Study of wheat phylogeny by coRI analysis of chloroplastic and mitochondrial DNAs

Analysis of ATP6 sequence diversity in the Triticum-Aegilops species group reveals the crucial role of rearrangement in mitochondrial genome evolution

Mutation and chromosomal rearrangements are the two main forces of increasing genetic diversity for natural selection to act upon, and ultimately drive the evolutionary process. Although genome evolution is a function of both forces, simultaneously, the ratio of each can be varied among different genomes and genomic regions. It is believed that in plant mitochondrial genome, rearrangements play a more important role than point mutations, but relatively few studies have directly addressed this phenomenon. To address this issue, we isolated and sequenced the ATP6-1 and ATP6-2 genes from 46 different euplasmic and alloplasmic wheat lines. Four different ATP6-1 orthologs were detected, two of them reported for the first time. Expression analysis revealed that all four orthologs are transcriptionally active. Results also indicated that both point mutation and genomic rearrangement are involved in the evolution of ATP6. However, rearrangement is the predominant force that triggers drastic variation. Data also indicated that speciation of domesticated wheat cultivars were simultaneous with the duplication of this gene. These results directly support the notion that rearrangement plays a significant role in driving plant mitochondrial genome evolution.

Chloroplast DNA from the fern Osmunda cinnamomea: physical organization, gene localization and comparison to angiosperm

Chloroplast DNA from the fern Osmunda einnamomea was isolated by a sucrose gradient procedure utilizing PEG to stabilize chloroplasts. Analysis with the restriction endonucleases PvuII, Sacl and BstEII indicates a chloroplast genome size of 144 kb. A physical map of the fragments produced by these three enzymes was constructed by filter hybridizations using purified PvuII fragments as hybridization probes. The Osmunda chloroplast genome is circular and contains an inverted repeat 8-13 kb in size.Gene probes from tobacco, corn and spinach were used to map the positions of six genes on the Osmunda chloroplast chromosome. The 16S and 23S ribosomal RNAs are encoded by duplicate genes which lie within the inverted repeat. Genes for the large subunit of ribulose-1,5-bisphosphate carboxylase, a photosystem II polypeptide, and the alpha and beta subunits of chloroplast coupling factor are located in three different segments of the large single copy region.The Osmunda chloroplast genome is remarkably similar in size, conformation, physical organization, and map positions of known genes, to chloroplast DNA from a number of angiosperms. The major difference between chloroplast DNA from this fern and angiosperms is that the inverted repeat is smaller in Osmunda (8-13 kb) than in angiosperms (22-25 kb).

Physical and gene mapping of cauliflower (Brassica oleracea) mitochondrial DNA

A physical map of the mitochondrial DNA isolated from B. oleracea (cauliflower) inflorescences was constructed with the restriction endonucleases Sall, Kpnl and Bgll. Physical mapping was made using the multi enzyme method with either unlabeled or labeled DNA fragments isolated by preparative electrophoresis and a clone bank prepared by inserting incomplete Sall restriction digests of mitochondrial DNA into a cosmid vector.The different mapping studies led to a circular map, about 217 kb in size, containing the entire sequence complexity of the genome. The 26S and 18S - 5S ribosomal RNA genes appeared to be separated by about 75 kb in this map. However, the particular cross-hybridization between several restriction fragments and the sequential diversity of some cosmids indicated that intra molecular recombination may occur naturally in higher plant mitochondria. Namely, one recombinational event resulted in the ribosomal RNA genes mapping closer together.

High-throughput discovery of chloroplast and mitochondrial DNA polymorphisms in Brassicaceae species by ORG-EcoTILLING

Background

Information on polymorphic DNA in organelle genomes is essential for evolutionary and ecological studies. However, it is challenging to perform high-throughput investigations of chloroplast and mitochondrial DNA polymorphisms. In recent years, EcoTILLING stands out as one of the most universal, low-cost, and high-throughput reverse genetic methods, and the identification of natural genetic variants can provide much information about gene function, association mapping and linkage disequilibrium analysis and species evolution. Until now, no report exists on whether this method is applicable to organelle genomes and to what extent it can be used.

