Direct amplification of minisatellite-region DNA with VNTR core sequences in the genus Oryza

 A polymerase chain reaction (PCR) application, involving the directed amplification of minisatellite-region DNA (DAMD) with several minisatellite core sequences as primers, was used to detect genetic variation in 17 species of the genus Oryza and several rice cultivars (O. sativa L.). The electrophoretic analysis of DAMD-PCR products showed high levels of variation between different species and little variation between different cultivars of O. sativa. Polymorphisms were also found between accessions within a species, and between individual plants within an accession of several wild species. The DAMD-PCR yielded genome-specific banding patterns for the species studied. Several DAMD-PCR-generated DNA fragments were cloned and characterized. One clone was capable of detecting multiple fragments and revealed individual-specific hybridization banding patterns using genomic DNA from wild species as well as rice cultivars. A second clone detected only a single polymorphic locus, while a third clone expressed a strong genome specificity by Southern analysis. The results demonstrated that DAMD-PCR is potentially useful for species and genome identification in Oryza. The DAMD-PCR technique also allows for the isolation of informative molecular probes to be utilized in DNA fingerprinting and genome identification in rice. Received: 1 October 1996 / Accepted: 25 April 1997     

Quantitative analysis of the effect of selection history on sugar yield adaptation of sugarcane clones

An objective of the CSR sugarcane breeding programme in Australia was to assess the scope for broadening the genetic base of the commercial sugarcane germ plasm through interspecific hybridization with Saccharum spontaneum clones. The contribution of both selection history and S. spontaneum to sugar yield and its components was investigated in the germ plasm pool assembled. The analysis was conducted on a data-set of 256 clones, consisting of parents and full-sib families generated from 32 biparental crosses, tested in six environments. The minimum number of generations back to S. spontaneum ancestor in the clone's pedigree was used as a germ plasm score. The geographical origin and selection history of each parent and their use in the biparental crosses were used to develop a selection history score for parents and offspring. The variation for seven attributes, cane yield, commercial cane sugar %, sugar yield, stalk number per stool, stalk weight, fibre % and ash % juice was partitioned according to the germ plasm and selection history scores. Significant (P<0.05) clone variation and clone x environment interaction for all attributes was present. The germ plasm scores accounted for a significant (P<0.05) component of the clone variation for all of the attributes except cane yield. There was an increase in sugar yield with an increase in the minimum number of generations back to a S. spontaneum clone. The selection history groups accounted for a high proportion of the variation among parental clones for all of the attributes except cane yield. This suggested that parents were the outcome of strong selection pressure for the commercial cane attributes. However, the selection history groups for the offspring produced by random mating of parents did not account for a high proportion of the variation for the attributes. Using the mixture method of classification we partitioned the 256 clones into five groups for patterns of performance for the seven attributes across the six environments. The five groups emphasized major differences in the patterns of performance for the seven attributes across environments. The distribution of germ plasm and selection history scores in each of the five groups indicated that their patterns of performance were associated with selection history and minimum generations to S. spontaneum. Therefore, both the analysis on selection history and germ plasm scores (extrinsic classification) and the analysis on the mixture method of classification (intrinsic classification) emphasized the influence of selection history on the sugar yield of sugarcane.     

A CHEMOTAXONOMIC STUDY OF LEMNACEAE

One hundred eighty-six clones of Lemnaceae, representing world-wide collections of 22 taxa, were grown in axenic cultures reproduced by clonal subcultures. Following morphological examinations under a range of culture conditions, a “key” clone was selected to represent each taxon. These key clones were completely representative of the qualitative flavonoid chemistry of the taxa as determined from a number of clones. With the exceptions of Spirodela polyrhiza and S. biperforala which produce identical flavonoids, the flavonoid associations of each species of Lemnaceae were unique in the family. Through paper chromatographic comparisons of purified compounds, plus visible and ultraviolet absorption spectroscopy of isolated individual flavonoids, a total of 47 different compounds was described. These substances included: glycosides of anthocyanidins (cyanidin and petunidin); glycosides of flavonols (kaempferol and quercetin); glycosides of flavones (apigenin and luteolin); and several glycoflavones (C-glycosyl-flavones). When grown under equivalent controlled conditions of culture, infraspecific variation in the qualitative production of these 47 flavonoids was detected in only one flavone glycoside of the species Lemna perpusilla. The reliability of the flavonoid patterns under various conditions of culture was investigated. Under 62 different regimes S. oligorhiza and S. polyrhiza showed only minor variations in their flavonoid glycosides. Studies of other taxa supported this generalization. Under controlled conditions, morphological intergradation obscured identification of many collections. Each could be conclusively identified by its flavonoid chemistry.     

