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Sample records for issr markers based

  1. Genetic diversity analysis in Opal cotton hybrids based on SSR, ISSR, and RAPD markers.

    PubMed

    Noormohammadi, Z; Hasheminejad-Ahangarani Farahani, Y; Sheidai, M; Ghasemzadeh-Baraki, S; Alishah, O

    2013-01-01

    Cotton is one of the most economically important crops in Iran; hybridization is a means to increase the genetic diversity and obtain new elite cultivars in this crop. We examined agronomic characteristics and molecular genetic diversity in the Opal cotton (Gossypium hirsutum) cultivar and in F(2) progenies. Ten homo-primers and seven hetero-primers of 26 RAPD primers produced 261 reproducible bands, with an average of 4.18 bands per primer and 22% polymorphism. The OPB12/OPH08 primer gave the highest effective number of alleles (N(E)), and the largest Shannon index (I), Nei's genetic diversity (H), and polymorphism information content (PIC) values. Some RAPD bands were present in the parental genotypes but were absent in their hybrids. Ten ISSR primers produced 206 reproducible bands, with 49.4% polymorphism. The UBC807 locus gave the highest N(E), I, H, and PIC values. Some ISSR bands occurred only in the parental genotype, while others were only present in the hybrid genotypes. Four microsatellite loci produced 12 alleles, ranging from 181 to 236 bp, with 54% polymorphism. The TMB1421 locus, with a monomorphic allele, was digested with three restriction enzymes (CAP-microsatellite) to evaluate sequence variations among samples. Association analysis between molecular markers and agronomic data revealed a significant correlation between ISSR-UBC807-1500 and yield. The Mantel test performed among the genetic distance matrices obtained from RAPD, ISSR and SSR showed a non-significant regression between RAPD versus ISSR and ISSR versus SSR, while RAPD versus SSR showed a significant regression; regression for ISSR and RAPD+ISSR+SSR combined data was also significant. Cluster analysis (UPGMA) based on these three types of molecular markers differentiated cotton genotypes and their progenies. Among the molecular markers, ISSR revealed more genetic variation among the genotypes. However, using all three types of molecular markers provided a better overall view of cotton

  2. Genetic diversity of Iranian honey bee (Apis mellifera meda Skorikow, 1829) populations based on ISSR markers.

    PubMed

    Rahimi, A; Mirmoayedi, A; Kahrizi, D; Zarei, L; Jamali, S

    2016-01-01

    Honey bee is one of the most important insects considering its role in agriculture,ecology and economy as a whole. In this study, the genetic diversity of different Iranian honey bee populations was evaluated using inter simple sequence repeat (ISSR) markers. During May to September 2014, 108 young worker honey bees were collected from six different populations in 30 different geoclimatic locations from Golestan, Mazendaran, Guilan, West Azerbaijan, East Azerbaijan, Ardebil provinces of Iran. DNA was extracted from the worker honey bees. The quality and quantity of extracted DNA were measured. A set of ten primers were screened with the laboratory populations of honey bees. The number of fragments produced in the different honey bee populations varied from 3 to 10, varying within 150 to 1500 bp. The used ten ISSR primers generated 40 polymorphic fragments, and the average heterozygosity for each primer was 0.266. Maximum numbers of bands were recorded for primer A1. A dendrogram based on the Unweighted Pair Group Method with Arithmetic mean (UPGMA) method generated two sub-clusters. Honey bee populations of Golestan, Mazendaran, Guilan provinces were located in the first group. The second group included honey bee populations of Ardebil, West Azerbaijan, East Azerbaijan provinces, but this group showed a close relationship with other populations. The results showed obviously the ability of the ISSR marker technique to detect the genetic diversity among the honey bee populations. PMID:27188735

  3. Genetic diversity of Iranian honey bee (Apis mellifera meda Skorikow, 1829) populations based on ISSR markers.

    PubMed

    Rahimi, A; Mirmoayedi, A; Kahrizi, D; Zarei, L; Jamali, S

    2016-04-30

    Honey bee is one of the most important insects considering its role in agriculture,ecology and economy as a whole. In this study, the genetic diversity of different Iranian honey bee populations was evaluated using inter simple sequence repeat (ISSR) markers. During May to September 2014, 108 young worker honey bees were collected from six different populations in 30 different geoclimatic locations from Golestan, Mazendaran, Guilan, West Azerbaijan, East Azerbaijan, Ardebil provinces of Iran. DNA was extracted from the worker honey bees. The quality and quantity of extracted DNA were measured. A set of ten primers were screened with the laboratory populations of honey bees. The number of fragments produced in the different honey bee populations varied from 3 to 10, varying within 150 to 1500 bp. The used ten ISSR primers generated 40 polymorphic fragments, and the average heterozygosity for each primer was 0.266. Maximum numbers of bands were recorded for primer A1. A dendrogram based on the Unweighted Pair Group Method with Arithmetic mean (UPGMA) method generated two sub-clusters. Honey bee populations of Golestan, Mazendaran, Guilan provinces were located in the first group. The second group included honey bee populations of Ardebil, West Azerbaijan, East Azerbaijan provinces, but this group showed a close relationship with other populations. The results showed obviously the ability of the ISSR marker technique to detect the genetic diversity among the honey bee populations.

  4. Molecular profiling for genetic variability in Capsicum species based on ISSR and RAPD markers.

    PubMed

    Thul, Sanjog T; Darokar, Mahendra P; Shasany, Ajit K; Khanuja, Suman P S

    2012-06-01

    The taxonomic identity of Capsicum species is found to be difficult as it displays variations at morpho-chemical characters. Twenty-two accessions of six Capsicum species, namely, C. annuum, C. baccatum, C. chinense, C. eximium, C. frutescens, and C. luteum were investigated for phenotypic diversity based on flower color and for genetic differences by molecular makers. The genetic cluster analyses of 27 RAPD and eight ISSR primers, respectively, revealed genetic similarities in the ranges of 23-88% and 11-96%. Principal component analysis of the pooled RAPD and ISSR data further supports the genetic similarity and groupings. Different species showed variations in relation to corolla shade of flower. C. annuum accessions formed a single cluster in the molecular analysis as maintaining their flower characteristic. C. chinense accession shared flower features with the accessions of C. frutescens and were found to be closer at genotypic level. C. luteum was found to be rather closer to C. baccatum complex, both phenotypically and genetically. The only accession of C. eximium presenting purple flowers falls apart from the groupings. The floral characteristics and the molecular markers are found to be useful toward the delineation of the species specificity in Capsicum collection and identification of genetic stock.

  5. Construction of intersubspecific molecular genetic map of lentil based on ISSR, RAPD and SSR markers.

    PubMed

    Gupta, Mamta; Verma, Bhawna; Kumar, Naresh; Chahota, Rakesh K; Rathour, Rajeev; Sharma, Shyam K; Bhatia, Sabhyata; Sharma, Tilak R

    2012-01-01

    Lentil (Lens culinaris ssp. culinaris), is a self-pollinating diploid (2n = 2x = 14), cool-season legume crop and is consumed worldwide as a rich source of protein (~24.0%), largely in vegetarian diets. Here we report development of a genetic linkage map of Lens using 114 F(2) plants derived from the intersubspecific cross between L 830 and ILWL 77. RAPD (random amplified polymorphic DNA) primers revealed more polymorphism than ISSR (intersimple sequence repeat) and SSR (simple sequence repeat) markers. The highest proportion (30.72%) of segregation distortion was observed in RAPD markers. Of the 235 markers (34 SSR, 9 ISSR and 192 RAPD) used in the mapping study, 199 (28 SSRs, 9 ISSRs and 162 RAPDs) were mapped into 11 linkage groups (LGs), varying between 17.3 and 433.8 cM and covering 3843.4 cM, with an average marker spacing of 19.3 cM. Linkage analysis revealed nine major groups with 15 or more markers each and two small LGs with two markers each, and 36 unlinked markers. The study reported assigning of 11 new SSRs on the linkage map. Of the 66 markers with aberrant segregation, 14 were unlinked and the remaining 52 were mapped. ISSR and RAPD markers were found to be useful in map construction and saturation. The current map represents maximum coverage of lentil genome and could be used for identification of QTL regions linked to agronomic traits, and for marker-assisted selection in lentil. PMID:23271013

  6. The first genetic linkage map of Luohanguo (Siraitia grosvenorii ) based on ISSR and SRAP markers.

    PubMed

    Liu, Lihua; Ma, Xiaojun; Wei, Jianhe; Qin, Jiaming; Mo, Changming

    2011-01-01

    In this study, the first genetic map of Luohanguo (Siraitia grosvenorii (Swingle) C. Jeffrey) was constructed with 150 F₂ population individuals using inter-simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) markers. A total of 100 ISSRs and 196 SRAP primer combinations generated 51 and 222 polymorphic markers, respectively. Among the 273 markers obtained, 199 markers (29 ISSRs and 170 SRAPs) were mapped to 25 linkage groups. The map covered 1463.3 cM with a mean map distance of 7.35 cM between adjacent markers and a maximum map distance of 52.6 cM between two markers. The markers were distributed randomly in 25 groups except for minor clusters in the distal region of linkage groups. All 25 linkage groups consisted of 2-36 loci ranging in length from 19.5 to 152.6 cM and accounted for 59.8% of the total map distance. This map provides reference information for future molecular breeding work on Luohanguo.

  7. Genetic diversity analysis of sweet kernel apricot in China based on SSR and ISSR markers.

    PubMed

    Liu, M P; Du, H Y; Zhu, G P; Fu, D L; Tana, W Y

    2015-08-19

    Simple sequence repeat (SSR) and inter-simple sequence repeat (ISSR) markers were used to evaluate genetic diversity among 22 sweet kernel apricot accessions and 12 cultivars in China to provide information on how to improve the utilization of kernel apricot germplasms. The results showed that 10 pairs of SSR primers screened from 40 primer pairs amplified 43 allelic variants, all of which were polymorphic (100%), and 9 ISSR primers selected from 100 primers amplified 67 allelic variants with 50 polymorphic bands (74.63%). There was a relatively distant genetic relationship between the 34 samples, where their genetic similarity coefficient was between 0.62 and 0.99. The UPGMA dendrogram constructed using combined data of the two marker systems separated the genotypes into three main clusters.

  8. Genetic diversity analysis of sweet kernel apricot in China based on SSR and ISSR markers.

    PubMed

    Liu, M P; Du, H Y; Zhu, G P; Fu, D L; Tana, W Y

    2015-01-01

    Simple sequence repeat (SSR) and inter-simple sequence repeat (ISSR) markers were used to evaluate genetic diversity among 22 sweet kernel apricot accessions and 12 cultivars in China to provide information on how to improve the utilization of kernel apricot germplasms. The results showed that 10 pairs of SSR primers screened from 40 primer pairs amplified 43 allelic variants, all of which were polymorphic (100%), and 9 ISSR primers selected from 100 primers amplified 67 allelic variants with 50 polymorphic bands (74.63%). There was a relatively distant genetic relationship between the 34 samples, where their genetic similarity coefficient was between 0.62 and 0.99. The UPGMA dendrogram constructed using combined data of the two marker systems separated the genotypes into three main clusters. PMID:26345904

  9. Genetic diversity analysis of Aspergillus flavus isolates from plants and air by ISSR markers.

    PubMed

    Mahmoud1, M A; El-Samawaty, A M A; Yassin, M A; Abd El-Aziz, A R M

    2016-04-28

    Aspergillus flavus is one of the most abundant and widely distributed fungi on earth. A. flavus produces aflatoxins (AFs), which are toxic secondary metabolites. AFs have harmful effects on public health (humans and animals) and agricultural crops. Inter-simple sequence repeat (ISSR) markers were used to analyze the genetic diversity of 30 A. flavus isolates from five agricultural crops and air. Genetic similarity coefficients (GSC) ranged from 0.51 to 0.10 based on three ISSR markers for the isolates tested. A. flavus isolates grouped into 6, 5, and 3 clusters using the unweighted pair-group method with arithmetic average of three ISSR markers. This study suggests that ISSR biotechnology is a highly useful tool for characterizing genetic diversity of A. flavus isolated from different sources.

  10. Prediction of industrial tomato hybrids from agronomic traits and ISSR molecular markers.

    PubMed

    Figueiredo, A S T; Resende, J T V; Faria, M V; Da-Silva, P R; Fagundes, B S; Morales, R G F

    2016-05-13

    Heterosis is a highly relevant phenomenon in plant breeding. This condition is usually established in hybrids derived from crosses of highly divergent parents. The success of a breeder in obtaining heterosis is directly related to the correct identification of genetically contrasting parents. Currently, the diallel cross is the most commonly used methodology to detect contrasting parents; however, it is a time- and cost-consuming procedure. Therefore, new tools capable of performing this task quickly and accurately are required. Thus, the purpose of this study was to estimate the genetic divergence in industrial tomato lines, based on agronomic traits, and to compare with estimates obtained using inter-simple sequence repeat (ISSR) molecular markers. The genetic divergence among 10 industrial tomato lines, based on nine morphological characters and 12 ISSR primers was analyzed. For data analysis, Pearson and Spearman correlation coefficients were calculated between the genetic dissimilarity measures estimated by Mahalanobis distance and Jaccard's coefficient of genetic dissimilarity from the heterosis estimates, combining ability, and means of important traits of industrial tomato. The ISSR markers efficiently detected contrasting parents for hybrid production in tomato. Parent RVTD-08 was indicated as the most divergent, both by molecular and morphological markers, that positively contributed to increased heterosis and by the specific combining ability in the crosses in which it participated. The genetic dissimilarity estimated by ISSR molecular markers aided the identification of the best hybrids of the experiment in terms of total fruit yield, pulp yield, and soluble solids content.

  11. Prediction of industrial tomato hybrids from agronomic traits and ISSR molecular markers.

    PubMed

    Figueiredo, A S T; Resende, J T V; Faria, M V; Da-Silva, P R; Fagundes, B S; Morales, R G F

    2016-01-01

    Heterosis is a highly relevant phenomenon in plant breeding. This condition is usually established in hybrids derived from crosses of highly divergent parents. The success of a breeder in obtaining heterosis is directly related to the correct identification of genetically contrasting parents. Currently, the diallel cross is the most commonly used methodology to detect contrasting parents; however, it is a time- and cost-consuming procedure. Therefore, new tools capable of performing this task quickly and accurately are required. Thus, the purpose of this study was to estimate the genetic divergence in industrial tomato lines, based on agronomic traits, and to compare with estimates obtained using inter-simple sequence repeat (ISSR) molecular markers. The genetic divergence among 10 industrial tomato lines, based on nine morphological characters and 12 ISSR primers was analyzed. For data analysis, Pearson and Spearman correlation coefficients were calculated between the genetic dissimilarity measures estimated by Mahalanobis distance and Jaccard's coefficient of genetic dissimilarity from the heterosis estimates, combining ability, and means of important traits of industrial tomato. The ISSR markers efficiently detected contrasting parents for hybrid production in tomato. Parent RVTD-08 was indicated as the most divergent, both by molecular and morphological markers, that positively contributed to increased heterosis and by the specific combining ability in the crosses in which it participated. The genetic dissimilarity estimated by ISSR molecular markers aided the identification of the best hybrids of the experiment in terms of total fruit yield, pulp yield, and soluble solids content. PMID:27323023

  12. Polymorphism analysis in advanced mutant population of oat (Avena sativa L.) using ISSR markers.

    PubMed

    Sharma, Pawan; Tiwari, Sharad; Tripathi, Niraj; Mehta, Anoop K

    2016-01-01

    Present investigation was carried out to evaluate genetic diversity among 38 M6 population of oat cv. JO-1. To validate the observed morpho-physiological variations, these lines were analyzed with 21 ISSR primers. A total of 132 loci were amplified by these 21 ISSR markers and 116 loci were found to be polymorphic (87.87 %). The genetic similarity coefficient values among 39 oat genotypes based on ISSR analysis ranged from 0.305 to 0.957. The cluster analysis divided the oat genotypes into two groups. Mutants JMO 81 and JMO 82 were found to be most divergent, hence can be used as parents in breeding program for the development of superior cultivars.

  13. Polymorphism analysis in advanced mutant population of oat (Avena sativa L.) using ISSR markers.

    PubMed

    Sharma, Pawan; Tiwari, Sharad; Tripathi, Niraj; Mehta, Anoop K

    2016-01-01

    Present investigation was carried out to evaluate genetic diversity among 38 M6 population of oat cv. JO-1. To validate the observed morpho-physiological variations, these lines were analyzed with 21 ISSR primers. A total of 132 loci were amplified by these 21 ISSR markers and 116 loci were found to be polymorphic (87.87 %). The genetic similarity coefficient values among 39 oat genotypes based on ISSR analysis ranged from 0.305 to 0.957. The cluster analysis divided the oat genotypes into two groups. Mutants JMO 81 and JMO 82 were found to be most divergent, hence can be used as parents in breeding program for the development of superior cultivars. PMID:27186025

  14. Genetic diversity and identification of Chinese-grown pecan using ISSR and SSR markers.

    PubMed

    Jia, Xiao-Dong; Wang, Tao; Zhai, Min; Li, Yong-Rong; Guo, Zhong-Ren

    2011-01-01

    Pecan is an important horticultural nut crop originally from North America and now widely cultivated in China for its high ecological, ornamental and economic value. Currently, there are over one hundred cultivars grown in China, including introduced American cultivars and Chinese seedling breeding cultivars. Molecular markers were used to assess the genetic diversity of these cultivars and to identify the pedigrees of fine pecan plants with good characteristics and no cultivar-related data. A total of 77 samples grown in China were studied, including 14 introduced cultivars, 12 domestic seedling breeding cultivars, and 49 fine pecan plants with no cultivar data, together with Carya cathayensis and Juglans nigra. A total of 77 ISSR and 19 SSR primers were prescreened; 10 ISSR and eight SSR primers were selected, yielding a total of 94 amplified bands (100% polymorphic) in the range of 140-1,950 bp for the ISSR and 70 amplified bands (100% polymorphic) in the range of 50-350 bp for SSR markers. Genetic diversity analyses indicated Chinese-grown pecan cultivars and fine plants had significant diversity at the DNA level. The dengrograms constructed with ISSR, SSR or combined data were very similar, but showed very weak grouping association with morphological characters. However, the progeny were always grouped with the parents. The great diversity found among the Chinese cultivars and the interesting germplasm of the fine pecan plants analyzed in this study are very useful for increasing the diversity of the pecan gene pool. All 77 accessions in this study could be separated based on the ISSR and SSR fingerprints produced by one or more primers. The results of our study also showed that ISSR and SSR techniques were both suitable for genetic diversity analyses and the identification of pecan resources. PMID:22146370

  15. Genetic diversity analysis of okra (Abelmoschus esculentus L.) by inter-simple sequence repeat (ISSR) markers.

    PubMed

    Yuan, C Y; Zhang, C; Wang, P; Hu, S; Chang, H P; Xiao, W J; Lu, X T; Jiang, S B; Ye, J Z; Guo, X H

    2014-04-25

    Okra (Abelmoschus esculentus L.) is not only a nutrient-rich vegetable but also an important medicinal herb. Inter-simple sequence repeat (ISSR) markers were employed to investigate the genetic diversity and differentiation of 24 okra genotypes. In this study, the PCR products were separated by electrophoresis on 8% nondenaturing polyacrylamide gel and visualized by silver staining. The 22 ISSR primers produced 289 amplified DNA fragments, and 145 (50%) fragments were polymorphic. The 289 markers were used to construct the dendrogram based on the unweighted pair-group method with arithmetic average (UPGMA) cluster analysis. The dendrogram indicated that 24 okras were clustered into 4 geographically distinct groups. The average polymorphism information content (PIC) was 0.531929, which showed that the majority of primers were informative. The high values of allele frequency, genetic diversity, and heterozygosity showed that primer-sample combinations produced measurable fragments. The mean distances ranged from 0.045455 to 0.454545. The dendrogram indicated that the ISSR markers succeeded in distinguishing most of the 24 varieties in relation to their genetic backgrounds and geographical origins.

  16. Genetic diversity analysis of okra (Abelmoschus esculentus L.) by inter-simple sequence repeat (ISSR) markers.

    PubMed

    Yuan, C Y; Zhang, C; Wang, P; Hu, S; Chang, H P; Xiao, W J; Lu, X T; Jiang, S B; Ye, J Z; Guo, X H

    2014-01-01

    Okra (Abelmoschus esculentus L.) is not only a nutrient-rich vegetable but also an important medicinal herb. Inter-simple sequence repeat (ISSR) markers were employed to investigate the genetic diversity and differentiation of 24 okra genotypes. In this study, the PCR products were separated by electrophoresis on 8% nondenaturing polyacrylamide gel and visualized by silver staining. The 22 ISSR primers produced 289 amplified DNA fragments, and 145 (50%) fragments were polymorphic. The 289 markers were used to construct the dendrogram based on the unweighted pair-group method with arithmetic average (UPGMA) cluster analysis. The dendrogram indicated that 24 okras were clustered into 4 geographically distinct groups. The average polymorphism information content (PIC) was 0.531929, which showed that the majority of primers were informative. The high values of allele frequency, genetic diversity, and heterozygosity showed that primer-sample combinations produced measurable fragments. The mean distances ranged from 0.045455 to 0.454545. The dendrogram indicated that the ISSR markers succeeded in distinguishing most of the 24 varieties in relation to their genetic backgrounds and geographical origins. PMID:24841648

  17. Molecular characterization of cultivated bromeliad accessions with Inter-Simple Sequence Repeat (ISSR) Markers.

    PubMed

    Zhang, Fei; Ge, Yaying; Wang, Weiyong; Yu, Xinying; Shen, Xiaolan; Liu, Jianxin; Liu, Xiaojing; Tian, Danqing; Shen, Fuquan; Yu, Yongming

    2012-01-01

    Bromeliads are of great economic importance in flower production; however little information is available with respect to genetic characterization of cultivated bromeliads thus far. In the present study, a selection of cultivated bromeliads was characterized via inter-simple sequence repeat (ISSR) markers with an emphasis on genetic diversity and population structure. Twelve ISSR primers produced 342 bands, of which 287 (~84%) were polymorphic, with polymorphic bands per primer ranging from 17 to 34. The Jaccard's similarity ranged from 0.08 to 0.89 and averaged ~0.30 for the investigated bromeliads. The Bayesian-based approach, together with the un-weighted paired group method with arithmetic average (UPGMA)-based clustering and the principal coordinate analysis (PCoA), distinctly grouped the bromeliads from Neoregelia, Guzmania, and Vriesea into three separately clusters, well corresponding with their botanical classifications; whereas the bromeliads of Aechmea other than the recently selected hybrids were not well assigned to a cluster. Additionally, ISSR marker was proven efficient for the identification of hybrids and bud sports of cultivated bromeliads. The findings achieved herein will further our knowledge about the genetic variability within cultivated bromeliads and therefore facilitate breeding for new varieties of cultivated bromeliads in future as well.