Methodology/Principal Findings

To address this problem, we adapted the CEL I-based heteroduplex cleavage strategy used in Targeting Induced Local Lesions in Genomes (TILLING) for the discovery of nucleotide polymorphisms in organelle genomes. To assess the applicability and accuracy of this technology, designated ORG-EcoTILLING, at different taxonomic levels, we sampled two sets of taxa representing accessions from the Brassicaceae with three chloroplast genes (accD, matK and rbcL) and one mitochondrial gene (atp6). The method successfully detected nine, six and one mutation sites in the accD, matK and rbcL genes, respectively, in 96 Brassica accessions. These mutations were confirmed by DNA sequencing, with 100% accuracy at both inter- and intraspecific levels. We also detected 44 putative mutations in accD in 91 accessions from 45 species and 29 genera of seven tribes. Compared with DNA sequencing results, the false negative rate was 36%. However, 17 SNPs detected in atp6 were completely identical to the sequencing results.

Conclusions/Significance

These results suggest that ORG-EcoTILLING is a powerful and cost-effective alternative method for high-throughput genome-wide assessment of inter- and intraspecific chloroplast and mitochondrial DNA polymorphisms. It will play an important role in evolutionary and ecological biology studies, in identification of related genes associated with agronomic importance such as high yield and improved cytoplasmic quality, and for identifying mitochondrial point mutations responsible for diseases in humans and other animals.

Variations in a hotspot region of chloroplast DNAs among common wheat and Aegilops revealed by nucleotide sequence analysis

The second largest BamHI fragment (B2) of the chloroplast DNA in Triticum (wheat) and Aegilops contains a highly variable region (a hotspot), resulting in four types of B2 of different size, i.e. B2l (10.5kb), B2m (10.2kb), B2 (9.6kb) and B2s (9.4kb). In order to gain a better understanding of the molecular nature of the variations in length and explain unexpected identity among B2 of Ae. ovata, Ae. speltoides and common wheat (T. aestivum), the nucleotide sequence between a stop codon of rbcL and a HindIII site in cemA in the hotspot was determined for Ae. ovata, Ae. speltoides, Ae. caudata and Ae. mutica. The total number of nucleotides in the region was 2808, 2810, 3302, and 3594 bp, for Ae. speltoides, Ae. ovata, Ae. caudata and Ae. mutica, respectively, and the sequences were compared with the corresponding ones of Ae. crassa 4x, T. aestivum and Ae. squarrosa. Compared with the largest B2l fragment of Ae. mutica, a 791bp and a 793 bp deletion were found in Ae. speltoides and Ae. ovata, respectively, and the possible site of deletion in the two species is the same as that of T. aestivum. However, a deleted segment in Ae. ovata is 2 bp longer than that of Ae. speltoides (and T. aestivum), demonstrating that recurrent deletions had occurred in the chloroplast genomes of both species. Comparison of the sequences from Ae. caudata and Ae. crassa 4x with that of Ae. mutica revealed a 289 bp and a 61 bp deletion at the same site in Ae. caudata and Ae. crassa 4x, respectively. Sequence comparison using wild Aegilops plants showed that the large length variations in a hotspot are fixed to each species. A considerable number of polymorphisms are observed in a loop in the 3' of rbcL. The study reveals the relative importance of the large and small indels and minute inversions to account for variations in the chloroplast genomes among closely related species.

