Microsatellite markers for the tetraploid halophyte Suaeda maritima (L.) Dumort. (Chenopodiaceae) and cross-species amplification in related taxa

We developed 12 polymorphic microsatellite markers for the tetraploid halophyte Suaeda maritima (Chenopodiaceae). Population genetic parameters were estimated for three populations from different habitats (coastal and inland), using the program Tetrasat. Between two and 15 alleles per locus were observed. Mean expected heterozygosities (H(E) ) and Shannon-Wiener Diversity Indices (H') per locus and population ranged from zero to 0.852, and from zero to 2.990, respectively. The two inland populations were less diverse than the coastal one at most of the loci. All markers cross-amplified in the closely related Suaeda salsa, and all but one were transferable to Suaeda spicata and Suaeda salinaria.     

Microsatellite markers developed for Corallodiscus lanuginosus (Gesneriaceae) and their cross-species transferability

• Premise of the study: Corallodiscus is widespread across China and in adjacent countries to the west and south, with C. lanuginosus covering the entire range of the genus. Microsatellite markers will be useful to address within-complex taxonomic and biogeographic structures of this species. • Methods and Results: Fourteen markers were developed using the Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) protocol. Polymorphism was assessed in 12 individuals each from two populations from West Yunnan, China. Nine primers displayed polymorphisms. The number of alleles per locus ranged from one to six (mean: 2.7). The observed and expected heterozygosities ranged from 0 to 1 and from 0 to 0.772 (average: 0.487 and 0.448). Only one of the polymorphic loci deviated from Hardy–Weinberg equilibrium. Among the four congeneric species, cross-amplification success ranged from two to eight markers. • Conclusions: The markers will be useful for population genetic and evolutionary history studies for C. lanuginosus and the allied species C. bhutanicus, C. cooperi, and C. kingianus.     

浙江拟漆姑草属一新变种

对浙江省石竹科Caryophyllaceae一新变种闭花拟漆姑草（Spergularia marina var. cleistogama) 进行了描述和绘图。与原变种的主要区别在于本变种托叶三角状卵形,萼片宽度不等,花瓣0~4枚,有的花瓣变为雄蕊,闭锁,雌蕊具0.2~0.3mm的柄,雄蕊5~7枚,蒴果为宿存的花萼所包被,种子扁平,卵形。     

A New Variety of Spergularia (Caryophyllaceae) from Zhejiang,China

Spergularia marina var. cleistogama, a new variety of Caryophyllaceae from Zhejiang Province, China is described and illustrated. It is similar to S.marina var. marina, but differs by having triangular ovate stipules, unequally width of sepals, and 0-4 petals, a few of which may change into stamens. It is also characterized by its cleistogamous flowers, pistils with 0.2-0.3mm long gynophores, 5-7 stamens, capsules wrapped with persistent calyxes, and ovate, flat seeds.     

Microsatellite markers in common carp (Cyprinus carpio L.)

Microsatellite markers of the poly (CA) type in common carp ( Cyprinus carpio L.) are described. Clones containing a (CA) repeat were isolated from a common carp genomic library and sequenced. The number of repeats found was high compared to mammals but comparable with other teleost fishes. Classification of the repeats (perfect, imperfect and compound) are compared with the Atlantic cod ( Gadus morhua L.), rainbow trout ( Oncorhynchus mykiss ), and Atlantic salmon ( Salmo salar L.). A total of 41 primer sets were designed and tested for polymorphism on a test panel of eight animals (derived from outbred lines, inbred lines and gynogenetic clones). Thirty-two markers were found to be polymorphic. The heterozygosity in the outbred animals was 60·4%, 51·1% in the inbred animals and 0% in the gynogenetic clones. The average number of alleles among the eight animals was 4·7 per marker. Six markers (18·8%) gave an additional polymorphic amplification product besides the polymorphic amplification product in the expected size range. The possibility that these loci are tetraploid is discussed. The polymorphic loci described for common carp will be valuable as genetic markers for use in population, breeding, and evolutionary studies.     

