Twelve polymorphic microsatellites in Oriental river prawn, Macrobrachium nipponense

Oriental river prawn, Macrobrachium nipponense, is a commercially important freshwater prawn species in China, Japan, Korea and Vietnam. Due to overfishing for food, the wild stocks M. nipponense are endangered. Twenty microsatellite loci were isolated from the M. nipponense. Twelve of these loci were polymorphic (seven to 16 alleles per locus), with expected heterozygosity ranging from 0.68 to 0.86 (n = 48). These polymorphic loci provide a valuable tool for assessing genetic diversity of wild and cultured populations.     

PCR primers for polymorphic microsatellite loci in the facultatively polygynous plant‐ant Petalomyrmex phylax (Formicidae)

Fourteen microsatellite loci were isolated and their level of polymorphism characterized in two populations of the facultatively polygynous plant‐ant Petalomyrmex phylax (Formicinae). High levels of within‐population variation were observed at most loci, with number of alleles ranging from two to 15, and heterozygosity from 0.050 to 0.925. Cross‐species amplification of these loci was also tested in four plant‐ant species belonging to three other genera, Aphomomyrmex, Cladomyrma (both Formicinae) and Cataulacus (Myrmicinae).     

Majority of random cDNA clones correspond to single loci in the tomato genome

Summary The number of loci corresponding to each of 34 unique, random cDNA clones has been determined for the diploid plant species Lycopersicon esculentum (tomato) (2n=24). Fifty-three percent of the clones are homologous to loci represented only once in the tomato chromosomes. Thirty-two percent of the clones correspond to two genetically independent loci. The remaining clones belong to gene families represented by 3–5 loci. To determine the number of gene copies per locus, reconstruction experiments were performed on six of the single locus clones. The majority of these loci were estimated to contain only 1 or 2 copies of the gene. These results support the concept that the majority of structural genes in this diploid plant species are arranged in single loci and present in low copy number. Multigene families, such as those for the small subunit of ribulose bisphosphate carboxylase, chlorophyll a/b binding polypeptide and actin are exceptions to this rule.     

Nine polymorphic microsatellite loci for the fennel Pondweed Potamogeton pectinatus L.

Fennel (= Sago) pondweed (Potamogeton pectinatus L.) is a submersed macrophyte of nearly cosmopolitan distribution. The plant is of worldwide ecological importance as structuring component of shallow lakes, and as food for waterfowl. We developed nine polymorphic microsatellite primers for the population genetic analysis of P. pectinatus. The loci were identified using a GA/CT‐enriched genomic library using subtractive hybridization with magnetic particles. All nine loci were highly polymorphic with 6–9 alleles and heterozygosities ranging from 0.23 to 0.80 in a subset of N = 40 genotypes from five locations.     

ASSOCIATION BETWEEN QUANTITATIVE TRAITS AND ALLOZYME HETEROZYGOSITY IN A TETRASOMIC SPECIES: DACTYLIS GLOMERATA

Tetraploid individuals of orchardgrass (Dactylis glomerata L. subsp. hispanica Roth.) sampled from a natural population were used to evaluate the correlation between both single and multilocus heterozygosity at 7 enzyme loci, and several quantitative traits (plant size at time of collection, leaf weight, and panicle number in experimental trials). Four hundred and forty-eight plants were studied at the 7 loci and 288 of these individuals were scored for an additional eighth locus. Five genotype classes (monogenic, simplex, and duplex digenic, trigenic, and tetragenic) were distinguished according to their heterozygosity level. Multilocus heterozygosity showed a significant positive correlation with both leaf and panicle yield in experimental conditions, but not with original plant size, which was found to be markedly influenced by environmental microheterogeneity. Multilocus heterozygosity, estimated from both the number of heterozygous loci and the number of distinct alleles per locus, had a significant influence on plant performance. Individual locus effects were positive and significant at two loci (GOT1 and PX1). Panicle number increased regularly with heterozygosity level (from monogenics to tetragenics) at the GOT1 locus, as did leaf weight and panicle number at the PX1 locus. Such variation would be predicted by overdominance at these loci or at linked loci. Significant relationships between leaf yield and heterozygosity level at the GOT1 locus distinguished the homozygotes from the heterozygotes (of any class) and was thus more consistent with inbreeding effects. No significant differences were observed among the five genotype classes for any quantitative trait at the six remaining loci. At both the GOT1 and PX1 loci, heterozygosity had a significant independent effect on leaf weight and panicle number even when the correlation between these traits was removed by analysis of covariance.     