Plasmon analyses of Triticum (wheat) and Aegilops: PCR-single-strand conformational polymorphism (PCR-SSCP) analyses of organellar DNAs

To investigate phylogenetic relationships among plasmons in Triticum and Aegilops, PCR-single-strand conformational polymorphism (PCR-SSCP) analyses were made of 14.0-kb chloroplast (ct) and 13. 7-kb mitochondrial (mt)DNA regions that were isolated from 46 alloplasmic wheat lines and one euplasmic line. These plasmons represent 31 species of the two genera. The ct and mtDNA regions included 10 and 9 structural genes, respectively. A total of 177 bands were detected, of which 40.6% were variable. The proportion of variable bands in ctDNA (51.1%) was higher than that of mtDNA (28. 9%). The phylogenetic trees of plasmons, derived by two different models, indicate a common picture of plasmon divergence in the two genera and suggest three major groups of plasmons (Einkorn, Triticum, and Aegilops). Because of uniparental plasmon transmission, the maternal parents of all but one polyploid species were identified. Only one Aegilops species, Ae. speltoides, was included in the Triticum group, suggesting that this species is the plasmon and B and G genome donor of all polyploid wheats. ctDNA variations were more intimately correlated with vegetative characters, whereas mtDNA variations were more closely correlated with reproductive characters. Plasmon divergence among the diploids of the two genera largely paralleled genome divergence. The relative times of origin of the polyploid species were inferred from genetic distances from their putative maternal parents.

Variation in coxII intron in the wild ancestral species of wheat

To study the maternal lineage and evolution of polyploid species of wheat, variation in mitochondrial DNA was investigated in Triticum and Aegilops by PCR-aided RFLP analysis. A 1.3 kb region containing the intron of coxII was studied using 20 accessions from five species of Sitopsis section of Aegilops, one species of Einkorn wheat, four species of tetraploid wheat, and one species of common wheat. Only three restriction site changes and a single deletion/insertion were found among 884 restriction fragments surveyed. This fact suggests the highly conserved nature of this region within Triticum and Aegilops. Four haplo-types were recognized in coxII intron. A parsimonious relationship indicated that three haplo-types were independently derived from one prototype which was found in wild Einkorn and Aegilops species except for Ae. speltoides. All but one accession of Ae. speltoides possessed a derivative haplo-type, common in Timopheevi wheat. The result supported the hypothesis that Ae. speltoides donated the G genome to Timopheevi wheat; however did not agree with that Ae. speltoides was the B genome donor to the Emmer and common wheat.

Relationships among Cichorium species and related genera as determined by analysis of mitochondrial RFLPs

Mitochondrial DNA polymorphism was employed to assess cytoplasmic diversity among cytoypes of the genus Cichorium and related genera of the tribe Lactuceae (Asteraceae). Hybridization patterns of total DNA using six restriction enzymes and five heterologous mtDNA probes were examined. From estimates of mtDNA diversity, Cichorium spinosum appeared as an ecotype of C. intybus rather than a separate species. Interspecific mtDNA polymorphism in the genus Cichorium was higher than that observed in Cicerbita Crepis, Lactuca and Tragopogon. Molecular data seemed to indicate that Catananche is very distant from the other genera examined. Intergeneric comparisons allowed the clustering of Cicerbita, Lactuca and Cichorium, genera which belong to different subtribes. However, further molecular investigations on a larger number of genera are needed to clarify the relationships among genera within and between subtribes of the tribe Lactuceae.

Paternal inheritance of mitochondria and chloroplasts in Festuca pratensis-Lolium perenne intergeneric hybrids

Organelle inheritance in intergeneric hybrids of Festuca pratensis and Lolium perenne was investigated by restriction enzyme and Southern blot analyses of chloroplast DNA (cpDNA) and mitochondrial DNA (mtDNA). All F1 hybrids exhibited maternal inheritance of both cpDNA and mtDNA. However, examination of backcross hybrids, obtained by backcrossing the intergeneric F1 hybrids to L. Perenne, indicated that both uniparental maternal organelle inheritance and uniparental paternal organelle inheritance can occur in different backcross hybrids.

