Experimental evolutionary studies on the genetic autonomy of the cytoplasmic genome "plasmon" in the Triticum (wheat)-Aegilops complex.

The term "plasmon" is used to indicate the whole cytoplasmic genetic system, whereas "genome" refers to the whole nuclear genetic system. Although maternal inheritance of the plasmon is well documented in angiosperms, its genetic autonomy from the coexisting nuclear genome still awaits critical examination. We tested this autonomy in two related studies: One was to determine the persistence of the genetic effect of the plasmon of Aegilops caudata (genome CC) on the phenotype of common wheat, Triticum aestivum strain "Tve" (genome AABBDD), during 63 y (one generation per year) of repeated backcrosses of Ae. caudata and its offspring with pollen of the same Tve wheat, and the second was to reconstruct an Ae. caudata strain from the genome of this strain and its plasmon that had been resident in Tve wheat for 50 generations, and to compare the phenotypic and organellar DNA characteristics between the native and reconstructed strains. Results indicated no change in the effect of Ae. caudata plasmon on Tve wheat during its stay in wheat for more than half a century, and no difference between the native and reconstructed caudata strains in their phenotype and simple sequence repeats in their organellar DNAs, thus demonstrating the prolonged genetic autonomy of the plasmon from the coexisting genomes of wheat and several other species that were used in the reconstruction of Ae. caudata The relationship between the proven genetic autonomy of the plasmon under changing nuclear conditions and its diversification during evolution of the Triticum-Aegilops complex is discussed.

Fine mapping of the first multi-fertility-restoring gene, Rf(multi), of wheat for three Aegilops plasmons, using 1BS-1RS recombinant lines.

KEY MESSAGE: Fertility-restoring genes, Rfv1, Rfm1 and Rfn1, respectively, for the male sterile cytoplasms of Aegilops kotschyi, Ae. mutica and Ae. uniaristata to common wheat were located on the same locus of Pavon wheat 1BS arm. The male sterile cytoplasm (plasmon) and the fertility-restoring gene are essential genetic components for breeding hybrid seed crops. This article represents information on the genetic similarity of three Aegilops plasmons usable as the male sterile cytoplasm for hybrid wheat and provides an evidence on the possible genetic unity of three fertility-restoring genes reported for these plasmons by their genetic mapping using the 1BS-1RS recombinant lines of Pavon 76 wheat on to a single subsegment of the 1BS chromosome arm less than 2.9 cM in size: the locus is designated Rf (multi) , meaning "Restoration of fertility in multiple CMS systems". Unresolved problems were discussed in the use of the present cytoplasmic male sterility-fertility restoration system for hybrid wheat breeding.

Interorganellar DNA transfer in wheat: dynamics and phylogenetic origin.

A homology search of wheat chloroplast (ct) and mitochondrial (mt) genomes identified 54 ctDNA segments that have homology with 66 mtDNA segments. The mtDNA segments were classified according to their origin: orthologs (prokaryotic origin), xenologs (interorganellar DNA transfer origin) and paralogs (intraorganellar DNA amplification origin). The 66 mtDNA sequences with homology to ctDNA segments included 14 paralogs, 18 orthologs and 34 xenologs. Analysis of the xenologs indicated that the DNA transfer occurred unidirectionally from the ct genome to the mt genome. The evolutionary timing of each interorganellar DNA transfer that generated a xenolog was estimated. This analysis showed that 2 xenologs originated early in green plant evolution, 4 in angiosperm evolution, 3 in monocotyledon evolution, 9 during cereal diversification and 8 in the evolution of wheat. Six other xenologs showed recurrent transfer from the ct to mt genomes in more than one taxon. The two remaining xenologs were uninformative on the evolutionary timing of their transfer. The wheat mt nad9 gene was found to be chimeric, consisting of the cereal nad9 gene and its 291 bp 5'-flanking region that included a 58 bp xenolog of the ct-ndhC origin.

Evolutionary dynamics of wheat mitochondrial gene structure with special remarks on the origin and effects of RNA editing in cereals.

