Microsatellite Development Research Articles

Comprehensive Review of RF MEMS Switches in Satellite Communications.

The miniaturization and low power consumption characteristics of RF MEMS (Radio Frequency Microelectromechanical System) switches provide new possibilities for the development of microsatellites and nanosatellites, which will play an increasingly important role in future space missions. This paper provides a comprehensive review of RF MEMS switches in satellite communication, detailing their working mechanisms, performance optimization strategies, and applications in reconfigurable antennas. It explores various driving mechanisms (electrostatic, piezoelectric, electromagnetic, thermoelectric) and contact mechanisms (capacitive, ohmic), highlighting their advantages, challenges, and advancements. The paper emphasizes strategies to enhance switch reliability and RF performance, including minimizing the impact of shocks, reducing driving voltage, improving contacts, and appropriate packaging. Finally, it discusses the enormous potential of RF MEMS switches in future satellite communications, addressing their technical advantages, challenges, and the necessity for further research to optimize design and manufacturing for broader applications and increased efficiency in space missions. The research findings of this review can serve as a reference for further design and improvement of RF MEMS switches, which are expected to play a more important role in future aerospace communication systems.

Development of genome-wide microsatellites from Primula denticulata and their utility in different species of the genus

The genus Primula (Primulaceae) harbours habitat-sensitive species. It is a valuable tool for monitoring and assessing the overall state of the ecosystem as it can serve as a reliable indicator of ecological health. Primula denticulata Sm. is one of the most prevalent Primrose species found in the Indian Himalayan region with a wide extent of distribution from 1500 m to 3500 m altitude. Considering the ecological importance of Primulas, it is imperative to develop microsatellite markers to study genetic variability which can offer valuable insights into the adaptive strategies of the plants in response to changing environmental conditions. In this study, we sequenced the P. denticulata genome by utilizing Illumina paired-end sequencing technology at ∼15X coverage. 27,196 sequences harbouring 31,584 microsatellite loci were identified. 100 primer pairs were synthesized and tested for amplification. Impressively, 84 of these primers exhibited robust amplification, and 64 of these displayed polymorphism. Primer pairs from trinucleotide motifs were identified as more polymorphic. To assess the broader applicability of these primers, we also tested cross-species transferability on 14 different Primula species representing different sections of the genus that were collected from different parts of Himalaya. Notably, one SSR locus, Next Generation Sequencing Primula_5 (NGSPr_5) was able to produce bands in all the species showing 100 % transferability. Primula atrodentata showed a maximum (88.23 %) while P. glabra exhibited minimum (19.60 %) cross-transferability. The UPGMA dendrogram clustered different sections of sub-genus Aleuritia, and species from subgenera Sphondylia and Auganthus separately into two major groups. The groupings are in accordance with the known relationship between the different species from the genus.

Characterization of 23 microsatellite markers and development of multiplex PCRs for the Amur viper Gloydius saxatilis (Viperidae) and cross-species amplification in other Gloydius species

Characterization of 23 microsatellite markers and development of multiplex PCRs for the Amur viper Gloydius saxatilis (Viperidae) and cross-species amplification in other Gloydius species

Genome-wide in silico characterization, validation, and cross-species transferability of microsatellite markers in Mallard and Muscovy ducks

BackgroundMicrosatellites are important markers for livestock including ducks. The development of microsatellites is expensive and labor-intensive. Meanwhile, the in silico approach for mining for microsatellites became a practicable alternative. Therefore, the current study aimed at comparing whole-genome and chromosome-wise microsatellite mining approaches in Muscovy and Mallard ducks and testing the transferability of markers between them. The GMATA software was used for the in silico study, and validation was performed using 26 primers. ResultsThe total number of the detected microsatellites using chromosome-wise was 250,053 and 226,417 loci compared to 260,059 and 238,462 loci using whole genome in Mallards and Muscovies. The frequencies of different motifs had similar patterns using the two approaches. Dinucleotide motifs were predominant (> 50%) in both Mallards and Muscovies. The amplification of the genomes revealed an average number of alleles of 5.08 and 4.96 in Mallards and Muscovies. One locus was monographic in Mallards, and two were monomorphic in Muscovies. The average expected heterozygosity was higher in Muscovy than in Mallards (0.45 vs. 0.43) with no significant difference between the two primer sets, which indicated the usefulness of cross-species amplification of different primers. ConclusionThe current study developed a whole-genome SSR panel for ducks for the first time, and the results could prove that using chromosome-wise mining did not generate different results compared to the whole-genome approach.