Cytoplasmic male sterility and fertility restoration in wheat are not associated with rearrangements of mitochondrial DNA in the gene regions for cob, coxII, or coxI

In comparing the genetic organization and exploring the molecular basis of cytoplasmic male sterility (CMS) in wheat, mitochondrial DNAs (mtDNA) from Triticum aestivum, T. timopheevi, CMS alloplasmic wheat with T. aestivum nucleus and T. timopheevi mitochondria, and fertility-restored lines were compared by hybridization analysis with specific probes for three gene regions: coxII, cob, and coxI. Minor differences between T. aestivum- and T. timopheevi-derived sources were found for gene regions for coxII and cob. For coxI, there are significant differences between T. timopheevi-derived mtDNAs and T. aestivum mtDNA extending beyond an 8 kb distance. All T. timopheevi-derived mtDNA sources have a chimeric gene region (orf256) with part of the upstream coxI gene region, including some coxI-coding region, preceding coxI. The part of orf256 that does not include any of coxI and the 3'-flanking region of CMS coxI are not found in T. aestivum mtDNA. Neither orf256 nor the CMS 3'-flanking region of coxI are found in T. timopheevi or T. aestivum chloroplastic or nuclear DNA. There do not appear to be DNA sequence differences for the three gene regions studied that are related to either CMS or fertility-restored states.

The molecular basis of genetic diversity among cytoplasms of Triticum and Aegilops : 7. Restriction endonuclease analysis of mitochondrial DNAs from polyploid wheats and their ancestral species

Many related species and strains of common wheat were compared by matching differences among their mitochondrial genomes with their "parent" nuclear genomes. We examined three species of Aegilops, section Sitopsis (Ae. bicornis, Ae. sharonensis, and Ae. speltoides), emmer wheat (Triticum dicoccoides, T. dicoccum, and T. durum), common wheat (T. spelta, T. aestivum, and T. compaction), and timopheevi wheat (T. araraticum, T. timopheevi, and T. zhukovskyi). A single source of the cytoplasm was used in all the species, except Ae. speltoides (two sources), T. araraticum (two), and T. aestivum (three). Following restriction endonuclease analyses, the mitochondrial genomes were found to comprise seven types, and a dendrogram showing their genetic relatedness was constructed, based upon the percentage of common restriction fragments. MtDNAs from T. dicoccum, T. durum, T. aestivum, and T. compactum yielded identical restriction fragment patterns; these differed from T. dicoccoides and T. spelta mtDNAs in only 2.3% of their fragments. The fragment patterns of T. timopheevi and T. zhukovskyi were identical, and these differed from T. araraticum mtDNA by only one fragment. In both the emmer-dinkel and timopheevi groups, mitochondrial genome differentiation is evident, suggesting a diphyletic origin of each group. MtDNAs from four accessions of the Sitopsis species of Aegilops differ greatly from one another, but those of Ae. bicornis, Ae. sharonensis, and Ae. searsii, belonging to the same subsection Emarginata, are relatively similar. MtDNAs of timopheevi species are identical, or nearly so, to those of Ae. speltoides accession (09), suggesting that the latter was the cytoplasm donor to the former, polyploid group. The origin of this polyploid group seems to be rather recent in that the diploid and polyploid species possess nearly identical mitochondrial genomes. We cannot determine, with precision, the cytoplasm donor to the emmer-dinkel group. However, our results do suggest that mitochondrial DNAs show larger evolutionary divergence than do the ctDNAs from these same strains.

An internal part of the chloroplast atpA gene sequence is present in the mitochondrial genome of Triticum aestivum: molecular organisation and evolutionary aspects

An internal part of the chloroplast atpA gene has been identified in the mitochondrial DNA of Triticum aestivum. It is located near the 18S-5S ribosomal genes and partially contained within a repeated sequence. Comparison of the transferred sequence with the original ct sequence reveals several nucleotide changes and shows that neither 5' nor 3' ends are present in the mt genome. No transcript of this region could be detected by Northern analysis. This sequence is present in mitochondrial genomes of other tetraploid and diploid species of Triticum, also in the vicinity of the 18S-5S ribosomal genes, suggesting a unique transfer event. The date of this event is discussed.