We investigated the evolutionary dynamics of wheat mitochondrial genes with respect to their structural differentiation during organellar evolution, and to mutations that occurred during cereal evolution. First, we compared the nucleotide sequences of three wheat mitochondrial genes to those of wheat chloroplast, alpha-proteobacterium and cyanobacterium orthologs. As a result, we were able to (1) differentiate the conserved and variable segments of the orthologs, (2) reveal the functional importance of the conserved segments, and (3) provide a corroborative support for the alpha-proteobacterial and cyanobacterial origins of those mitochondrial and chloroplast genes, respectively. Second, we compared the nucleotide sequences of wheat mitochondrial genes to those of rice and maize to determine the types and frequencies of base changes and indels occurred in cereal evolution. Our analyses showed that both the evolutionary speed, in terms of number of base substitutions per site, and the transition/transversion ratio of the cereal mitochondrial genes were less than two-fifths of those of the chloroplast genes. Eight mitochondrial gene groups differed in their evolutionary variability, RNA and Complex I (nad) genes being most stable whereas Complex V (atp) and ribosomal protein genes most variable. C-to-T transition was the most frequent type of base change; C-to-G and G-to-C transversions occurred at lower rates than all other changes. The excess of C-to-T transitions was attributed to C-to-U RNA editing that developed in early stage of vascular plant evolution. On the contrary, the editing of C residues at cereal T-to-C transition sites developed mostly during cereal divergence. Most indels were associated with short direct repeats, suggesting intra- and intermolecular recombination as an important mechanism for their origin. Most of the repeats associated with indels were di- or trinucleotides, although no preference was noticed for their sequences. The maize mt genome was characterized by a high incidence of indels, comparing to the wheat and rice mt genomes.

Structural dynamics of cereal mitochondrial genomes as revealed by complete nucleotide sequencing of the wheat mitochondrial genome.

The application of a new gene-based strategy for sequencing the wheat mitochondrial genome shows its structure to be a 452 528 bp circular molecule, and provides nucleotide-level evidence of intra-molecular recombination. Single, reciprocal and double recombinant products, and the nucleotide sequences of the repeats that mediate their formation have been identified. The genome has 55 genes with exons, including 35 protein-coding, 3 rRNA and 17 tRNA genes. Nucleotide sequences of seven wheat genes have been determined here for the first time. Nine genes have an exon-intron structure. Gene amplification responsible for the production of multicopy mitochondrial genes, in general, is species-specific, suggesting the recent origin of these genes. About 16, 17, 15, 3.0 and 0.2% of wheat mitochondrial DNA (mtDNA) may be of genic (including introns), open reading frame, repetitive sequence, chloroplast and retro-element origin, respectively. The gene order of the wheat mitochondrial gene map shows little synteny to the rice and maize maps, indicative that thorough gene shuffling occurred during speciation. Almost all unique mtDNA sequences of wheat, as compared with rice and maize mtDNAs, are redundant DNA. Features of the gene-based strategy are discussed, and a mechanistic model of mitochondrial gene amplification is proposed.

Memoir on the origin of wheat stocks used by Prof. Tetsu Sakamura, on the centennial of his discovery of the correct chromosome number and polyploidy in wheat.

Sakamura (1918) reported the discovery of a polyploid series among eight species of the genus Triticum; this series consisted of 2x, 4x and 6x species with 2n = 14, 28 and 42 chromosomes, respectively. He mentioned in this article that all the materials he used were gifted by T. Minami of the same department of Hokkaido University, Japan. In addition to carrying out an extensive collection of cereal germplasms in the period 1914 to 1916, Minami wrote on October 7, 1915 to K. A. Flaksberger, a wheat taxonomist at the Bureau of Applied Botany, Saint Petersburg, Russia, requesting seeds of Russian wheat and other cereals. He sent Flaksberger a letter of acknowledgement for seed stocks on May 19, 1916; thus, the requested seed package must have arrived from Flaksberger at some time between October 7, 1915 and May 19, 1916. Based on the available documents, there was a considerable period of time between these seed stocks reaching Minami and Sakamura's publication of the chromosome numbers with the discovery of polyploidy. In fact, the wheat species identified by Flaksberger (1915) and those studied by Sakamura (1918) were identical except for two wild species which appeared only in Flaksberger's list. The available information supports a proposal that the wheat species used by Sakamura (1918) in his discovery of polyploidy, and later by Kihara (1924, 1930) in his genome analysis, originated from Flaksberger's collection.

Aneuploid analyses of three chlorophyll abnormalities in Emmer wheat.