STUDY OF THE ESSENTIAL LEAF OILS OF THE GENUS MONARDA (LABIATAE)

Vapor-phase chromatographic patterns obtained from the distilled essential oils of 20 taxa in the genus Monarda (Labiatae) are discussed. The influence of leaf tissue maturity, plant habitat, and oil storage upon the composition of the essential oils was investigated, as well as similarities of leaf and flower oils in the same plant. The taxa of the subgenus Cheilyctis have very similar chromatographic “fingerprints” which confirm their homogeneity. On the other hand, the polyploid subgenus Monarda has heterogeneous patterns of essential oil composition among its species. A population of M. fistulosa gave evidence of being a chemical race.     

Genetic variation of NBS-LRR class resistance genes in rice lines

The use of plant disease resistance (R) genes in breeding programs needs an understanding of their variation patterns. In our current study, we investigated the polymorphisms of 44 NBS-LRR class R-genes among 21 rice cultivars and 14 wild rice populations. Our data suggested that there were four basic types of variations: conserved, diversified, intermediate-diversified, and present/absent patterns. Common characteristics at a locus of conserved R-genes were: copy-number uniformity, clear divergence (long branches) with other paralogs, and highly identical alleles. On the other hand, copy-number variability, a nearly equal and non-zero branch lengths, and high levels of nucleotide diversity were observed at the loci of highly diversified R-genes. Research suggests that the ratio of diverse alleles to the total number of genes at a locus is one of the best criteria to characterize the variation pattern of an R-gene. Our data suggested that a significant genetic reduction was detected only in four present/absent R-genes, compared with the variation observed in wild rice. In general, no difference was detected between wild rice and cultivars, japonica and indica rice, or between lines from different geographic regions. Our results also suggested that R-genes were under strong selection, which shaped R-gene variation patterns. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Sihai Yang and Tingting Gu contributed equally to this work.     

Causes and consequences of sectoriality in the clonal herb Glechoma hederacea

The causes of sectoriality and consequences for clone behaviour are examined using data from the stoloniferous herb Glechoma hederacea. The proximal causes of physiological integration patterns are investigated using anatomical studies, acid fuchsin dye to reveal patterns of xylem continuity between ramets, and ¹⁴C as a label to reveal quantitative photoassimilate translocation patterns in the phloem. Dye movement in the xylem was acropetal and sectorial, and the sectoriality was determined by phyllotaxy. Patterns of ¹⁴C-labelled photoassimilate allocation were qualitatively similar to those of xylem based resources, although there was some basipetal movement of photoassimilate. The patterns of physiological integration and independence between ramets are shown to be governed by rules which depend on vascular continuity and discontinuity between ramets. Physiological support to stolon apices results in acquisition of relative branch autonomy (branches become semi-autonomous integrated physiological units, IPUs).This paper evaluates whether observed physiological integration patterns may be modified by altering normal source-sink relationships or by modifying environmental conditions. An experiment using different defoliation intensities, and different defoliation patterns at the same overall intensity, demonstrated that the precise positions of leaves removed from a clone had unique consequences for its subsequent development. Individual ramets of a given clone may be located in microhabitats of differing quality. An experiment in which competition was either present or absent throughout the space occupied by the clone, or patchy in distribution, showed that G. hederacea did not respond to competition at the whole clone level. Instead, connected stolons (IPUs) responded independently to local competition. Sectoriality may promote the restriction of lethal, localised environmental factors within the affected IPU. A study investigating the uptake and translocation of zinc by clones revealed that quantified patterns of zinc distribution resembled patterns of ¹⁴C movement in the phloem, and that there was no significant transport of zinc from one stolon to another.Although sectorial patterns of resource movement in G. hederacea can be modified in the short term, in the long-term, physiological integration may not allow this species to integrate the effects of environmental heterogeneity. A mobile clonal species with a high growth rate and relatively short-lived ramets, such as G. hederacea, is likely to benefit from a semi-autonomous response to patch quality at the level of the stolon, since the alternative of widespread intra-clonal support may increase the residence time of the clone in unfavourable pathches.     

