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19 results for “SSRs”
Data from: "Discovery and characterization of 80 SNPs and 1,624 SSRs in the transcriptome of Atlantic mackerel (Scomber scombrus, L)" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015
This paper reports on SNP discovery in the Atlantic mackerel transcriptome, using next generation sequencing technologies and applying developed methodology already proven successful for the European anchovy. A total of 9,966 high quality transcriptome contigs were assembled, from which 951 putative SNPs were discovered. In all, 479 putative SNPs and 1,624 simple sequence repeats (SSRs) suitable for genotyping were identified. A subset of 96 was selected for genotyping; from these, 80 SNPs were considered polymorphic and reliably scored after genotyping of 105 individuals from three locations in the Eastern Atlantic Ocean. These markers will be valuable for future studies on population genetic structure assessment and for product tracing.
Data from: "Discovery and characterization of 80 SNPs and 1,624 SSRs in the transcriptome of Atlantic mackerel (Scomber scombrus, L)" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015
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Data from: Identification and analysis of novel salt responsive candidate gene based SSRs (cgSSRs) from rice (Oryza sativa L.)
Background: Majority of the Asian people depend on rice for nutritional energy. Rice cultivation and yield are severely affected by soil salinity stress worldwide. Marker assisted breeding is a rapid and efficient way to develop improved variety for salinity stress tolerance. Genomic microsatellite markers are an elite group of markers, but there is possible uncertainty of linkage with the important genes. In contrast, there are better possibilities of linkage detection with important genes if SSRs are developed from candidate genes. To the best of our knowledge, there is no such report on SSR markers development from candidate gene sequences in rice. So the present study was aimed to identify and analyse SSRs from salt responsive candidate genes of rice. Results: In the present study, based on the comprehensive literature survey, we selected 220 different salt responsive genes of rice. Out of them, 106 genes were found to contain 180 microsatellite loci with, tri-nucleotide motifs (56%) being most abundant, followed by di-(41%) and tetra nucleotide (2.8%) motifs. Maximum loci were found in the coding sequences (37.2%), followed by in 5′UTR (26%), intron (21.6%) and 3′UTR (15%). For validation, 19 primer sets were evaluated to detect polymorphism in diversity analysis among the two panels consisting of 17 salt tolerant and 17 susceptible rice genotypes. Except one, all primer sets exhibited polymorphic nature with an average of 21.8 alleles/primer and with a mean PIC value of 0.28. Calculated genetic similarity among genotypes was ranged from 19%-89%. The generated dendrogram showed 3 clusters of which one contained entire 17 susceptible genotypes and another two clusters contained all tolerant genotypes. Conclusion: The present study represents the potential of salt responsive candidate gene based SSR (cgSSR) markers to be utilized as novel and remarkable candidate for diversity analysis among rice genotypes differing in salinity response.
Data from: Level of genetic differentiation affects relative performances of EST- and genomic SSRs
Microsatellites, also called simple sequence repeats (SSRs) are markers of choice to estimate relevant parameters for conservation genetics, such as migration rates, effective population size and kinship. Cross-amplification of SSRs is the simplest way to obtain sets of markers and highly conserved SSRs have recently been developed from Expressed Sequence Tags (EST) to improve SRR cross-species utility. As EST-SSRs are located in coding regions, the higher stability of their flanking regions reduces the frequency of null alleles and improves cross-species amplification. However, EST-SSRs have generally less allelic variability than genomic SSRs, potentially leading to differences in estimates of population genetic parameters such as genetic differentiation. To assess the potential of EST-SSRs in studies of within-species genetic diversity, we compared the relative performance of EST- and genomic SSRs following a multi-species approach on passerine birds. We tested whether patterns and levels of genetic diversity within- and between-populations assessed from EST- and from genomic SSRs are congruent and we investigated how the relative efficiency of EST- and genomic SSRs is influenced by levels of differentiation. EST- and genomic SSRs ensured comparable inferences of population genetic structure in cases of strong genetic differentiation, and genomic SSRs performed slightly better than EST-SSRs when differentiation is moderate. However and interestingly, EST-SSRs had a higher power to detect weak genetic structure compared to genomic SSRs. Our study attests that EST-SRRs may be valuable molecular markers for conservation genetic studies in taxa such as birds, where the development of genomic SSRs is impeded by their low frequency.
