Species in the genus Engraulis show extensive intraspecific as well as interspecific morphological and genetic diversity. Since morphological differences do not necessarily correspond to genetic differences, it is necessary to clarify the relationship between morphological differences and genetic differences for a better understanding of the population structure. Fish morphology at a given standard length differs between cohorts of Japanese anchovy Engraulis japonicus during the early life stages in the Kii Channel, but it is unknown whether the differences are caused by genetic differences or not. The Kii Channel includes the boundary between the Pacific (southern side of the Kii Channel) and the Seto Inland Sea stocks (northern side), but stock separation is based primarily on demographic characteristics. In the present study, genetic analyses were conducted to examine the genetic differences among samples (month and area) based on mitochondrial DNA cytochrome b region (Cyt b), control region (CR) and microsatellite markers. AMOVA revealed that the percentage of genetic variation among samples was low at 0.11% for Cyt b, 0.30% for CR and 0.00% for microsatellite, and no significant genetic variation was observed among samples. Although two clades were identified in the unrooted neighbour-joining tree for Cyt b and CR, both Cyt b and CR sequences were similar between months and between areas. Accordingly, the morphological differences among cohorts can be attributed to phenotypic plasticity. Additionally, there were no genetic differences between samples from the southern side and the northern side of the Kii Channel, suggesting strong genetic connectivity in these areas.

Identification of sugarcane hybrids is difficult when selections are based solely on morphological traits. Our objective was to combine morphological traits and molecular marker analysis to select F1 hybrids from two separate crosses between Djatiroto, a clone of Saccharum spontaneum, and elite sugarcane clones, LCP 85-384 (Cross 97-3144) and CP 62-258 (Cross 97-3146). The maternal inflorescences of Djatiroto were emasculated by submersion in a circulating 45°C hot-water tank for 10 min to minimize self-fertilization. Cross 97-3144 produced 4.7 g of seeds with 338 viable seeds per gram and Cross 97-3146 produced 2.4 g of seeds with 166 viable seeds per gram. After greenhouse germination, 96 progeny from each cross were evaluated in a field plot. Evaluations were conducted on the ratoon crops for stalk diameter (mm), juice Brix (percentage soluble solids), and a randomly amplified polymorphic DNA (RAPD) marker OPA-11-366 that was reproducibly amplified through PCR from the elite clones, but not the maternal S. spontaneum clone. Fifty progeny (52.1%) from Cross 97-3144 and 36 progeny (37.5%) from Cross 97-3146 inherited the RAPD marker. Five putative F1 progeny were selected from each cross, namely US 99-43, US 99-44, US 99-45, US 99-46 and US 99-47 from Cross 97-3144, and US 99-48, US 99-49, US 99-50, US 99-51 and US 99-52 from Cross 97-3146, based on their relatively larger stalk diameter, higher Brix and inheritance of the RAPD marker. The hybrid nature of these selected progeny was verified with sugarcane microsatellite markers. This is the first report of the development of Saccharum hybrids with the cytoplasm of S. spontaneum for breeding purpose through a combination of conventional and molecular breeding approaches. Availability of these F1 hybrids could enhance the genetic diversity of Saccharum germplasm and has enabled sugarcane geneticists and breeders to explore the possible contribution of S. spontaneum cytoplasm in the development of new sugarcane cultivars.

An important route of introduction of some nonnative species that subsequently become invasive in the United States is through horticulture. One such plant is Euonymus fortunei (Turcz.) Hand.-Maz., commonly known as wintercreeper, an evergreen groundcover with more than 52 different horticultural varieties, which is still sold at many plant nurseries and garden centers in the midwestern United States. Although several states have recognized E. fortunei as an invasive species, it is unknown how its escape from cultivation has occurred and even the identity of spreading populations, including whether hybrids or cultivars are involved. Using codominant microsatellite markers, we sampled multiple invasive populations in Ohio, Kentucky, Kansas, and Minnesota and compared their genotypes with commercially available cultivars to determine how spread has occurred. All samples collected from invasive populations were genetically identical to one another and matched perfectly with the ‘Coloratus’ cultivar, the only cultivar to exhibit polyploidy. The data also suggest that E. fortunei may potentially reproduce via apomixis and/or clonally through propagule fragments, which can quickly fix favorable genotypes within a population. To curb continued invasive spread, we suggest that Coloratus be removed from commercial sale and distribution. We also propose that land managers, horticultural and landscaping businesses, and governmental agencies carefully monitor other Euonymus cultivars for invasive potential and spread.