Intraspecific variability in egg maturation patterns and associated life‐history trade‐offs in a polyembryonic parasitoid wasp

1. Life‐history theory predicts a trade‐off between the resources allocated to reproduction and those allocated to survival. Early maturation of eggs (pro‐ovigeny) is correlated with small body size and low adult longevity in interspecific comparisons among parasitoids, demonstrating this trade‐off. The handful of studies that have tested for similar correlations within species produced conflicting results. 2. Egg maturation patterns and related life‐history traits were studied in the polyembryonic parasitoid wasp, Copidosoma koehleri (Hymenoptera: Encyrtidae). Although the genus Copidosoma was previously reported to be fully pro‐ovigenic, mean egg loads of host‐deprived females almost doubled within their first 6 days of adulthood. 3. The initial egg‐loads of newly emerged females were determined and age‐specific realised fecundity curves were constructed for their clone‐mate twins. The females' initial egg loads increased with body size, but neither body size nor initial egg load was correlated with longevity and fecundity. 4. The variation in initial egg loads was lowest among clone‐mates, intermediate among non‐clone sisters and highest among non‐sister females. The within‐clone variability indicates environmental influences on egg maturation, while the between‐clone variation may be genetically based. 5. Ovaries of host‐deprived females contained fewer eggs at death (at ～29 days) than on day 6. Their egg loads at death were negatively correlated with life span, consistent with reduced egg production and/or egg resorption. Host deprivation prolonged the wasps' life span, suggesting a survival cost to egg maturation and oviposition. 6. It is concluded that adult fecundity and longevity were not traded off with pre‐adult egg maturation.     

Genetic variation in a host-parasite association: potential for coevolution and frequency-dependent selection

Abstract.— Models of host‐parasite coevolution assume the presence of genetic variation for host resistance and parasite infectivity, as well as genotype‐specific interactions. We used the freshwater crustacean Daphnia magna and its bacterial microparasite Pasteuria ramosa to study genetic variation for host susceptibility and parasite infectivity within each of two populations. We sought to answer the following questions: Do host clones differ in their susceptibility to parasite isolates? Do parasite isolates differ in their ability to infect different host clones? Are there host clone‐parasite isolate interactions? The analysis revealed considerable variation in both host resistance and parasite infectivity. There were significant host clone‐parasite isolate interactions, such that there was no single host clone that was superior to all other clones in the resistance to every parasite isolate. Likewise, there was no parasite isolate that was superior to all other isolates in infectivity to every host clone. This form of host clone‐parasite isolate interaction indicates the potential for coevolution based on frequency‐dependent selection. Infection success of original host clone‐parasite isolate combinations (i.e., those combinations that were isolated together) was significantly higher than infection success of novel host clone‐parasite isolate combinations (i.e., those combinations that were created in the laboratory). This finding is consistent with the idea that parasites track specific host genotypes under natural conditions. In addition, correspondence analysis revealed that some host clones, although distinguishable with neutral genetic markers, were susceptible to the same set of parasite isolates and thus probably shared resistance genes.     

Sources of intraspecific variation in the hostplant seeking behavior of Colias butterflies

Summary Egg-laying females of the legume-feeding butterfly Colias philodice eriphyle were observed within a high-altitude study site during 1977 and 1978. Average oviposition selectivity showed two patterns of seasonal variation. First, second-brood females laid eggs more frequently after alighting upon hostplants than did first-brood females in both years. Second, a consistent decline in post-alighting oviposition probability near the end of the second brood corresponded with a dramatic decrease in the water content of hostplant foliage near the end of the dry summer season. In addition to seasonal variation in oviposition behavior, individual females landed and oviposited upon widely varying sets of legume hostplant species. By sampling hostplant abundances along the flightpaths of observed females, we show that individuals varied in their tendency to land upon different hostplants. Females tended to specialize upon one or two species, at least in the short term, and the pattern of oligophagy for the population as a whole is partly generated by variation in the host-seeking behavior of individual females.     