  18. Molecular Characterization of Cultivated Bromeliad Accessions with Inter-Simple Sequence Repeat (ISSR) Markers

    PubMed Central

    Zhang, Fei; Ge, Yaying; Wang, Weiyong; Yu, Xinying; Shen, Xiaolan; Liu, Jianxin; Liu, Xiaojing; Tian, Danqing; Shen, Fuquan; Yu, Yongming

    2012-01-01

    Bromeliads are of great economic importance in flower production; however little information is available with respect to genetic characterization of cultivated bromeliads thus far. In the present study, a selection of cultivated bromeliads was characterized via inter-simple sequence repeat (ISSR) markers with an emphasis on genetic diversity and population structure. Twelve ISSR primers produced 342 bands, of which 287 (~84%) were polymorphic, with polymorphic bands per primer ranging from 17 to 34. The Jaccard’s similarity ranged from 0.08 to 0.89 and averaged ~0.30 for the investigated bromeliads. The Bayesian-based approach, together with the un-weighted paired group method with arithmetic average (UPGMA)-based clustering and the principal coordinate analysis (PCoA), distinctly grouped the bromeliads from Neoregelia, Guzmania, and Vriesea into three separately clusters, well corresponding with their botanical classifications; whereas the bromeliads of Aechmea other than the recently selected hybrids were not well assigned to a cluster. Additionally, ISSR marker was proven efficient for the identification of hybrids and bud sports of cultivated bromeliads. The findings achieved herein will further our knowledge about the genetic variability within cultivated bromeliads and therefore facilitate breeding for new varieties of cultivated bromeliads in future as well. PMID:22754348

  19. Molecular characterization of cultivated bromeliad accessions with Inter-Simple Sequence Repeat (ISSR) Markers.

    PubMed

    Zhang, Fei; Ge, Yaying; Wang, Weiyong; Yu, Xinying; Shen, Xiaolan; Liu, Jianxin; Liu, Xiaojing; Tian, Danqing; Shen, Fuquan; Yu, Yongming

    2012-01-01

    Bromeliads are of great economic importance in flower production; however little information is available with respect to genetic characterization of cultivated bromeliads thus far. In the present study, a selection of cultivated bromeliads was characterized via inter-simple sequence repeat (ISSR) markers with an emphasis on genetic diversity and population structure. Twelve ISSR primers produced 342 bands, of which 287 (~84%) were polymorphic, with polymorphic bands per primer ranging from 17 to 34. The Jaccard's similarity ranged from 0.08 to 0.89 and averaged ~0.30 for the investigated bromeliads. The Bayesian-based approach, together with the un-weighted paired group method with arithmetic average (UPGMA)-based clustering and the principal coordinate analysis (PCoA), distinctly grouped the bromeliads from Neoregelia, Guzmania, and Vriesea into three separately clusters, well corresponding with their botanical classifications; whereas the bromeliads of Aechmea other than the recently selected hybrids were not well assigned to a cluster. Additionally, ISSR marker was proven efficient for the identification of hybrids and bud sports of cultivated bromeliads. The findings achieved herein will further our knowledge about the genetic variability within cultivated bromeliads and therefore facilitate breeding for new varieties of cultivated bromeliads in future as well. PMID:22754348

  20. Genetic diversity analysis in Tunisian perennial ryegrass germplasm as estimated by RAPD, ISSR, and morpho-agronomical markers.

    PubMed

    Ghariani, S; Elazreg, H; Chtourou-Ghorbel, N; Chakroun, M; Trifi-Farah, N

    2015-01-01

    Tunisia is rich in diverse forage and pasture species including perennial ryegrass. In order to enhance forage production and improve agronomic performance of this local germplasm, a molecular analysis was undertaken. Random amplified polymorphic DNA (RAPD), inter simple sequence repeats (ISSR) and morpho-agronomical traits markers were used for genetic diversity estimation of ryegrass germplasm after screening 20 spontaneous accessions, including a local and an introduced cultivars. Same mean polymorphism information content values were obtained (0.37) for RAPD and ISSR suggesting that both marker systems were equally effective in determining polymorphisms. The average pairwise genetic distance values were 0.57 (morpho-agronomical traits), 0.68 (RAPD), and 0.51 (ISSR) markers data sets. A higher Shannon diversity index was obtained with ISSR marker (0.57) than for RAPD (0.54) and morpho-agronomical traits (0.36). The Mantel test based on genetic distances of a combination of molecular markers and morpho-agronomical data exhibited a significant correlation between RAPD and ISSR data, suggesting that the use of a combination of molecular techniques was a highly efficient method of estimating genetic variability levels among Tunisian ryegrass germplasm. In summary, results showed that combining molecular and morpho-agronomical markers is an efficient way in assessing the genetic variability among Tunisian ryegrass genotypes. In addition, the combined analysis provided an exhaustive coverage for the analyzed diversity and helped us to identify suitable accessions showed by Beja and Jendouba localities, which present large similarities with cultivated forms and can be exploited for designing breeding programmes, conservation of germplasm and management of ryegrass genetic resources. PMID:26782500

  1. Genetic diversity analysis in Tunisian perennial ryegrass germplasm as estimated by RAPD, ISSR, and morpho-agronomical markers.

    PubMed

    Ghariani, S; Elazreg, H; Chtourou-Ghorbel, N; Chakroun, M; Trifi-Farah, N

    2015-12-28

    Tunisia is rich in diverse forage and pasture species including perennial ryegrass. In order to enhance forage production and improve agronomic performance of this local germplasm, a molecular analysis was undertaken. Random amplified polymorphic DNA (RAPD), inter simple sequence repeats (ISSR) and morpho-agronomical traits markers were used for genetic diversity estimation of ryegrass germplasm after screening 20 spontaneous accessions, including a local and an introduced cultivars. Same mean polymorphism information content values were obtained (0.37) for RAPD and ISSR suggesting that both marker systems were equally effective in determining polymorphisms. The average pairwise genetic distance values were 0.57 (morpho-agronomical traits), 0.68 (RAPD), and 0.51 (ISSR) markers data sets. A higher Shannon diversity index was obtained with ISSR marker (0.57) than for RAPD (0.54) and morpho-agronomical traits (0.36). The Mantel test based on genetic distances of a combination of molecular markers and morpho-agronomical data exhibited a significant correlation between RAPD and ISSR data, suggesting that the use of a combination of molecular techniques was a highly efficient method of estimating genetic variability levels among Tunisian ryegrass germplasm. In summary, results showed that combining molecular and morpho-agronomical markers is an efficient way in assessing the genetic variability among Tunisian ryegrass genotypes. In addition, the combined analysis provided an exhaustive coverage for the analyzed diversity and helped us to identify suitable accessions showed by Beja and Jendouba localities, which present large similarities with cultivated forms and can be exploited for designing breeding programmes, conservation of germplasm and management of ryegrass genetic resources.

  2. Genetic diversity of Cosmos species revealed by RAPD and ISSR markers.

    PubMed

    Rodríguez-Bernal, A; Piña-Escutia, J L; Vázquez-García, L M; Arzate-Fernández, A M

    2013-12-04

    The genus Cosmos is native of America and is constituted by 34 species; 28 of them are endemic of Mexico. The cosmos are used as a nematicide, antimalarial, and antioxidative agent. The aim of this study was to estimate the genetic diversity among 7 cosmos species based on random amplified polymorphic DNA (RAPD) and inter-simple sequences repeats (ISSR) markers. With RAPD markers, the obtained polymorphism was 91.7 % and the genetic diversity was 0.33, whereas these values were 65.6%, and 0.22 from ISSR markers, respectively, indicating the presence of high genetic diversity among the Cosmos species that were analyzed. The unweighted pair group method with arithmetic mean dendrograms that were obtained with both markers were notably similar, revealing 2 clusters and indicating a clear genetic differentiation among the Cosmos species that were assessed. The first cluster comprised the species Cosmos sulphureus, Cosmos pacificus, and Cosmos diversifolius, while the second cluster included the species Cosmos purpureus, Cosmos crithmifolius, Cosmos bipinnatus, and Cosmos parviflorus. Besides this, the Cosmos species were clustered according to their collection sites. The Mantel test corroborates the correlation between the genetic distance and the geographic altitude of each Cosmos species. The results suggest that it is necessary to preserve the Cosmos species in their natural habitat in addition to the germoplasm collection for ex situ conservation.

  3. Comparison of RAPD, ISSR, and AFLP Molecular Markers to Reveal and Classify Orchardgrass (Dactylis glomerata L.) Germplasm Variations.

    PubMed

    Costa, Rita; Pereira, Graça; Garrido, Inmaculada; Tavares-de-Sousa, Manuel María; Espinosa, Francisco

    2016-01-01

    Three different DNA-based techniques, Random Amplified Polymorphic DNA (RAPD), Inter Simple Sequence Repeat (ISSR) and Amplified Fragment Length Polymorphism (AFLP) markers, were used for fingerprinting Dactylis glomerata genotypes and for detecting genetic variation between the three different subspecies. In this study, RAPD assays produced 97 bands, of which 40 were polymorphic (41.2%). The ISSR primers amplified 91 bands, and 54 showed polymorphism (59.3%). Finally, the AFLP showed 100 bands, of which 92 were polymorphic (92%). The fragments were scored as present (1) or absent (0), and those readings were entered in a computer file as a binary matrix (one for each marker). Three cluster analyses were performed to express--in the form of dendrograms--the relationships among the genotypes and the genetic variability detected. All DNA-based techniques used were able to amplify all of the genotypes. There were highly significant correlation coefficients between cophenetic matrices based on the genetic distance for the RAPD, ISSR, AFLP, and combined RAPD-ISSR-AFLP data (0.68, 0.78, 0.70, and 0.70, respectively). Two hypotheses were formulated to explain these results; both of them are in agreement with the results obtained using these three types of molecular markers. We conclude that when we study genotypes close related, the analysis of variability could require more than one DNA-based technique; in fact, the genetic variation present in different sources could interfere or combine with the more or less polymorphic ability, as our results showed for RAPD, ISSR and AFLP markers. Our results indicate that AFLP seemed to be the best-suited molecular assay for fingerprinting and assessing genetic relationship among genotypes of Dactylis glomerata.

  4. Comparison of RAPD, ISSR, and AFLP Molecular Markers to Reveal and Classify Orchardgrass (Dactylis glomerata L.) Germplasm Variations

    PubMed Central

    Costa, Rita; Pereira, Graça; Garrido, Inmaculada; Tavares-de-Sousa, Manuel María; Espinosa, Francisco

    2016-01-01

    Three different DNA-based techniques, Random Amplified Polymorphic DNA (RAPD), Inter Simple Sequence Repeat (ISSR) and Amplified Fragment Length Polymorphism (AFLP) markers, were used for fingerprinting Dactylis glomerata genotypes and for detecting genetic variation between the three different subspecies. In this study, RAPD assays produced 97 bands, of which 40 were polymorphic (41.2%). The ISSR primers amplified 91 bands, and 54 showed polymorphism (59.3%). Finally, the AFLP showed 100 bands, of which 92 were polymorphic (92%). The fragments were scored as present (1) or absent (0), and those readings were entered in a computer file as a binary matrix (one for each marker). Three cluster analyses were performed to express–in the form of dendrograms–the relationships among the genotypes and the genetic variability detected. All DNA-based techniques used were able to amplify all of the genotypes. There were highly significant correlation coefficients between cophenetic matrices based on the genetic distance for the RAPD, ISSR, AFLP, and combined RAPD-ISSR-AFLP data (0.68, 0.78, 0.70, and 0.70, respectively). Two hypotheses were formulated to explain these results; both of them are in agreement with the results obtained using these three types of molecular markers. We conclude that when we study genotypes close related, the analysis of variability could require more than one DNA-based technique; in fact, the genetic variation present in different sources could interfere or combine with the more or less polymorphic ability, as our results showed for RAPD, ISSR and AFLP markers. Our results indicate that AFLP seemed to be the best-suited molecular assay for fingerprinting and assessing genetic relationship among genotypes of Dactylis glomerata. PMID:27070939

  5. Comparison of RAPD, ISSR, and AFLP Molecular Markers to Reveal and Classify Orchardgrass (Dactylis glomerata L.) Germplasm Variations.

    PubMed

    Costa, Rita; Pereira, Graça; Garrido, Inmaculada; Tavares-de-Sousa, Manuel María; Espinosa, Francisco

    2016-01-01

    Three different DNA-based techniques, Random Amplified Polymorphic DNA (RAPD), Inter Simple Sequence Repeat (ISSR) and Amplified Fragment Length Polymorphism (AFLP) markers, were used for fingerprinting Dactylis glomerata genotypes and for detecting genetic variation between the three different subspecies. In this study, RAPD assays produced 97 bands, of which 40 were polymorphic (41.2%). The ISSR primers amplified 91 bands, and 54 showed polymorphism (59.3%). Finally, the AFLP showed 100 bands, of which 92 were polymorphic (92%). The fragments were scored as present (1) or absent (0), and those readings were entered in a computer file as a binary matrix (one for each marker). Three cluster analyses were performed to express--in the form of dendrograms--the relationships among the genotypes and the genetic variability detected. All DNA-based techniques used were able to amplify all of the genotypes. There were highly significant correlation coefficients between cophenetic matrices based on the genetic distance for the RAPD, ISSR, AFLP, and combined RAPD-ISSR-AFLP data (0.68, 0.78, 0.70, and 0.70, respectively). Two hypotheses were formulated to explain these results; both of them are in agreement with the results obtained using these three types of molecular markers. We conclude that when we study genotypes close related, the analysis of variability could require more than one DNA-based technique; in fact, the genetic variation present in different sources could interfere or combine with the more or less polymorphic ability, as our results showed for RAPD, ISSR and AFLP markers. Our results indicate that AFLP seemed to be the best-suited molecular assay for fingerprinting and assessing genetic relationship among genotypes of Dactylis glomerata. PMID:27070939

  6. Genetic characterization of Iranian safflower (Carthamus tinctorius) using inter simple sequence repeats (ISSR) markers.

    PubMed

    Panahi, Bahman; Ghorbanzadeh Neghab, Mahmoud

    2013-04-01

    Safflower (Carthamus tinctorious L.) is valued as a source of high quality vegetable oil. 20 ISSR primers were used to assess the genetic diversity of 18 accessions of safflower collected from different geographical regions of Iran. The ISSR primers combinations revealed 57.6 % polymorphism, among 338 genetic loci amplified from the accessions. The sum of effective number of alleles and observed number of alleles were 29.76 and 36.77, respectively. To understand genetic relationships among these cultivars, Jacquards' similarity coefficient and UPGMA clustering algorithm were applied to the ISSR marker data set. ISSR markers grouped accessions into two main clusters and four sub clusters. Also, the principal coordinate analysis (PCoA) supported the cluster analysis results. The results showed these genotypes have high genetic diversity, and can be used for alternative safflower breeding program.

  7. [Construction of the first genetic linkage map of Salvia miltiorrhiza Bge. using SSR, SRAP and ISSR markers].

    PubMed

    Zong Cheng-kun; Song, Zhen-qiao; Chen, Hai-mei; Liu, Chang; Wang, Jian-hua; Guo, Lin-lin; Liu, Tian; Pan, Yu-ling

    2015-03-01

    The first genetic linkage map of Salvia miltiorrhiza was constructed in 94 F1 individuals from an intraspecific cross by using simple sequence repeat (SSR), sequence-related amplified polymorphism (SRAP) and inter-simple sequence repeat (ISSR) markers. A total of 93 marker loci in the linkage map, consisting of 53 SSR, 38 SRAP and 2 ISSR locus were made up of eight linkage groups, covered a total length of 400.1 cm with an average distance of 4.3 cm per marker. The length of linkage groups varied from 3.3 -132 cm and each of them included 2-23 markers, separately. The result will provide important basis for QTL mapping, map-based cloning and association studies for commercially important traits in S. miltiorrhiza.

  8. Assessment of genetic diversity in Trigonella foenum-graecum and Trigonella caerulea using ISSR and RAPD markers

    PubMed Central

    Dangi, Rakhee S; Lagu, Meena D; Choudhary, Lal B; Ranjekar, Prabhakar K; Gupta, Vidya S

    2004-01-01

    Background Various species of genus Trigonella are important from medical and culinary aspect. Among these, Trigonella foenum-graecum is commonly grown as a vegetable. This anti-diabetic herb can lower blood glucose and cholesterol levels. Another species, Trigonella caerulea is used as food in the form of young seedlings. This herb is also used in cheese making. However, little is known about the genetic variation present in these species. In this report we describe the use of ISSR and RAPD markers to study genetic diversity in both, Trigonella foenum-graecum and Trigonella caerulea. Results Seventeen accessions of Trigonella foenum-graecum and nine accessions of Trigonella caerulea representing various countries were analyzed using ISSR and RAPD markers. Genetic diversity parameters (average number of alleles per polymorphic locus, percent polymorphism, average heterozygosity and marker index) were calculated for ISSR, RAPD and ISSR+RAPD approaches in both the species. Dendrograms were constructed using UPGMA algorithm based on the similarity index values for both Trigonella foenum-graecum and Trigonella caerulea. The UPGMA analysis showed that plants from different geographical regions were distributed in different groups in both the species. In Trigonella foenum-graecum accessions from Pakistan and Afghanistan were grouped together in one cluster but accessions from India and Nepal were grouped together in another cluster. However, in both the species accessions from Turkey did not group together and fell in different clusters. Conclusions Based on genetic similarity indices, higher diversity was observed in Trigonella caerulea as compared to Trigonella foenum-graecum. The genetic similarity matrices generated by ISSR and RAPD markers in both species were highly correlated (r = 0.78 at p = 0.001 for Trigonella foenum-graecum and r = 0.98 at p = 0.001 for Trigonella caerulea) indicating congruence between these two systems. Implications of these observations in

  9. Genetic stability of micropropagated plants of Crambe abyssinica Hochst using ISSR markers.

    PubMed

    Werner, E T; Soares, T C B; Gontijo, A B P L; Souza Neto, J D; do Amaral, J A T

    2015-12-09

    Crambe (Crambe abyssinica) is a non-edible annual herb, which was first cultivated to extract oil for industry, and now has great potential for biodiesel production. The objective of this investigation was to evaluate the genetic stability of micropropagated plants of the C. abyssinica Hochst cultivar 'FMS brilhante' using polymerase chain reaction techniques based on inter-simple sequence repeat (ISSR) molecular markers. The aim was to develop a protocol for the in vitro regeneration of these plants with low genetic variation as compared to the donor plant. For micropropagation, shoot tips from in vitro germinated seedlings were used as explants and were initially cultivated for 90 days on MS medium with 5.0 μM 6-benzylaminopurine (BAP), which at 90 days, led to the highest number of shoots per explant (NSE) (12.20 shoots) being detected. After 120 days, the interaction between BAP concentration and naphthalene acetic acid (NAA) was tested, and the highest NSE was observed following exposure to 0.0/0.5 μM BAP/NAA (11.40 shoots) and 1.0/0.0 μM BAP/NAA (11.00 shoots). The highest proportion of rooting phase were observed following exposure to 0.5 μM NAA (30%). The 13 ISSR primers used to analyze genetic stability produced 91 amplification products, of which only eight bands were polymorphic and 83 were monomorphic for all 10 regenerated crambe plants, compared to the donor plant explant. These results indicate that crambe shoot tips are a highly reliable explant that can be used to micropropagate genetically true-to-type plants or to maintain genetic stability, as verified using ISSR markers.

  10. Genetic diversity revealed by morphological traits and ISSR markers in 48 Okras (Abelmoschus escullentus L.).

    PubMed

    Yuan, Cong-Ying; Wang, Ping; Chen, Pang-Pang; Xiao, Wen-Jun; Zhang, Cheng; Hu, Shuai; Zhou, Ping; Chang, Hong-Ping; He, Zhuang; Hu, Rong; Lu, Xiu-Tao; Ye, Jia-Zhuo; Guo, Xin-Hong

    2015-07-01

    Okra is a widely distributed crop in the tropics, subtropics, and warmer areas of the temperate zones. Its major potential uses as a vegetable, oil and protein source, and source of paper pulp and fuel, or biomass are compatible. It is expected to have high value of exploitation and application. Due to the limited number of molecular studies focused on okras, the methods of morphological and ISSR markers were used to analysis the genetic diversity of 48 okras in the present study. The 22 primers were picked for ISSR-PCR, and a total of 154 fragments were amplified with an overall average polymorphism of 54.55 %. We used the 154 markers to construct the dendrogram based on the unweighted pair group method with arithmetic means (UPGMA). A high level of genetic diversity was found among 48 individuals. The 48 Okras was divided into four clusters at Dice's coefficient of 0.19 with clustering analysis. Based on these data of the genetic diversity, it will be possible to exploit the available resources of okra in more valuable ways.