Nitrate reductases in hexaploid and tetraploid wheats and Aegilops

Nitrate reductase activity (NR activity), protein content (NR protein) and polypeptides were compared in shoots of Triticum aestivum ssp. vulgare (L.) cv Fidel (bread wheat, AABBDD genome), Triticum dicoccum cv Vernal (AABB genome), Aegilops squarrosa var. strangulata (DD genome) and the amphiploid 365 (AABBDD genome), produced by crossing T. dicoccum cv Vernal and Ae. squarrosa var. strangulata. Constitutive NR protein and activity were found in shoots of all seedlings grown without nitrate, with the highest activity in the bread wheat. The inducible NR protein and activity developed upon the addition of nitrate. A 116-K polypeptide was identified as the main component of the NR from the bread wheat, while a faint, sometimes discernable 94-K band appeared on Western blots. Only one NR polypeptide could be identified in Ae. squarrosa -the 94 K. An intermediary situation was observed with the tetraploid T. dicoccum and the amphiploid: The 94-K polypeptide was the only one separated from NR of seedlings grown in the absence of nitrate. The 116-K polypeptide appeared after the addition of nitrate. The intensity of its band on the gel increased with the duration of the nitrate treatment. When comparing Ae. squarrosa and T. dicoccum, the constitutive isozyme (94-K polypeptide) was found in the D as well as in the AB genomes, while the inducible NR (116-K polypeptide) was absent from the D genome. Addition of the D genome into the AB genome slightly reinforced the expression of the inducible form (AB genome expression) in the amphiploid wheat. We postulate that the inducible form of NR in the bread wheat resulted from an evolutionary selection pressure favoured by cultivation.

Species relationships in the Hordeum murinum aggregate viewed from chloroplast DNA restriction fragment patterns

Three annual widespread species of Hordeum were investigated by the fragment pattern method on their chloroplast (cp) DNA. The species were H. glaucum, H. leporinum and H. murinum; H. vulgare was surveyed for comparison. Twelve restriction enzymes were used, nine recognizing 6 bp, one 5 bp and two 4 bp, thus, randomly surveyed, a total of 2,113 bp or 1.6% of the cp genome. Differences in patterns were found in three enzymes, HindIII, CfoI and MspI. CfoI characterizes H. glaucum from the other two species. HindIII and MspI revealed polymorphisms within species. These results confirm previous numerical taxonomic relationships among these three closely related species. Furthermore, cpDNA polymorphism in Hordeum is discussed in view of earlier reports on cpDNA polymorphism in H. vulgare. The taxonomic implications of cpDNA polymorphism are discussed after reviewing several articles using the fragment pattern method on cpDNA. The importance of using material from several populations representative of a species is stressed.

Mitochondrial DNA variation in pearl millet and related species

Mitochondrial DNA (mtDNA) restriction endonuclease fragment patterns and patterns of mtDNA hybridized by mitochondrial gene probes were used to study phylogenetic relationships of seven Pennisetum species, including five P. americanum (pearl millet) ecotypes and a reference species from the distantly related genus, Panicum. The restriction patterns of the pearl millet ecotypes were uniform with the exception of the ecotype collected in Ethiopia. The probe hybridization method revealed more variability, with both the Rhodesian and Ethiopian ecotypes differing from the others and from each other. Considerable restriction pattern polymorphism was noted among different species of Pennisetum, and Panicum. Significant relationships were noted of Pennisetum polystachyon to P. pedicellatum and of P. purpureum to P. squamulatum using the restriction pattern method. In addition to those relationships, the hybridization method showed relationships of pearl millet to P. purpureum and to P. squamulatum. The relationships noted between species by the hybridization method agreed more closely to the cytological data than those indicated by the restriction pattern method. Therefore, the hybridization method appeared to be the preferred method for studying species relationships. The mitochondrial genome size of pearl millet was calculated to be 407 kb and the mitochondrial genome sizes of other Pennisetum species ranged from 341 to 486 kb.