Polymorphic Microsatellite Development, Genetic Diversity, Population Differentiation and Sexual State of Phytophthora capsici on Commercial Peppers in Three Provinces of Southwest China.

Pepper blight, caused by the oomycete pathogen Phytophthora capsici (P. capsici), is one of the most destructive soilborne diseases worldwide. Between 2019 and 2020, 235 single spore isolates of P. capsici were collected from 36 commercial pepper planting areas in Sichuan, Chongqing, and Guizhou provinces in China. A novel full set of 323 high-quality polymorphic microsatellites was obtained by resequencing 10 isolates. In total, 163 isolates with two alleles per microsatellite locus were used for population analysis and resulted in 156 genotypes on 10 microsatellite loci. The genetic diversity, population differentiation, principal component, genetic structure, and genetic relationships analyses showed an extensive variety of the P. capsici in Sichuan and Guizhou with clonal lineages, two shared genotypes, and no geographic differentiation. The population from Chongqing was differentiated from that of Sichuan and Guizhou and had the highest genetic diversity. There was no significant distinction between the populations of the two sampling years, but there was a small differentiation between the populations from bell peppers and hot peppers. The isolates from Southwest China were largely distant from the two reference isolates from the USA. The analysis of molecular variance showed that the major variance of the populations was within populations. The linkage equilibrium test, mating type composition, and oospore detection indicated that only P. capsici from the Jiulongpo district of Chongqing had appeared in sexual recombination. Overall, this study revealed that the high and complex genetic diversity population of P. capsici in Sichuan, Chongqing, and Guizhou with uneven geographic variation and limited sexual reproductive behavior in Chongqing, potentially driven by differences in the geographical environment, reproductive patterns, different cultivars, and artificial long-distance transfers. IMPORTANCE Phytophthora capsici, a notorious soilborne and rapidly evolving pathogen with a wide range of hosts, is a huge threat to pepper production worldwide. However, the detailed genetic structure and dynamics of P. capsici in most Chinese provinces are still unclear, even though China is the world's largest producer and consumer of peppers. Here, a novel full set of high-quality polymorphic microsatellites, obtained by genome resequencing data of 10 isolates from Southwest China, was provided for future population analyses. In this study, we further investigated and established the genetic structure, sexual recombination, geographic subdivisions, interannual stability, differentiation in different types of host peppers, and member relationships of P. capsici from three provinces in Southwest China. These results reveal the genetic structure and dynamics of P. capsici in three provinces of Southwest China and help us to execute more effective management strategies in the future.

Development and characterization of microsatellite markers for Chaeturichthys stigmatias (Actinopterygii: Gobiiformes: Gobiidae) based on restriction site-associated DNA sequencing (RAD-seq)

Chaeturichthys stigmatias Richardson, 1844, a fish species of the family Gobiidae, is an offshore warm-temperate fish species and a dominant component of estuarine ecosystems. In this study, restriction site-associated DNA sequencing was adopted to analyze the traits of candidate microsatellite markers for C. stigmatias, and 30 polymorphic loci were developed. A total of 5631 microsatellites with primer fragments were detected, among which trinucleotide repeats (57.56% of the total simple sequence repeats) were the most abundant, followed by di- (23.30%), tetra- (11.79%), penta- (4.14%), and hexa- (3.21%) nucleotide repeats type. The numbers of alleles per locus ranged from 6 to 14 with the mean value of 10.4. The mean value of observed heterozygosity and the expected heterozygosity were 0.349 and 0.870, respectively. The microsatellite locus with the lowest polymorphic information content (PIC) was 0.749, which indicated that all sites were highly polymorphic (PIC > 0.50). This is the first microsatellite development and characterization of this species to be reported.