  11. Genetic diversity revealed by morphological traits and ISSR markers in 48 Okras (Abelmoschus escullentus L.).

    PubMed

    Yuan, Cong-Ying; Wang, Ping; Chen, Pang-Pang; Xiao, Wen-Jun; Zhang, Cheng; Hu, Shuai; Zhou, Ping; Chang, Hong-Ping; He, Zhuang; Hu, Rong; Lu, Xiu-Tao; Ye, Jia-Zhuo; Guo, Xin-Hong

    2015-07-01

    Okra is a widely distributed crop in the tropics, subtropics, and warmer areas of the temperate zones. Its major potential uses as a vegetable, oil and protein source, and source of paper pulp and fuel, or biomass are compatible. It is expected to have high value of exploitation and application. Due to the limited number of molecular studies focused on okras, the methods of morphological and ISSR markers were used to analysis the genetic diversity of 48 okras in the present study. The 22 primers were picked for ISSR-PCR, and a total of 154 fragments were amplified with an overall average polymorphism of 54.55 %. We used the 154 markers to construct the dendrogram based on the unweighted pair group method with arithmetic means (UPGMA). A high level of genetic diversity was found among 48 individuals. The 48 Okras was divided into four clusters at Dice's coefficient of 0.19 with clustering analysis. Based on these data of the genetic diversity, it will be possible to exploit the available resources of okra in more valuable ways. PMID:26261400

  12. Genetic diversity analysis of Capparis spinosa L. populations by using ISSR markers.

    PubMed

    Liu, C; Xue, G P; Cheng, B; Wang, X; He, J; Liu, G H; Yang, W J

    2015-01-01

    Capparis spinosa L. is an important medicinal species in the Xinjiang Province of China. Ten natural populations of C. spinosa from 3 locations in North, Central, and South Xinjiang were studied using morphological trait inter simple sequence repeat (ISSR) molecular markers to assess the genetic diversity and population structure. In this study, the 10 ISSR primers produced 313 amplified DNA fragments, with 52% of fragments being polymorphic. Unweighted pair-group method with arithmetic average (UPGMA) cluster analysis indicated that 10 C. spinosa populations were clustered into 3 geographically distinct groups. The Nei gene of C. spinosa populations in different regions had Diversity and Shannon's information index ranges of 0.1312-0.2001 and 0.1004-0.1875, respectively. The 362 markers were used to construct the dendrogram based on the UPGMA cluster analysis. The dendrogram indicated that 10 populations of C. spinosa were clustered into 3 geographically distinct groups. The results showed these genotypes have high genetic diversity, and can be used for an alternative breeding program.

  13. Efficacy of RAPD, ISSR and DAMD markers in assessment of genetic variability and population structure of wild Musa acuminata colla.

    PubMed

    Lamare, Animos; Rao, Satyawada Rama

    2015-07-01

    North east India is considered as one of the major biodiversity hotspots worldwide and centre of origin of several plant species including Musa. Musa acuminata Colla is known to be one of the wild progenitors of cultivated bananas and plantains. Three single primer based DNA marker techniques viz., random amplified polymorphic DNA (RAPD), inter simple sequence repeat (ISSR) and directed amplification of minisatellites DNA (DAMD) were used for diversity diagnostics among 25 genotypes of wild M. acuminata collected from Meghalaya province of north east India. A total of 58 primers (26-RAPD, 21-ISSR, and11-DAMD) yielded 451 DNA fragments, of which 395 (87.58 %) were found to be polymorphic in nature. The polymorphic information content (PIC) values were almost identical for each marker system. The resolving power of the marker system was found to be highest in RAPD (3.96) whereas ISSR resolved highest marker index (16.39) in the study. Selected amplicon data obtained through single primer amplification reactions were utilized for determination of diversity within and among the populations of M. acuminata. Nei's genetic differentiation (Gst) value (0.451) indicated higher proportion of the genetic variation within the populations which is supported by the AMOVA analysis (88 %). The study provides insight into the efficacy of RAPD, ISSR and DAMD to analyse the genetic variation existing in the wild Musa germplasm, which can further be exploited for quality trait improvement and domestication of such important horticultural crops. The genetic diversity based population structure may shed light on the genetic basis of speciation and evolution of various species within the genus Musa.

  14. Application of ISSR markers to analyze molecular relationships in Iranian jasmine (Jasminum spp.) accessions.

    PubMed

    Ghasemi Ghehsareh, Masood; Salehi, Hassan; Khosh-Khui, Morteza; Niazi, Ali

    2015-01-01

    There are many species of jasmines in different regions of Iran in natural or cultivated form, and there is no information about their genetic status. Therefore, inter-simple sequence repeat (ISSR) analysis was used to evaluate genetic variations of the 53 accessions representing eight species of Jasminum collected from different regions of Iran. A total of 21 ISSR primers were used which generated 981 bands of different sizes. Mean percentage of polymorphic bands was 90.64 %. Maximum resolving power, polymorphic information content average, and marker index values were 21.55, 0.35, and 14.42 for primers of 3, 4, and 3 respectively. The unweighted pair group method with arithmetic mean dendrogram based on Jaccard's coefficients indicated that 53 accessions were divided into two major clusters. The first major cluster was divided into two subclusters; the subcluster A included Jasminum grandiflorum L., J. officinale L., and J. azoricum L. and the subcluster B consisted of three forms of J. sambac L. (single, semi-double, and double flowers). The second major cluster was divided into two subclusters; the first subcluster (C) included J. humile L., J. primulinum Hemsl., J. nudiflorum Lindl. and the second subcluster (D) consisted of J. fruticans L. At the species level, the highest percentage of polymorphism (34.05 %), numbers of effective alleles (1.16), Shannon index (0.151), and Nei's genetic diversity (0.098) were observed in J. officinale. The lowest values of percentage polymorphism (0.011), number of effective alleles (1.009), Shannon index (0.007), and Nei's genetic diversity (0.005) were obtained for J. nudiflorum. Based on pairwise population matrix of Nei's unbiased genetic identity, the highest identity (0.85) was found between J.officinale and J. azoricum and the lowest identity (0.69) was between J. grandiflorum and J. perimulinum. Based on analysis of molecular variance, the amount of genetic variations among the eight populations was 83 %. This study

  15. Population genetics of Sargassum horneri (Fucales, Phaeophyta) in China revealed by ISSR and SRAP markers

    NASA Astrophysics Data System (ADS)

    Yu, Shenhui; Chong, Zhuo; Zhao, Fengjuan; Yao, Jianting; Duan, Delin

    2013-05-01

    Sargassum horneri is a common brown macro-alga that is found in the inter-tidal ecosystems of China. To investigate the current status of seaweed resources and provide basic data for its sustainable development, ISSR (inter simple sequence repeat) and SRAP (sequence related amplified polymorphism) markers were used to analyze the population genetics among nine natural populations of S. horneri. The nine studied populations were distributed over 2 000 km from northeast to south China. The percentage of polymorphic loci P % (ISSR, 99.44%; SRAP, 100.00%), Nei's genetic diversity H (ISSR, 0.107-0.199; SRAP, 0.100-0.153), and Shannon's information index I (ISSR, 0.157-0.291; SRAP, 0.148-0.219) indicated a fair amount of genetic variability among the nine populations. Moreover, the high degree of gene differentiation G st (ISSR, 0.654; SRAP, 0.718) and low gene flow N m (ISSR, 0.265; SRAP, 0.196) implied that there was significant among-population differentiation, possibly as a result of habitat fragmentation. The matrices of genetic distances and fixation indices ( F st) among the populations correlated well with their geographical distribution (Mantel test R =0.541 5, 0.541 8; P =0.005 0, 0.002 0 and R =0.728 6, 0.641 2; P =0.001 0, 0.001 0, respectively); the Rongcheng population in the Shandong peninsula was the only exception. Overall, the genetic differentiation agreed with the geographic isolation. The fair amount of genetic diversity that was revealed in the S. horneri populations in China indicated that the seaweed resources had not been seriously affected by external factors.

  16. Varietal Discrimination and Genetic Variability Analysis of Cymbopogon Using RAPD and ISSR Markers Analysis.

    PubMed

    Bishoyi, Ashok Kumar; Sharma, Anjali; Kavane, Aarti; Geetha, K A

    2016-06-01

    Cymbopogon is an important genus of family Poaceae, cultivated mainly for its essential oils which possess high medicinal and economical value. Several cultivars of Cymbopogon species are available for commercial cultivation in India and identification of these cultivars was conceded by means of morphological markers and essential oil constitution. Since these parameters are highly influenced by environmental factors, in most of the cases, it is difficult to identify Cymbopogon cultivars. In the present study, Random amplified polymorphic DNA (RAPD) and Inter-simple sequence repeat (ISSR) markers were employed to discriminate nine leading varieties of Cymbopogon since prior genomic information is lacking or very little in the genus. Ninety RAPD and 70 ISSR primers were used which generated 63 and 69 % polymorphic amplicons, respectively. Similarity in the pattern of UPGMA-derived dendrogram of RAPD and ISSR analysis revealed the reliability of the markers chosen for the study. Varietal/cultivar-specific markers generated from the study could be utilised for varietal/cultivar authentication, thus monitoring the quality of the essential oil production in Cymbopogon. These markers can also be utilised for the IPR protection of the cultivars. Moreover, the study provides molecular marker tool kit in both random and simple sequence repeats for diverse molecular research in the same or related genera. PMID:26922722

  17. Genetic and chemical diversity of high mucilaginous plants of Sida complex by ISSR markers and chemical fingerprinting.

    PubMed

    Thul, Sanjog T; Srivastava, Ankit K; Singh, Subhash C; Shanker, Karuna

    2011-09-01

    A method was developed based on multiple approaches wherein DNA and chemical analysis was carried out toward differentiation of important species of Sida complex that is being used for commercial preparation. Isolated DNA samples were successfully performed through PCR amplification using ISSR markers and degree of genetic diversity among the different species of Sida is compared with that of chemical diversity. For genetic fingerprint investigation, selected 10 ISSR primers generating reproducible banding patterns were used. Among the total of 63 amplicons, 62 were recorded as polymorphic, genetic similarity index deduced from ISSR profiles ranged from 12 to 51%. Based on similarity index, S. acuta and S. rhombifolia found to be most similar (51%). High number of species-specific bands played pivotal role to delineate species at genetic level. Investigation based on HPTLC fingerprints analysis revealed 23 bands representing to characteristic chemicals and similarity index ranged from 73 to 91%. Prominent distinguishable bands were observed only in S. acuta, while S. cordifolia and S. rhombifolia shared most bands making them difficult to identify on chemical fingerprint basis. This report summarizes the genotypic and chemotypic diversity and the use of profiles for authentication of species of Sida complex.

  18. [Genetic diversity revealed by ISSR molecular marker in common wheat, spelt, compactum and progeny of recurrent selection].

    PubMed

    Du, Jin-Kun; Yao, Ying-Yin; Ni, Zhong-Fu; Peng, Hui-Ru; Sun, Qi-Xin

    2002-05-01

    It is important to estimate the genetic diversity between the parents for improving the heterosis of hybrid wheat. In this study, ISSR(inter-simple sequence repeat) marker was used to measure the genetic diversity within and among common wheat (Triticum aestivum L.), spelt (Triticum spelta L.), compactum (Triticum compactum Host.) and progeny of foreign wheat-based recurrent selection, and the possibility of establishing the new heterotic group was also assessed. Forty seven genotypes were used for ISSR analysis, which included 14 common wheat, 10 spelt wheat, 11 compactum and 12 progeny of recurrent selection. Eleven of 33 ISSR primers that can produce distinguishable bands were selected for PCR amplification. A total of 238 bands were amplified, among which 207 (87%) bands were polymorphic. The polymorphic bands amplified by each primer ranged from 11 to 38, with an averaged of 18.8. The percentage of polymorphic band (80.3%) in common wheat was higher than that in progeny of recurrent selection (78.7%), spelt (75.0%) and compactum (74.9%). The 238 polymorphic products were used to calculate Nei's similarity index (GS) and the genetic distance (GD). It was found that the mean genetic distance between different wheat types (0.3115-0.3442) was obviously higher than that within common wheat (0.2743), spelt (0.2351), compactum (0.2622). In addition, progeny of recurrent selection also showed much higher genetic distance with other three wheat types (0.3217, 0.3256, 0.3198). The cluster analysis was performed based on the genetic distance (GD) matrix by using UPGMA method. Common wheat, spelt, compactum and progeny of recurrent selection were classified into four different groups. In this study, ISSR marker was firstly used to assess genetic diversity among common wheat, spelt, compactum and progeny of recurrent selection, and can differentiate the wheat cultivars (lines) that selected from the same cross combination. It was concluded that spelt, compactum and progeny

  19. Comprehensive genetic discrimination of Leonurus cardiaca populations by AFLP, ISSR, RAPD and IRAP molecular markers.

    PubMed

    Khadivi-Khub, Abdollah; Soorni, Aboozar

    2014-06-01

    Leonurus cardiaca is well known for its medicinal importance. In this investigation, genotypic characterization of this species from six eco-geographical regions of Iran was evaluated by four molecular techniques (AFLP, RAPD, ISSR and IRAP). A total of 899 polymorphic fragments were detected by used molecular markers (AFLP = 356, RAPD = 325, ISSR = 113 and IRAP = 105) with an overall average polymorphism of 81.24%. Genetic variation calculated using Shannon's Information index (I) and Nei's gene diversity index (H) showed high genetic diversity in studied germplasm. Also, analysis of molecular variance showed high genetic variation among (55%) and within populations (45%). UPGMA dendrogram constructed from combined data of molecular markers distinguished studied populations in accordance with the results obtained by each marker which all individuals were clearly differentiated into two major clusters. The correlation coefficients were statistically significant for all marker systems with the highest correlation between similarity matrixes of RAPD and ISSR markers (r = 0.82). The present results have an important implication for L. cardiaca germplasm characterization, improvement, and conservation. Furthermore, the characterized individuals exhibited a great deal of molecular variation and they seem to have a rich gene pool for breeding programs.

  20. Analysis of genetic diversity in Larix gmelinii (Pinaceae) with RAPD and ISSR markers.

    PubMed

    Zhang, L; Zhang, H G; Li, X F

    2013-01-01

    Dahurian larch (Larix gmelinii), a deciduous conifer, is the northernmost tree, native to eastern Siberia and nearby regions of China. We used growth traits and molecular markers to assess genetic variation in different L. gmelinii growing regions; 105 individual samples were collected from seven regions of the Qingshan Forestry Centre, Heilongjiang Province, China. The greatest genetic regional variation was seen in the Youhao area, based on coefficients of variation for tree height, diameter and volume (14.73, 28.25, and 55.27%, respectively). Analysis using molecular markers showed rich genetic diversity. The RAPD and ISSR methods both indicated that most variation came from within populations. The seven regions were divided into two groups (Daxing'an and Xiaoxing'an Mountain ranges) by RAPD cluster analysis: Tianchi, Xiaojiuya, Yuanjiang, and Taiping regions were placed in the first group at a genetic distance of 0.08; while the other regions were in the second group. The correlation between RAPD markers and geographical distance was significant, with a correlation coefficient of 0.752.

  1. Genetic variation assessment of acid lime accessions collected from south of Iran using SSR and ISSR molecular markers.

    PubMed

    Sharafi, Ata Allah; Abkenar, Asad Asadi; Sharafi, Ali; Masaeli, Mohammad

    2016-01-01

    Iran has a long history of acid lime cultivation and propagation. In this study, genetic variation in 28 acid lime accessions from five regions of south of Iran, and their relatedness with other 19 citrus cultivars were analyzed using Simple Sequence Repeat (SSR) and Inter-Simple Sequence Repeat (ISSR) molecular markers. Nine primers for SSR and nine ISSR primers were used for allele scoring. In total, 49 SSR and 131 ISSR polymorphic alleles were detected. Cluster analysis of SSR and ISSR data showed that most of the acid lime accessions (19 genotypes) have hybrid origin and genetically distance with nucellar of Mexican lime (9 genotypes). As nucellar of Mexican lime are susceptible to phytoplasma, these acid lime genotypes can be used to evaluate their tolerance against biotic constricts like lime "witches' broom disease".

  2. Identification and validation of a new male sex-specific ISSR marker in pointed gourd (Trichosanthes dioica Roxb.).

    PubMed

    Adhikari, Sinchan; Saha, Soumen; Bandyopadhyay, Tapas Kumar; Ghosh, Parthadeb

    2014-01-01

    The aim of the present study was to develop a genetic sex marker for the pointed gourd (Trichosanthes dioica Roxb.) to allow gender determination at any stage in the life cycle. Screening of genomic DNA with intersimple sequence repeat (ISSR) primers was used to discover sex-specific touch-down polymerase chain reaction (Td-PCR) amplification products. Using pooled DNA from male and female genotypes and 42 ISSR primers, a putative male specific marker (~550 bp) was identified. DNA marker specific to male is an indication of existence of nonepigenetic factors involved in gender development in pointed gourd. The ISSR technique has proved to be a reliable technique in gender determination of pointed gourd genotypes at the seedling phenophase. The sex marker developed here could also be used as a starting material towards sequence characterization of sex linked genes for better understanding the developmental as well as evolutionary pathways in sexual dimorphism. PMID:25538949

  3. Identification and Validation of a New Male Sex-Specific ISSR Marker in Pointed Gourd (Trichosanthes dioica Roxb.)

    PubMed Central

    Adhikari, Sinchan; Saha, Soumen; Bandyopadhyay, Tapas Kumar

    2014-01-01

    The aim of the present study was to develop a genetic sex marker for the pointed gourd (Trichosanthes dioica Roxb.) to allow gender determination at any stage in the life cycle. Screening of genomic DNA with intersimple sequence repeat (ISSR) primers was used to discover sex-specific touch-down polymerase chain reaction (Td-PCR) amplification products. Using pooled DNA from male and female genotypes and 42 ISSR primers, a putative male specific marker (~550 bp) was identified. DNA marker specific to male is an indication of existence of nonepigenetic factors involved in gender development in pointed gourd. The ISSR technique has proved to be a reliable technique in gender determination of pointed gourd genotypes at the seedling phenophase. The sex marker developed here could also be used as a starting material towards sequence characterization of sex linked genes for better understanding the developmental as well as evolutionary pathways in sexual dimorphism. PMID:25538949

  4. Genetic diversity in three natural populations of Pitcairnia flammea (l.) John (Bromeliaceae) estimated by ISSR markers.

    PubMed

    Souza-Sobreira, F B; Souza, G B; Rosado, C C G; Miranda, F D; Soares, T C B; Gontijo, A B P L

    2015-01-01

    Bromeliads are greatly represented in the Atlantic Forest, although many species are threatened with extinction owing to habitat fragmentation and intense extraction for ornamental purposes. Therefore, it is necessary to conduct studies generating knowledge about genetic diversity and the distribution of this diversity among and within natural populations to establish conservation strategies. These studies can be performed with the use of molecular markers. Molecular markers are advantageous for studies of natural populations, for conservation programs, and to aid in properly classifying plant species. This study aimed to evaluate the genetic diversity among and within natural populations of Pitcairnia flammea, occurring in three fragments of the Atlantic Forest in the southern State of Espírito Santo through the use of inter-simple sequence repeat (ISSR) markers. DNA samples from 55 individuals were amplified with 18 ISSR primers, generating 180 bands, 159 of which were polymorphic. The Shannon genetic diversity index ranged from 0.348 to 0.465, with an average of 0.412. The Bayesian approach for the molecular data indicated the existence of two genetic groups. Analysis of molecular variance indicated the existence of 90.3% diversity within the population and 9.74% among populations. The amount of genetic differentiation of populations was moderate (0.0974), indicating that gene flow rates may be enough to counteract the effects of genetic drift. Greater genetic variability found in population B indicates that this area is an important source of genetic variability. PMID:26634557

  5. Genetic diversity in three natural populations of Pitcairnia flammea (l.) John (Bromeliaceae) estimated by ISSR markers.

    PubMed

    Souza-Sobreira, F B; Souza, G B; Rosado, C C G; Miranda, F D; Soares, T C B; Gontijo, A B P L

    2015-12-03

    Bromeliads are greatly represented in the Atlantic Forest, although many species are threatened with extinction owing to habitat fragmentation and intense extraction for ornamental purposes. Therefore, it is necessary to conduct studies generating knowledge about genetic diversity and the distribution of this diversity among and within natural populations to establish conservation strategies. These studies can be performed with the use of molecular markers. Molecular markers are advantageous for studies of natural populations, for conservation programs, and to aid in properly classifying plant species. This study aimed to evaluate the genetic diversity among and within natural populations of Pitcairnia flammea, occurring in three fragments of the Atlantic Forest in the southern State of Espírito Santo through the use of inter-simple sequence repeat (ISSR) markers. DNA samples from 55 individuals were amplified with 18 ISSR primers, generating 180 bands, 159 of which were polymorphic. The Shannon genetic diversity index ranged from 0.348 to 0.465, with an average of 0.412. The Bayesian approach for the molecular data indicated the existence of two genetic groups. Analysis of molecular variance indicated the existence of 90.3% diversity within the population and 9.74% among populations. The amount of genetic differentiation of populations was moderate (0.0974), indicating that gene flow rates may be enough to counteract the effects of genetic drift. Greater genetic variability found in population B indicates that this area is an important source of genetic variability.