Effects of nutrient availability on primary sexual traits and their response to selection in Spergularia marina (Caryophyllaceae)

Abstract Theoretical models of the evolution of sex allocation generally assume a negative genetic correlation between components of male and female investment or function. To test this assumption, and to determine whether the expression of the correlation is sensitive to environmental conditions, we conducted an artificial selection experiment targeting primary sexual traits in the autogamous herb, Spergularia marina. Mass selection favouring individuals with high (or low) pollen and ovule production per flower had previously been conducted for two generations under uniform conditions. Following a third episode of selection (reported here) within the high‐pollen‐, high‐ovule‐, low‐pollen‐ and low‐ovule‐producing lineages, selected maternal seed families were replicated and cultivated in three nutrient treatments. With this design, we observed the effects of nutrient availability on: floral phenotype, the realized response to selection and the expression of genetic variation in, and covariation between, male and female investment. The first two episodes of selection Mazer et al. 1999 (Evolution 53:717–731) detected evidence for a genetically based negative correlation between ovule and anther production. Following the third episode of selection, phenotypic differences among the selected lines were maintained in all treatments, but evidence for a negative correlation between male and female investment nearly disappeared. Only under low‐nutrient conditions, in which plants selected for low ovule production exhibited elevated anther production, was a genetic trade‐off expressed. Either genetic drift or the combination of novel growing conditions (relative to previous generations) and G × E interactions may have caused the change in the expression of the genetic correlation. This experiment also allowed us to test the prediction that autogamous selfers should exhibit higher canalization of the ratio of male to female investment than of its components. Supporting this prediction, the A : O ratio was more strongly buffered against environmental variation than either anther or ovule production per flower.     

Genetic structure of coastal and inland populations of <Emphasis Type=Italic>Spergularia media</Emphasis> (L.) C. Presl (Caryophyllaceae) in Central Europe

In Central Europe, salt-influenced habitats are restricted mainly to the coastlines of the North Sea and the Baltic Sea. The few natural inland salt sites suffer from size reduction and loss in biodiversity, while anthropogenic salt sites around potash mining dumps experienced recent and massive de novo colonization by numerous halophytes. Our study aimed to elucidate the general patterns of gene flow among coastal and inland salt habitats. We used amplified fragment length polymorphisms to assess the genetic diversity and genetic structure of 18 European populations of the halophyte Spergularia media (Caryophyllaceae), sampled from inland and coastal salt sites of Germany, the Netherlands, Denmark, Austria, France and Italy. Estimates of genetic diversity on the population level were generally low, especially within inland salt habitats. Analyses of molecular variance showed comparatively strong differentiation among populations. Multivariate ordination (principal coordinate analysis) and a NeighborNet analysis revealed four distinct groups of populations that showed good correspondence to their geographic origins. A Bayesian analysis performed with the program Structure as well as high pairwise Φ _ST values supported the results of the phenetic analyses. The observed patterns of diversity and differentiation among inland populations of S. media are best explained by the isolated nature of suitable salt habitats, with concomitant reduction of gene flow to and among these sites. Our data support the hypothesis that the colonization of anthropogenic salt sites by S. media originated from natural inland habitats.     

Covariation among floral traits in Spergularia marina (Caryophyllaceae): geographic and temporal variation in phenotypic and among-family correlations

Strong covariation among traits suggests the presence of constraints on their independent evolution due to pleiotropy, to linkage, or to selective forces that maintain particular trait combinations. We examined floral trait covariation among individuals, among maternal families within and across populations, and over time, in greenhouse-raised plants of the autogamous Spergularia marina. We had three aims. First, since the phenotype of traits expressed by modular organs often changes as individuals age, estimates of the degree of genetic covariation between such traits may also change over time. To seek evidence for this, we measured weekly (for five weeks) an array of floral traits among plants representing ～ 10 maternal families from each of four populations. The statistical significance of the phenotypic and among-family correlations among traits changed over time. Second, we compared populations with respect to trait covariation to determine whether populations or traits appear to be evolving independently of one another. Differences observed among populations suggest that they have diverged genetically. Third, we sought correlations that might reflect constraints on the independent evolution of floral traits. Investment in another and ovule production per flower vary independently among maternal families; there was no evidence for a “trade-off” between male and female investment. We propose that in autogamous taxa one should not find a negative correlation between pollen and ovule production per flower, as such taxa cannot evolve sexual specialization and should be under strong selection to maintain an efficient pollen:ovule ratio, preventing the evolution of male-biased or female-biased genotypes. We found that other pairs of floral traits, however, expressed highly signficant correlation coefficients, suggesting the presence of some evolutionary constraints, at least within some populations, although their strength depended on exactly when flowers were sampled.     