Unraveling hierarchical genetic structure of tea green leafhopper, Matsumurasca onukii, in East Asia based on SSRs and SNPs
<p><em>Matsumurasca onukii</em> (Matsuda, 1952), one of the dominant pests in major tea production areas in Asia, currently is known to occur in Japan, Vietnam, and China, and severely threatens tea production, quality, and international export trade. To elucidate the population genetic structure of this species, 1633 single nucleotide polymorphisms (SNPs) and 18 microsatellite markers (SSRs) were used to genotype samples from 27 sites representing 18 geographical populations distributed throughout the known range of the species in East Asia. Analyses of both SNPs and SSRs showed that <em>M</em>. <em>onukii</em> populations in Yunnan exhibit high genetic differentiation and structure compared to other populations. The Kagoshima (JJ) and Shizuoka (JS) populations from Japan were separated from populations from China by SNPs but clustered with Jinhua (JH), Yingde (YD), Guilin (GL), Fuzhou (FZ), Hainan (HQ), Leshan (CT), Chongqing (CY) and Zunyi (ZY) tea areas in China and the Vietnamese Vinh Phuc (VN) population based on SSR data. On the contrary, CT, CY, ZY, and Shaanxi (SX) populations clustered together based on SNPs, but were separated by SSRs. Both marker datasets identified significant geographic differentiation among the 18 populations. Various environmental and anthropogenic factors, including the geographical barriers to migration, human transport of hosts (<em>Camellia sinesis</em> (L.) O. Kuntze), and adaptability of <em>M. onukii</em> to various climatic zones possibly account for the rapid spread of this pest in Asia. The results demonstrate that SNPs from high-throughput genotyping data can be used to reveal subtle genetic substructure at broad scales in r-strategist insects.</p>
Data from: Ex situ conservation of underutilised fruit tree species: establishment of a core collection for Ficus carica L. using microsatellite markers (SSRs)
Ex situ germ plasm collections of woody crops are necessary to ensure the optimal use of plant genetic resources. The fig tree (Ficus carica L.) germ plasm bank, consisting of 229 accessions, is located in Centro de Investigación 'La Orden'. Despite great progress in conservation, ex situ collections face size and organization problems. Core collections obtained from structured samples of bigger collections are a useful tool to improve germ plasm management. In this work, we used simple sequence repeat (SSR) markers to establish a core collection in this underutilised Mediterranean fruit tree species. Four approaches have been carried out (random sampling, maximization, simulated annealing and stepwise clustering) to determine the best method to develop a core collection in this woody plant. The genetic diversity obtained with each subset was compared with that of the complete collection. It was found that the most efficient way to achieve the maximum diversity was the maximization strategy, which, with 30 accessions, recovers all the SSR alleles and does not show significant differences in allele frequency distribution in any of the loci or in the variability parameters (H O, H E) between the whole and core collections. Thus, this core collection, a representative of most fig diversity conserved in the germ plasm bank, could be used as a basis for plant material exchange among researchers and breeders.
Evaluation of a Novel CT-On-Rails or Trilogy Stereotactic Spine Radiotherapy System (SSRS)
ClinicalTrials.gov study NCT00508443. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Data from: Level of genetic differentiation affects relative performances of EST- and genomic SSRs
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Data from: Ex situ conservation of underutilised fruit tree species: establishment of a core collection for Ficus carica L. using microsatellite markers (SSRs)
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Data from: Identification and analysis of novel salt responsive candidate gene based SSRs (cgSSRs) from rice (Oryza sativa L.)
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Unraveling hierarchical genetic structure of tea green leafhopper, Matsumurasca onukii, in East Asia based on SSRs and SNPs
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Genetic diversity and population structure in Chrysolepis chrysophylla (golden chinquapin; Fagaceae): SSRs vs SNPs
<p>Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) genotypes on the same plant samples of <i>Chrysolepis chrysophylla</i> (Fagaceae; golden chinquapin) from 22 sites were used to determine genetic diversity and population structure. One site of <i>C. sempervirens</i> allowed <i>inter</i>specific vs.<i> intra</i>specific comparison. SSRs and SNPs yielded many similar results. Among-site variation contributed 13% to 17% of the genetic variation and Fst estimates of 0.14 to 0.17 were in the range expected among Fagaceae species rather than among populations within a species. The northern sites tended to group separately on the first two axes of multivariate scatterplots from southern sites. Sites in two geographically isolated areas were divergent: 1) the Hood Canal, Washington population was relatively more genetically distant from other golden chinquapin sites than was our <i>C. sempervirens</i> site; 2) three coastal southern California sites were moderately diverged. The Hood Canal site had a negative inbreeding coefficient, fewer alleles, lower heterozygosity, and differed from the Skamania County, Washington site as well as all other sites. Hood Canal trees are distinguished by disjunct geography and by these molecular results. This suggests that the golden chinquapin near Hood Canal be treated as a management unit, and potential conservation actions are discussed.</p>
SSRs data from 12 populations in China and North America
<p>The project is the SSRs data of 12 populations in China and North America. The Chinese populations include Panjin (PJ), Tianjin (TJ), Tangshan (TS), Lianyungang (LYG), Yancheng (YC), Zhoushan (ZS), Putian (PT), Zhangzhou (ZZ), and Zhanjiang (ZJ) and the North American populations include Commonwealth of Virginia (VI), Lange Eylandt (LE), and Rhode Island (RL). The markers involved in this data are 7, including RUMM017, RUMM018, RUMM020, RUMM021, RUMM032, RUMM034, and RUMM047.</p>
SSRs data from 12 populations in China and North America
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Genetic diversity and population structure in Chrysolepis chrysophylla (golden chinquapin; Fagaceae): SSRs vs SNPs
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Involved Versus Elective Target SSRS for Spinal Metastases
ClinicalTrials.gov study NCT04033536. IPD Sharing: NO. Countries: 1. Publications: 0.
Pilot Study to Assess Feasibility, Reliability and Validity of the e-SSRS-IVR
ClinicalTrials.gov study NCT00921466. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Single Versus Multiple Fractionated SSRS for Spinal Metastases
ClinicalTrials.gov study NCT02608866. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Phase I Study of Feasibility of Single Session Spine Stereotactic Radiosurgery (SSRS) in the Primary Management in Patients With Inoperable, Previously Unirradiated Metastatic Epidural Spinal Cord Com
ClinicalTrials.gov study NCT01254903. IPD Sharing: Not stated. Countries: 1. Publications: 0.
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