  6. Multilocus ISSR Markers Reveal Two Major Genetic Groups in Spanish and South African Populations of the Grapevine Fungal Pathogen Cadophora luteo-olivacea

    PubMed Central

    Gramaje, David; León, Maela; Santana, Marcela; Crous, Pedro W.; Armengol, Josep

    2014-01-01

    Cadophora luteo-olivacea is a lesser-known fungal trunk pathogen of grapevine which has been recently isolated from vines showing decline symptoms in grape growing regions worldwide. In this study, 80 C. luteo-olivacea isolates (65 from Spain and 15 from South Africa) were studied. Inter-simple-sequence repeat-polymerase chain reaction (ISSR-PCR) generated 55 polymorphic loci from four ISSR primers selected from an initial screen of 13 ISSR primers. The ISSR markers revealed 40 multilocus genotypes (MLGs) in the global population. Minimum spanning network analysis showed that the MLGs from South Africa clustered around the most frequent genotype, while the genotypes from Spain were distributed all across the network. Principal component analysis and dendrograms based on genetic distance and bootstrapping identified two highly differentiated genetic clusters in the Spanish and South African C. luteo-olivacea populations, with no intermediate genotypes between these clusters. Movement within the Spanish provinces may have occurred repeatedly given the frequent retrieval of the same genotype in distant locations. The results obtained in this study provide new insights into the population genetic structure of C. luteo-olivacea in Spain and highlights the need to produce healthy and quality planting material in grapevine nurseries to avoid the spread of this fungus throughout different grape growing regions. PMID:25310345

  7. Morphological and molecular profiling of Spirogyra from northeastern and northern Thailand using inter simple sequence repeat (ISSR) markers

    PubMed Central

    Wongsawad, Pheravut; Peerapornpisal, Yuwadee

    2014-01-01

    Green algae, Spirogyra (Chlorophyta), are found in a wide range of habitats including small stagnant water bodies, rivers, and streams. Species identification of Spirogyra based on morphological characteristics has proven to be a difficult process. An accurate identification method is required to evaluate genetic variations. This study is aimed at investigating the molecular profiling of 19 samples of Spirogyra from northern and northeastern Thailand. The morphological characteristics of each sample were recorded, viz. cell dimensions (width and length), along with the number and arrangement of chloroplast spirals/pyrenoids. With regard to a correlation of the biological and ecological parameters, conductivity was clearly significantly related to the number of pyrenoids. While DO is negatively related to the number of chloroplast spirals. Molecular studies with 10 ISSR primers were amplified to examine the DNA fingerprints. Morphological characters were determined to be significantly different by revealing 5 traits (P < 0.05) for all specimens. In addition, the DNA markers of all specimens were investigated using 10 ISSR primers. The results show that the PCR technique amplified 108 fragments. An analysis of the DNA fragments grouped all samples by ISRR-PCR, which were then separated into two groups according to their distribution. PMID:26150742

  8. Morphological and molecular profiling of Spirogyra from northeastern and northern Thailand using inter simple sequence repeat (ISSR) markers.

    PubMed

    Wongsawad, Pheravut; Peerapornpisal, Yuwadee

    2015-07-01

    Green algae, Spirogyra (Chlorophyta), are found in a wide range of habitats including small stagnant water bodies, rivers, and streams. Species identification of Spirogyra based on morphological characteristics has proven to be a difficult process. An accurate identification method is required to evaluate genetic variations. This study is aimed at investigating the molecular profiling of 19 samples of Spirogyra from northern and northeastern Thailand. The morphological characteristics of each sample were recorded, viz. cell dimensions (width and length), along with the number and arrangement of chloroplast spirals/pyrenoids. With regard to a correlation of the biological and ecological parameters, conductivity was clearly significantly related to the number of pyrenoids. While DO is negatively related to the number of chloroplast spirals. Molecular studies with 10 ISSR primers were amplified to examine the DNA fingerprints. Morphological characters were determined to be significantly different by revealing 5 traits (P < 0.05) for all specimens. In addition, the DNA markers of all specimens were investigated using 10 ISSR primers. The results show that the PCR technique amplified 108 fragments. An analysis of the DNA fragments grouped all samples by ISRR-PCR, which were then separated into two groups according to their distribution.

  9. Analysis of the genetic diversity of Chinese native Cannabis sativa cultivars by using ISSR and chromosome markers.

    PubMed

    Zhang, L G; Chang, Y; Zhang, X F; Guan, F Z; Yuan, H M; Yu, Y; Zhao, L J

    2014-01-01

    Hemp (Cannabis sativa) is an important fiber crop, and native cultivars exist widely throughout China. In the present study, we analyzed the genetic diversity of 27 important Chinese native hemp cultivars, by using inter-simple sequence repeats (ISSR) and chromosome markers. We determined the following chromosome formulas: 2n = 20 = 14m + 6sm; 2n = 20 = 20m; 2n = 20 = 18m + 2sm; 2n = 20 = 16m + 4sm; and 2n = 20 = 12m + 8sm. The results of our ISSR analysis revealed the genetic relationships among the 27 cultivars; these relationships were analyzed by using the unweighted pair-group method based on DNA polymorphism. Our results revealed that all of the native cultivars showed considerable genetic diversity. At a genetic distance of 0.324, the 27 varieties could be classified into five categories; this grouping corresponded well with the chromosome formulas. All of the investigated hemp cultivars represent relatively primitive types; moreover, the genetic distances show a geographical distribution, with a small amount of regional hybridity. PMID:25511032

  10. Analysis of the genetic diversity of Chinese native Cannabis sativa cultivars by using ISSR and chromosome markers.

    PubMed

    Zhang, L G; Chang, Y; Zhang, X F; Guan, F Z; Yuan, H M; Yu, Y; Zhao, L J

    2014-12-12

    Hemp (Cannabis sativa) is an important fiber crop, and native cultivars exist widely throughout China. In the present study, we analyzed the genetic diversity of 27 important Chinese native hemp cultivars, by using inter-simple sequence repeats (ISSR) and chromosome markers. We determined the following chromosome formulas: 2n = 20 = 14m + 6sm; 2n = 20 = 20m; 2n = 20 = 18m + 2sm; 2n = 20 = 16m + 4sm; and 2n = 20 = 12m + 8sm. The results of our ISSR analysis revealed the genetic relationships among the 27 cultivars; these relationships were analyzed by using the unweighted pair-group method based on DNA polymorphism. Our results revealed that all of the native cultivars showed considerable genetic diversity. At a genetic distance of 0.324, the 27 varieties could be classified into five categories; this grouping corresponded well with the chromosome formulas. All of the investigated hemp cultivars represent relatively primitive types; moreover, the genetic distances show a geographical distribution, with a small amount of regional hybridity.

  11. Genetic diversity analysis of wild close relatives of barley from Tibet and the Middle East by ISSR and SSR markers.

    PubMed

    Wang, Aihua; Yu, Zhiyong; Ding, Yi

    2009-04-01

    The genetic diversity analysis of 90 barley samples, including 45 wild close relatives of barley from the Tibet region of China and 45 wild accessions from different countries throughout the Middle East, were carried out using ISSR and SSR markers. The results showed that Tibetan wild close relatives of barley had a higher genetic diversity than those from the Middle East. Ten ISSR primers amplified 91 allelic variants, of which 79 were polymorphic (86.81%), in the Tibetan genotypes and 82 allelic variants, of which 66 were polymorphic (80.49%), in the Middle East genotypes. Eleven primer pairs of SSR markers amplified 100 allelic variants among the Tibetan genotypes with 100 polymorphic bands (100%). Among the Middle East genotypes, 78 allelic variants were produced containing 77 polymorphic bands (98.72%). Moreover, the total gene diversity analysis (HT) values of Tibetan barley (0.227 for ISSRs and 0.126 for SSRs) were higher than those of Middle East (0.212 for ISSRs and 0.102 for SSRs). Cluster analysis of the ISSR and SSR results by the UPGMA method revealed two distinct groups correlated with the geographic origin of sampling. These results offer a new evidence for the theory of the origin of Hordeum vulgare L. PMID:19304270

  12. Genetic diversity in mazandaranian native cattle: a comparison with Holstein cattle, using ISSR marker.

    PubMed

    Pashaei, S; Azari, M A; Hasani, S; Khanahmadi, A; Rostamzadeh, J

    2009-05-01

    This study was carried out to investigate genetic diversity in Mazandaranian native cattle population comparised to the Holstein breed, using Inter Simple Sequence Repeats (ISSR) marker. A total of 175 animals, including 71 native and 104 cattle of Holstein breed were screened. The extraction of DNA samples were carried out, using modified salting out method. A 19-mer oligonucleotide, (GA)9C, was used as primer in PCR reactions. The PCR products showed 15 different fragments with length ranged from 120 to 1600 bp in the two breeds.. Genetic variation indexes, including effective number of alleles, Shannon index, Nei's gene diversity and standard genetic distance were estimated, using POPGene software. Generally, the estimated genetic variation indexes showed low levels of diversity in the two breeds. However, Nei's gene diversity and Shannon index estimation was observed almost two folds in native cattle compared to Holstein breed. Less levels of diversity in Holstein cattle may be because of applying intensive selection programs. Conversely, native cattle have been less affected by selection. Therefore, it seems that Mazandaranian native cattle probably are better for breeding programs than Holstein cattle. Results showed that ISSR Markers are reliable and can be used in genetic diversity investigations. PMID:19634477

  13. Molecular identification and phylogenetic relationship of green algae, Spirogyra ellipsospora (Chlorophyta) using ISSR and rbcL markers.

    PubMed

    Wongsawad, Pheravut; Peerapornpisal, Yuwadee

    2014-11-01

    Spirogyra is found in a wide range of habitats, including small stagnant water bodies, rivers, and streams. Spirogyra ellipsospora is common in northern Thailand. Species identification of the Spirogyra species based only on morphological characteristics can be difficult. A reliable and accurate method is required to evaluate genetic variations. This study aims to apply molecular approaches for the identification of S. ellipsospora using microsatellites and rbcL markers. Based on DNA sequencing, the rbcL gene was sequenced and the data was analyzed using the BLAST (Basic Local Alignment Search Tool) program in the NCBI (National Center for Biotechnology Information) database. The sequence of S. ellipsospora from this study revealed definitive identity matches in the range of 99% for the consensus sequences of S. ellipsospora. The 10 primers of ISSR could be amplified by 92 amplification fragments. The DNA fragments and the rbcL sequence data grouped the Spirogyra specimens into two distinct clusters.

  14. Dataset of SSR markers for ISSR-Suppression-PCR to detect genetic variation in Garcinia mangostana L. in Peninsular Malaysia.

    PubMed

    Samsir, Sri A'jilah; Bunawan, Hamidun; Yen, Choong Chee; Noor, Normah Mohd

    2016-09-01

    In this dataset, we present 15 Simple Sequence Repeat (SSR) markers with the motifs (AC)n, (GA)n, and (AC)n(AG)n using a ISSR-Suppression-PCR technique in order to discriminate Garcinia mangostana from diverse geographical origins in Peninsular Malaysia. A few loci showed differences between 3 and 6 bp in allele size, indicating that there are some polymorphisms between individuals correlating to the number of SSR repeats that may be useful for differentiate of genotypes. Collectively, these data show that the ISSR-Suppression-PCR is a valuable method to illustrate genetic variation of selected G. mangostana in Malaysia. PMID:27617279

  15. Dataset of SSR markers for ISSR-Suppression-PCR to detect genetic variation in Garcinia mangostana L. in Peninsular Malaysia.

    PubMed

    Samsir, Sri A'jilah; Bunawan, Hamidun; Yen, Choong Chee; Noor, Normah Mohd

    2016-09-01

    In this dataset, we present 15 Simple Sequence Repeat (SSR) markers with the motifs (AC)n, (GA)n, and (AC)n(AG)n using a ISSR-Suppression-PCR technique in order to discriminate Garcinia mangostana from diverse geographical origins in Peninsular Malaysia. A few loci showed differences between 3 and 6 bp in allele size, indicating that there are some polymorphisms between individuals correlating to the number of SSR repeats that may be useful for differentiate of genotypes. Collectively, these data show that the ISSR-Suppression-PCR is a valuable method to illustrate genetic variation of selected G. mangostana in Malaysia.

  16. Genetic diversity of Toona sinensis Roem in China revealed by ISSR and SRAP markers.

    PubMed

    Xing, P Y; Liu, T; Song, Z Q; Li, X F

    2016-07-29

    Toona sinensis Roem has an important value as a type of traditional vegetable and Chinese medicinal herb, and is also a valuable source of wood in China. In this study, we used the inter-simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) markers to assess the level and pattern of genetic diversity in five domesticated T. sinensis populations in China. Our results indicated a relatively low level of genetic diversity both at species (Hs = 0.1662, 0.2098, respectively) and population levels (Hs = 0.0978, 0.1145, respectively). Molecular variance analyses revealed a relatively high degree of differentiation among populations (GST = 0.3901, 0.4498), and low levels of gene flow (Nm = 0.7816 and 0.6116). We divided the five populations into two groups by cluster analysis: group one consists of populations collected from the south part of China (e.g., Yuxi, Yunan Province and Zuanjiang, Chongqing Municipality), and group two contains those cultivated in north part of China (e.g., Hengshui, Hebei Province, Jinan and Rizhao, Shandong Province). The correlation of genetic relationships among populations fits well with their geographical distribution (Mantel test; r = 0.7236 and 0.6789, respectively). Asexual propagation, limited gene flow and geographic isolation are most likely the key factors associated with the observed genetic structure of T. sinensis grown in China. The present study indicated that both ISSR and SRAP markers were effective and reliable for assessing the degree of T. sinensis genetic variations.

  17. Assessment of diversity in Harpagophytum with RAPD and ISSR markers provides evidence of introgression.

    PubMed

    Muzila, Mbaki; Werlemark, Gun; Ortiz, Rodomiro; Sehic, Jasna; Fatih, Moneim; Setshogo, Moffat; Mpoloka, Wata; Nybom, Hilde

    2014-10-01

    The genus Harpagophytum has two species: H. procumbens which is an important medicinal plant in southern Africa, and H. zeyheri. Genetic diversity in 96 samples, obtained by germinating seeds collected from Botswana, was assessed using six inter-simple sequence repeat (ISSR) and 10 random amplified polymorphic DNA (RAPD) primers. These DNA markers yielded a total of 138 polymorphic bands. Polymorphism information content (PIC) ranged from 0.06 to 0.39 for ISSR primers, and from 0.09 to 0.43 for RAPD primers. Jaccard's similarity coefficients were highest when seedlings derived from the same fruit capsule were compared, while seedlings from different fruits on the same plant had intermediate values. The lowest values were recorded among seedlings from different plants. These results were consistent with an outcrossing breeding system in Harpagophytum. Analysis of molecular variance revealed significant differentiation (P<0.01) between taxonomic units within Harpagophytum. About 39% of the variability occurred between the two species, H. procumbens and H. zeyheri. Plants with an intermediate morphology, i.e. putative hybrids (PH), showed 21% differentiation when compared with H. procumbens ssp. procumbens (PP), and 19% when compared with H. procumbens ssp. transvaalense (PT) or with H. zeyheri (ZZ). In addition, a deviating variant of PT was identified, here termed 'procumbens new variety' (PN). PN showed only 9% differentiation when compared with PT, 22% when compared with PP or with PH, and 41% when compared with ZZ. Considerable differentiation between the two Harpagophytum species was revealed also by a cluster analysis. Introgression was, however, suggested by the intermediate position of the putative hybrid plants in a principal component analysis while inter-specific gene flow was shown by a Bayesian genetic structure analysis. PMID:25363276

  18. Analysis of genetic diversity through AFLP, SAMPL, ISSR and RAPD markers in Tribulus terrestris, a medicinal herb.

    PubMed

    Sarwat, Maryam; Das, S; Srivastava, P S

    2008-03-01

    Tribulus terrestris is well known for its medicinal importance in curing urino-genital disorders. Amplified fragment length polymorphism (AFLP), selective amplification of microsatellite polymorphic loci (SAMPL), inter-simple sequence repeat (ISSR) and randomly amplified polymorphic DNA (RAPD) markers were used for the first time for the detection of genetic polymorphism in this medicinal herb from samples collected from various geographical regions of India. Six assays each of AFLP and SAMPL markers and 21 each of ISSR and RAPD markers were utilized. AFLP yielded 500 scorable amplified products, of which 82.9% were polymorphic. SAMPL primers amplified 488 bands, 462 being polymorphic (94.7%). The range of amplified bands was 66 [(TC)(8)G + M-CAG] to 98 [(CA)(6)AG + M-CAC] and the percentage polymorphism, 89.9 [from (CT)(4)C (AC)(4)A + M-CTG] to 100 [from (GACA)(4) + M-CTA]. The ISSR primers amplified 239 bands of 0.4-2.5 kb, 73.6% showed polymorphism. The amplified products ranged from 5 to 16 and the percentage polymorphism 40-100. RAPD assays produced 276 bands, of which 163 were polymorphic (59%). Mantel test employed for detection of goodness of fit established cophenetic correlation values above 0.9 for all the four marker systems. The dendrograms and PCA plots derived from the binary data matrices of the four marker systems are highly concordant. High bootstrap values were obtained at major nodes of phenograms through WINBOOT software. The relative efficiency of the four molecular marker systems calculated on the basis of multiplex ratio, marker index and average heterozygosity revealed SAMPL to be the best. Distinct DNA fingerprinting profile, unique to every geographical region could be obtained with all the four molecular marker systems. Clustering can be a good indicator for clear separation of genotypes from different regions in well-defined groups that are supported by high bootstrap values.

  19. Genetic diversity of Paris polyphylla var. yunnanensis, a traditional Chinese medicinal herb, detected by ISSR markers.

    PubMed

    He, Jun; Wang, Hong; Li, De-Zhu; Chen, Shao-Feng

    2007-10-01

    Paris polyphylla Smith var. yunnanensis (Franch.) Hand.-Mazz. is an important Chinese medicinal herb. Because of overharvesting, the wild populations of this herb have greatly declined and become fragmentized. In this paper, ISSR markers were used to determine the genetic diversity and genetic structure of this variety represented by a total of 153 individuals from three natural populations and three cultivated populations. Fourteen primers produced a total of 251 bands, of which 227 were polymorphic (PPB=90.44%). For the natural populations, the results showed that genetic differentiation was mainly within populations (GST=0.1952), with low genetic diversity at the population level. At the population level, genetic diversity of the cultivated populations was relatively higher than that of the natural populations (PPB=57.24% vs. 53.38%, HE=0.153 vs. 0.151, HO=0.241 vs. 0.235). This pattern can be explained by the recent introduction and artificial selection of cultivars from comparatively wide areas of origin, and subsequent gene flow among populations in cultivation. Although the neighbour-joining cluster analysis seemed to suggest that there was conspicuous genetic differentiation between the natural and cultivated populations, the AMOVA showed that only 4.84% of the total variance existed between groups of natural and cultivated populations, while 67.51% of the variance occurred within populations. In the end, some suggestions for conservation of this important herb are proposed. PMID:17973204

  20. Genetic diversity of Paris polyphylla var. yunnanensis, a traditional Chinese medicinal herb, detected by ISSR markers.

    PubMed

    He, Jun; Wang, Hong; Li, De-Zhu; Chen, Shao-Feng

    2007-10-01

    Paris polyphylla Smith var. yunnanensis (Franch.) Hand.-Mazz. is an important Chinese medicinal herb. Because of overharvesting, the wild populations of this herb have greatly declined and become fragmentized. In this paper, ISSR markers were used to determine the genetic diversity and genetic structure of this variety represented by a total of 153 individuals from three natural populations and three cultivated populations. Fourteen primers produced a total of 251 bands, of which 227 were polymorphic (PPB=90.44%). For the natural populations, the results showed that genetic differentiation was mainly within populations (GST=0.1952), with low genetic diversity at the population level. At the population level, genetic diversity of the cultivated populations was relatively higher than that of the natural populations (PPB=57.24% vs. 53.38%, HE=0.153 vs. 0.151, HO=0.241 vs. 0.235). This pattern can be explained by the recent introduction and artificial selection of cultivars from comparatively wide areas of origin, and subsequent gene flow among populations in cultivation. Although the neighbour-joining cluster analysis seemed to suggest that there was conspicuous genetic differentiation between the natural and cultivated populations, the AMOVA showed that only 4.84% of the total variance existed between groups of natural and cultivated populations, while 67.51% of the variance occurred within populations. In the end, some suggestions for conservation of this important herb are proposed.

  1. Analysis of genetic diversity of Brassica rapa var. chinensis using ISSR markers and development of SCAR marker specific for Fragrant Bok Choy, a product of geographic indication.

    PubMed

    Shen, X L; Zhang, Y M; Xue, J Y; Li, M M; Lin, Y B; Sun, X Q; Hang, Y Y

    2016-04-25

    Non-heading Chinese cabbage [Brassica rapa var. chinensis (Linnaeus) Kitamura] is a popular vegetable and is also used as a medicinal plant in traditional Chinese medicine. Fragrant Bok Choy is a unique accession of non-heading Chinese cabbage and a product of geographic indication certified by the Ministry of Agriculture of China, which is noted for its rich aromatic flavor. However, transitional and overlapping morphological traits can make it difficult to distinguish this accession from other non-heading Chinese cabbages. This study aimed to develop a molecular method for efficient identification of Fragrant Bok Choy. Genetic diversity analysis, based on inter-simple sequence repeat molecular markers, was conducted for 11 non-heading Chinese cabbage accessions grown in the Yangtze River Delta region. Genetic similarity coefficients between the 11 accessions ranged from 0.5455 to 0.8961, and the genetic distance ranged from 0.0755 to 0.4475. Cluster analysis divided the 11 accessions into two major groups. The primer ISSR-840 amplified a fragment specific for Fragrant Bok Choy. A pair of specific sequence-characterized amplified region (SCAR) primers based on this fragment amplified a target band in Fragrant Bok Choy individuals, but no band was detected in individuals of other accessions. In conclusion, this study has developed an efficient strategy for authentication of Fragrant Bok Choy. The SCAR marker described here will facilitate the conservation and utilization of this unique non-heading Chinese cabbage germplasm resource.

