The low-molecular-weight glutenin subunit proteins of primitive wheats. II. The genes from A-genome species

 Three accessions of T. boeoticum were selected for the cloning and sequencing of novel low-molecular-weight glutenin subunit (LMW-GS) genes, based on the results of SDS-PAGE and PCR analyses of the LMW-GS diversity in A-genome wheat (Lee et al. 1998 a). A comparison of the nucleotide and deduced amino-acid sequences of three cloned genes, LMWG-E2, LMWG-E4 and LMWG-AQ1, both to each other and to other known LMW-GS genes was carried out. The N-terminal domains showed one variable position; GAG (coding for a glutamic acid) for the E-type, and GAT (coding for an aspartic acid) for the Q-type. The comparisons of the LMW-GSs in the literature and this paper define three different types of N-terminal sequences; METSCIPGLERPW and MDTSCIPGLERPW from the durum and A-genome wheats, and METRCIPGLERPW from the hexaploid and D-genome wheats. The repetitive domains were AC-rich at the nucleotide level and coded for a large number of glutamine residues; this region showed 16 variable positions changing 12 amino-acid residues, three triple nucleotide deletions/additions, a large deletion of 18 nucleotides in LMWG-E4 and a deletion of 12 nucleotides in LMWG-E2. In the C-terminal domains 26 variable positions were found and 12 of these mutations changed amino-acid residues; no deletions/ additions were present in this region. It was shown that the LMWG-E2 and LMWG-E4 genes could be expressed in bacteria and this allowed the respective protein products to be related back to the proteins defined as LMW-GSs in vivo. Received: 24 November 1997 / Accepted: 18 August 1998     

Genetic variation in rice

Completion of the genomic sequencing of rice has enhanced the discovery of new genes. Wild rice relatives are good sources for extending the genetic variation of cultivated rice. Reproductive barriers are commonly found in distant crosses of rice and are attracting attention. The combination of genetic analyses and molecular tools has greatly facilitated the molecular cloning of rice genes based on the classical approach and enabled the tracking of dissemination of the alleles for domestication. Basic information for population genetics study in rice is still being collected and is expected to provide an alternative approach for finding new genes. The wide genetic variation available in wild rice relatives and the combination of various genetic approaches will allow the analysis and understanding of genetic variation at the nucleotide sequence level, as well as the discovery of novel alleles by sequence-based approaches.     

Seed storage protein variation in Arachis species.

Seventy-two accessions, representing 22 species from sections Arachis, Erectoides, Extranervosae, and Triseminalae of the genus Arachis, were screened for seed storage protein polymorphism. Variation was detected between sections, between genome types, between species, and in some cases between different accessions of the same species or different seeds of the same accession. Arachis duranensis and one accession of A. cardenasii were found to have identical protein patterns. The greatest dissimilarity was found between species of the section Extranervosae and species of the section Triseminalae. Those of section Erectoides showed much similarity with some species of section Arachis. Protein polymorphism was shown to distinguish the two subspecies of A. hypogaea (fastigiata and hypogaea) in 27 of 28 cases. The seed protein profile of A. monticola was a combination of seed protein profiles from the two A. hypogaea subspecies. The relatedness between the various species was calculated and those that had the greatest similarity with A. hypogaea were A. spegazzinii and A. batizocoi.     

Enzyme variation in Eimeria species of the chicken.

A method for the biochemical identification of protozoa belonging to the genus Eimeria is described for the first time. Starch gel electrophoresis of the enzymes lactate dehydrogenase, glucose phosphate isomerase, 6-phosphogluconate dehydrogenase and glucose-6-phosphate dehydrogenase from parasite extracts revealed both intra- and inter-species differences when 11 strains representative of 6 species of Eimeria were examined. Oocysts were the most accessible parasite stage for investigation but sporozoites and merozoites of an embryo-adapted strain of E. tenella were also examined for enzyme activity.     

DNA variation in tissue-culture-derived rice plants

Summary Regenerants of rice were examined by RFLP analysis to determine the occurrence and extent of somaclonal variation. DNA polymorphisms were observed both among plants regenerated from different callus cultures as well as among sibling plants derived from a single callus. Regardless of the basal medium, a higher degree of genetic instability was found among plants regenerated from callus cultures maintained for longer incubation periods (67 days) than among those from shorter incubation periods (28 days). Detailed analysis showed that in several regenerants, there was a close correlation among those plants exhibiting DNA rearrangements and those with apparent methylation changes. Such alterations were observed with both structural and housekeeping genes.     