The molecular basis of genetic diversity among cytoplasms of Triticum and Aegilops : 5. Mitochondrial genome diversity among Aegilops species having identical chloroplast genomes

Restriction fragment patterns of mtDNA isolated from the cytoplasm of three groups of Aegilops species (or accessions) which are known to carry the identical chloroplast genome but distinctly different cytoplasmic genomes (plasmons) have been analysed using five restriction endonucleases. Two to four different mitochondrial genomes are found in each group, between which the percent common restriction fragments amounts to 86-97%, whereas the same parameter obtained between mitochondrial genomes of the different groups ranges from 34 to 42%. Mitochondrial genome diversity is far more extensive than the chloroplast genome diversity, and the former provides a useful key for the phylogenetic relationships between cytoplasms of closely related species or even different accessions of the same species. The mitochondrial and chloroplast genome differentiation most certainly accounts for the plasmon variability known in this genus.

Nicotiana cybrids with Petunia chloroplasts

Protoplasts of a chloroplast-defective cultivar of Nicotiana tabacum were fused with gamma-irradiated protoplasts of Petunia hybrida. Over 100 photoautotrophic plants were regenerated; of these 94 were tested for Petunia chloroplast traits and all but one had Petunia chloroplasts based on their sensitivity to the fungal toxin, tentoxin. Chloroplast DNA was analysed for 3 of the sensitive plants and was shown to be identical to Petunia chloroplast DNA. Most of the plants (about 70%) appeared to be normal N. tabacum plants, based on morphology and chromosome number. They were fully fertile with normal pollen viability, seed set, and seed viability. The remaining 30% of the plants showed varying degrees of vegetative and reproductive abnormalities.

Chloroplast DNA variation between the common cultivated potato (Solanum tuberosum ssp. tuberosum) and several South American relatives

Chloroplast DNA (ctDNA) from the tuberbearing Solanum species tuberosum, vernei, phureja, and chacoense has been compared by restriction endonuclease analysis. Digestion by Hind III or Xba I reveal no differences, but digestion with Bam HI and Eco RI reveals minor differences in the ctDNA among these species. The ctDNA restriction patterns of the tetraploid common cultivated potato of North America and Europe, S. tuberosum ssp. tuberosum and the South American tetraploid, S. tuberosum ssp. andigena are identical for all four restriction endonucleases. These data suggest that ssp. tuberosum and ssp. andigena contain similar ctDNA and therefore may share a common ancestor, or direct lineage. The ctDNA restriction patterns of S. vernei and S. chacoense are identical for all four restriction endonucleases, and S. phureja ctDNA, can be distinguished from the other diploid ctDNAs by digestion with Bam HI. None of the diploids analyzed contain ctDNA identical to the tetraploids and therefore either did not contribute their chloroplast genomes to the evolution of the tetraploids, or the ctDNA has diverged since this evolutionary event. The ctDNAs studied did not contain restriction polymorphisms which could be correlated to cytoplasmic male sterility in Solanum. This is the first demonstration of ctDNA diversity in the tuber-bearing Solanum species.

Variation of plastid and mitochondrial DNAs in the genus Hedysarum

Plastid and mitochondrial DNAs from Hedysarum species of the western Mediterranean basin, H. spinosissimum ssp eu-spinosissimum, H. spinosissimum ssp capitatum, H. carnosum, H. coronarium and H. flexuosum, were compared by restriction endonuclease fragment analysis. ctDNA fragment patterns for ssp eu-spinosissimum and ssp capitatum were indistinguishable in different enzyme digests. An identical ctDNA variation was found in Hpa II digests with two Sardinian populations of ssp capitatum. Each of the two subspecies was characterized by specific mt DNA patterns with Pst I, Bam HI, Sma I and EcoRI. No variation was detected in populations of different geographical origins for a given subspecies. H. carnosum, H. coronarium and H. flexuosum generated specific ct and mt DNA patterns. Comparison of mitochondrial fragments indicated: - a strong homology between the two subspecies, - a closer homology among the three other diploids, each being closer to the other two than to H. spinosissimum subspecies - as was also the case for the plastid genomes.