  2. Analysis of genetic diversity of Brassica rapa var. chinensis using ISSR markers and development of SCAR marker specific for Fragrant Bok Choy, a product of geographic indication.

    PubMed

    Shen, X L; Zhang, Y M; Xue, J Y; Li, M M; Lin, Y B; Sun, X Q; Hang, Y Y

    2016-01-01

    Non-heading Chinese cabbage [Brassica rapa var. chinensis (Linnaeus) Kitamura] is a popular vegetable and is also used as a medicinal plant in traditional Chinese medicine. Fragrant Bok Choy is a unique accession of non-heading Chinese cabbage and a product of geographic indication certified by the Ministry of Agriculture of China, which is noted for its rich aromatic flavor. However, transitional and overlapping morphological traits can make it difficult to distinguish this accession from other non-heading Chinese cabbages. This study aimed to develop a molecular method for efficient identification of Fragrant Bok Choy. Genetic diversity analysis, based on inter-simple sequence repeat molecular markers, was conducted for 11 non-heading Chinese cabbage accessions grown in the Yangtze River Delta region. Genetic similarity coefficients between the 11 accessions ranged from 0.5455 to 0.8961, and the genetic distance ranged from 0.0755 to 0.4475. Cluster analysis divided the 11 accessions into two major groups. The primer ISSR-840 amplified a fragment specific for Fragrant Bok Choy. A pair of specific sequence-characterized amplified region (SCAR) primers based on this fragment amplified a target band in Fragrant Bok Choy individuals, but no band was detected in individuals of other accessions. In conclusion, this study has developed an efficient strategy for authentication of Fragrant Bok Choy. The SCAR marker described here will facilitate the conservation and utilization of this unique non-heading Chinese cabbage germplasm resource. PMID:27173238

  3. ISSR markers in wild species of Passiflora L. (Passifloraceae) as a tool for taxon selection in ornamental breeding.

    PubMed

    Sousa, A G R; Souza, M M; Melo, C A F; Sodré, G A

    2015-01-01

    Inter simple sequence repeat (ISSR) molecular markers were developed and used to investigate interspecific genetic variation in 25 wild species of Passiflora preserved in an active germplasm bank (BAG-Passifloras); intraspecific diversity was also analyzed in P. cincinnata accessions. Of 31 primers tested, 20 identified polymorphic loci with a total of 331 bands, suggesting high polymorphism in the sample. Interspecific polymorphism was greater than intraspecific polymorphism. This is a common finding in studies of genetic variation using dominant markers. The ISSRs revealed species-specific amplification bands in 11 species; these bands ranged from 200 to 1000 bp, and they will be of use for developing SCAR markers for the identification of germplasm in further studies. The use of Jaccard's similarity coefficient to obtain a dendrogram by the UPGMA clustering method distributed the taxa into five major groups, with differences among grouping with respect to principal coordinate analysis. Despite the high cophenetic correlation coefficient (r = 0.94) of the dendrogram, taxonomic inconsistencies were observed; similar irregularities have been reported previously in studies using dominant markers. Intraspecific analysis of P. cincinnata accessions revealed a larger genetic distance between those from Bahia (P2) and from Minas Gerais (P2), indicating that both accessions have considerable potential as parents in a genetic improvement program for this species. PMID:26782501

  4. [Genetic relationship and parent selection of some Sarcandra glabra resources based on ISSR].

    PubMed

    Wei, Yi-Cong; Chen, Ying; Luo, Lin-Quan; Yang, Qun-Xiong; Chen, Yi-Juan; Liang, Yi-Chi

    2014-12-01

    The study is aimed to assess the genetic diversity and genetic relationship of 18 Sarcandra glabra resources from different populations,and guide parent selection of cross breeding between these resources. The molecular marker technique ISSR was used to investigate the genetic diversity of the 18 resources. Data was analyzed by POPGEN 32, and a cluster diagram was presented by UPGMA. One hundred and ninety-eight amplified fragments were obtained using 23 ISSR primers. One hundred and eighty-four polymorphic loci were identified. Nei's genetic diversity index (h) was 0.32, Shannon diversity index (I) was 0.485 4. The genetic similarity coefficient among the resources ranged from 0.383 8 to 0.878 8 in an average of 0.661 2. The genetic distance between sample S2 and sample S18 was the farthest, so as between sample S3 and sample S18 both Nei's genetic distance was 0.957 5, The genetic distance between sample S4 and sample S5 was the closest, the Nei's genetic distance was 0.129 2,and the sample S1, S2, S3, S7, S10 were significantly different from the others based on the clustering analysis, the three groups S2 vs S3, S2 vs S6, S2 vs S18 were the best parent group selection. There was a middle level of genetic differentiation in the resources. The genetic distance between resources gives useful information to guide parent selection of cross breeding.

  5. Genetic stability of micropropagated almond plantlets, as assessed by RAPD and ISSR markers.

    PubMed

    Martins, M; Sarmento, D; Oliveira, M M

    2004-12-01

    Almond shoots produced by axillary branching from clone VII derived from a seedling of cultivar Boa Casta were evaluated for somaclonal variation using randomly amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) analysis. To verify genetic stability we compared RAPD and ISSR patterns of plantlets obtained after 4 and 6 years of in vitro multiplication. A total of 64 RAPD and 10 ISSR primers gave 326 distinct and reproducible band classes, monomorphic across all 22 plantlets analysed. Thus, a total of 7,172 bands were generated, exhibiting homogeneous RAPD and ISSR patterns for the plantlets tested. These results suggest that the culture conditions used for axillary branching proliferation are appropriate for clonal propagation of almond clone VII, as they do not seem to interfere with the integrity of the regenerated plantlets. These results allowed us to establish the use of axillary branching plantlets (mother-plants) as internal controls for the analysis of somaclonal variation of shoots regenerated from other in vitro culture processes performed with clone VII (adventitious regeneration, regeneration from meristem culture, virus sanitation programs and genetic engineering).

  6. Assessment of genetic diversity through RAPD, ISSR and AFLP markers in Podophyllum hexandrum: a medicinal herb from the Northwestern Himalayan region.

    PubMed

    Naik, Pradeep Kumar; Alam, Md Afroz; Singh, Harvinder; Goyal, Vinod; Parida, Swarup; Kalia, Sanjay; Mohapatra, T

    2010-04-01

    Total synthesis of podophyllotoxin is an expensive process and availability of the compound from the natural resources is an important issue for pharmaceutical companies that manufacture anticancer drugs. In order to facilitate reasoned scientific decisions on its management and conservation for selective breeding programme, genetic analysis of 28 populations was done with 19 random primers, 11 ISSR primers and 13 AFLP primer pairs. A total of 92.37 %, 83.82 % and 84.40 % genetic polymorphism among the populations of Podophyllum were detected using RAPD, ISSR and AFLP makers, respectively. Similarly the mean coefficient of gene differentiation (Gst) were 0.69, 0.63 and 0.51, indicating that 33.77 %, 29.44 % and 26 % of the genetic diversity resided within the population. Analysis of molecular variance (AMOVA) indicated that 53 %, 62 % and 64 % of the genetic diversity among the studied populations was attributed to geographical location while 47 %, 38 % and 36 % was attributed to differences in their habitats using RAPD, ISSR and AFLP markers. An overall value of mean estimated number of gene flow (Nm) were 0.110, 0.147 and 0.24 from RAPD, ISSR and AFLP markers indicating that there was limited gene flow among the sampled populations.

  7. Genetic Homogeneity Revealed Using SCoT, ISSR and RAPD Markers in Micropropagated Pittosporum eriocarpum Royle- An Endemic and Endangered Medicinal Plant

    PubMed Central

    Thakur, Julie; Dwivedi, Mayank D.; Sourabh, Pragya; Uniyal, Prem L.; Pandey, Arun K.

    2016-01-01

    Pittosporum eriocarpum Royle, a medicinally important taxon, is endemic to Uttarakhand region of Himalaya. It has become endangered due to over-collection and the loss of habitats. As raising plants through seeds in this plant is problematic, a reliable protocol for micropropagation using nodal explants has been developed. High shoot regeneration (95%) occurred in MS medium augmented with BA 0.4mg/l in combination IBA 0.6mg/l. In vitro regenerated shoots were rooted in MS medium supplemented with three auxins, of which 0.6 mg/l indole butyric acid proved to be the best for rooting (90%) with maximum number of roots per shoot. Thereafter, rooted plants were hardened and nearly 73% of rooted shoots were successfully acclimatized and established in the field. Start codon targeted (SCoT), inter simple sequence repeats (ISSR) and random amplified polymorphic DNA (RAPD) markers were used to validate the genetic homogeneity amongst nine in vitro raised plantlets with mother plant. DNA fingerprints of in vitro regenerated plantlets displayed monomorphic bands similar to mother plant, indicating homogeneity among the micropropagated plants with donor mother plant. The similarity values were calculated based on SCoT, ISSR and RAPD profiles which ranged from 0.89 to 1.00, 0.91 to 1.00 and 0.95 to 1.00 respectively. The dendrograms generated through Unweighted Pair Group Method with arithmetic mean (UPGMA) analysis revealed 97% similarity amongst micropropagated plants with donor mother plant, thus confirming genetic homogeneity of micropropagated clones. This is the first report on micropropagation and genetic homogeneity assessment of P. eriocarpum. The protocol would be useful for the conservation and large scale production of P. eriocarpum to meet the demand for medicinal formulations and also for the re-introduction of in vitro grown plants in the suitable natural habitats to restore the populations. PMID:27434060

  8. Genetic Homogeneity Revealed Using SCoT, ISSR and RAPD Markers in Micropropagated Pittosporum eriocarpum Royle- An Endemic and Endangered Medicinal Plant.

    PubMed

    Thakur, Julie; Dwivedi, Mayank D; Sourabh, Pragya; Uniyal, Prem L; Pandey, Arun K

    2016-01-01

    Pittosporum eriocarpum Royle, a medicinally important taxon, is endemic to Uttarakhand region of Himalaya. It has become endangered due to over-collection and the loss of habitats. As raising plants through seeds in this plant is problematic, a reliable protocol for micropropagation using nodal explants has been developed. High shoot regeneration (95%) occurred in MS medium augmented with BA 0.4mg/l in combination IBA 0.6mg/l. In vitro regenerated shoots were rooted in MS medium supplemented with three auxins, of which 0.6 mg/l indole butyric acid proved to be the best for rooting (90%) with maximum number of roots per shoot. Thereafter, rooted plants were hardened and nearly 73% of rooted shoots were successfully acclimatized and established in the field. Start codon targeted (SCoT), inter simple sequence repeats (ISSR) and random amplified polymorphic DNA (RAPD) markers were used to validate the genetic homogeneity amongst nine in vitro raised plantlets with mother plant. DNA fingerprints of in vitro regenerated plantlets displayed monomorphic bands similar to mother plant, indicating homogeneity among the micropropagated plants with donor mother plant. The similarity values were calculated based on SCoT, ISSR and RAPD profiles which ranged from 0.89 to 1.00, 0.91 to 1.00 and 0.95 to 1.00 respectively. The dendrograms generated through Unweighted Pair Group Method with arithmetic mean (UPGMA) analysis revealed 97% similarity amongst micropropagated plants with donor mother plant, thus confirming genetic homogeneity of micropropagated clones. This is the first report on micropropagation and genetic homogeneity assessment of P. eriocarpum. The protocol would be useful for the conservation and large scale production of P. eriocarpum to meet the demand for medicinal formulations and also for the re-introduction of in vitro grown plants in the suitable natural habitats to restore the populations. PMID:27434060

  9. [Clonal micropropagation of a rare species Hedysarum theinum Krasnob (Fabaceae) and assessment of the genetic stability of regenerated plants using ISSR markers].

    PubMed

    Erst, A A; Svyagina, N S; Novikova, T I; Dorogina, O V

    2015-02-01

    In the present study, a protocol was developed for the in vitro propagation of a rare medicinal plant, Hedysarum theinum (tea sweetvetch), from axillary buds, and identification of the regenerants was performed with the use of ISSR markers. It was demonstrated that Gamborg and Eveleigh medium supplemented with 5 μM 6-benzylaminopurine was the best for H. theinum for initial multiplication. On the other hand, half-strength Murashige and Skoog (MS) basal medium supplemented with 7 μM α-naphthaleneacetic acid proved to be the best for explant rooting. Molecular genetic analysis of the H. theinum mother plants and the obtained regenerants was performed with six ISSR markers. Depending on the primer, four to ten amplified fragments with sizes ranging from 250 to 3000 bp were identified. Our results confirmed the genetic stability of regenerants obtained in five passages and their identity to the mother plant.

  10. Insight into the Migration Routes of Plutella xylostella in China Using mtCOI and ISSR Markers.

    PubMed

    Yang, Jiaqiang; Tian, Lixia; Xu, Baoyun; Xie, Wen; Wang, Shaoli; Zhang, Youjun; Wang, Xiangjing; Wu, Qingjun

    2015-01-01

    The larvae of the diamondback moth, Plutella xylostella, cause major economic losses to cruciferous crops, including cabbage, which is an important vegetable crop in China. In this study, we used the mitochondrial COI gene and 11 ISSR markers to characterize the genetic structure and seasonal migration routes of 23 P. xylostella populations in China. Both the mitochondrial and nuclear markers revealed high haplotype diversity and gene flow among the populations, although some degree of genetic isolation was evident between the populations of Hainan Island and other sampling sites. The dominant haplotypes, LX1 and LX2, differed significantly from all other haplotypes both in terms of the number of individuals with those haplotypes and their distributions. Haplotypes that were shared among populations revealed that P. xylostella migrates from the lower reaches of the Yangtze River to northern China and then to northeastern China. Our results also revealed another potential migration route for P. xylostella, i.e., from southwestern China to both northwestern and southern China.

  11. Insight into the Migration Routes of Plutella xylostella in China Using mtCOI and ISSR Markers.

    PubMed

    Yang, Jiaqiang; Tian, Lixia; Xu, Baoyun; Xie, Wen; Wang, Shaoli; Zhang, Youjun; Wang, Xiangjing; Wu, Qingjun

    2015-01-01

    The larvae of the diamondback moth, Plutella xylostella, cause major economic losses to cruciferous crops, including cabbage, which is an important vegetable crop in China. In this study, we used the mitochondrial COI gene and 11 ISSR markers to characterize the genetic structure and seasonal migration routes of 23 P. xylostella populations in China. Both the mitochondrial and nuclear markers revealed high haplotype diversity and gene flow among the populations, although some degree of genetic isolation was evident between the populations of Hainan Island and other sampling sites. The dominant haplotypes, LX1 and LX2, differed significantly from all other haplotypes both in terms of the number of individuals with those haplotypes and their distributions. Haplotypes that were shared among populations revealed that P. xylostella migrates from the lower reaches of the Yangtze River to northern China and then to northeastern China. Our results also revealed another potential migration route for P. xylostella, i.e., from southwestern China to both northwestern and southern China. PMID:26098353

  12. Genetic fidelity and variability of micropropagated cassava plants (Manihot esculenta Crantz) evaluated using ISSR markers.

    PubMed

    Vidal, Á M; Vieira, L J; Ferreira, C F; Souza, F V D; Souza, A S; Ledo, C A S

    2015-07-14

    Molecular markers are efficient for assessing the genetic fidelity of various species of plants after in vitro culture. In this study, we evaluated the genetic fidelity and variability of micropropagated cassava plants (Manihot esculenta Crantz) using inter-simple sequence repeat markers. Twenty-two cassava accessions from the Embrapa Cassava & Fruits Germplasm Bank were used. For each accession, DNA was extracted from a plant maintained in the field and from 3 plants grown in vitro. For DNA amplification, 27 inter-simple sequence repeat primers were used, of which 24 generated 175 bands; 100 of those bands were polymorphic and were used to study genetic variability among accessions of cassava plants maintained in the field. Based on the genetic distance matrix calculated using the arithmetic complement of the Jaccard's index, genotypes were clustered using the unweighted pair group method using arithmetic averages. The number of bands per primer was 2-13, with an average of 7.3. For most micropropagated accessions, the fidelity study showed no genetic variation between plants of the same accessions maintained in the field and those maintained in vitro, confirming the high genetic fidelity of the micropropagated plants. However, genetic variability was observed among different accessions grown in the field, and clustering based on the dissimilarity matrix revealed 7 groups. Inter-simple sequence repeat markers were efficient for detecting the genetic homogeneity of cassava plants derived from meristem culture, demonstrating the reliability of this propagation system.

  13. Development of single-locus DNA microsatellite markers using 5'anchored ISSR-PCR method for the mangrove horseshoe crab, Carcinoscorpius rotundicauda (Latreille, 1802) in Peninsular Malaysia.

    PubMed

    Adibah, A B; Ling, L Pui; Tan, S G; Faridah, Q Z; Christianus, A

    2012-04-01

    Horseshoe crabs are said to be declining worldwide. However, there is still no published report on the status of horseshoe crabs in Malaysia. Thus, we report here eight informative microsatellite markers that were developed using the 5'-anchored ISSR-PCR enrichment procedure to diagnose the population genetic structure of the mangrove horseshoe crab, Carcinoscorpius rotundicauda from Peninsular Malaysia. This set of markers was tested on 127 samples and showed polymorphism in this species. Hence they should be useful in future essential population genetic studies of these living fossils in the Southeast Asian region. PMID:21744263

  14. Development of single-locus DNA microsatellite markers using 5'anchored ISSR-PCR method for the mangrove horseshoe crab, Carcinoscorpius rotundicauda (Latreille, 1802) in Peninsular Malaysia.

    PubMed

    Adibah, A B; Ling, L Pui; Tan, S G; Faridah, Q Z; Christianus, A

    2012-04-01

    Horseshoe crabs are said to be declining worldwide. However, there is still no published report on the status of horseshoe crabs in Malaysia. Thus, we report here eight informative microsatellite markers that were developed using the 5'-anchored ISSR-PCR enrichment procedure to diagnose the population genetic structure of the mangrove horseshoe crab, Carcinoscorpius rotundicauda from Peninsular Malaysia. This set of markers was tested on 127 samples and showed polymorphism in this species. Hence they should be useful in future essential population genetic studies of these living fossils in the Southeast Asian region.

  15. In vitro clonal propagation and genetic fidelity of the regenerants of Spilanthes calva DC. using RAPD and ISSR marker.

    PubMed

    Razaq, Mohd; Heikrujam, Monika; Chetri, Siva K; Agrawal, Veena

    2013-04-01

    An efficient in vitro protocol has been established for clonal propagation of elite plant of Spilanthes calva DC., an important source of spilanthol, an antimalarial larvicidal compound. Nodal explants excised from field grown plant of S. calva DC. when reared on Murashige and Skoog's medium augmented with different cytokinins, viz. N(6)-Benzyladenine (BA), N(6)-(2-isopentenyl) adenine (2iP) and 6-furfuryl aminopurine (Kn), differentiated multiple shoots from the axils. BA at 10 μM proved optimum for elicitation of multiple shoots in 91.6 % cultures with an average of 7.12 shoots per explant within 6 weeks. The excised shoots rooted on half strength Murashige and Skoog's medium supplemented with 0.1 μM IBA. Micropropagated plants were hardened and transferred to field for acclimatization, where 95 % plants survived and were phenotypically similar to the donor plant. Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers were employed to evaluate the genetic fidelity amongst the regenerants. Eleven individuals, randomly chosen amongst a population of 120 regenerants were compared with the donor plant. A total of 71 scorable bands, ranging in size from 100 bp to 1,100 bp were generated by a combination of the two markers in the aforesaid plants. All banding profiles from micropropagated plants were monomorphic and similar to those of mother plant. The similarity values amongst the aforesaid plants varied from 0.967 to 1.000. The dendrogram generated through UPGMA (Unweighted Pair Group Method with arithmetic mean) analysis revealed 98 % similarity amongst them, thus confirming the genetic fidelity of the in vitro clones. PMID:24431493

  16. Genetic diversity and phylogenetic relationships of two closely related northeast China Vicia species revealed with RAPD and ISSR markers.

    PubMed

    Han, Ying; Wang, Hao-You

    2010-06-01

    RAPD and ISSR analyses revealed genetic diversity and relationships among 11 populations of two closely related northeast China Vicia species, Vicia ramuliflora and V. unijuga. Both methods yielded similar and complementary results, showing high genetic diversity. Vicia ramuliflora had 100% polymorphic loci in both RAPD and ISSR, and V. unijuga had 100% polymorphic loci for RAPD and 98.96% for ISSR. Genetic differentiation was moderate among populations of each species. Genetic variation was distributed mainly within populations for the two species. The high level of gene flow was important for the allocation of genetic variation. The UPGMA dendrogram and principal coordinates analysis at the level of individuals and populations showed that V. ramuliflora and V. unijuga were more closely related than either of them was to the outgroup species, V. cracca. The small molecular variance of V. ramuliflora and V. unijuga supports the conclusion that these two species had a common ancestor.