Biological species and variation in arthroderma

Summary The distinctive peridial appendages ofArthroderma were of little value for the delimitation of species. The peridial appendages as well as the conidia of certain species were so similar as to be value-less for the delimitation of species. Further, morphological and physiological variation was found to be as great within, as between, species. The usual morphological methods for classifying species were, therefore, inadequate and the concept of biological species was considered.The following points were found to favor the applicability of biological species concepts. Nine of ten species were heterothallic which assured crossing. A gene pool, the result of sexual reproduction and an essential requirement of a biological species, was maintained. This was evidenced by complete fertility between isolates of the same species from diverse geographic areas. Finally, no hybridization between species was evident in over one hundred attempted crosses.Strains which were readily compatible and produced viable ascospores were considered to be members of the same species. Conversely, incompatible strains were differentiated into separate species. In this way over fifty strains from more than one hundred isolations were found to be members of ten species. Six of the species correlated with species previously described on morphological bases, and confirmed their validity. Four species were considered to be new. All four were previously confused withA. quadrifidum orA. cuniculi because they possessed similar types of conidia. Once separated on an incompatibility basis, they were found to possess characteristics of distinct species. The only reliable method for their differentiation, however, was found to be interspecific incompatibility.Several strains, some pathogens, were crossed with soil borne species ofArthroderma. Some mated but others did not. Several incompatible strains possessedArthroderma-like appendages and partial compatibility was indicated. Partial compatibility also occurred in certain interspecific crosses.     

Protoclonal variation of plant regeneration in rice

Protoplasts were isolated from callus derived from a single homozygous seed of Oryza sativa L. var. Norin 8. Thirty protoclones were randomly selected and these showed variation in regeneration frequency ranging from 0–87% with an average of 52%. The potential for regeneration of each protoclone as reflected in the regeneration frequency was analyzed five times over a period of 250 days and showed that the protoclones can be classified into three types, namely: protoclones with high regeneration frequency; protoclones with low regeneration frequency, both of which maintained their respective levels of regeneration potential; and protoclones with gradually decreasing regeneration frequency. Secondary protoclones established from protoplasts isolated from some of these protoclones and regenerated 2–3 times for a period of 120 days also showed further reduction in regeneration frequency. The polypeptide composition analyzed by two dimensional gel electrophoresis suggests the presence of specific polypeptides related to regeneration potential. Analysis of ploidy level based on plant morphology and pollen size suggests the predominance of tetraploids among the regenerated plants.     

Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes

The A-genome group in Oryza consists of eight diploid species and is distributed world-wide. Here we reconstructed the phylogeny among the A-genome species based on sequences of nuclear genes and MITE (miniature inverted-repeat transposable elements) insertions. Thirty-seven accessions representing two cultivated and six wild species from the A-genome group were sampled. Introns of four nuclear single-copy genes on different chromosomes were sequenced and analysed by both maximum parsimony (MP) and Bayesian inference methods. All the species except for Oryza rufipogon and Oryza nivara formed a monophyletic group and the Australian endemic Oryza meridionalis was the earliest divergent lineage. Two subspecies of Oryza sativa (ssp. indica and ssp. japonica) formed two separate monophyletic groups, suggestive of their polyphyletic origin. Based on molecular clock approach, we estimated that the divergence of the A-genome group occurred c. 2.0 million years ago (mya) while the two subspecies (indica and japonica) separated c. 0.4 mya. Intron sequences of nuclear genes provide sufficient resolution and are informative for phylogenetic inference at lower taxonomic levels.     

Mitochondrial DNA variation and genetic relationships of Populus species.