Muskmelon, which is an important cucurbit of the tropical and subtropical region of the world, shows great diversity, with six different botanical or horticultural groups and fifteen varietal groups. In this study, a total of fifty (50) simple sequence repeat (SSR) markers were used to investigate the genetic diversity and population structure of 46 muskmelon accessions of different horticultural or varietal groups. Thirty-eight (38) of the fifty SSR markers were highly polymorphic. A total of 99 alleles were generated by the polymorphic markers, with an average of 2.06 alleles per loci. Heterozygosity among accessions for individual loci varied from 0.00 to 0.21, with the highest (0.21) reported for the CMCTN71 marker. The gene diversity and polymorphism information content (PIC) values varied between 0.08 to 0.72 and 0.07 to 0.67, with an average of 0.47 and 0.38, respectively. The primer that showed the highest gene diversity and PIC values was DM0913. The unweighted pair-group method for arithmetic average (UPGMA)-based dendrogram classified all the 46 accessions into two major clusters. Population structure analysis classified 46 muskmelon accessions into 2 subpopulations. The subpopulation I contained 29 accessions from the cantalupensis group, and subpopulation II contained 17 accessions from momordica, inodorus and conomon groups, respectively. Analysis of variance indicated that 18 and 68% of variance was due to subpopulations and differences among individuals, respectively. The present study supports the existence of sufficient variation among musk melon genetic resources in India, and their classification based on molecular markers will be helpful to accelerate the breeding programme for specific traits.

Oaks are model species due to their importance in various ecosystems, worldwide distribution, high economic value and emerging genomic resources. As such, knowledge on population differentiation across their distribution range is of high importance for sustainable forest management. As in most angiosperms, chloroplasts are maternally (via seeds) inherited in oak species and acorns are dispersed over comparably short distances. Consequently, chloroplast markers reveal comparatively high differentiation between populations, making them highly viable for the analysis of historic migration patterns and the certification of reproductive material. Despite the existence of various white oak (section: Quercus) chloroplast markers, red oak (section: Lobatae) chloroplast markers remain limited. Northern red oak is one of the most important North American oak species and a widespread non-native plantation tree species in European forests. We took advantage of chloroplast genomes of Q. rubra L. and related oak chloroplast genomes to develop a set of robust and easy-to-use chloroplast microsatellite primers for northern red oak. Furthermore, we tested transferability of those novel red oak primer pairs to Q. robur L. and Q. petraea Matt. Liebl. The new set of fifteen polymorphic chloroplast microsatellite markers revealed three additional northern red oak haplotypes after screening 80 northern red oak individuals representing seven haplotypes, identified based on formerly available markers. Therefore, they provide a higher resolution of haplotypes as compared to currently available markers.

Genetic structure may be highly variable across seabird species, and particularly among those that are distributed over large geographical areas. The Adélie penguin (Pygoscelis adeliae) is a numerically dominant Antarctic seabird that is considered to be a key species in coastal ecosystems. Since the Last Glacial Maximum, penguin colonization of the Antarctic coastline occurred at varying geographical and temporal scales, contributing to an incomplete understanding of how modern colonies relate to each other at local or regional scales. We assessed the population genetic structure of Adélie penguins (n = 86 individuals) from three adjacent colonies along the Victoria Land coast using molecular genetic markers (i.e. seven microsatellite loci isolated through next-generation sequencing). Our results indicate meta-population dynamics and possibly relationships with habitat quality. A generally low genetic diversity (Nei's index: 0.322–0.667) was observed within each colony, in contrast to significant genetic heterogeneity among colonies (pairwise FST = 0.071–0.148), indicating that populations were genetically structured. Accordingly, an assignment test correctly placed individuals within the respective colonies from which they were sampled. The presence of inter-colony genetic differentiation contrasts with previous studies on this species that showed a lack of genetic structure, possibly due to higher juvenile or adult dispersal. Our sampled colonies were not panmictic and suggest a lower migration rate, which may reflect relatively stable environmental conditions in the Ross Sea compared to other regions of Antarctica, where the ocean climate is warming.