  17. Analysis of genetic diversity of Laeliinae (Orchidaceae) in the State of Sergipe using ISSR markers.

    PubMed

    Arrigoni-Blank, M F; Santos, M S; Blank, A F; Rabbani, A R C; Silva-Mann, R; Santos, J B; Costa, A S; Menezes, T S A

    2016-01-01

    The Orchidaceae represent one of the largest and most diverse families on the planet. However, this family is constantly threatened by predators and by the advancement of urban centers over its natural habitats. The objective of this study was to use inter-simple sequence repeat markers to evaluate the genetic diversity between orchid accessions of the Laeliinae subtribe, which comprise part of the Orchidaceae study collection at the Department of Agronomic Engineering of the Federal University of Sergipe. DNA was extracted from each specimen by using an adapted 2% cetyltrimethyl ammonium bromide protocol. Similarity between individuals was calculated using the Jaccard method. Clustering was carried out by the unweighted pair group method with arithmetic mean method, with resampling and 10,000 bootstraps. Eighty-seven fragments were obtained, all of which were polymorphic, revealing high variability between accessions. The mean similarity was 35.77% between Encyclia sp individuals, and 35.90% between specimens of Cattleya tigrina. For Epidendrum secundum, a relationship between geographic and genetic distances was observed, and the accession collected in the southern part of the State of Sergipe (Serra de Itabaiana National Park) was more divergent than that of the other parts of the state. The data generated in this study will guide further research aimed at the ex situ conservation of these materials. PMID:27323130

  18. Molecular genetic variation and structure of Southeast Asian crocodile (Tomistoma schlegelii): Comparative potentials of SSRs versus ISSRs.

    PubMed

    Shafiei-Astani, Behnam; Ong, Alan Han Kiat; Valdiani, Alireza; Tan, Soon Guan; Yien, Christina Yong Seok; Ahmady, Fatemeh; Alitheen, Noorjahan Banu; Ng, Wei Lun; Kuar, Taranjeet

    2015-10-15

    Tomistoma schlegelii, also referred to as the "false gharial", is one of the most exclusive and least known of the world's fresh water crocodilians, limited to Southeast Asia. Indeed, lack of economic value for its skin has led to neglect the biodiversity of the species. The current study aimed to investigate the mentioned case using 40 simple sequence repeat (SSR) primer pairs and 45 inter-simple sequence repeat (ISSR) primers. DNA analysis of 17 T. schlegelii samples using the SSR and ISSR markers resulted in producing a total of 49 and 108 polymorphic bands, respectively. Furthermore, the SSR- and ISSR-based cluster analyses both generated two main clusters. However, the SSR based results were found to be more in line with the geographical distributions of the crocodile samples collected across the country as compared with the ISSR-based results. The observed heterozygosity (HO) and expected heterozygosity (HE) of the polymorphic SSRs ranged between 0.588-1 and 0.470-0.891, respectively. The present results suggest that the Malaysian T. schlegelii populations had originated from a core population of crocodiles. In cooperation with the SSR markers, the ISSRs showed high potential for studying the genetic variation of T. schlegelii, and these markers are suitable to be employed in conservation genetic programs of this endangered species. Both SSR- and ISSR-based STRUCTURE analyses suggested that all the individuals of T. schlegelii are genetically similar with each other.

  19. Molecular genetic variation and structure of Southeast Asian crocodile (Tomistoma schlegelii): Comparative potentials of SSRs versus ISSRs.

    PubMed

    Shafiei-Astani, Behnam; Ong, Alan Han Kiat; Valdiani, Alireza; Tan, Soon Guan; Yien, Christina Yong Seok; Ahmady, Fatemeh; Alitheen, Noorjahan Banu; Ng, Wei Lun; Kuar, Taranjeet

    2015-10-15

    Tomistoma schlegelii, also referred to as the "false gharial", is one of the most exclusive and least known of the world's fresh water crocodilians, limited to Southeast Asia. Indeed, lack of economic value for its skin has led to neglect the biodiversity of the species. The current study aimed to investigate the mentioned case using 40 simple sequence repeat (SSR) primer pairs and 45 inter-simple sequence repeat (ISSR) primers. DNA analysis of 17 T. schlegelii samples using the SSR and ISSR markers resulted in producing a total of 49 and 108 polymorphic bands, respectively. Furthermore, the SSR- and ISSR-based cluster analyses both generated two main clusters. However, the SSR based results were found to be more in line with the geographical distributions of the crocodile samples collected across the country as compared with the ISSR-based results. The observed heterozygosity (HO) and expected heterozygosity (HE) of the polymorphic SSRs ranged between 0.588-1 and 0.470-0.891, respectively. The present results suggest that the Malaysian T. schlegelii populations had originated from a core population of crocodiles. In cooperation with the SSR markers, the ISSRs showed high potential for studying the genetic variation of T. schlegelii, and these markers are suitable to be employed in conservation genetic programs of this endangered species. Both SSR- and ISSR-based STRUCTURE analyses suggested that all the individuals of T. schlegelii are genetically similar with each other. PMID:26112832

  20. Analysis of drought-tolerant sugar beet (Beta vulgaris L.) mutants induced with gamma radiation using SDS-PAGE and ISSR markers.

    PubMed

    Sen, Ayse; Alikamanoglu, Sema

    2012-01-01

    Drought is one of the major environmental stresses which greatly affect the plant growth and productivity. In the present study, various doses (0-75Gy) of gamma rays were applied to investigate the effect of radiation on shoot tip explants. It was observed that the regeneration rates and plant fresh weights decreased significantly with an increase in radiation dose. The optimal irradiation doses for mutation induction were determined at 15 and 20Gy. Afterwards, the induction of somatic mutation in sugar beet (Beta vulgaris L.) was investigated by irradiation of shoot tips with 15 and 20Gy gamma rays. Irradiated shoot tips were sub-cultured and M(1)V(1)-M(1)V(3) generations were obtained. Mutants tolerant to drought stress were selected on MS medium, supplemented with 10 and 20gl(-1) PEG6000. Of the M(1)V(3) plantlets, drought-tolerant mutants were selected. Leaf soluble proteins obtained from the control and drought-tolerant mutants were analyzed by SDS-PAGE. A total of 22 protein bands were determined and 2 of them were observed to be drought-tolerant mutants except the control. Polymorphism was also detected among the control and drought-tolerant mutants by DNA fingerprinting using ISSR markers. A total of 106 PCR fragments were amplified with 19 ISSR primers and 91 of them were polymorphic. The dendrograms were separated into two main clusters. First cluster included M8 mutant plant, which was applied 20Gy gamma radiation and regenerated on selective culture media containing 10gl(-1) PEG6000 concentration, and the second cluster was further divided into five sub-clusters.

  1. Applicability of ISSR and DAMD markers for phyto-molecular characterization and association with some important biochemical traits of Dendrobium nobile, an endangered medicinal orchid.

    PubMed

    Bhattacharyya, Paromik; Kumaria, Suman; Tandon, Pramod

    2015-09-01

    Dendrobium nobile is an important medicinal orchid having profound importance in traditional herbal drug preparations and pharmacopeias worldwide. Due to various anthropogenic pressures the natural populations of this important orchid species are presently facing threats of extinction. In the present study, genetic and chemical diversity existing amongst 6 natural populations of D. nobile were assessed using molecular markers, and the influence of genetic factors on its phytochemical activity especially antioxidant potential was determined. Molecular fingerprinting of the orchid taxa was performed using ISSR and DAMD markers along with the estimation of total phenolics, flavonoids and alkaloid contents. Antioxidant activity was also measured using DPPH and FRAP assays which cumulatively revealed a significant level of variability across the sampled populations. The representatives from Sikkim in Northeast India revealed higher phytochemical activity whereas those from Mizoram showed lesser activity. Analysis of molecular variance (AMOVA) revealed that variation amongst the populations was significantly higher than within the populations. The data generated by UPGMA and Bayesian analytical models were compared in order to estimate the genetic relationships amongst the D. nobile germplasm sampled from different geographical areas of Northeast India. Interestingly, identical grouping patterns were exhibited by both the approaches. The results of the present study detected a high degree of existing genetic and phytochemical variation amongst the populations in relation to bioclimatic and geographic locations of populations. Our results strongly establish that the cumulative marker approach could be the best suited for assessing the genetic relationships with high accuracy amongst distinct D. nobile accessions.

  2. Genetic diversity of Pleurotus pulmonarius revealed by RAPD, ISSR, and SRAP fingerprinting.

    PubMed

    Yin, Yonggang; Liu, Yu; Li, Huamin; Zhao, Shuang; Wang, Shouxian; Liu, Ying; Wu, Di; Xu, Feng

    2014-03-01

    Pleurotus pulmonarius is one of the most widely cultivated and popular edible fungi in the genus Pleurotus. Three molecular markers were used to analyze the genetic diversity of 15 Chinese P. pulmonarius cultivars. In total, 21 random amplified polymorphic DNA (RAPD), 20 inter-simple sequence repeat (ISSR), and 20 sequence-related amplified polymorphism (SRAP) primers or primer pairs were selected for generating data based on their clear banding profiles produced. With the use of these RAPD, ISSR, and SRAP primers or primer pairs, a total of 361 RAPD, 283 ISSR, and 131 SRAP fragments were detected, of which 287 (79.5 %) RAPD, 211 (74.6 %) ISSR, and 98 (74.8 %) SRAP fragments were polymorphic. Unweighted Pair-Group Method with Arithmetic Mean (UPGMA) trees of these three methods were structured similarly, grouping the 15 tested strains into four clades. Subsequently, visual DNA fingerprinting and cluster analysis were performed to evaluate the resolving power of the combined RAPD, ISSR, and SRAP markers in the differentiation among these strains. The results of this study demonstrated that each method above could efficiently differentiate P. pulmonarius cultivars and could thus be considered an efficient tool for surveying genetic diversity of P. pulmonarius.

  3. Phylogeny, Floral Evolution, and Inter-Island Dispersal in Hawaiian Clermontia (Campanulaceae) Based on ISSR Variation and Plastid Spacer Sequences

    PubMed Central

    Givnish, Thomas J.; Bean, Gregory J.; Ames, Mercedes; Lyon, Stephanie P.; Sytsma, Kenneth J.

    2013-01-01

    Previous studies based on DNA restriction-site and sequence variation have shown that the Hawaiian lobeliads are monophyletic and that the two largest genera, Cyanea and Clermontia, diverged from each other ca. 9.7 Mya. Sequence divergence among species of Clermontia is quite limited, however, and extensive hybridization is suspected, which has interfered with production of a well-resolved molecular phylogeny for the genus. Clermontia is of considerable interest because several species posses petal-like sepals, raising the question of whether such a homeotic mutation has arisen once or several times. In addition, morphological and molecular studies have implied different patterns of inter-island dispersal within the genus. Here we use nuclear ISSRs (inter-simple sequence repeat polymorphisms) and five plastid non-coding sequences to derive biparental and maternal phylogenies for Clermontia. Our findings imply that (1) Clermontia is not monophyletic, with Cl. pyrularia nested within Cyanea and apparently an intergeneric hybrid; (2) the earliest divergent clades within Clermontia are native to Kauài, then Òahu, then Maui, supporting the progression rule of dispersal down the chain toward progressively younger islands, although that rule is violated in later-evolving taxa in the ISSR tree; (3) almost no sequence divergence among several Clermontia species in 4.5 kb of rapidly evolving plastid DNA; (4) several apparent cases of hybridization/introgression or incomplete lineage sorting (i.e., Cl. oblongifolia, peleana, persicifolia, pyrularia, samuelii, tuberculata), based on extensive conflict between the ISSR and plastid phylogenies; and (5) two origins and two losses of petaloid sepals, or—perhaps more plausibly—a single origin and two losses of this homeotic mutation, with its introgression into Cl. persicifolia. Our phylogenies are better resolved and geographically more informative than others based on ITS and 5S-NTS sequences and nuclear SNPs, but agree

  4. Genetic relationship of Curcuma species from Northeast India using PCR-based markers.

    PubMed

    Das, Archana; Kesari, Vigya; Satyanarayana, Vinod M; Parida, Ajay; Rangan, Latha

    2011-09-01

    Molecular genetic fingerprints of nine Curcuma species from Northeast India were developed using PCR-based markers. The aim involves elucidating there intra- and inter-specific genetic diversity important for utilization, management, and conservation. Twelve random amplified polymorphic DNA (RAPD), 19 Inter simple sequence repeats (ISSRs), and four amplified fragment length polymorphism (AFLP) primers produced 266 polymorphic fragments. ISSR confirmed maximum polymorphism of 98.55% whereas RAPD and AFLP showed 93.22 and 97.27%, respectively. Marker index and polymorphic information content varied in the range of 8.64-48.1, 19.75-48.14, and 25-28 and 0.17-0.48, 0.19-0.48, and 0.25-0.29 for RAPD, ISSR, and AFLP markers, respectively. The average value of number of observed alleles, number of effective alleles, mean Nei's gene diversity, and Shannon's information index were 1.93-1.98, 1.37-1.62, 0.23-0.36, and 0.38-0.50, respectively, for three DNA markers used. Dendrograms based on three molecular data using unweighted pair group method with arithmetic mean (UPGMA) was congruent and classified the Curcuma species into two major clusters. Cophenetic correlation coefficient between dendrogram and original similarity matrix were significant for RAPD (r = 0.96), ISSR (r = 0.94), and AFLP (r = 0.97). Clustering was further supported by principle coordinate analysis. High genetic polymorphism documented is significant for conservation and further improvement of Curcuma species.

  5. Parentage and relatedness in polyandrous comb-crested jacanas using ISSRs

    USGS Publications Warehouse

    Haig, Susan M.; Mace, Terrence R.; Mullins, Thomas D.

    2003-01-01

    In this article we present the first analysis of parentage and relatedness in a natural vertebrate population, using Intersimple Sequence Repeat (ISSR) markers. Thus, 28 ISSR markers were used in a study of a sex-role reversed, simultaneously polyandrous shorebird from northeastern Australia, the comb-crested jacana (Irediparra gallinacea). Assessment of parentage was based on comparison of field observations, novel bands, individual-specific bands found in 7/9 males and 4/6 females, and a 99% CI exclusion criteria. Integrating results from these approaches resulted in confirmation of paternity in all 36 chicks. In only one case (2.8% of chicks) was a co-mate assigned paternity. Thus, comb-crested jacanas appear to be genetically monogamous. These results showed resemblance to sequentially polyandrous birds but differed from the simultaneously polyandrous wattled jacana ( Jacana jacana; Emlen et al. 1998). A significant relationship between relatedness and ISSR similarity resulted in recognition that 14/15 adults sampled may be related to at least one other adult by 0.25 or more. Lack of dispersal may be explained by physical limitations and adequate regional habitat. ISSRs proved to be simple and helpful in resolving these issues.

  6. Assessing molecular and morpho-agronomical diversity and identification of ISSR markers associated with fruit traits in quince (Cydonia oblonga).

    PubMed

    Ganopoulos, I; Merkouropoulos, G; Pantazis, S; Tsipouridis, C; Tsaftaris, A

    2011-01-01

    Quince is a deciduous tree known to the countries around the Mediterranean since antiquity. Nowadays, quince is used as an ornamental plant, and as a rootstock for pear trees, with its fruit being appreciated mainly for production of jam and sweets rather than for raw consumption. Quince leaves contain compounds with antioxidant, antimicrobial and anticancerous properties that have been the focus of recent research on pharmaceutical and medical uses as well as for food preservatives. An orchard has been established in Greece, composed of quince varieties (Cydonia oblonga, N = 49) collected from different sites of the country (mainly from home gardens), constituting a unique quince gene bank collection for southeast Europe. We made a phenotypic analysis using 26 morphological plus seven agronomical descriptors coupled with molecular techniques in order to examine the genetic diversity within the collection. Principal component analysis using the 33 descriptors identified 10 components explaining the existence of more than 70% of the total variation. Subsequent cluster analysis classified most of the previously identified productive varieties of the quince orchard in the same clade of a dendrogram. Molecular analysis generated by 13 inter-simple sequence repeat primers amplified 139 bands, including 109 polymorphic bands, indicating a level of polymorphism of 79%; mean gene diversity was calculated to be 0.309. Using stepwise multiple regression analysis, a number of markers significantly associated with fire blight susceptibility, yield, mean fruit weight, citric acid content, soluble solid content, and fruit drop were identified. Hence, data extracted by multiple regression analysis could be useful in marker-assisted breeding programs, especially when no previous genetic information is available. PMID:22095599

  7. RAPD and ISSR based evaluation of genetic stability of micropropagated plantlets of Morus alba L. variety S-1

    PubMed Central

    Saha, Soumen; Adhikari, Sinchan; Dey, Tulsi; Ghosh, Parthadeb

    2015-01-01

    Plant regeneration through rapid in vitro clonal propagation of nodal explants of Morus alba L. variety S-1 was established along with genetic stability analysis of regenerates. Axillary shoot bud proliferation was achieved on Murashige and Skoog (MS) medium in various culture regimes. Highest number of shoots (5.62 ± 0.01), with average length 4.19 ± 0.01 cm, was initially achieved with medium containing 0.5 mg/l N6-benzyladenine (BA) and 3% sucrose. Repeated subculturing of newly formed nodal parts after each harvest up to sixth passage, yielded highest number of shoots (about 32.27) per explants was obtained after fourth passage. Rooting of shoots occurred on 1/2 MS medium supplemented with 1.0 mg/1 Indole-3-butyric acid (IBA). About 90% (89.16) of the plantlets transferred to the mixture of sand:soil:organic manure (2:2:1) in small plastic pots acclimatized successfully. Genetic stability of the discussed protocol was confirmed by two DNA-based fingerprinting techniques i.e. RAPD (random amplified polymorphic DNA) and ISSR (inter-simple sequence repeat). This protocol can be used for commercial propagation and for future genetic improvement studies. PMID:26693403

  8. RAPD and ISSR based evaluation of genetic stability of micropropagated plantlets of Morus alba L. variety S-1.

    PubMed

    Saha, Soumen; Adhikari, Sinchan; Dey, Tulsi; Ghosh, Parthadeb

    2016-02-01

    Plant regeneration through rapid in vitro clonal propagation of nodal explants of Morus alba L. variety S-1 was established along with genetic stability analysis of regenerates. Axillary shoot bud proliferation was achieved on Murashige and Skoog (MS) medium in various culture regimes. Highest number of shoots (5.62 ± 0.01), with average length 4.19 ± 0.01 cm, was initially achieved with medium containing 0.5 mg/l N(6)-benzyladenine (BA) and 3% sucrose. Repeated subculturing of newly formed nodal parts after each harvest up to sixth passage, yielded highest number of shoots (about 32.27) per explants was obtained after fourth passage. Rooting of shoots occurred on 1/2 MS medium supplemented with 1.0 mg/1 Indole-3-butyric acid (IBA). About 90% (89.16) of the plantlets transferred to the mixture of sand:soil:organic manure (2:2:1) in small plastic pots acclimatized successfully. Genetic stability of the discussed protocol was confirmed by two DNA-based fingerprinting techniques i.e. RAPD (random amplified polymorphic DNA) and ISSR (inter-simple sequence repeat). This protocol can be used for commercial propagation and for future genetic improvement studies. PMID:26693403

  9. Genetic diversity among the Eurytemora affinis species complex in the Scheldt estuary and its tributaries using ISSR-PCR marker assay

    NASA Astrophysics Data System (ADS)

    Gasmi, S.; Ferval, M.; Pelissier, C.; D'Amico, F.; Maris, T.; Tackx, M.; Legal, L.

    2014-05-01

    As an estuary being restored, the Scheldt (Belgium/The Netherlands) offers an interesting setting to study the response of organisms and ecosystems to changing conditions. This study specifically deals with this with regard to the spatio-temporal distribution and possible genetic differentiation among the species complex Eurytemora affinis (copepoda, calanoida). Until the 1990s, E. affinis typically occurred downstream the Scheldt estuary (Belgium/The Netherlands). In parallel to water quality improvement, E.affinis has recently also occurred upstream the estuary and in some of the tributaries. This paper aims to assess the origin of the copepod sibling species complex E. affinis occurring upstream the Scheldt estuary through genetic characterization. Using the Inter Simple Sequence Repeat (ISSR) technique, we explored genetic pools of the E. affinis complex in three Scheldt localities (downstream, middle-estuary and upstream) and two of its tributaries. Four ISSR primers produced 75 polymorphic loci. Bayesian and hierarchical analysis revealed different but close genetic entities in both down and upstream localities. The middle-estuary individuals were genetically a composite mix of downstream and upstream populations (84% from downstream and 16% from upstream). A distinctive separation of the tributaries and the main Scheldt stream populations suggests that two fully independent genetic pools are present. It is of note that the tributaries showed a lack of genetic subdivision, that upstream and downstream E. affinis populations are closely related, and that the downstream population is most likely at the origin of the upstream one, which implies the necessity to guarantee sufficient oxygen concentration levels throughout the estuarine continuum to guarantee the presence of this species upstream. The results of the ISSR technique are discussed in comparison with genetic studies on E. affinis using COI barcoding.

  10. ISSR and RAPD based evaluation of genetic stability of encapsulated micro shoots of Glycyrrhiza glabra following 6 months of storage.

    PubMed

    Mehrotra, Shakti; Khwaja, O; Kukreja, A K; Rahman, L

    2012-11-01

    In vitro grown axillary micro shoots of Glycyrrhiza glabra were encapsulated in alginate beads. Following 6 months of normal storage at 25 ± 2°C the re growth of encapsulated G. glabra micro shoots, reached 98% within 30 days of incubation on MS medium supplemented with 0.1 mg/l IAA. Re growth was characterized by the development of both shoot and root from single encapsulated micro shoot. Healthy plants were established to glass house with 95% survival. The genetic fidelity of plants obtained after conversion of alginate beads was ascertained through 10 RAPD and 13 ISSR primers. Of the 10 RAPD primers tested, 6 of them produced 14 clear and reproducible amplicons with an average of 2.3 bands per primer out of which 28.57% were polymorphic generated by only two primers. Eight ISSR primers produced total 37 bands ranging between 300 and 3,500 bp length. Number of scorable bands for each primer varied from 3 to 8 with an average of 4.6 bands per primer. Cluster analysis from ISSR and RAPD showed that all the tested plants including the mother plant distributed in two major groups with similarity coefficient ranging from 0.91 to 0.96 for RAPD and 0.89 to 0.97 for ISSR.

