of a fertile Petunia line has been identified. The coding region of the two genes are identical and they share homology for at least 800 bp downstream. The genes diverge 117 bp upstream of the nad3 start codon. Transcripts of the S-pcf/S-nad3 transcripts are similar in tissues of a fertility-restored line and a CMS line.