Microsatellite markers for Bromus tectorum (cheatgrass)

Bromus tectorum (cheatgrass) is a flourishing invasive weed in the western United States. The objective of our study is to characterize its genetic diversity. We made a B. tectorum genomic library in lambda phage and screened approximately 4000 clones for poly CA and poly CT dinucleotide repeats. Of 38 sequences with dinucleotide repeats isolated from the library, we designed primer sets for 18 loci. A preliminary screen of 40 individuals from four populations indicated that seven loci were polymorphic. These loci will be valuable for elucidation of cheatgrass genetic diversity and population structure.     

The neighborhood matters: effects of neighbor number and sibling (or kin) competition on floral traits in Spergularia marina (Caryophyllaceae)

Abstract.— Effects of abiotic factors on the expression of floral and gender traits have been well documented in wild plant species; by contrast, little is known of the effect(s) on an individual's floral phenotype of the genetic composition of its neighboring conspecifics. Here we report the results of a greenhouse experiment conducted to detect the effects of genetic attributes of an individual's local environment on the expression of floral traits in the selfing annual, Spergularia marina (Caryophyllaceae). First, to test the hypothesis that negative effects of intraspecific competition are stronger when an individual competes with genetically similar individuals than when it competes with unrelated genotypes, we evaluated the effects of the number of nearest-neighbor kin (vs. unrelated individuals) on floral traits. Plants adjacent to two kin produced significantly fewer stamens per flower than plants adjacent to one or no siblings, indicating that kin competition reduced allocation to male function. Second, to test the hypothesis that the genetic diversity of a neighborhood influences the phenotype of a focal plant, we determined whether the number of maternal families represented among an individual's nearest neighbors influences its phenotype. The number of maternal families surrounding a focal plant did not affect floral trait expression. These results suggest that in S. marina , male function is more sensitive than female function to the genetic environment and that as an individual's genetic similarity to its neighbors increases, so do the negative effects of competition for limited resources.     

Microsatellite markers for the Indian golden silkmoth, Antheraea assama (Saturniidae: Lepidoptera)

Antheraea assama, an economically important and scientifically unexplored Indian wild silkmoth, is unique among saturniid moths. For this species, a total of 87 microsatellite markers was derived from 35 000 expressed sequence tags and a microsatellite‐enriched sub‐genomic library. Forty individuals collected from Tura and West Garo Hills region of Northeast India were screened for each of these loci. Ten loci from expressed sequence tags and one from genomic library were found to be polymorphic. These microsatellite markers will be useful resources for population genetic studies of A. assama and other closely related species of saturniids. This is the first report on development of microsatellite markers for any saturniid species.     

Relationships between seed germinability of Spergularia marina (Caryophyllaceae) and the formation of zonal communities in an inland salt marsh