  11. High gene flow and genetic diversity in three economically important Zanthoxylum Spp. of Upper Brahmaputra Valley Zone of NE India using molecular markers.

    PubMed

    Medhi, K; Sarmah, D K; Deka, M; Bhau, B S

    2014-12-01

    The genetic diversity in Zanthoxylum species viz.  Zanthoxylum nitidum, Zanthoxylum oxyphyllum and Zanthoxylum rhesta collected from the Upper Brahmaputra Valley Zone of Assam (NE India) was amplified using 13 random amplified polymorphic DNA (RAPD) markers and 9 inter-simple sequence repeat (ISSR) markers. RAPD markers were able to detect 81.82% polymorphism whereas ISSR detected 98.02% polymorphism. The genetic similarities were analyzed from the dendrogram constructed by RAPD and ISSR fingerprinting methods which divided the 3 species of Zanthoxylum into 3 clear different clusters. The principle component analysis (PCA) was carried out to confirm the clustering pattern of RAPD and ISSR analysis. Analysis of molecular variance (AMOVA) revealed the presence of significant variability between different Zanthoxylum species and within the species by both RAPD and ISSR markers. Z. nitidum was found to be sharing a high degree of variation with the other two Zanthoxylum species under study. The Nei's gene diversity (h), Shannon's information index (I), observed number of alleles (na) and effective number of alleles (ne) were also found to be higher in ISSR markers (0.3526, 0.5230, 1.9802 and 1.6145) than in RAPD markers (0.3144, 0.4610, 1.8182 and 1.5571). The values for total genotype diversity for among population (HT), within population diversity (Hs) and gene flow (Nm) were more in ISSR (0.3491, 0.2644 and 1.5610) than RAPD (0.3128, 0.2264 and 1.3087) but the mean coefficient of gene differentiation (GST) was more in RAPD (0.2764) than ISSR (0.2426). A comparison of this two finger printing methods was done by calculating MR, EMI and MI. The correlation coefficient between data matrices of RAPD and ISSR based on Mantel test was found to be significant (r = 0.65612). PMID:25606454

  12. High gene flow and genetic diversity in three economically important Zanthoxylum Spp. of Upper Brahmaputra Valley Zone of NE India using molecular markers

    PubMed Central

    Medhi, K.; Sarmah, D.K.; Deka, M.; Bhau, B.S.

    2014-01-01

    The genetic diversity in Zanthoxylum species viz.  Zanthoxylum nitidum, Zanthoxylum oxyphyllum and Zanthoxylum rhesta collected from the Upper Brahmaputra Valley Zone of Assam (NE India) was amplified using 13 random amplified polymorphic DNA (RAPD) markers and 9 inter-simple sequence repeat (ISSR) markers. RAPD markers were able to detect 81.82% polymorphism whereas ISSR detected 98.02% polymorphism. The genetic similarities were analyzed from the dendrogram constructed by RAPD and ISSR fingerprinting methods which divided the 3 species of Zanthoxylum into 3 clear different clusters. The principle component analysis (PCA) was carried out to confirm the clustering pattern of RAPD and ISSR analysis. Analysis of molecular variance (AMOVA) revealed the presence of significant variability between different Zanthoxylum species and within the species by both RAPD and ISSR markers. Z. nitidum was found to be sharing a high degree of variation with the other two Zanthoxylum species under study. The Nei's gene diversity (h), Shannon's information index (I), observed number of alleles (na) and effective number of alleles (ne) were also found to be higher in ISSR markers (0.3526, 0.5230, 1.9802 and 1.6145) than in RAPD markers (0.3144, 0.4610, 1.8182 and 1.5571). The values for total genotype diversity for among population (HT), within population diversity (Hs) and gene flow (Nm) were more in ISSR (0.3491, 0.2644 and 1.5610) than RAPD (0.3128, 0.2264 and 1.3087) but the mean coefficient of gene differentiation (GST) was more in RAPD (0.2764) than ISSR (0.2426). A comparison of this two finger printing methods was done by calculating MR, EMI and MI. The correlation coefficient between data matrices of RAPD and ISSR based on Mantel test was found to be significant (r = 0.65612). PMID:25606454

  13. Inter simple sequence repeat (ISSR) analysis of genetic diversity in tef [Eragrostis tef (Zucc.) Trotter].

    PubMed

    Assefa, Kebebew; Merker, Arnulf; Tefera, Hailu

    2003-01-01

    The DNA polymorphism among 92 selected tef genotypes belonging to eight origin groups was assessed using eight inter simple sequence repeat (ISSR) primers. The objectives were to examine the possibility of using ISSR markers for unravelling genetic diversity in tef, and to assess the extent and pattern of genetic diversity in the test germplasm with respect to origin groups. The eight primers were able to separate or distinguish all of the 92 tef genotypes based on a total of 110 polymorphic bands among the test lines. The Jaccard similarity coefficient among the test genotypes ranged from 0.26 to 0.86, and at about 60 % similarity level the clustering of this matrix using the unweighted pair-group method based on arithmetic average (UPGMA) resulted in the formation of six major clusters of 2 to 37 lines with further eight lines remaining ungrouped. The standardized Nei genetic distance among the eight groups of origin ranged between 0.03 and 0.32. The UPGMA clustering using the standardized genetic distance matrix resulted in the identification of three clusters of the eight groups of origin with bootstrap values ranging from 56 to 97. The overall mean Shannon Weaver diversity index of the test lines was 0.73, indicating better resolution of genetic diversity in tef with ISSR markers than with phenotypic (morphological) traits used in previous studies. This can be attributed mainly to the larger number of loci generated for evaluation with ISSR analysis as compared to the few number of phenotypic traits amenable for assessment and which are further greatly affected by environment and genotype x environment interaction. Analysis of variance of mean Shannon Weaver diversity indices revealed substantial (P < or = 0.05) variation in the level of diversity among the eight groups of origin. In conclusion, our results indicate that ISSR can be useful as DNA-based molecular markers for studying genetic diversity and phylogenetic relationships, DNA fingerprinting for the

  14. ISSR-based analysis of genetic diversity among sorghum landraces growing in some parts of Saudi Arabia and Yemen.

    PubMed

    Basahi, Mohammed

    2015-11-01

    Inter simple sequence repeats (ISSR) analysis was used to determine the genetic diversity among 15 genotypes of sorghum [Sorghum bicolor (L.) Moench] growing in some parts of Saudi Arabia and Yemen. A total of 92 alleles were amplified, with an average of 13 ISSR alleles per primer. Cluster analysis divided the 15 genotypes into two main groups. Group A consisted of five genotypes with white grains from Jazan and Abha with a similarity coefficient range of 0.527 to 0.818. Group B was comprised of 10 genotypes; two genotypes from Al-Qassim were clearly delimited from the remaining eight samples with a coefficient range from 0.709 to 0.490. The eight genotypes were divided into two clusters; one was comprised of landraces with dark grains from Abha in Saudi Arabia and Ab in Yemen, with a similarity coefficient range between 0.563 and 0.781, and the other cluster was differentiated into three white-colored-grain genotypes and one colored-grain genotype; all samples from North Yemen had a similarity coefficient range from 0.454 to 0.800. The current results encourage further collection and authentication of sorghum landraces in the gene banks of Saudi Arabia.

  15. Biogeographic pattern of genetic diversity detected by RAPD and ISSR analysis in Gypsophila (Caryophyllaceae) species from Turkey.

    PubMed

    Korkmaz, M; Dogan, N Y

    2015-01-01

    Gypsophila L. is the 3rd-largest genus of Caryophyllaceae in Turkey, a country that includes 60 taxa belonging to 56 species of the 126 recognized in the genus. A total of 35 taxa are endemic to Turkey, with an approximately 60% endemism ratio. In this study, the genetic diversity of 14 Gypsophila species from Turkey was analyzed using random amplification of polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. Sixteen RAPD and 6 ISSR primers produced 132 polymorphic bands. RAPD, ISSR, and RAPD + ISSR primers for the 14 species showed 92.7, 93.8, and 92.9% polymorphism, respectively. Our results indicate that RAPD and ISSR markers are reliable and effective for assessing the genetic diversity of Gypsophila species. Gypsophila species studied were separated into 2 clusters. Our analysis shows that the clusters correlated with geographic and phytogeographic regions.

  16. Genetic variation and population differentiation in a medical herb Houttuynia cordata in China revealed by inter-simple sequence repeats (ISSRs).

    PubMed

    Wei, Lin; Wu, Xian-Jin

    2012-01-01

    Houttuynia cordata is an important traditional Chinese herb with unresolved genetics and taxonomy, which lead to potential problems in the conservation and utilization of the resource. Inter-simple sequence repeat (ISSR) markers were used to assess the level and distribution of genetic diversity in 226 individuals from 15 populations of H. cordata in China. ISSR analysis revealed low genetic variations within populations but high genetic differentiations among populations. This genetic structure probably mainly reflects the historical association among populations. Genetic cluster analysis showed that the basal clade is composed of populations from Southwest China, and the other populations have continuous and eastward distributions. The structure of genetic diversity in H. cordata demonstrated that this species might have survived in Southwest China during the glacial age, and subsequently experienced an eastern postglacial expansion. Based on the results of genetic analysis, it was proposed that as many as possible targeted populations for conservation be included. PMID:22942696

  17. An improved micropropagation of Arnebia hispidissima (Lehm.) DC. and assessment of genetic fidelity of micropropagated plants using DNA-based molecular markers.

    PubMed

    Phulwaria, Mahendra; Rai, Manoj K; Shekhawat, N S

    2013-07-01

    An efficient and improved in vitro propagation method has been developed for Arnebia hispidissima, a medicinally and pharmaceutically important plant species of arid and semiarid regions. Nodal segments (3-4 cm) with two to three nodes obtained from field grown plants were used as explants for shoot proliferation. Murashige and Skoog's (MS) medium supplemented with cytokinins with or without indole-3-acetic acid (IAA) or naphthalene acetic acid was used for shoot multiplication. Out of different PGRs combinations, MS medium containing 0.5 mg l(-1) 6-benzylaminopurine and 0.1 mg l(-1) IAA was optimal for shoot multiplication. On this medium, explants produced the highest number of shoots (47.50 ± 0.38). About 90 % of shoots rooted ex vitro on sterile soilrite under the greenhouse condition when the base (2-4 mm) of shoots was treated with 300 mg l(-1) of indole-3-butyric acid for 5 min. The plantlets were hardened successfully in the greenhouse with 85-90 % survival rate. Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers were employed to assess the genetic stability of in vitro-regenerated plants of A. hispidissima. Out of 40 (25 RAPD and 15 ISSR) primers screened, 15 RAPD and 7 ISSR primers produced a total number of 111 (77 RAPD and 34 ISSR) reproducible amplicons. The amplified products were monomorphic across all the micropropagated plants and were similar to the mother plant. To the best of our knowledge, it is the first report on the assessment of the genetic fidelity in micropropagated plants of A. hispidissima.

  18. Assessment of genetic diversity in Mucuna species of India using randomly amplified polymorphic DNA and inter simple sequence repeat markers.

    PubMed

    Patil, Ravishankar R; Pawar, Kiran D; Rane, Manali R; Yadav, Shrirang R; Bapat, Vishwas A; Jadhav, Jyoti P

    2016-04-01

    Genus Mucuna which is native to China and Eastern India comprises of perennial climbing legume with long slender branches, trifoliate leaves and bear green or brown pod covered with soft or rigid hairs that cause intense irritation. The plants of this genus are agronomically and economically important and commercially cultivated in India, China and other regions of the world. The high degrees of taxonomical confusions exist in Mucuna species that make authentic identification and classification difficult. In the present study, the genetic diversity among the 59 accessions of six species and three varieties of M. pruriens has been assessed using DNA fingerprinting based molecular markers techniques namely randomly amplified polymorphic DNA (RAPD), inter simple sequence repeats (ISSR) and combined dataset of RAPD and ISSR. Also, genetic relationship among two endemic species of Mucuna namely M. imbricata and M. macrocarpa and two varieties namely IIHR hybrid (MHR) and Dhanwantari (MD) with other species under study was investigated by using cluster analysis and principal coordinate analysis. The cluster analysis of RAPD, ISSR and combined dataset of RAPD and ISSR clearly demonstrated the existence of high interspecific variation than intra-specific variation in genus Mucuna. The utility and efficacy of RAPD and ISSR for the study of intra species and interspecies genetic diversity was evident from AMOVA and PCoA analysis. This study demonstrates the genetic diversity in Mucuna species and indicates that these markers could be successfully used to assess genetic variation among the accessions of Mucuna species. PMID:27436912

  19. Analysis of genetic stability of in vitro propagated potato microtubers using DNA markers.

    PubMed

    Tiwari, Jagesh K; Chandel, Poonam; Gupta, Shruti; Gopal, Jai; Singh, B P; Bhardwaj, Vinay

    2013-10-01

    The genetic stability of in vitro propagated potato microtubers was assessed using random amplified polymorphic DNA (RAPD), inter simple sequence repeat (ISSR), simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers. Microtubers were developed through in vitro from potato microplants using standardized protocols. The microtubers were conserved for 1 year under three different culture media and consequently microplants were regenerated for the DNA analyses. During the study, a total of 38 (10 RAPD, 11 ISSR, 12 SSR and 5 AFLP) primers produced a total of 407 (58 RAPD, 56 ISSR, 96 SSR and 197 AFLP) clear, distinct and reproducible amplicons. Cluster analysis revealed 100 % genetic similarity among the mother plant and its derivatives within the clusters by SSR, ISSR and RAPD analyses, whereas AFLP analysis revealed from 85 to 100 % genetic similarity. Dendrogram analysis based on the Jaccard's coefficient classified the genotypes into five clusters (I-V), each cluster consisting of mother plant and its derivatives. Principal component analysis (PCA) also plotted mother plant and its genotypes of each cluster together. Based on our results, it is concluded that AFLP is the best method followed by SSR, ISSR and RAPD to detect genetic stability of in vitro conserved potato microtubers. The in vitro conservation medium (T2) is a safe method for conservation of potato microtubers to produce true-to-type plans. PMID:24431528

  20. Highly informative nature of inter simple sequence repeat (ISSR) sequences amplified using tri- and tetra-nucleotide primers from DNA of cauliflower (Brassica oleracea var. botrytis L.).

    PubMed

    Bornet, B; Muller, C; Paulus, F; Branchard, M

    2002-10-01

    Inter simple sequence repeat (ISSR) sequences as molecular markers can lead to the detection of polymorphism and also be a new approach to the study of SSR distribution and frequency. In this study, ISSR amplification with nonanchored primer was performed in closely related cauliflower lines. Fourty-four different amplified fragments were sequenced. Sequences of PCR products are delimited by the expected motifs and number of repeats, which validates the ISSR nonanchored primer amplification technique. DNA and amino acids homology search between internal sequences and databases (i) show that the majority of the internal regions of ISSR had homologies with known sequences, mainly with genes coding for proteins implicated in DNA interaction or gene expression, which reflected the significance of amplified ISSR sequences and (ii) display long and numerous homologies with the Arabidopsis thaliana genome. ISSR amplifications revealed a high conservation of these sequences between Arabidopsis thaliana and Brassica oleracea var. botrytis. Thirty-four of the 44 ISSRs had one or several perfect or imperfect internal microsatellites. Such distribution indicates the presence in genomes of highly concentrated regions of SSR, or "SSR hot spots." Among the four nonanchored primers used in this study, trinucleotide repeats, and especially (CAA)5, were the most powerful primers for ISSR amplifications regarding the number of amplified bands, level of polymorphism, and their nature.

  1. Molecular diversity and population structure of the forage grass Hemarthria compressa (Poaceae) in south China based on SRAP markers.

    PubMed

    Huang, L-K; Zhang, X-Q; Xie, W-G; Zhang, J; Cheng, L; Yan, H D

    2012-08-16

    Hemarthria compressa is one of the most important and widely utilized forage crops in south China, owing to its high forage yield and capability of adaptation to hot and humid conditions. We examined the population structure and genetic variation within and among 12 populations of H. compressa in south China using sequence-related amplified polymorphism (SRAP) markers. High genetic diversity was found in these samples [percentage polymorphic bands (PPB) = 82.21%, Shannon's diversity index (I) = 0.352]. However, there was relatively low level of genetic diversity at the population level (PPB = 29.17%, I = 0.155). A high degree of genetic differentiation among populations was detected based on other measures and molecular markers (Nei's genetic diversity analysis: G(ST) = 54.19%; AMOVA analysis: F(ST) = 53.35%). The SRAP markers were found to be more efficient than ISSR markers for evaluating population diversity. Based on these findings, we propose changes in sampling strategies for appraising and utilizing the genetic resources of this species.

  2. Molecular identification of Aquilaria spp. by using inter-simple sequence repeat (ISSR)

    NASA Astrophysics Data System (ADS)

    Azhari, Hanif; Mohamad, Azhar; Othman, Roohaida

    2015-09-01

    Aquilaria species are very important economic plant for production of resin locally known as gaharu in Malaysia. There are five species that can be found in Malaysia and the most important Aquilaria species for gaharu production is A. malaccensis. Molecular markers for Aquilaria species are still insufficient and require more efficient, robust and reproducible molecular marker. Inter-simple sequence repeat (ISSR) markers are highly polymorphic and have high reproducibility which will be useful in areas of genetic diversity, phylogenetic studies, gene tagging, genome mapping and evolutionary biology in a wide range of crop species. Five selected ISSR primers were used to identify four Aquilaria species commonly found in Malaysia namely A. malaccensis, A. sub-integra, A. crassna and A. hirta. All the primers showed sufficient polymorphism to distinguish between the four species. Hence, the markers derived from ISSR can be used for molecular identification of Aquilaria spp. in ensuring homogenous species for plantation which may improve the quality of resin derived from known and certified materials.

  3. Plant genotyping using fluorescently tagged inter-simple sequence repeats (ISSRs): basic principles and methodology.

    PubMed

    Prince, Linda M

    2015-01-01

    Inter-simple sequence repeat PCR (ISSR-PCR) is a fast, inexpensive genotyping technique based on length variation in the regions between microsatellites. The method requires no species-specific prior knowledge of microsatellite location or composition. Very small amounts of DNA are required, making this method ideal for organisms of conservation concern, or where the quantity of DNA is extremely limited due to organism size. ISSR-PCR can be highly reproducible but requires careful attention to detail. Optimization of DNA extraction, fragment amplification, and normalization of fragment peak heights during fluorescent detection are critical steps to minimizing the downstream time spent verifying and scoring the data.

  4. Evaluation of genetic fidelity among micropropagated plants of Gloriosa superba L. using DNA-based markers--a potential medicinal plant.

    PubMed

    Yadav, Kuldeep; Aggarwal, Ashok; Singh, Narender

    2013-09-01

    Malabar glory lily (Gloriosa superba L.) is a medicinally potent plant species used for the production of alkaloid colchicine. With ever increasing demand, there is a pressing need to conserve it through biotechnological approaches. A large number of complete plantlets were obtained by direct regeneration from the non-dormant tuber explants on Murashige and Skoog (MS) medium supplemented with 2.0 mg/l 6-benzylaminopurine (BAP)+0.5 mg/l α-naphthalene acetic acid (NAA). Large number of plants can be produced in vitro under aseptic conditions, but there is always a danger of producing somaclonal variants by tissue culture technology. Thus, the genetic stability of micropropagated clones was evaluated using random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) analysis. During the study a total of 80 (50 RAPD and 30 ISSR) primers were screened, out of which 10 RAPD and 7 ISSR primers produced a total of 98 (49 RAPD and 49 ISSR) clear, distinct and reproducible amplicons. The amplification products of the regenerated plants showed similar banding patterns to that of the mother plant thus demonstrating the homogeneity of the micropropagated plants. This is the first report that evaluates the use of genetic markers to establish genetic fidelity of micropropagated G. superba using RAPD and ISSR, which can be successfully applied for the mass multiplication, germplasm conservation and further genetic transformation assays for colchicine production to meet the ever increasing demand of this medicinally potent plant for industrial and pharmaceutical uses.

  5. [Comparative Estimate of the Sheep Breed Gene Pools using ISSR Analysis].

    PubMed

    Nesteruk, L V; Makarova, N N; Evsyukov, A N; Svishcheva, G R; Lhasaranov, B B; Stolpovsky, Yu A

    2016-03-01

    Using the ISSR-PCR technique, the genetic structure of nine sheep breeds (Ovis aries) bred on the territories of Russia and Mongolia was examined. Species-specific and breed-specific DNA fragments were identified. For the first time, data on the genetic diversity of Telengit and Buubey sheep breeds were obtained. The main parameters of the genetic diversity and the breed structure were assessed, and the phylogenetic relationships and genetic distances between the studied breeds were determined. Using the method of hierarchical frequency averaging, the prototypal sheep gene pool was reconstructed. The three-tiered analysis of diversity based on the ISSR fingerprinting data showed that 15.8% of variability was found between the breeds, 31.4% of variability was found between the populations within the breeds, and the diversity among the individuals within the populations constituted 52.8%. PMID:27281855

  6. Markers

    ERIC Educational Resources Information Center

    Healthy Schools Network, Inc., 2011

    2011-01-01

    Dry erase whiteboards come with toxic dry erase markers and toxic cleaning products. Dry erase markers labeled "nontoxic" are not free of toxic chemicals and can cause health problems. Children are especially vulnerable to environmental health hazards; moreover, schools commonly have problems with indoor air pollution, as they are more densely…

  7. Genetic diversity of Fusarium oxysporum f.sp. cubense isolates (Foc) of India by inter simple sequence repeats (ISSR) analysis.

