Large-scale advances in SSR markers with high-throughput sequencing in Euphorbia fischeriana Steud

BACKGROUND: Euphorbia fischeriana Steud is a very important medicinal herb and has significant medical value for healing cancer, edema and tuberculosis in China. The lack of molecular markers for Euphorbia fischeriana Steud is a dominant barrier to genetic research. For the purpose of developing many simple sequence repeat (SSR) molecular markers, we completed transcriptome analysis with the Illumina HiSeq 2000 platform. RESULTS: Approximately 9.1 million clean reads were acquired and then assembled into approximately 186.3 thousand nonredundant unigenes, 53,146 of which were SSR-containing unigenes. A total of 76,193 SSR loci were identified. Of these SSR loci, 28,491 were detected at the terminal position of ESTs, which made it difficult to design SSR primers for these SSR-containing sequences, and the residual SSRs were thus used to design primer pairs. Analyzing the results of these markers revealed that the mononucleotide motif A/T (44,067, 57.83% of all SSRs) was the most abundant, followed by the dinucleotide type AG/CT (9430, 12.38%). Using 100 randomly selected primer pairs, 77 primers were successfully amplified in Euphorbia fischeriana Steud, and 79 were successfully amplified in three other related species. The markers developed displayed relatively high quality and cross-species transferability. CONCLUSIONS: The large number of EST-SSRs exploited successfully in Euphorbia fischeriana Steud for the first time could provide genetic information for research on linkage maps, variety identification, genetic diversity analysis, and molecular marker-assisted breeding.

Linkage and mapping of quantitative trait loci associated with angular leaf spot and powdery mildew resistance in common beans

Abstract Angular leaf spot (ALS) and powdery mildew (PWM) are two important fungi diseases causing significant yield losses in common beans. In this study, a new genetic linkage map was constructed using single sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), in a segregating population derived from the AND 277 x SEA 5 cross, with 105 recombinant inbred lines. Phenotypic evaluations were performed in the greenhouse to identify quantitative trait loci (QTLs) associated with resistance by means of the composite interval mapping analysis. Four QTLs were identified for ALS resistance. The QTL ALS11AS, linked on the SNP BAR 5054, mapped on chromosome Pv11, showed the greatest effect (R2 = 26.5%) on ALS phenotypic variance. For PWM resistance, two QTLs were detected, PWM2AS and PWM11AS, on Pv2 and Pv11, explaining 7% and 66% of the phenotypic variation, respectively. Both QTLs on Pv11 were mapped on the same genomic region, suggesting that it is a pleiotropic region. The present study resulted in the identification of new markers closely linked to ALS and PWM QTLs, which can be used for marker-assisted selection, fine mapping and positional cloning.

The Reliability and Validity of the Korean Version of Columbia-Suicide Severity Rating Scale in Alcohol Dependent Patients / 신경정신의학

OBJECTIVES: This study was designed to evaluate the reliability and validity of the Korean version of Columbia-Suicide Severity Rating Scale (C-SSRS) in alcohol-dependent patients. METHODS: The participants were 31 patients with alcohol dependence disorder. All participants were tested using the Korean version of C-SSRS. To test the concurrent validity, Beck Hopelessness Scale, Beck Depression Inventory, and Scale for Suicidal Ideation were applied. Reliability and validity were assessed by comparison of cronbach-alpha coefficients, Pearson's correlation coefficients. RESULTS: The Korean version of C-SSRS was proved to be a reliable and valid method for assessment of suicidal risk by verification of internal consistency and concurrent validity. CONCLUSION: These results support that the Korean version of C-SSRS is a reliable and valid tool for prediction of suicidal risk in a clinical setting.

Use of EST database markers from M. truncatula in the transferability to other forage legumes.

In general tropical forage legumes lack microsatellites or simple sequence repeat (SSR) markers. Development of genic SSR markers from expressed sequence tagged (EST) database is an alternate and efficient approach to generate the standard DNA markers for genome analysis of such crop species. In the present paper a total of 816 EST-SSRs containing perfect repeats of mono (33.5%), di (14.7%), tri (39.3%), tetra (2.7%), penta (0.7%) and hexa (0.4%) nucleotides were identified from 1,87,763 ESTs of Medicago truncatula. Along with, 70 (8.5%) SSRs of a compound type were also observed. Seven primer pairs of tri repeats were tested for cross transferability in 19 accessions of forage legumes comprising 11 genera. At two different annealing temperatures (55 and 60oC) all primer pairs except AJ410087 reacted with many accessions of forage legumes. A total of 51 alleles were detected with six M. truncatula EST-SSRs primer-pairs against DNA from 19 accessions representing 11 genera where number of alleles ranged from 2 to 13. The cross-transferability of these EST-SSRs was 40.6% at 55oC and 32.3% at 60oC annealing temperature. 24 alleles of the total 50 (48%) at 55oC and 27 of 51 (53%) at 60oC were polymorphic among the accessions. These 27 polymorphic amplicons identified could be used as DNA markers. This study demonstrates the developed SSR markers from M. truncatula ESTs as a valuable genetic markers and also proposes the possibility of transferring these markers between species of different genera of the legumes of forage importance. It was evident from the results obtained with a set of Desmanthus virgatus accessions where Sequential Agglomerative Hierarchical and Nested (SAHN) cluster analysis based on Dice similarity and Unweighted Pair Group Method with Arithmetic mean Algorithm (UPGMA) revealed significant variability (24 to 74%) among the accessions. High bootstrap values (>30) supported the nodes generated by dendrogram analysis of accessions.