Evolutionary significance of genotypic variation in developmental reaction norms for a perennial grass under competitive stress

The developmental reaction norm (DRN) represents the set of ontogenetic trajectories that can be produced by a genotype exposed to different environmental conditions. Genetic variation in the DRN for growth traits and in the patterns of biomass allocation is critical to phenotypic evolution in heterogeneous environments. The DRN and patterns of biomass allocation were investigated in 11 clones of the caespitose, corm-forming, perennial grass Phleum pratense in relation to competitive stress imparted by Lolium perenne in a 16 week glasshouse experiment. A separate experiment assessed the ability of basal buds flanking a corm to sprout and the relationship of corm mass to sprout mass for the same clones. Corm fresh mass varied among clones and was significantly correlated with the dry mass of the tillers that sprouted from basal buds. In the competition experiment, clones in competitive environments varied significantly from those in non-competetive environments in terms of their DRNs for number of tillers and shoot dry mass. Thus, selection of DRNs would favour different genotypes in the two environments and at different times. Significant negative genetic correlations were detected for tiller number and mean tiller mass in the noncompetitive, but not the competitive, environment. Biomass allocation to stem bases was significantly greater for clones under competitive stress. Allocation to storage tissues such as corms may be adaptive if it enhances persistence in the competitive field environments typically occupied by caespitose grasses. Root and shoot allocation showed a significant clone by competition interaction. For P. pratense, genotypic variation in growth trajectories plays an important role in determining variation in individual performance, a condition necessary for the continued evolution of the DRN.     

CHLOROPLAST DNA SYSTEMATICS OF LILIOID MONOCOTS: RESOURCES,FEASIBILITY, AND AN EXAMPLE FROM THE ORCHIDACEAE

Although chloroplast DNA (cpDNA) analysis has been widely and successfully applied to systematic and evolutionary problems in a wide variety of dicots, its use in monocots has thus far been limited to the Poaceae. The cpDNAs of grasses are significantly altered in arrangement relative to the genomes of most vascular plants, and thus the available clone banks of grasses are not particularly useful in studying variation in the cpDNA of other monocots. In this report, we present mapping studies demonstrating that cpDNAs of four lilioid monocots (Allium cepa, Alliaceae; Asparagus sprengeri, Asparagaceae; Narcissus × hybridus, Amaryllidaceae; and Oncidium excavatum, Orchidaceae), which, while varying in size over as much as 18 kilobase pairs, conform to the genome arrangement typical of most vascular plants. A nearly complete (99.2%) clone bank was constructed from restriction fragments of the chloroplast genome of Oncidium excavatum; this bank should be useful in cpDNA analysis among the monocots and is available upon request. As an example of the utility of filter hybridization using this clone bank to detect systematically useful variation, we present a Wagner parsimony analysis of restriction site data from the controversial genus Trichocentrum and several sections of Oncidium, popularly known as the “mule ear” and “rat tail oncidiums.” Because of their vastly different floral morphology, the species of Trichocentrum have never been placed in Oncidium, although several authors have recently suggested a close relationship to this vegetatively modified group. The analysis of cpDNA presented here supports this affinity; in fact, it places Trichocentrum as a derivative of the mule ear oncidiums.     

Clonal fingerprinting in the genus <Emphasis Type="Italic">Populus</Emphasis> L. by nuclear microsatellite loci regarding differences between sections,species and hybrids

Reliable methods for clone identification are desired to characterise and distinguish breeding products within the genus Populus L. (Salicaceae). Ten nuclear microsatellite loci (PMGC14, PMGC456, PMGC2163, PTR2, PTR7, WPMS05, WPMS09, WPMS14, WPMS15 and WPMS20) were applied on a clone collection with several species and hybrids belonging to the sections Tacamahaca (balsam poplars), Aigeiros (black poplars, cottonwoods) and Populus (white poplars and aspens) and intersectional hybrids between black and balsam poplars. The members of the different sections and species do not always share their allelic ladders. Some shifts of one or two nucleotides in allele length were observed for several loci. This could be explained by nucleotide sequence differences in the flanking regions of loci in diverse taxonomic groups. Such shifts of allelic ladders result in irregular patterns in hybrid genotypes. The set of loci should have a sufficient amount of variation for a differentiation between clones, even if they are full siblings originating from crossing experiments.     