Chloroplast DNA evolution and the origin of amphidiploid Brassica species

The origin and evolution of a hybrid species complex in the genus Brassica (cabbage, turnip, mustard, rapeseed oil) has been explored through mutational analysis of the maternally inherited chloroplast genome. A detailed chloroplast DNA phylogeny enables identification of the maternal parent for most of the amphidiploids examined and permits quantitative resolution of the relative time of hybridization as well as the relative divergence of the diploid parents. Contradictory chloroplast and nuclear phylogenies obtained for two accessions of the amphidiploid B. napus (rapeseed oil) lead to the hypothesis that introgressive hybridization has also figured in their recent evolution.

Chloroplast DNA variation between species of Triticum and Aegilops. Location of the variation on the chloroplast genome and its relevance to the inheritance and classification of the cytoplasm

Restriction endonuclease analysis revealed interspecific and intraspecific variation between the chloroplast DNAs and therefore between the cytoplasms of 14 selected species of Triticum and Aegilops. Eleven distinct chloroplast DNA types were detected, the differences between them residing in the varied combination of a relatively few DNA alterations.The variation was simple enough for chloroplast DNA analysis to be used as a basis for the identification and classification of the Triticum and Aegilops cytoplasms. There was good agreement with the classification based on analysis of the phenotypic effects of the cytoplasm when combined with the T. aestivum nucleus in nuclear-cytoplasmic hybrids (Tsunewaki et al. 1976). There was however no correlation between specific chloroplast DNA alterations and any of the phenotypic effects known to be associated with specific cytoplasms.Although the diploid species examined included all those which have been suggested as possible donors of the cytoplasm and the B genome to T. aestivum, none of the chosen accessions belonged to the same cytoplasmic class as T. aestivum itself, except that of the tetraploid T. dicoccoides. Therefore, none of the diploid accessions analysed was the B genome donor. The analyses did however support several other suggestions which have been made concerning wheat ancestry. Scoring the different chloroplast DNA types according to the rarity of their banding patterns indicated that four of the eleven cytoplasms are of relatively recent origin.The DNA alterations most easily detectable by the limited comparison of the eleven Triticum/Aegilops chloroplast DNA types using only 4 endonucleases were insertions and deletions. These ranged between approximately 50 bp and 1,200 bp in size and most of them were clustered in 2 segments of the large single-copy region of the genome. Only two examples of the loss of restriction endonuclease sites through possible point mutations were observed. No variation was detected in the inverted repeat regions. Several of the deletions and insertions map close to known chloroplast protein genes, and there is also an indication that the more variable regions of the chloroplast genome may contain sequences which have allowed DNA recombination and rearrangement to occur.

Chloroplast and mitochondrial DNA variation as indicator of phylogenetic relationships in the genus Coffea L

Chloroplast and mitochondrial DNA from nine species or taxons of coffee-trees were compared as to their phylogenetic relationship by restriction endonuclease fragment analysis. Three types of chloroplast DNA (cp DNA) were detected indicating relationships as follows: (i) C. arabica, C. eugenioides; (ii) C. canephora, C. congensis, "nana" taxon; (iii) C. liberica. The mitochondrial DNA (mt DNA) separated into five types: (i) C. arabica, C. eugenioides, C. congensis; (ii) C. canephora, "nana" taxon; (iii) C. excelsa; (iv) C. liberica; (v) Paracoffea ebracteolata. The divergence in organelle DNAs agrees with the phylogenetic relationship deduced by conventional methods and is presented in some detail. Restriction patterns of the cp and mt DNAs isolated from a clone of C. arabusta have been compared to those of the parents and were found to be inherited from the mother. Cp and mt DNA analyses in the genus Coffea support the hypothesis that C. canephora diverged from C. congensis, whereafter the latter species differentiated into C. eugenioides and C. arabica.

Effect of the D genome and of selection on photosynthesis in wheat

Photosynthesis and transpiration in wheats and in their progenitors were analyzed in relation to their genome, ploidy and selection. The values of these parameters markedly depend on a specific effect of the D genome and on leaf enlargement in the course of evolution in wheats. Leaf enlargement has had a marked effect on photosynthesis in the genotypes that are devoid of the D genome; in addition, their photosynthetic capacity is greater in forms with lower leaf area. The increase in the mesophyll resistance rm to CO2 transfer is in relation to the increase in leaf area and is mainly responsible for the decrease in photosynthesis rate.Owing to its stomatal regulation, Triticum aestivum L. is characterized by good water use efficiency in spite of its large leaves and of its low net photosynthesis. On the basis of the photosynthesis rate, the "large leaf factor does not appear to be a good selection criterion for the Triticum durum genotypes that are devoid of the D genome.