Genetic variation of soybean collection based on microsatellite DNA markers related to plant height

Soybean is a relatively new crop in Kazakhstan, and the development of new competitive cultivars with high productivity and quality is an important direction in the local breeding program. Previously, one of the major approaches for the development of new cultivars was breeding projects based on the evaluation of key morphological traits, including flowering time and plant height (PH). However, with the development of soybean genetics new molecular tools have emerged, including the development of DNA microsatellites, or simple sequence repeats (SSRs). In this study, a collection of hundred accessions grown in the southeast of Kazakhstan in 2020-2021 was assessed using eight agronomic traits, including plant height (PH), the height of lowest pod, number of lateral branches, number of fertile nodes, number of seeds per plant, thousand seeds weight, yield per square meter (YP2), and maturity group. The assessment of field trials showed a wide range of variability in agronomic traits and suggested that PH is significantly correlated with all studied traits, including YP2. The collection was genotyped using eight SSRs associated with PH. The results suggested that three SSRs (Satt244, Satt288, and Satt371) were the most polymorphic, and five out of eight SSRs were associated with six important agronomic traits, including flowering time, PH, and yield per square meters. Obtained results can be efficiently used in soybean breeding based on a marker-assisted selection approach.

AN OVERVIEW ON INNOVATIVE COMPOSITE MATERIALS EMPLOYED IN THE CONSTRUCTION OF MICROSATELLITES

The space industry has a growing interest in microsatellite missions, which are frequently employed in the defense, agriculture, business intelligence, in case of disasters, in communications. The paper presents recent findings from the literature regarding the structure and properties of composite materials, in order to establish the possibilities of their use in the development of microsatellites, in the context of a sustainable development. Innovative composites must have dimensional stability during exposure to thermal cycling in space, low degree of outgassing, high resistance to microcracking, UV radiation, atomic oxygen, proton irradiation and orbital debris.

Mining and characterization of genic-microsatellites associated with sucrose synthesis and their utility in population structure analysis in sugarcane

Sucrose content is a highly valued trait in sugarcane breeding that is regulated by several genes. Tracking of multiple genes involved in the expression of a complex trait in a highly heterozygous crop like sugarcane during the breeding programme is a huge challenge. Trait tagging through expressed sequence tags (ESTs) derived molecular markers has been considered as powerful tool because they are encoded by functionally relevant elements of the genome and directly linked with the target traits. Functional markers related to sucrose content are very limited in sugarcane, which hindered the genetic improvement of this trait. Seventy-three sucrose rich and fifteen low sucrose clones chosen from twelve full-sib families were used for the study on the development and characterization of genic microsatellites associated with sucrose synthesis. A total of 186 alleles were obtained, with an average of 6.20 alleles per microsatellite marker. Polymorphism Information Content (PIC) values were ranged from 0.31 to 0.83, with a mean value of 0.61. The average values of gene diversity (GD) and resolving power (RP) were 0.60 and 5.14, respectively. The present study identified genic SSR markers for four major enzymes viz., CA076844187 (FK), CA155160295 (SREBF), CA163325191,213 (SREBF), TA38405-4547232 (PPFK), and CA135596178, 225 (DFPP) which could be useful to identify sucrose rich clones in the initial testing stages of the selection programme in sugarcane. Analysis of molecular variance (AMOVA) showed 74 per cent of the total variation within population and 26 per cent among population. The EST-SSR primers showed a high allelic polymorphism, as demonstrated by high genetic diversity estimates (I =1.17, Ho = 0.78). The low mean values of fixation index (FST = 0.078) and the high estimates of gene flow (Nm = 4.166) indicates the low level of population differentiation and maximum genetic exchange between two populations. Based on SSR marker data, eighty-eight clonal accessions were classified broadly into high and low sugar population which corresponded to the molecular diversity of the sucrose specific alleles through structure analysis and principal coordinate analysis. Key wordsSugarcane, sucrose content, genic-microsatellites, AMOVA, population structure