Characterization of novel genic SSR markers in Linum usitatissimum (L. ) and their transferability across eleven Linum species

Little is known about the evolutionary relationships among Linum species, basically because of the lack of transferable molecular markers. Currently, expressed sequence tags available in public databases provide an opportunity for the rapid and inexpensive development of simple sequence repeat (SSR) markers in wild flax species. In this regard, fifty expressed sequence tag-derived microsatellite markers (EST-SSRs) were evaluated for polymorphism and transferability in 50 Linum usitatissimum cultivars/accessions and 11 Linum species. Among them 23 EST-SSRs were polymorphic in L. usitatissimum, while 2-4 alleles were detected (average 2.26 per locus). The polymorphism information content value ranged from 0.08 to 0.55 (average 0.38). Forty one genic markers (95.3 percent) produced strong amplicons in at least two of the 11 Linum species. The percentage of cross amplification ranged from 34.1 percent to 92.7 percent in L. tauricum and L. bienne, respectively. Moreover, the rate of transferability was associated positively with the botanical section. Our results suggest that the high degree of EST-SSRs transferability to Linum species can be a useful enhancement of the current database of SSR markers for future genetic and evolutionary studies.

Genetic diversity in cultivated carioca common beans based on molecular marker analysis

A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats - SSRs and amplified fragment length polymorphisms - AFLPs) for assessing the genetic diversity of carioca beans. The amount of information provided by Roger's modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98 percent and Fst = 0.83, respectively) than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm.

Aplicação de marcadores microssatélites para o estudo de Culicidae (Diptera): revisão com especial referência a Haemagogus / Aplicación de marcadores microsatélites para el estudio de Culicidae (Diptera): una revisión con especial referencia a Haemagogus / Application of microsatellite markers for the study of Culicidae (Diptera): a review with special reference to Haemagogus

Marcadores moleculares microssatélites se caracterizam pela neutralidade, alto polimorfismo e elevada abundância com ampla distribuição pelo genoma de eucariotos. O seu emprego em estudos relacionados a espécies de mosquitos vetoras é ideal para o mapeamento genético e físico, para a identificação e discriminação de genótipos e estudos de genética de populações. Esta revisão sumariza e fornece informações sobre estudos envolvendo culicídeos através da utilização de marcadores microssatélites e propõe sugestões de pesquisas para uma melhor compreensão da biologia e dinâmica de transmissão do vírus da febre amarela por espécies do gênero Haemagogus.

Los marcadores moleculares microsatelitales se caracterizan por su neutralidad, alto polimorfismo y elevada abundancia con amplia distribución en el genoma de eucariotas. Su empleo en estudios relacionados a especies de mosquitos vectores es ideal para el mapeo genético y físico, para la identificación y discriminación de genotipos y estudios de genética de poblaciones. Esta revisión sintetiza y provee información sobre estudios de mosquitos que utilizan marcadores microsatelitales y propone nuevas líneas de investigación para una mejor comprensión de la biología y dinámica de transmisión del virus de la Fiebre Amarilla por especies del género Haemagogus.

Microsatellite molecular markers are characterized by neutrality, high polymorphism and wide distribution with high abundance in the genome of eukaryotes. Its use in studies related to species of mosquito vectors is ideal for genetic and physical mapping, for the identification and discrimination of genotypes and genetic studies of populations. This review summarizes and provides information on studies involving mosquitoes by using microsatellite markers and suggests avenues of research to better understand the biology and dynamics of transmission of Yellow Fever virus by Haemagogus mosquitoes.