This paper provides a solution to the active vibration control of a microsatellite with two solar panels. At first, the microsatellite is processed as a finite element model containing a rigid body and two flexible bodies, according to the principles of mechanics, and that the dynamic characteristics are solved by modal analysis. Secondly, the equation involving vibration control is established according to the finite element calculation results. There are several actuators composed of macro fibre composite on the two solar panels for outputting control force. Furthermore, the control voltage for driving actuator is calculated by using fuzzy algorithm. It is clear that the smart structure consists of the flexible bodies and actuators. Finally, the closed-loop control simulation for suppressing harmful vibration is established. The simulation results illustrate that the responses to the external excitation are decreased significantly after adopting fuzzy control.

Introduced from Europe to North America in the early 19th century as an ornamental shrub and for medicinal purposes, common buckthorn (Rhamnus cathartica L.) has since spread and naturalized throughout regions of the United States and Canada. The purpose of this study was to investigate levels of genetic variation and population differentiation in R.cathartica in its introduced range in North America compared with its native range in Europe to better understand patterns of spread. By analyzing introduced and native populations using microsatellite markers, we found that introduced populations generally exhibited similar or slightly lower levels of genetic variation compared with native populations, consistent with a slight bottleneck effect. Introduced populations contained many different genotypes, indicating genetic admixture, rather than one or few genotypes. In a few cases, populations had been misidentified in the field and were glossy buckthorn (Frangula alnus Mill.; syn. Rhamnus frangula L.). Overall, there was no substantial genetic differentiation detected between native and introduced populations of R. cathartica. Invasive spread in this species is likely due to its past horticultural history as well as adaptive biological traits such as competitive behavior, potential allelopathy, and seed dispersal via birds.

Two X-linked microsatellites, (AC)n repeats at the monoamine oxidase (MAO) A locus and (TG)n repeats at the MAO-B locus, were typed by using a PCR-based procedure in 89 nuclear families consisting of mothers, fathers and female affected offspring with schizophrenia or mothers and male affected offspring. A haplotype-based haplotype relative risk (HHRR) approach was applied to detect allelic association of these two microsatellites with schizophrenia. In the families of male patients, a significant difference in frequency distribution was found between transmitted and non-transmitted (TG)n repeats (χ2 = 15.13, df = 6, P = 0.019), and Fisher's exact test showed that allelic frequency of the transmitted (TG)24 was significantly higher than that of the non-transmitted (TG)24 (Fisher's P = 0.003). However, no significant differences in frequency distribution between mother- or father-transmitted and non-transmitted (TG)n repeats were found in the families of female patients. No significant differences in frequency distribution were found between transmitted and non-transmitted (AC)n repeats in the families of either male patients or female patients. The present study suggests that the MAO-B gene may be associated with schizophrenia, and the underlying genetic mechanism of schizophrenia may differ between male and female schizophrenic individuals.

Invasions can be genetically diverse, and that diversity may have implications for invasion management in terms of resistance or tolerance to control methods. We analyzed the population genetics of Russian-olive (Elaeagnus angustifolia L.), an ecologically important and common invasive tree found in many western U.S. riparian areas. We found three cpDNA haplotypes and, using 11 microsatellite loci, identified three genetic clusters in the 460 plants from 46 populations in the western United States. We found high levels of polymorphism in the microsatellites (5 to 15 alleles per locus; 106 alleles total). Our native-range sampling was limited, and we did not find a genetic match for the most common cpDNA invasive haplotype or a strong confirmation of origin for the most common microsatellite genetic cluster. We did not find geographic population structure (isolation by distance) across the U.S. invasion, but we did identify invasive populations that had the most diversity, and we suggest these as choices for initial biological control–release monitoring. Accessions from each genetic cluster, which coarsely represent the range of genetic diversity found in the invasion, are now included in potential classical biological control agent efficacy testing.