We examined variation in and around the region coding for the cytochrome c oxidase I (coxI) and ATPase 6 (atp6) genes in the mitochondrial genomes of four Populus species (P. nigra, P. deltoides, P. maximowiczii, and P. tremuloides) and the natural hybrid P. x canadensis (P. deltoides x P. nigra). Total cellular DNAs of these poplars were digested with 16 restriction endonucleases and probed with maize mtDNA-specific probes (CoxI and Atp6). The only variant observed for Atp6 was interspecific, with P. maximowiczii separated from the other species as revealed by EcoRI digestions. No intraspecific mtDNA variation was observed among individuals of P. nigra, P. maximowiczii, P. x canadensis, or P. tremuloides for the CoxI probe. However, two varieties of P. deltoides were distinct because of a single site change in the KpnI digestions, demonstrating that P. deltoides var. deltoides (eastern cottonwood) and var. occidentalis (plains cottonwood) have distinct mitochondrial genomes in the region of the coxI gene. Populus x canadensis shared the same restriction fragment patterns as its suspected maternal parent P. deltoides. Nucleotide substitutions per base in and around the coxI and atp6 genes among the Populus species and the hybrid ranged from 0.0017 to 0.0077. The interspecific estimates of nucleotide substitution per base suggested that P. tremuloides was furthest removed from P. deltoides and P. x canadensis and least diverged from P. nigra. Populus maximowiczii was placed between these two clusters.     

Mhc-DQB repertoire variation in hominoid and Old World primate species.

Comparison of 87 distinct Mhc-DQB sequences, obtained from 13 primate species, demonstrates that five out of eight trans-species Mhc-DQB allele lineages are at least 30 million years old and predate divergence of hominoid and Old World primate species. One lineage may be much older because its members are not only traced back in higher primates, but also are present in a New World primate species. Comparing Mhc-DQB repertoire variation in distinct species, allows one to pinpoint when certain polymorphisms were lost or gained in primate evolution. Heterogeneity observed among members of trans-species Mhc-DQB allele lineages can be explained in major part by point mutations, whereas intraexonic crossing-over is a potent mechanism in generating new allele lineages. The stability of Mhc-DQB polymorphisms is influenced by selective forces because distinct allele lineages appear to have accumulated nucleotide substitutions and amino acid replacements at different rates.     

Biological variation in Trichinella species and genotypes

At present, the genus Trichinella comprises seven species of which five have encapsulated muscle larvae (T. spiralis, T. nativa, T. britovi, T. nelsoni and T. murrelli) and two do not (T. pseudospiralis and T. papuae) plus three genotypes of non-specific status (T6, T8 and T9). The diagnostic characteristics of these species are based on biological, biochemical and genetic criteria. Of biological significance is variation observed among species and isolates in parameters such as infectivity and immunogenicity. Infectivity of Trichinella species or isolates is determined, among other considerations, by the immune status of the host in response to species- or isolate-specific antigens. Common and particular antigens determine the extent of protective responses against homologous or heterologous challenge. The kinetics of isotype, cytokine and inflammatory responses against T. spiralis infections are isolate-dependent. Trichinella spiralis and T. pseudospiralis induce different dose-dependent T-cell polarizations in the early host response, with T. spiralis initially preferentially promoting Th1-type responses before switching to Th2 and T. pseudospiralis driving Th2-type responses from the outset.     

B chromosome in a rice aneuploid variation

An awned rice plant was discovered among the progeny of the triploid Zhongxian 3037. Cytological investigation showed that this awned plant was a variation with extra chromosomes. Based on the properties of the extra chromosomes during both meiosis and mitosis – e.g., short stature, darkly staining, instability in chromosome number, and lack of synapsis with A chromosomes – they could be considered to be B chromosomes in rice. The B chromosome(s) in both asexual and sexual progenies exhibited a unique segregation that is different from that of telotrisomics and other aneuploids. Moreover molecular marker analysis detected no dosage effects between the B-chromosome plant and the normal diploid of Zhongxian 3037, indicating that the B chromosomes might not be directly derived from any A-chromosome fragments in rice. Received: 8 June 1999 / Accepted: 30 December 1999     

Cell-cycle-related variation in proteins in suspension-cultured rice cells

To understand the cell cycle process in plants, we searched for proteins that quantitatively change during the cell cycle in suspension-cultured rice (Oryza sativa L.) cells. The proteins were analyzed by a two-dimensional polyacrylamide gel electrophoresis image-analysis system. We detected 11 proteins that quantitatively changed during the cell cycle, among which -tubulins and a calreticulin-like protein were identified. The amounts of -tubulin proteins were low in the M phase and high in the G1 phase. In contrast, mRNAs for two of the three types of -tubulin were high in the M phase of the cell cycle. The addition of protease inhibitors MG132 or E64d to the cells decreased the -tubulin proteins during 24 h, suggesting that -tubulin proteins are degraded in vivo by proteases other than those whose activities are inhibited by MG132 or E64d.     