Of the various chlorophyll abnormalities that occur in polyploid wheats, genetic bases of only two types, chlorina and virescence, are known. Here, for the first time, the chromosomal bases of three other chlorophyll abnormalities, striato-virescence, delayed virescence, and albino, which occur in Emmer wheat (2n = 4x = 28, genome constitution AABB) are reported. A set of disomic substitution lines of Langdon durum was used for chromosome identification. All three abnormalities are controlled by two duplicated recessive genes (carrier chromosome in parentheses); striato-virescence by sv1 (3A) and sv2 (2A), delayed virescence by dv1 (2B) and dv2 (supposedly 2A), and albino by abn1 (2A) and abn2 (2B). Genes on the same chromosome are located in different loci and are recombined with each other. The Chinese Spring cultivar of common wheat (2n = 6x = 42, genome constitution AABBDD) carries wild-type homoeoalleles for these abnormalities; Sv3 (2D), Dv3 (2D), and Abn3 (2D).

Plasmon analysis of Triticum (wheat) and Aegilops. 2. Characterization and classification of 47 plasmons based on their effects on common wheat phenotype.

This article comprises our final remarks on the phenotypic effects of alien plasmons on common wheat. Twenty-one vegetative, reproductive, and seed characters of 551 alloplasmic lines of 12 common wheat genotypes with 46 alloplasmons, and as the control, their euplasmic lines were investigated. Effects of genotype, plasmon, and their interaction had high statistical significance for all the characters investigated, whereas phenotypic variations attributable to the alien plasmons were relatively small. Individual plasmon types are characterized by their primary effects on 21 characters. Genotype x plasmon effects on two representative characters, heading date and plant height, are described in detail. Cluster and principal component analyses of the phenotypic effects of the 47 plasmons yielded 22 groups. The relationships between these phenotype-based groups and those defined by molecular differences in organellar genomes were examined. A significant correlation was found with some explainable discrepancies. For efficient plasmon identification, use of six of the present 12 genotypes is proposed. The key for plasmon classification is provided. Our findings indicate that alien plasmons may be of limited value in future wheat breeding, but that the plasmon diversity that exists in Triticum and Aegilops species is of great significance for understanding the evolution of these genera.

Genetic effect of the Aegilops caudata plasmon on the manifestation of the Ae. cylindrica genome.

In the course of reconstructing Aegilops caudata from its own genome (CC) and its plasmon, which had passed half a century in common wheat (genome AABBDD), we produced alloplasmic Ae. cylindrica (genome CCDD) with the plasmon of Ae. caudata. This line, designated (caudata)-CCDD, was found to express male sterility in its second substitution backcross generation (SB2) of (caudata)-AABBCCDD pollinated three times with the Ae. cylindrica pollen. We repeatedly backcrossed these SB2 plants with the Ae. cylindrica pollen until the SB5 generation, and SB5F2 progeny were produced by self-pollination of the SB5 plants. Thirteen morphological and physiological characters, including pollen and seed fertilities, of the (caudata)-CCDD SB5F2 were compared with those of the euplasmic Ae. cylindrica. The results indicated that the male sterility expressed by (caudata)-CCDD was due to genetic incompatibility between the Ae. cylindrica genome and Ae. caudata plasmon that did not affect any other characters of Ae. cylindrica. Also, we report that the genome integrity functions in keeping the univalent transmission rate high.

Whole chloroplast genome comparison of rice, maize, and wheat: implications for chloroplast gene diversification and phylogeny of cereals.

The fully sequenced chloroplast genomes of maize (subfamily Panicoideae), rice (subfamily Bambusoideae), and wheat (subfamily Pooideae) provide the unique opportunity to investigate the evolution of chloroplast genes and genomes in the grass family (Poaceae) by whole-genome comparison. Analyses of nucleotide sequence variations in 106 cereal chloroplast genes with tobacco sequences as the outgroup suggested that (1) most of the genic regions of the chloroplast genomes of maize, rice, and wheat have evolved at similar rates; (2) RNA genes have highly conservative evolutionary rates relative to the other genes; (3) photosynthetic genes have been under strong purifying selection; (4) between the three cereals, 14 genes which account for about 28% of the genic region have evolved with heterogeneous nucleotide substitution rates; and (5) rice genes tend to have evolved more slowly than the others at loci where rate heterogeneity exists. Although the mechanism that underlies chloroplast gene diversification is complex, our analyses identified variation in nonsynonymous substitution rates as a genetic force that generates heterogeneity, which is evidence of selection in chloroplast gene diversification at the intrafamilial level. Phylogenetic trees constructed with the variable nucleotide sites of the chloroplast genes place maize basal to the rice-wheat clade, revealing a close relationship between the Bambusoideae and Pooideae.