The plerocercoid (sparganum) of Spirometra erinaceieuropaei is the main aetiological agent of human sparganosis. To improve the current knowledge on S. erinaceieuropaei evolution, we performed multi-locus microsatellite typing of sparganum isolates from China for the first time. All available expressed sequence tag (EST) sequences for the Spirometra were downloaded from the GenBank. The identification and localization of microsatellites in ESTs was accomplished by MISA. Based on the selected microsatellites, the genetic structure of 64 sparganum isolates collected from 11 geographical locations in southwest China were investigated through principal component analysis, STRUCTURE analysis and neighbour-joining clustering. A total of 522 non-redundant ESTs containing 915 simple sequence repeats were identified from 12 481 ESTs screened. Five primer pairs were finally selected. Using these loci, a total of 12 alleles were detected in 64 sparganum isolates. Little variability was observed within each of geographical population, especially among isolates derived from Kunming of Yunnan (YN-KM) province. Both STRUCTURE analysis and the clustering analysis supported that two genotypes existed among the sparganum isolates from southwest China. In conclusion, five microsatellite markers were successfully developed, and sparganum population was observed to harbour low genetic variation, further investigation with deeper sampling was needed to elucidate the population structure.

Camellia oleifera is an important woody plant producing healthy edible oils. People need a large number of molecular markers, especially microsatellite, in breeding of C. oleifera. In this study, we sequenced the root transcriptomes of C. oleifera, and then designed a novel set of microsatellite markers based on the root-expressed genes. We assembled a total of 57,121 unigenes with a length of 42.63 Mb, which harboured 15,902 microsatellites. Among these microsatellites, di-nucleotide repeat motifs were the most abundant group (56.45%), then followed by tri- (25.20%), mono- (12.12%), hexa- (3.21%), penta- (2.18%) and quad-nucleotide ones (0.84%). In total, 6738 primer pairs were designed successfully to amplify the microsatellite loci. To test these microsatellite markers, 48 primer pairs were randomly selected and synthesized and validated in C. oleifera and its eight relatives. Up to 75% of the primer pairs amplified in C. oleifera and its relatives, and 62.5% displayed polymorphism. The transferability and diverse alleles across its eight relatives were detected for each polymorphic primer pair. The novel set of microsatellites derived from the root transcriptomes here provided a useful resource for future molecular genetics improvement of C. oleifera and its relatives.

The genus Narcissus L. (Amaryllidaceae) provides a model system to study the evolution and maintenance of sexual polymorphisms. In this study, we characterized microsatellite markers for N. dubius, N. cuatrecasasii, N. assoanus and N. rupicola for studies of genetic diversity and paternity analyses to investigate the stability of stylar dimorphism. We proved 40 new primer pairs from a genomic library of N. papyraceus and 12 microsatellite markers characterized also for N. papyraceus in a previous study (52 primer pairs overall). Twenty markers amplified, but their transferability and variability were different among species. Polymorphism was tested at least on 74 individuals and one population per species. The number of polymorphic loci per species ranged from four to eight. The number of alleles per locus ranged from two to 19 and the observed heterozygosity and gene diversity, from 0.107 to 0.729 and 0.103 to 0.894, respectively. These markers can be used for studies of genetic diversity and paternity analyses among individuals of N. dubius, N. cuatrecasasii, N. assoanus and N. rupicola to study the stability of stylar dimorphism.

Digitaria exilis is an important indigenous cereal in West Africa. The first fonio reference transcriptome was released and became a key tool for developing new molecular markers contributing to a better understanding of its genetic diversity. A total of 126 new putative primer pairs were successfully designed in 37,327 unigenes from the D. exilis transcriptome. Thirty-seven primer pairs were randomly selected and tested for their ability to cross-amplify to related species. Clear amplification patterns were observed on 24 primer pairs. Of these, 71, 74 and 35% showed polymorphism in three species: D. exilis, D. longiflora and D. iburua. The transferability from D. exilis was 96% to D. longiflora and 71% to D. iburua. The new SSR markers confirmed the close genetic proximity of D. exilis with D. longiflora and its stronger genetic difference of D. exilis from D. iburua. These markers will be valuable for completing future knowledge on Digitaria evolutionary history, and for testing gene flows between related species.