Genetic divergence of rubber tree estimated by multivariate techniques and microsatellite markers

Genetic diversity of 60 Hevea genotypes, consisting of Asiatic, Amazonian, African and IAC clones, and pertaining to the genetic breeding program of the Agronomic Institute (IAC), Brazil, was estimated. Analyses were based on phenotypic multivariate parameters and microsatellites. Five agronomic descriptors were employed in multivariate procedures, such as Standard Euclidian Distance, Tocher clustering and principal component analysis. Genetic variability among the genotypes was estimated with 68 selected polymorphic SSRs, by way of Modified Rogers Genetic Distance and UPGMA clustering. Structure software in a Bayesian approach was used in discriminating among groups. Genetic diversity was estimated through Nei's statistics. The genotypes were clustered into 12 groups according to the Tocher method, while the molecular analysis identified six groups. In the phenotypic and microsatellite analyses, the Amazonian and IAC genotypes were distributed in several groups, whereas the Asiatic were in only a few. Observed heterozygosity ranged from 0.05 to 0.96. Both high total diversity (H T' = 0.58) and high gene differentiation (Gst' = 0.61) were observed, and indicated high genetic variation among the 60 genotypes, which may be useful for breeding programs. The analyzed agronomic parameters and SSRs markers were effective in assessing genetic diversity among Hevea genotypes, besides proving to be useful for characterizing genetic variability.

Transferability and characterization of microsatellite markers in two Neotropical Ficus species

Microsatellite markers were transferred and characterized for two Neotropical fig tree species, Ficus citrifolia and Ficus eximia. Our study demonstrated that microsatellite markers developed from different subgenera of Ficus can be transferred to related species. In the present case, 12 of the 15 primer pairs tested (80 percent) were successfully transferred to both of the above species. Eleven loci were polymorphic when tested across 60 F. citrifolia and 60 F. eximia individuals. For F. citrifolia, there were 4 to 15 alleles per locus, whereas expected heterozygosities ranged from 0.31 to 0.91. In the case of F. eximia, this was 2 to 12 alleles per locus and expected heterozygosities from 0.42 to 0.87.

Adaptação transcultural e avaliação da consistência interna da versão em português da Spirituality Self Rating Scale (SSRS) / Transcultural adaptation and evaluation of the internal consistency of the Portuguese version of the Spirituality Self Rating Scale (SSRS)

CONTEXTO: A espiritualidade pode ser considerada uma dimensão pessoal para a compreensão de questões sobre a vida, sobre significados e sobre o relacionamento com o sagrado ou transcendente, pelo qual pode (ou não) estar relacionada com rituais religiosos. OBJETIVO: Avaliar a consistência interna da versão traduzida e adaptada para o Brasil do instrumento Spirituality Self Rating Scale (SSRS). MÉTODOS: Estudo descritivo, de corte transversal. Aplicou-se a SSRS para estudar sua consistência interna em uma amostra constituída de 138 (69 por cento) homens usuários de substâncias psicoativas vinculados a diferentes serviços para reabilitação ou participando de grupo de mútua ajuda. RESULTADOS: A consistência interna, analisada pelo coeficiente de alfa de Cronbach, apresentou valor global de 0,8355, variando de 0,7028 a 0,8878. CONCLUSÕES: A versão brasileira da SSRS apresentou valores de consistência interna semelhantes aos da versão original em inglês e podem ser considerados bons.

CONTEXT: Spirituality can be considered a personal dimension to understand questions about life, about meanings and the relationship with the sacred or transcendent, which may (or not) be related to religious rituals. OBJECTIVE: To evaluate the internal consistency of translated and adapted for Brazil version of the instrument Spirituality Self Rating Scale (SSRS). METHODS: Descriptive, cross sectional study. The SSRS has been applied to study it the internal consistency in a sample consisted of 138 (69 percent) males psychoactive substance users linked to different services for rehabilitation or participating in group of mutual-help. RESULTS: The internal consistency, evaluated by the coefficient of Chronbach's alpha, showed overall value of 0.8355, ranging from 0.7028 to 0.8878. CONCLUSIONS: The Brazilian version of SSRS showed value of internal consistency similar to the original version in English and can be considered good.

Comparison of simple sequence repeats in 19 Archaea

All organisms that have been studied until now have been found to have differential distribution of simple sequence repeats (SSRs), with more SSRs in intergenic than in coding sequences. SSR distribution was investigated in Archaea genomes where complete chromosome sequences of 19 Archaea were analyzed with the program SPUTNIK to find di- to penta-nucleotide repeats. The number of repeats was determined for the complete chromosome sequences and for the coding and non-coding sequences. Different from what has been found for other groups of organisms, there is an abundance of SSRs in coding regions of the genome of some Archaea. Dinucleotide repeats were rare and CG repeats were found in only two Archaea. In general, trinucleotide repeats are the most abundant SSR motifs; however, pentanucleotide repeats are abundant in some Archaea. Some of the tetranucleotide and pentanucleotide repeat motifs are organism specific. In general, repeats are short and CG-rich repeats are present in Archaea having a CG-rich genome. Among the 19 Archaea, SSR density was not correlated with genome size or with optimum growth temperature. Pentanucleotide density had an inverse correlation with the CG content of the genome.