Studies on maternal inheritance in polyploid wheats with cytoplasmic DNAs as genetic markers

Restriction fragment patterns of DNA fragments obtained after EcoRI cleavage of chloroplastic (cp) and mitochondrial (mt) DNAs isolated from different wheat species were compared. T. aestivum, T. timopheevi, Ae. speltoides, Ae. sharonensis and T. urartu gave species specific mt DNA patterns. Consequently, the cytoplasmic genomes of wheat cannot have originated from contemporary Ae. speltoides, Ae. sharonensis and T. urartu species. It is shown that cp and mt DNAs of Ae. ventricosa, a tetraploid used to transfer eyespot resistance into T. aestivum, contains cp and mt DNAs differing from DNAs isolated from T. aestivum and other wheats. In contrast, the cytoplasmic DNAs of Ae. ventricosa and Ae. squarrosa reveal an important homology, suggesting that Ae. squarrosa was the female parent of Ae. ventricosa. Disomic addition lines (T. aestivum - Ae. ventricosa) in both Ae. ventricosa cytoplasm and T. aestivum cytoplasm contained cytoplasmic DNAs identical to those of the maternal parent. Restriction patterns of the cp and mt DNAs isolated from eight lines of Triticale differing in their cytoplasm have been compared to those of the maternal parent. A strict maternal inheritance has been observed in each case.

Cytoplasmic DNA variation and relationships in cereal genomes

Chloroplast (cp) and mitochondrial (mt) DNAs were isolated from four cereal genomes (cultivated wheat, rye, barley and oats) and compared by restriction nuclease analysis. Cleavage of cp and mt DNAs by Sal I, Kpn I, Xho I and EcoR I enzymes indicated that each cereal group contains specific cytoplasmic DNAs. A phylogenetic tree of cereal evolution has been obtained on the basis of cp DNA homologies. It is suggested that wheat and rye diverged after their common ancestor had diverged from the ancestor of barley. This was preceded by the divergence of the common ancestor of wheat, rye and barley and the ancestor of oats.The molecular weight of the different cp DNAs was determined from the Sal I and Kpn I patterns. cp DNAs from wheat, rye, barley and oats appeared to be characterized by a very similar molecular weight of about 80-82.10(6) d.In the case of the mt DNAs, the great number of restriction fragments obtained with the restriction enzymes used prevented precise comparisons and determination of molecular weights.

The presence of DNA in ribosome-deficient plastids of heat-bleached rye leaves

In leaves of rye seedlings (Secale cereale L.) grown at 32 degrees C the formation of plastid (70-S) ribosomes is specifically prevented. The resulting plastid-ribosome-deficient leaves can be used as a suitable system to identify chloroplast proteins which are translation products of cytosolic (80-S) ribosomes. The ribosome deficiency in plastids is accompanied by a bleaching of the leaves in light. In experiments aimed at finding the primary heat-sensitive event leading to ribosome deficiency the DNA of rye chloroplasts has been identified. Its properties are similar to those of chloroplast DNAs from other higher plants. The ribosome-deficient plastids isolated from heat-bleached rye leaves contained a DNA species which was indistinguishable from that of chloroplasts with regard to buoyant density in CsCl equilibrium gradients, reassociation properties and fragment patterns obtained upon cleavage by restriction endonucleases. Its quantity was comparable to that of chloroplast DNA of green leaves grown at a permissive temperature (22 degrees C). These results suggest that, unlike the effect in heat-bleached Euglena strains, lack of chloroplast DNA cannot be considered as the reason for the primary effect of high temperature in rye leaves but steps in the biosynthetic pathway of plastid ribosomes themselves must be affected more directly.