DNA polymorphisms and haplotype patterns of transcription factors involved in barley endosperm development are associated with key agronomic traits

Background  

Association mapping is receiving considerable attention in plant genetics for its potential to fine map quantitative trait loci (QTL), validate candidate genes, and identify alleles of interest. In the present study association mapping in barley (Hordeum vulgare L.) is investigated by associating DNA polymorphisms with variation in grain quality traits, plant height, and flowering time to gain further understanding of gene functions involved in the control of these traits. We focused on the four loci BLZ1, BLZ2, BPBF and HvGAMYB that play a role in the regulation of B-hordein expression, the major fraction of the barley storage protein. The association was tested in a collection of 224 spring barley accessions using a two-stage mixed model approach.     

The effect of direct and indirect defenses in two wild brassicaceous plant species on a specialist herbivore and its gregarious endoparasitoid

Most studies on plant defenses against insect herbivores investigate direct and indirect plant defenses independently. However, these defenses are not necessarily mutually exclusive. Plant metabolites can be transmitted through the food chain and can also affect the herbivore's natural enemies. A conflict may arise when a natural enemy is attracted to a plant that is suboptimal in terms of its own fitness. In addition, plant defenses are often studied in cultivated plant species in which artificial selection may have resulted in reduced resistance against insect herbivores. In this study, we investigated both direct and indirect plant defenses in two closely related wild brassicaceous plant species, Brassica nigra L. and Sinapis arvensis L. The herbivore Pieris brassicae L. (Lepidoptera: Pieridae), which is specialized on brassicaceous plant species, developed faster and attained higher pupal mass when reared on B. nigra than on S. arvensis. In contrast, Cotesia glomerata L. (Hymenoptera: Braconidae), which is a gregarious endoparasitoid of P. brassicae caterpillars, developed equally well on P. brassicae irrespective of the food plant on which its host had been reared. The feeding strategy of the parasitoid larvae, that is, selectively feeding on hemolymph and fat body, is likely to allow for a much wider host‐size range without affecting the size or development time of the emerging parasitoids. In flight chamber experiments, C. glomerata, which had an oviposition experience in a host that fed on Brussels sprout, exhibited significant preference for host‐damaged B. nigra over host‐damaged S. arvensis plants. Headspace analysis revealed quantitative and qualitative differences in volatile emissions between the two plant species. This parasitoid species may use a range of cues associated with the host and the host's food plant in order to recognize the different plant species on which the host can feed. These results show that there is no conflict between direct and indirect plant defenses for this plant–host–parasitoid complex.     

Microbial influence on gene-for-gene interactions in legume-Rhizobium symbioses

Recent advances in our understanding of the molecular genetics of legume-Rhizobium symbioses have indicated that relatively few bacterial genes are required for nodulation. While some of these genes are functionally similar and shared among microsymbionts nodulating genetically diverse legumes, others appear to encode host-specific nodulation (hsn) functions which allow for nodulation of plants within a given legume genus. More recently, genotype-specific nodulation (GSN) determinants have been identified in R. leguminosarum bv. viceae strain TOM and in B. japonicum strain USDA 110. GSN determinants refer to those bacterial sequences that allow for nodulation of specific plant genotypes within a given legume species. In contrast to the avr loci of several plant pathogens, rhizobia host-range determinants (hsn and GSN) have been shown to positively affect nodulation. That is, the introduction of exogenous hsn and GSN loci extends host-range. Since GSN loci have been reported to interact with single host plant alleles, it suggests that gene-for-gene interactions occur in rhizobial-legume symbioses and contribute to nodulation specificity at the host genotype level.     