Cultivar variation in methane efflux from tropical rice

Wide variation in CH4 flux was noticed among the ten rice cultivars grown under uniform field conditions. Cumulative CH4 flux ranged from 4.61 g m-2 to 20.25 g m-2. The rice cultivars could be ranked into three groups based on their CH4 flux potential. Rice cultivars could also be arranged based on their peak CH4 emission occurring either at vegetative, reproductive or at both growth stages. Of the several variables studied (root region redox potential, above- and underground biomass, grain and straw yield, duration of the crop, percent area occupied by the air space and root oxidase activity), only oxidase activity of the root tip exhibited a significant (negative) correlation with CH4 flux indicating an indirect effect of root oxidation potential on CH4 flux. Data presented in this study, demonstrate inherent variation in CH4 flux among different rice cultivars that can be used for developing future mitigation options.     

Population and species variation of minisatellite DNA in Plantago

Three Plantago species were surveyed for within- and between-population variation at DNA sequences detected with the M13 minisatellite probe. The levels and patterns of variation detected by this probe correspond to those expected from the mating systems of the species. The highly-selfing species P. major has a relatively low variability of minisatellite sequences within populations and considerable differentiation between populations. The outcrossing species P. lanceolata exhibits higher minisatellite variability within populations and moderate differentiation between populations. P. coronopus, with a mixed mating system, has levels of variation intermediate between P. major and P. lanceolata. The levels of variation within and between populations corresponds, in general, to the levels of allozyme variation determined in an earlier study. Mating system and population structure appear to have a major influence on M13-detected fragment variation.     

Effects of genotype variation in the cultivated rice species on the biology and galling characteristics of the African rice gall midge,Orseolia oryzivora (Diptera: Cecidomyiidae)

This study assessed the effects of genotype variations in two cultivated rice species: Oryza glaberrima and Oryza sativa on the biology and galling characteristics of the African rice gall midge (AfRGM), Orseolia oryzivora Harris and Gagné. The study was conducted in the screen house at ambient temperature (27 ± 3°C), 70 ± 5% relative humidity and 12:12 h photoperiod. Shoot galling, the most visible response of rice genotypes to attack by the insect, was greatly suppressed, being only 0.7 cm long in the O. glaberrima genotypes compared to 34 cm in the O. sativa species. Larval mortality (70–88%) in the O. glaberrima genotypes was significantly higher at the first instar compared to O. sativa. Gall setting was confirmed to be an irredeemable tiller loss. Even in the susceptible O. sativa genotypes, where many larvae may colonize a tiller, only one survived to the second instar. Resistant and susceptible rice genotypes had significantly different effects on the development and reproductive anatomy of the AfRGM. The female reproductive anatomy which consists of two ovaries, each with a potential complement of 192 eggs was affected by interspecific variation in rice genotypes causing reduced potential fecundity (32); morphological distortion, 60% reduction of egg size of F1 emergent in O. glaberrima compared to emergent from the susceptible O. sativa genotypes.     

The local introduction of strongly interacting species and the loss of geographic variation in species and species interactions

Species introductions into nearby communities may seem innocuous, however, these introductions, like long-distance introductions (e.g. trans- and intercontinental), can cause extinctions and alter the evolutionary trajectories of remaining community members. These 'local introductions' can also more cryptically homogenize formerly distinct populations within a species. We focus on several characteristics and the potential consequences of local introductions. First, local introductions are commonly successful because the species being introduced is compatible with existing abiotic and biotic conditions; many nearby communities differ because of historical factors and the absence of certain species is simply the result of barriers to dispersal. Moreover, the species with which they interact most strongly (e.g. prey) may have, for example, lost defences making the establishment even more likely. The loss or absence of defences is especially likely when the absent species is a strongly interacting species, which we argue often includes mammals in terrestrial communities. Second, the effects of the introduction may be difficult to detect because the community is likely to converge onto nearby communities that naturally have the introduced species (hence the perceived innocuousness). This homogenization of formerly distinct populations eliminates the geographic diversity of species interactions and the geographic potential for speciation, and reduces regional species diversity. We illustrate these ideas by focusing on the introduction of tree squirrels into formerly squirrel-less forest patches. Such introductions have eliminated incipient species of crossbills (Loxia spp.) co-evolving in arms races with conifers and will likely have considerable impacts on community structure and ecosystem processes.