Development of genetic tools for the redbait species Pyura herdmani and P. stolonifera, important bioengineers along African coastlines

The development of new genetic resources is key for biological conservation in an era when the preservation of biodiversity is crucial. Here, we report the development of microsatellites and mitochondrial markers for the redbait species Pyura herdmani and P. stolonifera, both important bioengineers along African coastlines. Specifically, we identified microsatellites by means of pyrosequencing and variable regions in the mitochondrial genome using RAD-seq libraries that were generated with Illumina sequencing. A total of 4 339 putative microsatellites were found, of which 32 were tested on individuals collected along the southeast coast of South Africa. Of those, five microsatellites cross-amplified consistently in both species, and these were tested on a total of 260 samples. Additionally, we mapped the partial mitochondrial genome of a small number of individuals from both species and identified the most-variable regions by comparing a small number of individuals from all regions where these species have been recorded (including western South Africa and northwest Africa). The genetic markers developed here can be used to conduct population genetic studies, to monitor range shifts under contemporary climate change, and to help in preserving ecosystem functioning along African coastlines.

Microsatellite characterization and development of unified STR panel for big cats in captivity: a case study from a Seoul Grand Park Zoo, Republic of Korea.

The zoos manage small populations of endangered big cat species like tiger, lion, and leopard for display, research, and conservation breeding. Genetic management of these populations is essential to ensure long term survival and conservation utility. Here we propose a simple and cost effective microsatellite based protocol for the genetic management of captive big cats. We sampled 36 big cat individuals from Seoul Grand Park Zoo (Republic of Korea) and amplified 33 published microsatellite loci. Overall, allelic richness and gene diversity was found highest for leopards, followed by lions and tigers. Twelve of the thirty-three markers showed a high degree of polymorphism across all target species. These microsatellites provide a high degree of discrimination for tiger (1.45 × 10-8), lion (1.54 × 10-10), and leopard (1.88 × 10-12) and thus can be adopted for the genetic characterization of big cats in accredited zoos globally. During captive breeding, zoo authorities rely on pedigree records maintained in studbooks to ensure mating of genetically fit unrelated individuals. Several studies have reported errors in studbook records of big cat species. Microsatellites are simple and cost effective tool for DNA fingerprinting, estimation of genetic diversity, and paternity assessment. Our unified microsatellite panel (12-plex) for big cats is efficient and can easily be adopted by zoo authorities for regular population management.

Development of microsatellite markers for horse-chestnut (Aesculus hippocastanum), their polymorphism in natural Greek populations, and cross-amplification in related species

New nuclear microsatellite markers (SSRs) were developed for Aesculus hippocastanum, a relict tree species from the Balkan Peninsula. The development of microsatellites was done using the Illumina MiSeq PE300 platform. Out of a set of 500 SSRs designed, a subset of 13 loci was tested using 290 individ­uals from seven natural populations. Twelve species-specific loci were polymorphic. The number of alleles per locus ranged from 2 to 17 and expected heterozygosity from 0.089 to 0.800 with a mean value of 0.484. The population of Kalampaka had the lowest value of allelic richness (2.63) and gene diversity in compari­son to the remaining populations. STRUCTURE analysis confirmed isolation of population Mariolata from the southern edge of the species range and genetic similarity among populations from the Pindos Mts. Ad­ditionally, the utility of new SSRs in 29 individuals from nine other Aesculus taxa was tested. Eleven markers gave polymorphic products for all tested species. For 24 individuals, a high-quality product was obtained for each marker. Results confirmed the utility of specific markers for future population genetics studies.

In silico development of microsatellites associated with resistance genes to powdery mildew in Vitis vinifera L.

In silico development of microsatellites associated with resistance genes to powdery mildew in Vitis vinifera L.

In silico microsatellite development based on genome analysis of Vitis vinifera L.

In silico microsatellite development based on genome analysis of <i>Vitis vinifera</i> L.

Fast sequence-based microsatellite genotyping development workflow.