The white-backed planthopper, Sogatella furcifera (Horváth) (Hemiptera, Delphacidae), has emerged as a serious rice pest in Asia. In the present study, 12 microsatellite markers were employed to investigate the genetic structure, diversity and migration route of 43 populations sampled from seven Asian countries (Bangladesh, China, Korea, Laos, Nepal, Thailand, and Vietnam). According to the isolation by distance analysis, a significant positive correlation was observed between genetic and geographic distances by the Mantel test (r2 = 0.4585, P = 0.01), indicating the role of geographic isolation in the genetic structure of S. furcifera. A population assignment test using the first-generation migrants detection method (thresholds a = 0.01) revealed southern China and northern Vietnam as the main sources of S. furcifera in Korea. Nepal and Bangladesh might be additional potential sources via interconnection with Vietnam populations. This paper provides useful data for the migration route and origin of S. furcifera in Korea and will contribute to planthopper resistance management.

We developed novel and polymorphic microsatellite primers for Spathoglottis plicata, a tropical and subtropical terrestrial orchid, to investigate the genetic patterns and population structure among wild populations, and also to identify the varieties and hybrids of S. plicata in horticultural industry. The 12 novel microsatellites from S. plicata were developed by using polymerase chain reaction (PCR)-based isolation of microsatellite arrays. These markers that were successfully PCR amplified exhibited polymorphisms in S. plicata. The number of alleles, observed heterozygosity, expected heterozygosity and polymorphism information content values across loci ranged from 2.000 to 8.000, 0.000 to 0.756, 0.208 to 0.813 and 0.405 to 0.805 in total populations, respectively. The newly developed microsatellite markers exhibited variation in S. plicata. These markers can be used as a tool to further investigate the genetic diversity, conservation genetics and variety/hybrid identification of S. plicata.

Genome sequencing has greatly contributed to our understanding of parasitic protozoa. This is particularly the case for Cryptosporidium species (phylum Apicomplexa) which are difficult to propagate. Because of their polymorphic nature, simple sequence repeats have been used extensively as genotypic markers to differentiate between isolates, but no global analysis of amino acid repeats in Cryptosporidium genomes has been reported. Taking advantage of several newly sequenced Cryptosporidium genomes, a comparative analysis of single-amino-acid repeats (SAARs) in seven species was undertaken. This analysis revealed a striking difference between the SAAR profile of the gastric and intestinal species which infect mammals and one species which infects birds. In average, total SAAR length in gastric species is only 25% of the cumulative SAAR length in the genome of Cryptosporidium parvum, Cryptosporidium hominis and Cryptosporidium meleagridis, species infectious to humans. The SAAR profile in the avian parasite Cryptosporidium baileyi stands out due to the presence of long asparagine repeats. Cryptosporidium baileyi proteins with repeats ⩾20 residues are significantly enriched in regulatory functions. As postulated for the related apicomplexan species Plasmodium falciparum, these observations suggest that Cryptosporidium SAARs evolve in response to selective pressure. The putative selective mechanisms driving SAAR evolution in Cryptosporidium species are unknown.

Compared with conventional identification methods, DNA-based genetic approaches such as single nucleotide polymorphisms (SNPs) and satellites are much more reliable for pig identification and meat traceability. In this study, multiallelic amplification fragments with multiple SNPs, incorporating the advantages of both SNPs and microsatellites, were explored for the first time for pig identification and meat traceability. Primer pairs for multiallelic fragments and their optimal SNPs were successfully selected and used for identification of individuals from Suzhong and Duroc populations. Meanwhile, the combined panel of the above mentioned primer pairs together with their optimal SNPs for Suzhong and/or Duroc pigs were validated for identification of the hybrids (Suzhong×Duroc). Therefore, we have successfully selected multiallelic amplification fragments with multiple SNPs to identify pigs and their meat samples from Suzhong, Duroc or their hybrids. Our study demonstrates that our method is more powerful for pig identification or meat traceability than SNPs or microsatellites.