Nine polymorphic microsatellite markers in Centaurea stoebe L. [subspecies C. s. stoebe and C. s. micranthos (S. G. Gmelin ex Gugler) Hayek] and C. diffusa Lam. (Asteraceae)

Centaurea stoebe (subspecies C. s. stoebe and C. s. micranthos[S. G. Gmelin ex Gugler) Hayek] and Centaurea diffusa are Eurasian plant species that have invaded much of North America. We isolated seven microsatellite loci from C. stoebe and two loci from C. diffusa. All loci described here amplify in both species and have between six and 25 alleles each. These markers will be useful in examining population structure and addressing questions regarding these invasions.     

RFLP-based mapping of three mutant loci in rye (Secale cereale L.) and their relation to homoeologous loci within the Gramineae

 Three mutant loci of rye determining absence of ligules (al), waxless plant (wa1) and waxy endosperm (Wx) characters were mapped in a single F₂ population, comprising 84 individual plants. The three loci could be clearly tagged in relation to 7 (al on chromosome 2R), 4 (wa1 on chromosome 7R) or 6 (Wx on chromosome 4R) RFLP markers. The mapping data are compared with existing data for homoeologous regions containing equivalent mutants of wheat, barley, rice and maize. It is shown that the loci analysed are highly conserved across the cereal species, including rye. Received: 14 March 1997 / Accepted: 21 March 1997     

Isolation and characterization of polymorphic microsatellite markers in Zabrotes subfasciatus Boheman (Coleoptera: Bruchidae)

Bruchid beetles of the genus Zabrotes (Coleoptera: Bruchidae) are important worldwide pests of legume seeds. Samples of Zabrotes subfasciatus and Z. sylvestris were collected from seeds of two Phaseolus species throughout Mexico to assess the role of host plant variation and plant domestication on the evolution of host use in this species. For this purpose six polymorphic microsatellite loci were isolated and characterized for the bruchid Z. subfasciatus. Cross‐species amplification tests were performed on Z. sylvestris and revealed that three loci amplified successfully and were polymorphic in this closely related species.     

The effect of different host plants on the reproduction and longevity of Nysius natalensis

Nysius natalensis Evans (Hemiptera: Orsillidae) is a pest of sunflower in South Africa. Adults invade sunflower fields from their weedy hosts which occur inside crop fields and on surrounding headlands. The host plant suitability for survival and reproduction as well as the effect of within‐generation host switching was studied on different wild host plants and sunflower. Life history parameters used to assess host plant suitability were F₁ adult survival, pre‐oviposition period, fecundity, and longevity. Nymphs and adults were provided with stems and seeds of five host plants, viz., Amaranthus hybridus L. (Amaranthaceae), Portulaca oleracea L. (Portulacaceae), Chenopodium album L. (Chenopodiaceae), Conyza albida Spreng. (Asteraceae), and sunflower, Helianthus annuus L. (Asteraceae). Nymphs were reared on crushed seed of the five plant species. After completion of the nymphal stage, emerging adults of each host plant group were provided with seed of a different host plant species for food. Adults did not survive long on stems only and very few eggs were laid. Seeds of the host plant species were shown to be an essential source of nutrients for N. natalensis reproduction, whereas the vegetative plant parts were unsuitable. Nymphal food and host‐plant switching between the nymphal and adult stages significantly affected the pre‐oviposition period. Nymphal and adult food source also affected female longevity. The number of eggs laid was not influenced by nymphal food, but was influenced by adult food and the switch between nymphal and adult food. The comparative attractiveness of sunflower and wild host plants for oviposition was also investigated and showed that females preferred to lay eggs on wild host plants, compared with sunflower. These results may explain why N. natalensis will lay their eggs on sunflower after weeds in the vicinity are controlled, or senesce toward the end of the growing season.     