Application of high-throughput sequencing technologies to microsatellite genotyping (SSRseq) has been shown to remove many of the limitations of electrophoresis-based methods and to refine inference of population genetic diversity and structure. We present here a streamlined SSRseq development workflow that includes microsatellite development, multiplexed marker amplification and sequencing, and automated bioinformatics data analysis. We illustrate its application to five groups of species across phyla (fungi, plant, insect and fish) with different levels of genomic resource availability. We found that relying on previously developed microsatellite assay is not optimal and leads to a resulting low number of reliable locus being genotyped. In contrast, de novo ad hoc primer designs gives highly multiplexed microsatellite assays that can be sequenced to produce high quality genotypes for 20–40 loci. We highlight critical upfront development factors to consider for effective SSRseq setup in a wide range of situations. Sequence analysis accounting for all linked polymorphisms along the sequence quickly generates a powerful multi-allelic haplotype-based genotypic dataset, calling to new theoretical and analytical frameworks to extract more information from multi-nucleotide polymorphism marker systems.

Development and characterization of microsatellites from the sweetpotato weevil, Cylas formicarius elegantulus

AbstractTo conduct population genetics analyses on sweetpotato weevils (Cylas formicarius elegantulus) collected from three populations in the United States, microsatellite loci were developed from sweetpotato weevil transcriptome sequences obtained from a publicly available database. Nineteen of 27 microsatellite loci tested were usable for population analyses. Sweetpotato weevil individuals from Georgia (N = 17), Hawaii (N = 16) and South Carolina (N = 12) were analysed. Here, we present microsatellite primer sequences for 19 loci and population genetics statistics, including diversity, population differences and relatedness. Thirty‐nine alleles were detected in the 45 individuals, and four private alleles were observed in individuals from the Hawaii and South Carolina populations. Observed heterozygosities ranged from 0.00 to 1.00, and expected heterozygosities ranged from 0.00 to 0.44. The mean Shannon's information index ranged from 0.30 to 0.49 for the three populations. Pairwise differences among populations (FST estimates) from individuals ranged from a low of 0.022 between Georgia and Hawaii to a high of 0.036 between Georgia and South Carolina, and cluster analysis (PCA and Structure) indicated two populations independent of geographical location.

First development and characterization of 27 novel microsatellite markers in the dobsonfly Neoneuromus ignobilis (Megaloptera: Corydalidae) at genome-scale level

The dobsonfly species Neoneuromus ignobilis Navas (Megaloptera: Corydalidae) is endemic to but widely distributed from eastern and southeastern Asia, being an important insect indicator for freshwater biomonitoring. At present, there is no report on the development of microsatellites of Megaloptera. Here, we developed 27 novel microsatellite markers of N. ignobilis from 850,920 candidate microsatellites with the stringent screening criteria considering the amplification success rate, the presence or absence of stutter peaks, the peak intensity, the polymorphism of the loci, the heterozygosity, and the number of alleles. The allele number of 27 microsatellite markers ranges from 3 to 12 with an average value of 6.19 per locus. The observed heterozygosity (HO) and expected heterozygosity (HE) revealed a range from 0.000 to 0.947 and 0.000 to 0.842, respectively. We constructed three panels (MP panel, most polymorphic; SS panel, most stringent strategy; ALL panel, total 27 microsatellite markers) and compared the analyses on population genetic diversity and structure. The result showed that the MP panel can significantly improve the analyses of individual assignment and genetic diversity. Accordingly, we advocate selecting the most polymorphic microsatellite marker for analyzing population genetics based on microsatellite data. The present work represents the first study on the microsatellite development of Megaloptera.

A Novel Software and Method for the Efficient Development of Polymorphic SSR Loci Based on Transcriptome Data.