Cryptic Appearance of a New Clone of Vibrio cholerae Serogroup O1 Biotype El Tor in Calcutta,India

In this study, pulsed-field gel electrophoresis (PFGE) was applied to determine if the Vibrio cholerae O1 strains which reappeared after being temporarily displaced in Calcutta by the O139 serogroup were different from those isolated before the advent of the O139 serogroup. NotI digestion generated a total of 11 different patterns among the 24 strains of V. cholerae randomly selected to represent different time frames. Among the V. cholerae O1 strains isolated after July 1993, 4 PFGE banding patterns designated as H through K were observed with pattern H dominating. Pattern H was distinctly different from all other patterns encountered in this study including patterns A, B and C of V. cholerae O1 El Tor, which dominated before November 1992, and pattern F, which was the dominant V. cholerae O139 pattern. Further, pattern H was also different from the NotI banding patterns of the representative strains of the 4 toxigenic clonal groups of V. cholerae O1 El Tor currently prevailing in different parts of the world. NotI fragments of the new clone of V. cholerae O1 did not hybridize with an O139 specific DNA probe, indicating that there was no O139 genetic material in the new clone of V. cholerae O1. Hybridization data with an O1-specific DNA probe again differentiated between the clones of V. cholerae O1 existing before the genesis of the O139 serogroup and the O1 strains currently prevalent.     

Population consequences of changes in an ant-seed mutualism in Sanguinaria canadensis

Summary Seed dispersal by ants was studied in three populations of the myrmecochore, Sanguinaria canadensis, located in three habitats, each of which showed a different level of disturbance. Frequency of seed removal and the distances seeds were carried by ants were related to plant density, dispersion and the relative proportions of sexual and asexual reproduction in each population. Seeds in the least disturbed habitat were removed frequently and carried, by a wide variety of ants, distances of up to 12 m. Plant density was low and clone size was small. There was a relatively low level of sexual (seed) reproduction but seeds were generally transported well beyond the boundaries of the parent clones. By contrast, at the most disturbed site, plant density was high and clone size was very large. While there was a high level of seed production, seeds were rarely moved by ants and since removal distances were short, the probability of a seed being relocated beyond the limits of the parent clone was miniscule. The third population from a habitat which was intermediate in disturbance yielded data intermediate to the others. The data show that habitat disturbance, in disrupting the ant fauna and hence the ant-seed mutualism, has profound effects upon population density, dispersion and patterns of reproduction. Density-dependent regulation of sexual output predicted, for example, by the Strawberry-Coral model (Williams 1975), is maladaptive when the antseed mutualism is disturbed. We discuss the implications of this for theoretical modeling, the significance of mutualisms and the assessment of disturbance for conservation.     

A comparative study of isoenzyme patterns ofHydrilla verticillata (L.f.) Royle in Japan

Isoenzyme patterns of 226 accessions ofHydrilla verticillata collected in Japan were compared. 17 and 23 electrophoretic phenotypes were identifiable in diploid and triploid accessions, respectively, in dioecious ones. To the contrary, monoecious plants showed no variation of banding patterns and were assumed to be rametes of the same clone. The cytological change from diploid to triploid was suggested to occur many times in dioecious plants.     

Spatial patterns in abundance of a damselfish reflect availability of suitable habitat

For species with metapopulation structures, variation in abundance among patches can arise from variation in the input rate of colonists. For reef fishes, variability in larval supply frequently is invoked as a major determinant of spatial patterns. We examined the extent to which spatial variation in the amount of suitable habitat predicted variation in the abundance of the damselfish Dascyllus aruanus, an abundant planktivore that occupies live, branched coral throughout the Indo-Pacific. Reef surveys established that size, branching structure and location (proximity to sand) of the coral colonies together determined the ”suitability” of microhabitats for different ontogenetic stages of D. aruanus. Once these criteria were known, patterns of habitat use were quantified within lagoons of five Pacific islands. Availability of suitable habitat generally was an excellent predictor of density, and patterns were qualitatively consistent at several spatial scales, including among different lagoons on the same island, among different islands and between the central (French Polynesia and Rarotonga) and western (Great Barrier Reef, Australia) South Pacific. A field experiment that varied the amount of suitable coral among local plots indicated that habitat for settlers accounted for almost all of the spatial variation in the number of D. aruanus that settled at that location, suggesting that spatial patterns of abundance can be established at settlement without spatial variation in larval supply. Surveys of four other species of reef-associated fish revealed that a substantial fraction of their spatial variation in density also was explained by availability of suitable reef habitat, suggesting that habitat may be a prevalent determinant of spatial patterns. The results underscore the critical need to identify accurately the resource requirements of different species and life stages when evaluating causes of spatial variation in abundance of reef fishes. Received: 18 May 1999 / Accepted: 9 January 1999     