A large-scale study of rice plants transformed with different T-DNAs provides new insights into locus composition and T-DNA linkage configurations

Transgenic locus composition and T-DNA linkage configuration were assessed in a population of rice plants transformed using the dual-binary vector system pGreen (T-DNA containing the bar and gus genes)/pSoup (T-DNA containing the aphIV and gfp genes). Transgene structure, expression and inheritance were analysed in 62 independently transformed plant lines and in around 4,000 progeny plants. The plant lines exhibited a wide variety of transgenic locus number and composition. The most frequent form of integration was where both T-DNAs integrated at the same locus (56% of loci). When single-type T-DNA integration occurred (44% of loci), pGreen T-DNA was preferentially integrated. In around half of the plant lines (52%), the T-DNAs integrated at two independent loci or more. In these plants, both mixed and single-type T-DNA integration often occurred concurrently at different loci during the transformation process. Non-intact T-DNAs were present in 70–78% of the plant lines causing 14–21% of the loci to contain only the mid to right border part of a T-DNA. In 53–66% of the loci, T-DNA integrated with vector backbone sequences. Comparison of transgene presence and expression in progeny plants showed that segregation of the transgene phenotype was not a reliable indicator of either transgene inheritance or T-DNA linkage, as only 60–80% of the transgenic loci were detected by the expression study. Co-expression (28% of lines) and backbone transfer (53–66% of loci) were generally a greater limitation to the production of marker-free T₁ plants expressing the gene of interest than co-transformation (71% of lines) and unlinked integration (44% of loci).     

Isolation and characterization of polymorphic microsatellites in the tropical plant‐ant Cataulacus mckeyi (Formicidae: Myrmicinae)

Eleven microsatellite loci were isolated from the plant‐ant Cataulacus mckeyi (Hymenoptera: Myrmicinae) and their polymorphism was characterized. High levels of within‐population variation were observed at most loci, with number of alleles ranging from one to 16, and heterozygosity from 0 to 0.929 per population sample. Cross‐species amplification of these loci was also tested in four other species of the ant genus Cataulacus.     

Tracking genes of ecological relevance using a genome scan in two independent regional population samples of Arabis alpina

Understanding the genetic basis of adaptation in response to environmental variation is fundamental as adaptation plays a key role in the extension of ecological niches to marginal habitats and in ecological speciation. Based on the assumption that some genomic markers are correlated to environmental variables, we aimed to detect loci of ecological relevance in the alpine plant Arabis alpina L. sampled in two regions, the French (99 locations) and the Swiss (109 locations) Alps. We used an unusually large genome scan [825 amplified fragment length polymorphism loci (AFLPs)] and four environmental variables related to temperature, precipitation and topography. We detected linkage disequilibrium among only 3.5% of the considered AFLP loci. A population structure analysis identified no admixture in the study regions, and the French and Swiss Alps were differentiated and therefore could be considered as two independent regions. We applied generalized estimating equations (GEE) to detect ecologically relevant loci separately in the French and Swiss Alps. We identified 78 loci of ecological relevance (9%), which were mainly related to mean annual minimum temperature. Only four of these loci were common across the French and Swiss Alps. Finally, we discuss that the genomic characterization of these ecologically relevant loci, as identified in this study, opens up new perspectives for studying functional ecology in A. alpina, its relatives and other alpine plant species.     

Isolation and characterization of polymorphic microsatellite markers from Primula nutans (Primulaceae)

Seven polymorphic microsatellite loci were developed for a perennial seashore plant, Primula nutans. Degenerate oligonucleotide‐primed (DOP)–polymerase chain reaction (PCR)‐amplified DNA was ligated to TOPO TA vector and screened with radioactively labelled dinucleotide repeat probes. A sample of 378 individuals from Finland, Norway and Russia were used to characterize those loci, which exhibited two to four alleles per locus with observed heterozygosity of 0.003–0.229 and expected heterozygosity of 0.016–0.527. No linkage disequilibrium was found between these seven loci. These are the first microsatellite markers reported for P. nutans.     