Traditional methods for developing polymorphic microsatellite loci without reference sequences are time-consuming and labor-intensive, and the polymorphisms of simple sequence repeat (SSR) loci developed from expressed sequence tag (EST) databases are generally poor. To address this issue, in this study, we developed a new software (PSSRdt) and established an effective method for directly obtaining polymorphism details of SSR loci by analyzing diverse transcriptome data. The new method includes three steps, raw data processing, PSSRdt application, and loci extraction and verification. To test the practicality of the method, we successfully obtained 1940 potential polymorphic SSRs from the transcript dataset combined with 44 pea aphid transcriptomes. Fifty-two SSR loci obtained by the new method were selected for validating the polymorphic characteristics by genotyping in pea aphid individuals. The results showed that over 92% of SSR loci were polymorphic and 73.1% of loci were highly polymorphic. Our new software and method provide an innovative approach to microsatellite development based on RNA-seq data, and open a new path for the rapid mining of numerous loci with polymorphism to add to the body of research on microsatellites.

Identification and evaluation of a core microsatellite panel for use in white-tailed deer (Odocoileus virginianus)

BackgroundMicrosatellite loci have been used extensively over the past two decades to study the genetic characteristics of non-model species. The ease of microsatellite development and ability to adapt markers from related species has led to the proliferation of available markers for many commonly studied species. Because it is often infeasible to genotype individuals across all available loci, researchers generally rely on subsets of markers. Marker choice can bias inferences made using disparate suites of loci. This has been a primary motivation for efforts to identify uniform marker panels. Here, we use the geographic distribution of previous studies to identify microsatellite loci for white-tailed deer (Odocoileus virginianus) with the potential for widespread use, and we evaluate the effectiveness of this panel in a portion of the range where few previous studies have been conducted. The purpose was to consolidate the numerous genetic resources for this species into a manageable panel and to provide a uniform methodology that improves comparisons between past and future studies.ResultsWe reviewed microsatellite panels from 58 previous or ongoing projects and identified 106 candidate loci. We developed a multiplex protocol and evaluated the efficacy of 17 of the most commonly used loci using 720 DNA samples collected from the Mid-Atlantic region of the United States of America. Amplification errors were detected in six of these loci. The 11 remaining loci were highly polymorphic, exhibited low frequencies of null alleles, and were easy to interpret with the aid of allele binning software.ConclusionsThe development of broadly-applicable, core microsatellite panels has the potential to improve repeatability and comparative ability for commonly studied species. The properties of the consolidated 11 microsatellite panel suggest that they are applicable for many common research objectives for white-tailed deer. The geographic distribution of previous studies using these markers provides a greater degree of confidence regarding the robustness to common sources of error related to amplification anomalies, such as null alleles, relative to loci with more limited use. While this does not replace further evaluation of genotyping errors, it does provide a common platform that benefits future research studies.

Development and characterization of polymorphic microsatellite markers in northern fulmar, Fulmarus glacialis (Procellariiformes), and cross-species amplification in eight other seabirds.

In the North Pacific, northern fulmar (Fulmarus glacialis) forms extensive colonies in few locales, which may lead to limited gene flow and locale-specific population threats. In the Atlantic, there are thousands of colonies of varying sizes and in Europe the species is considered threatened. Prior screens and classical microsatellite development in fulmar failed to provide a suite of markers adequate for population genetics studies. The objective of this study was to isolate a suite of polymorphic microsatellite loci with sufficient variability to quantify levels of gene flow, population affinity, and identify familial relationships in fulmar. We also performed a cross-species screening of these markers in eight other species. We used shotgun sequencing to isolate 26 novel microsatellite markers in fulmar to screen for variability using individuals from two distinct regions: the Pacific (Chagulak Island, Alaska) and theAtlantic (Hafnarey Island, Iceland). Polymorphism was present in 24 loci in Chagulak and 23 in Hafnarey, while one locus failed to amplify in either colony. Polymorphic loci exhibited moderate levels of genetic diversity and this suite of loci uncovered genetic structuring between the regions. Among the other species screened, polymorphism was present in one to seven loci. The loci yielded sufficient variability for use in population studies and estimation of familial relationships; as few as five loci provide resolution to determine individual identity. These markers will allow further insight into the global population dynamics and phylogeography of fulmars. We also demonstrated some markers are transferable to other species.