High variation in host adaptation among clones of the pea aphid,Acyrthosiphon pisum on peas,Pisum sativum

The performance of one clone of the pea aphid,Acyrthosiphon pisum (Harris), was assessed on 37 different cultivars and species ofPisum L. In addition, random samples of 36 pea aphid clones collected on alfalfa and clover were tested on a selection of fivePisum sativum L. cultivars. Aphid performance was evaluated in terms of the mean relative growth rate (MRGR) during the first five days of life or other life history variables. The MRGR of the first-mentioned pea aphid clone differed little between cultivars. No significant differences in MRGR were found between wild and cultivatedPisum species or between modern and oldP. sativum cultivars. There was considerable variation in host adaptation among the 36 pea aphid clones within each sampled field. The pea aphid clones showed no consistent pattern in performance on four of the five pea cultivars i.e. there was a significant pea aphid genotype —pea genotype interaction. On one of the cultivars all clones performed well. Pea aphid clones collected from red clover generally performed relatively poorly on pea cultivars, in contrast to the pea aphid clones collected on alfalfa. There was no difference in performance between the two pea aphid colour forms tested. Possible reasons for the high variation and the observed adaptation patterns are discussed. The fact that all clones were collected in two adjacent fields indicates thatA. pisum shows high local intraspecific variability in terms of host adaptation.     

Allozyme Variation Patterns and Multiple Hybridization Origins: Clonal Variation Among Four Sibling Parthenogenetic Caucasian Rock Lizards

Allozyme electrophoresis of four sibling parthenogenetic Caucasian rock lizards Darevskia unisexualis, D.uzzelli, D.sapphirina, and D.bendimahiensis found seven clones and five variable loci. The data supported the hypothesis that D.raddei and D.valentini are the parental species of all four parthenogens. Variation patterns in Darevskia were summarized. Species that originated from a single F₁ typically consisted of one widespread clone with a few rare clones. Species with multiple origins displayed variation only slightly higher than species with a single origin. This is contrary to other genera of parthenogenetic lizards, in which cases massive clonal variations were observed. This revised version was published online in August 2006 with corrections to the Cover Date.     

Host plant and competitor identity matter in genotype × genotype × environment interactions between vetch and pea aphids

1. Selection does not only operate in a genotype (G) × environment (E) context, but can also be modulated by the activities of organisms interacting with their environment (G × G × E). 2. The influences of aphid clonal identity and host plant (Vicia faba) intraspecific genetic variation on the performance of five genotypes of pea aphid (Acyrthosiphon pisum) were investigated – with and without interaction with a competing heterospecific clone of vetch aphid (Megoura viciae) – across three cultivars of V. faba. 3. Pea aphid performance in the presence of a competing vetch aphid clone (G × G × E) compared with the absence of competition (G × E) revealed strong context‐dependent, genotype‐specific shifts in performance, influenced by plant cultivar, competitor presence and their interaction. 4. The performance of vetch aphid in competition with each pea aphid clone was also compared. Here, competitor's genotype and abundance underlay a remarkably varied response by vetch aphid across interactions. 5. The study shows that aphid genotypes exhibit a varying degree of risk spreading, contingent on competitor identity and the patterns of aggregation across three plant cultivars. Owing to feedback loops between species activities and selective forces acting on them, our findings suggest that there are context‐dependent responses by competitors that are shaped via the interplay of the co‐occurring species and their biotic environment. 6. This work highlights the complexity of species interactions and the importance of investigating reciprocity between competition and intraspecific genetic variation. A better understanding of the eco‐evolutionary interactions between phloem‐feeding insects and their host plants can potentially be used to enhance crop protection and pest control.