Gain of function assays identify non- rol genes from Agrobacterium rhizogenes TL-DNA that alter plant morphogenesis or hormone sensitivity

This study tested the morphogenetic potential of 15 open reading frames of the TL-DNA of Agrobacterium rhizogenes strain HRI. These open reading frames were expressed individually under the control of the 35S RNA promoter in transgenic tobacco plants ( Nicotiana tabacum L.). Expression of three T-DNA loci, ORF3n, ORF8 and ORF13, alters plant morphogenesis or the response of transgenic tissues to plant hormones. ORF3n transgenic plants are characterized by retarded flowering, altered internode elongation, altered leaf shape and, in particular, leaf tip necrosis. ORF3n and ORF8 expression reduces the sensitivity to auxin and cytokinin in combination or auxin alone. Tetracycline-dependent expression of ORF13 overcomes a selection of low levels of expression during plant regeneration and reveals a strong inhibitory effect of the ORF13 gene product on cell division and cell elongation. We conclude that the A. rhizogenes TL-DNA harbors genetic information that is important for pathogenicity apart from the well studied rol genes. We propose that these genes play mainly a negative regulatory role during pathogenesis. Moreover, these loci might be relevant to successful infections in specific host plants.     

Variation of allele composition and protein locus expression in the course of genetic differentiation of taxa of different ranks in the mammals

The contributions of different groups of loci, namely those identical (i), similar (s), and different (d) with respect to allele composition and the loci expressed in only one of two compared objects (0), into the differentiation of marsupial and placental mammals have been evaluated. An increase in the proportions of d and 0 loci with increasing taxon rank has been demonstrated. At the intraspecific level, identical loci are prevailing, and d loci are rare; the latter are more common in subspecies. At the species level, the proportions of different (d) and similar (s) loci are increased, but the proportion of i loci is still the highest. Only at the genus level does the proportion of different loci reach 41–49%; 0 loci are found in marsupials and small placental mammals, and the number of s loci is decreased. In large placental mammals, this trend is disrupted at the subspecies level, where the contribution of s loci is drastically increased, while the proportion of identical ones (i) is decreased. Comparison with data on other groups of vertebrates shows that the ratios between these groups of loci reflect the specificity of differentiation processes at the intraspecific level and the levels of species and taxa of higher ranks in all classes of animal analyzed. However, the species differentiation in amphibians approximately corresponds to the genus level in mammals and the family level in birds.     

Isolation and characterization of microsatellite loci in the highland papaya Vasconcellea × heilbornii V. Badillo (Caricaceae)

Nine polymorphic microsatellite loci were identified in the tropical plant Vasconcellea ×heilbornii and used to estimate allelic diversity in two populations of southern Ecuador. Allelic richness ranged from two to five alleles, observed heterozygosity ranged from 0.150 to 0.947 and expected heterozygosity ranged from 0.186 to 0.701. Most of these markers also amplified microsatellite loci in two other Vasconcellea species (Vasconcellea stipulata and Vasconcellea cundinamarcensis). Hence, these markers will be useful for population genetic analysis and the evaluation of genetic diversity and gene flow in these species.     

Characterization of polymorphic microsatellites in the castration parasite plant‐ant Allomerus octoarticulatus cf. demerarae (Formicidae: Myrmicinae)

Fifteen microsatellite loci were isolated from the Peruvian tropical plant‐ant Allomerus octoarticulatus cf. demerarae (Hymenoptera: Myrmicinae) and their polymorphism was characterized. High levels of within‐population variation were observed at most loci, with number of alleles ranging from one to 21, and heterozygosity from 0 to 1 per population sample. Cross‐species amplification of these loci was also tested in one other species of the ant genus Allomerus (Allomerus decemarticulatus), displaying similar life history.