BACKGROUND AND AIMS: The formation of zonal communities may be attributed to differences in germination across the community and to timing of germination of seeds present in the seed bank. Our goals were two-fold: (1) to assess the annual germination pattern of Spergularia marina; and (2) to determine whether germination of S. marina differed across zonal communities. METHODS: Fresh seeds were buried in an experimental garden in polyester bags. Bags were harvested monthly for 1 year and exposed to differing 12 h/12 h temperature regimes (5/15 degrees C, 5/25 degrees C, 15/25 degrees C and 20/35 degrees C) with a 12 h dark/12 h light photoperiod. Replicate seeds were exposed to 24 h dark. Seeds were also placed in different zonal communities to assess germinability in the field. KEY RESULTS: Spergularia marina has a primary physiological dormancy. Conditional dormancy occurs from December to May and non-dormancy from June to November. Field germination initiates in the spring when temperatures are cool and salinity is low due to flooding, and ceases in the summer when temperatures exceed germination requirements. Spergularia marina has a light requirement for germination. CONCLUSIONS: If seeds become buried in the field or are light inhibited by Phragmites australis, they will remain dormant until they receive an adequate amount of light for germination. Since S. marina can germinate across all zones in a salt-marsh community, the formation of zonal communities is not determined at the germination stage, but at some later stage of development.     

Microsatellite markers for Sachalin fir (Abies sachalinensis Masters)

We developed eight polymorphic microsatellite markers from the Sachalin fir (Abies sachalinensis Masters). The number of alleles per locus ranged from eight to 31, with an average of 21.4. The observed and expected heterozygosities ranged from 0.656 to 0.937 and from 0.710 to 0.945, respectively. These markers will be available for population genetic studies and parentage analysis.     

Microsatellite markers for northern red oak (Fagaceae: Quercus rubra)

We provide primer sequences for 14 (GA) _n microsatellite loci developed from northern red oak, an important timber species. We screened loci using two sets of samples. A parent–offspring set included DNA from seven acorns collected from one mother tree along with maternal DNA, to determine that all progeny carried a maternal allele at each locus. The other set was comprised of 10 adult trees sampled from Indiana old‐growth forest, providing a measure of diversity revealed by each locus.     

Isolation and characterization of nine microsatellite markers for Brachypodium sylvaticum (Huds.) Beauv., a recently invasive grass species in Oregon

The patterns of genetic diversity caused by rapid range expansions following recent colonizations are best observed using highly polymorphic genetic markers. We characterized nine microsatellite markers for Brachypodium sylvaticum, a bunchgrass invasive in the Northwestern United States and native to Eurasia. Loci exhibited from two to 10 alleles, and generally had high F(IS) values. These loci will help identify sources of new populations in the region, and they will be useful for studying patterns of genetic diversity during rapid range expansions.     

Development and cross-species/genera transferability of microsatellite markers discovered using 454 genome sequencing in chokecherry (Prunus virginiana L.)

Chokecherry (Prunus virginiana L.) (2n?=?4x?=?32) is a unique Prunus species for both genetics and disease-resistance research due to its tetraploid nature and X-disease resistance. However, no genetic and genomic information on chokecherry is available. A partial chokecherry genome was sequenced using Roche 454 sequencing technology. A total of 145,094 reads covering 4.8?Mbp of the chokecherry genome were generated and 15,113 contigs were assembled, of which 11,675 contigs were larger than 100?bp in size. A total of 481 SSR loci were identified from 234 (out of 11,675) contigs and 246 polymerase chain reaction (PCR) primer pairs were designed. Of 246 primers, 212 (86.2?%) effectively produced amplification from the genomic DNA of chokecherry. All 212 amplifiable chokecherry primers were used to amplify genomic DNA from 11 other rosaceous species (sour cherry, sweet cherry, black cherry, peach, apricot, plum, apple, crabapple, pear, juneberry, and raspberry). Thus, chokecherry SSR primers can be transferable across Prunus species and other rosaceous species. An average of 63.2 and 58.7?% of amplifiable chokecherry primers amplified DNA from cherry and other Prunus species, respectively, while 47.2?% of amplifiable chokecherry primers amplified DNA from other rosaceous species. Using random genome sequence data generated from next-generation sequencing technology to identify microsatellite loci appears to be rapid and cost-efficient, particularly for species with no sequence information available. Sequence information and confirmed transferability of the identified chokecherry SSRs among species will be valuable for genetic research in Prunus and other rosaceous species. Key message A total of 246 SSR primers were identified from chokecherry genome sequences. Of which, 212 were confirmed amplifiable both in chokecherry and other 11 other rosaceous species.