    PubMed

    Thangavelu, R; Kumar, K Muthu; Devi, P Ganga; Mustaffa, M M

    2012-07-01

    To find out the genetic diversity of Indian Foc isolates of banana, a total of 107 isolates of Fusarium which includes 98 Foc isolates obtained from different banana growing regions of India and seven Foc isolates belong to all known VCGs obtained from Australia and two non-pathogenic Fusarium oxysporum (npFo) isolates were subjected to ISSR analysis. In the initial screening of ISSR primers, out of 34, 10 primers which generated more polymorphic bands were selected for further analysis. The Phylogenetic analysis carried out based on the fingerprints obtained through ISSR analysis indicated the presence of wide genetic diversity among the Foc isolates of India and also its polyphyletic nature. Totally, seven different clusters were obtained and these clusters differentiated the Foc isolates of India based on the races/VCGs. Besides, the cluster analysis clearly distinguished the freshly emerged Foc strain obtained from cv. Grand Naine (Cavendish-AAA) and Poovan (Mysore-AAB) from the other Foc isolates. The non-pathogenic F. oxysporum isolates which have been included for comparison purpose also clustered separately. All these above said findings indicates for the first time the discriminatory power of ISSR to clearly distinguish and separate the Foc isolates according to its race/VCGs and also its virulence. This study would be useful not only to design and develop effective management strategies but also useful for quarantine purposes.

  8. Phylogeography of two East Asian species in Croomia (Stemonaceae) inferred from chloroplast DNA and ISSR fingerprinting variation.

    PubMed

    Li, En-Xiang; Yi, Sun; Qiu, Ying-Xiong; Guo, Jiang-Tao; Comes, Hans Peter; Fu, Cheng-Xin

    2008-12-01

    The genus Croomia (Stemonaceae) comprises three herbaceous perennial species that are distributed in temperate-deciduous forests in Southeastern North America (C.pauciflora) and East Asia (C. japonica, C. heterosepala). The two Asian species have abutting ranges in South Japan, but C. japonica also occurs disjunctively on the adjacent Asiatic mainland in East China. In our phylogenetic analysis of Croomia, based on chloroplast (cp) DNA sequence variation of the trnL-F region, and rooted with Stemona spp., the two Asian species are identified as sister that likely diverged in the Mid-to-Late Pleistocene (0.84-0.13 mya), whereas the divergence of C. pauciflora dates back to the Late Plio-/Pleistocene (<2.6 mya). Phylogeographical analysis of the two East Asian species detected seven cpDNA (trnL-F) haplotypes across 16 populations surveyed, and all of those were fixed for a particular cpDNA haplotype (H(E)=0.0, G(ST)=1). A survey of inter-simple sequence repeats (ISSRs) markers also detected remarkably low levels of within-population diversity (C. japonica: H(E)=0.085; C. heterosepala: H(E)=0.125), and high levels of inter-population differentiation (C. japonica: Phi(ST)=0.736; C. heterosepala: Phi(ST)=0.550), at least partly due to pronounced regional genetic substructure within both species. Non-overlapping distributions of cpDNA haplotypes and strong genetic (cpDNA/ISSR) differentiation among populations and/or regions accord with findings of a nested clade analysis, which inferred allopatric fragmentation as the major process influencing the spatial haplotype distribution of the two species. Based on mismatch distribution analysis and neutrality tests, we do not find evidence of population expansion in both species. Overall, we conclude that components of temperate-deciduous forest types in South Japan and East China are particularly sensitive to range fragmentation, isolation, and enhanced (incipient) species formation through climate-induced expansions of other

  9. Construction of a genetic linkage map of black gram, Vigna mungo (L.) Hepper, based on molecular markers and comparative studies.

    PubMed

    Gupta, S K; Souframanien, J; Gopalakrishna, T

    2008-08-01

    A genetic linkage map of black gram, Vigna mungo (L.) Hepper, was constructed with 428 molecular markers using an F9 recombinant inbred population of 104 individuals. The population was derived from an inter-subspecific cross between a black gram cultivar, TU94-2, and a wild genotype, V. mungo var. silvestris. The linkage analysis at a LOD score of 5.0 distributed all 428 markers (254 AFLP, 47 SSR, 86 RAPD, and 41 ISSR) into 11 linkage groups. The map spanned a total distance of 865.1 cM with an average marker density of 2 cM. The largest linkage group spanned 115 cM and the smallest linkage group was of 44.9 cM. The number of markers per linkage group ranged from 11 to 86 and the average distance between markers varied from 1.1 to 5.6 cM. Comparison of the map with other published azuki bean and black gram maps showed high colinearity of markers, with some inversions. The current map is the most saturated map for black gram to date and will provide a useful tool for identification of QTLs and for marker-assisted selection of agronomically important characters in black gram.

  10. Virulence Structure of Blumeria graminis f. sp. tritici and Its Genetic Diversity by ISSR and SRAP Profiling Analyses.

    PubMed

    Liu, Na; Liu, Z Lewis; Gong, Guoshu; Zhang, Min; Wang, Xu; Zhou, You; Qi, Xiaobo; Chen, Huabao; Yang, Jizhi; Luo, Peigao; Yang, Chunping

    2015-01-01

    Blumeria graminis f. sp. tritici, which causes wheat powdery mildew, is an obligate biotrophic pathogen that can easily genetically adapt to its host plant. Understanding the virulence structure of and genetic variations in this pathogen is essential for disease control and for breeding resistance to wheat powdery mildew. This study investigated 17 pathogenic populations in Sichuan, China and classified 109 isolates into two distinct groups based on pathogenicity analysis: high virulence (HV, 92 isolates) and low virulence (LV, 17 isolates). Populations from Yibin (Southern region), Xichang (Western region), and Meishan (Middle region) showed lower virulence frequencies than populations from other regions. Many of the previously known resistance genes did not confer resistance in this study. The resistance gene Pm21 displayed an immune response to pathogenic challenge with all populations in Sichuan, and Pm13, Pm5b, Pm2+6, and PmXBD maintained resistance. AMOVA revealed significantly higher levels of variation within populations and lower levels of variation among populations within regions. High levels of gene flow were detected among populations in the four regions. Closely related populations within each region were distinguished by cluster analyses using ISSR and SRAP alleles. Both ISSR and SRAP allele profiling analyses revealed high levels of genetic diversity among pathogenic populations in Sichuan. Although ISSR and SRAP profiling analysis showed similar resolutions, the SRAP alleles appeared to be more informative. We did not detect any significant association between these alleles and the virulence or pathogenicity of the pathogen. Our results suggest that ISSR and SRAP alleles are more efficient for the characterization of small or closely related populations versus distantly related populations. PMID:26098844

  11. Virulence Structure of Blumeria graminis f. sp. tritici and Its Genetic Diversity by ISSR and SRAP Profiling Analyses

    PubMed Central

    Liu, Na; Liu, Z. Lewis; Gong, Guoshu; Zhang, Min; Wang, Xu; Zhou, You; Qi, Xiaobo; Chen, Huabao; Yang, Jizhi; Luo, Peigao; Yang, Chunping

    2015-01-01

    Blumeria graminis f. sp. tritici, which causes wheat powdery mildew, is an obligate biotrophic pathogen that can easily genetically adapt to its host plant. Understanding the virulence structure of and genetic variations in this pathogen is essential for disease control and for breeding resistance to wheat powdery mildew. This study investigated 17 pathogenic populations in Sichuan, China and classified 109 isolates into two distinct groups based on pathogenicity analysis: high virulence (HV, 92 isolates) and low virulence (LV, 17 isolates). Populations from Yibin (Southern region), Xichang (Western region), and Meishan (Middle region) showed lower virulence frequencies than populations from other regions. Many of the previously known resistance genes did not confer resistance in this study. The resistance gene Pm21 displayed an immune response to pathogenic challenge with all populations in Sichuan, and Pm13, Pm5b, Pm2+6, and PmXBD maintained resistance. AMOVA revealed significantly higher levels of variation within populations and lower levels of variation among populations within regions. High levels of gene flow were detected among populations in the four regions. Closely related populations within each region were distinguished by cluster analyses using ISSR and SRAP alleles. Both ISSR and SRAP allele profiling analyses revealed high levels of genetic diversity among pathogenic populations in Sichuan. Although ISSR and SRAP profiling analysis showed similar resolutions, the SRAP alleles appeared to be more informative. We did not detect any significant association between these alleles and the virulence or pathogenicity of the pathogen. Our results suggest that ISSR and SRAP alleles are more efficient for the characterization of small or closely related populations versus distantly related populations. PMID:26098844

  12. [Application of ISSR technology in genetic diversity detection of jute].

    PubMed

    Qi, Jianmin; Zhou, Dongxin; Wu, Weiren; Lin, Lihui; Wu, Jianmei; Fang, Pingping

    2003-09-01

    The genetic diversity among 27 accessions of Corchorus, including 10 Jute species, was investigated with ISSR technique. 283 DNA bands were amplified with 25 ISSR primers, among which, 263 (92.85%) were polymorphic, with 10.48 bands per primer in average. A further systemic cluster analysis indicated that the accessions could be clustered into three groups, and the group II (including two cultispecies and their close wild species) was obviously genetically different from the groups I and III (including eight wild species). Moreover, 16 accessions in group II presented a higher intraspecific genetic resemblance, while 11 accessions among groups I & III showed an abundant interspecific genetic diversity. After synthesized the relevant findings of morphology and DNA classification, it's found that C. urticifolius could be one of the original wild species, C. tilaculariszic was a variation of C. tilaculari, and Tian Jute could be an untitled wild species.

  13. Ghost marker detection and elimination in marker-based optical tracking systems for real-time tracking in stereotactic body radiotherapy

    SciTech Connect

    Yan, Guanghua Li, Jonathan; Huang, Yin; Mittauer, Kathryn; Lu, Bo; Liu, Chihray

    2014-10-15

    Purpose: To propose a simple model to explain the origin of ghost markers in marker-based optical tracking systems (OTS) and to develop retrospective strategies to detect and eliminate ghost markers. Methods: In marker-based OTS, ghost markers are virtual markers created due to the cross-talk between the two camera sensors, which can lead to system execution failure or inaccuracy in patient tracking. As a result, the users have to limit the number of markers and avoid certain marker configurations to reduce the chances of ghost markers. In this work, the authors propose retrospective strategies to detect and eliminate ghost markers. The two camera sensors were treated as mathematical points in space. The authors identified the coplanar within limit (CWL) condition as the necessary condition for ghost marker occurrence. A simple ghost marker detection method was proposed based on the model. Ghost marker elimination was achieved through pattern matching: a ghost marker-free reference set was matched with the optical marker set observed by the OTS; unmatched optical markers were eliminated as either ghost markers or misplaced markers. The pattern matching problem was formulated as a constraint satisfaction problem (using pairwise distances as constraints) and solved with an iterative backtracking algorithm. Wildcard markers were introduced to address missing or misplaced markers. An experiment was designed to measure the sensor positions and the limit for the CWL condition. The ghost marker detection and elimination algorithms were verified with samples collected from a five-marker jig and a nine-marker anthropomorphic phantom, rotated with the treatment couch from −60° to +60°. The accuracy of the pattern matching algorithm was further validated with marker patterns from 40 patients who underwent stereotactic body radiotherapy (SBRT). For this purpose, a synthetic optical marker pattern was created for each patient by introducing ghost markers, marker position

  14. Expression Marker-Based Strategy to Improve Beef Quality.

    PubMed

    Cassar-Malek, Isabelle; Picard, Brigitte

    2016-01-01

    For beef cattle research, a main objective is to control concomitantly the development of muscles and the qualities of beef cuts. Beef quality is a complex phenotype that is only detectable after slaughter and is highly variable. The beef industry is in need of tools to estimate beef quality of live cattle or online in abattoirs, with specific attention towards sensory attributes (tenderness, juiciness, flavour, and colour). Identification of relevant genetic and genomic markers is ongoing, especially for tenderness--a top priority quality attribute. In this paper, we describe the steps of an expression marker-based strategy to improve beef sensory quality, from the discovery of biomarkers that identify consistent beef and the biological functions governing beef tenderness to the integration of the knowledge into detection tests for desirable animals. These tools should soon be available for the management of sensory quality in the beef production chain for meeting market's demands and assuring good quality standards. PMID:27066527

  15. Expression Marker-Based Strategy to Improve Beef Quality

    PubMed Central

    Cassar-Malek, Isabelle; Picard, Brigitte

    2016-01-01

    For beef cattle research, a main objective is to control concomitantly the development of muscles and the qualities of beef cuts. Beef quality is a complex phenotype that is only detectable after slaughter and is highly variable. The beef industry is in need of tools to estimate beef quality of live cattle or online in abattoirs, with specific attention towards sensory attributes (tenderness, juiciness, flavour, and colour). Identification of relevant genetic and genomic markers is ongoing, especially for tenderness—a top priority quality attribute. In this paper, we describe the steps of an expression marker-based strategy to improve beef sensory quality, from the discovery of biomarkers that identify consistent beef and the biological functions governing beef tenderness to the integration of the knowledge into detection tests for desirable animals. These tools should soon be available for the management of sensory quality in the beef production chain for meeting market's demands and assuring good quality standards. PMID:27066527

  16. PNA-based microbial pathogen identification and resistance marker detection

    PubMed Central

    Miller, Nancy S; Frank-Kamenetskii, Maxim D

    2010-01-01

    With the rapidly growing availability of the entire genome sequences of microbial pathogens, there is unmet need for increasingly sensitive systems to monitor the gene-specific markers for diagnosis of bacteremia that enables an earlier detection of causative agent and determination of drug resistance. To address these challenges, a novel FISH-type genomic sequence-based molecular technique is proposed that can identify bacteria and simultaneously detect antibiotic resistance markers for rapid and accurate testing of pathogens. The approach is based on a synergistic combination of advanced Peptide Nucleic Acid (PNA)-based technology and signal-enhancing Rolling Circle Amplification (RCA) reaction to achieve a highly specific and sensitive assay. A specific PNA-DNA construct serves as an exceedingly selective and very effective biomarker, while RCA enhances detection sensitivity and provide with a highly multiplexed assay system. Distinct-color fluorescent decorator probes are used to identify about 20-nucleotide-long signature sequences in bacterial genomic DNA and/or key genetic markers of drug resistance in order to identify and characterize various pathogens. The technique's potential and its utility for clinical diagnostics are illustrated by identification of S. aureus with simultaneous discrimination of methicillin-sensitive (MSSA) versus methicillin-resistant (MRSA) strains. Overall these promising results hint to the adoption of PNA-based rapid sensitive detection for diagnosis of other clinically relevant organisms. Thereby, new assay enables significantly earlier administration of appropriate antimicrobial therapy and may, thus have a positive impact on the outcome of the patient. PMID:21686242

  17. ISSR and isozyme characterization of androgenetic dihaploids reveals tetrasomic inheritance in tetraploid somatic hybrids between Solanum melongena and Solanum aethiopicum group Gilo.

    PubMed

    Toppino, Laura; Mennella, Giuseppe; Rizza, Fulvia; D'Alessandro, Antonietta; Sihachakr, Darasinh; Rotino, Giuseppe L

    2008-01-01

    Gene exchanges between Solanum melongena and its allied relative Solanum aethiopicum are a crucial prerequisite for introgression of useful traits from the allied species into the cultivated eggplant. In order to evaluate the extent of genetic recombination between the 2 species, biochemical and molecular markers were employed. A dihaploid population obtained through anther culture of the corresponding tetraploid somatic hybrids was genetically analyzed. The extent of disomic/tetrasomic inheritance and segregation ratios of 3 isozyme systems and intersimple sequence repeat (ISSR) markers were evaluated. The dihaploids, being derived from microspores, allowed for simple, complete, and accurate analyses. The segregation of 280 ISSR markers (110 aethiopicum-specific, 104 melongena-specific, and 66 monomorphic) were evaluated in 71 dihaploids. According to the genetic constitution (simplex/duplex/triplex), almost 64% of the fragments revealed the tetrasomic and/or disomic inheritance. With regard to the assigned species-specific fragments, 68% and 4% were unambiguously the result of tetrasomic and disomic inheritance, respectively. Twenty-four of the 66 monomorphic ISSRs were inherited according to random chromatid segregation. The phenotypes of glucose-6-phosphate dehydrogenase (G-6-PDH), 6-phosphogluconate dehydrogenase (6-PGDH), and shikimate dehydrogenase (SKDH) were studied in 70 dihaploids and inferences were made about the allelic state of their 5 loci. The isozyme markers segregated in the dihaploids in a distorted manner, their segregations did not fit in with any of the expected segregation ratios. However, tetrasomic inheritance might be suggested for G-6-PDH 2 and SKDH 1 loci. Our results demonstrated that gene exchanges occurred readily in the somatic hybrids between S. melongena and S. aethiopicum gr. Gilo.

  18. Fluorescent marker-based and marker-free discrimination between healthy and cancerous human tissues using hyper-spectral imaging

    NASA Astrophysics Data System (ADS)

    Arnold, Thomas; De Biasio, Martin; Leitner, Raimund

    2015-06-01

    Two problems are addressed in this paper (i) the fluorescent marker-based and the (ii) marker-free discrimination between healthy and cancerous human tissues. For both applications the performance of hyper-spectral methods are quantified. Fluorescent marker-based tissue classification uses a number of fluorescent markers to dye specific parts of a human cell. The challenge is that the emission spectra of the fluorescent dyes overlap considerably. They are, furthermore disturbed by the inherent auto-fluorescence of human tissue. This results in ambiguities and decreased image contrast causing difficulties for the treatment decision. The higher spectral resolution introduced by tunable-filter-based spectral imaging in combination with spectral unmixing techniques results in an improvement of the image contrast and therefore more reliable information for the physician to choose the treatment decision. Marker-free tissue classification is based solely on the subtle spectral features of human tissue without the use of artificial markers. The challenge in this case is that the spectral differences between healthy and cancerous tissues are subtle and embedded in intra- and inter-patient variations of these features. The contributions of this paper are (i) the evaluation of hyper-spectral imaging in combination with spectral unmixing techniques for fluorescence marker-based tissue classification, (ii) the evaluation of spectral imaging for marker-free intra surgery tissue classification. Within this paper, we consider real hyper-spectral fluorescence and endoscopy data sets to emphasize the practical capability of the proposed methods. It is shown that the combination of spectral imaging with multivariate statistical methods can improve the sensitivity and specificity of the detection and the staging of cancerous tissues compared to standard procedures.

  19. Determining the genetic stability of micropropagated sugarcane using inter-simple sequence repeat markers.

    PubMed

    Hsie, B S; Brito, J Z; Vila Nova, M X; Borges-Paluch, L R; Silva, M V; Donato, V M S T

    2015-12-22

    Sugarcane culture is an important source of income for the Brazilian economy. The aim of this study was to identify somaclonal variation in sugarcane varieties RB943365 and RB92579 arising from micropropagation using inter-simple sequence repeat (ISSR) DNA markers. The evaluated plants were generated from the in vitro propagation of shoot tips grown in MS medium supplemented with vitamins, myoinositol, glycine, and sucrose, without the use of growth regulators. Fifteen consecutive subcultures with intervals of 14 days were carried out, and DNA was extracted from young leaves obtained from each of the subcultures. The DNA was amplified with ISSR markers and separated by electrophoresis on 2% agarose gels. No evidence of polymorphism was observed in subcultures of the varieties analyzed, suggesting the absence of somaclonal variants. In this way, the ISSR marker was efficient at analyzing somaclonal variation, and in vitro propagation of sugarcane can be considered efficient for 15 consecutive subcultures of the varieties analyzed.

  20. Genetic relationships among Heliconia (Heliconiaceae) species based on RAPD markers.

    PubMed

    Marouelli, L P; Inglis, P W; Ferreira, M A; Buso, G S C

    2010-07-13

    The family Heliconiaceae contains a single genus, Heliconia, with approximately 180 species of Neotropical origin. This genus was formerly allocated to the family Musaceae, but today forms its own family, in the order Zingiberales. The combination of inverted flowers, a single staminode and drupe fruits is an exclusive characteristic of Heliconia. Heliconias are cultivated as ornamental garden plants, and are of increasing importance as cut flowers. However, there are taxonomic confusions and uncertainties about the number of species and the relationships among them. Molecular studies are therefore necessary for better understanding of the species boundaries of these plants. We examined the genetic variability and the phylogenetic relationships of 124 accessions of the genus Heliconia based on RAPD markers. Phenetic and cladistic analyses, using 231 polymorphic RAPD markers, demonstrated that the genus Heliconia is monophyletic. Groupings corresponding to currently recognized species and some subgenera were found, and cultivars and hybrids were found to cluster with their parents. RAPD analysis generally agreed with morphological species classification, except for the position of the subgenus Stenochlamys, which was found to be polyphyletic.

  1. Opportunities of marker-assisted selection for rice fragrance through marker-trait association analysis of microsatellites and gene-based markers.

    PubMed

    Golestan Hashemi, F S; Rafii, M Y; Razi Ismail, M; Mohamed, M T M; Rahim, H A; Latif, M A; Aslani, F

    2015-09-01

    Developing fragrant rice through marker-assisted/aided selection (MAS) is an economical and profitable approach worldwide for the enrichment of an elite genetic background with a pleasant aroma. The PCR-based DNA markers that distinguish the alleles of major fragrance genes in rice have been synthesised to develop rice scent biofortification through MAS. Thus, the present study examined the aroma biofortification potential of these co-dominant markers in a germplasm panel of 189 F2 progeny developed from crosses between a non-aromatic variety (MR84) and a highly aromatic but low-yielding variety (MRQ74) to determine the most influential diagnostic markers for fragrance biofortification. The SSRs and functional DNA markers RM5633 (on chromosome 4), RM515, RM223, L06, NKSbad2, FMbadh2-E7, BADEX7-5, Aro7 and SCU015RM (on chromosome 8) were highly associated with the 2AP (2-acetyl-1-pyrroline) content across the population. The alleles traced via these markers were also in high linkage disequilibrium (R(2) > 0.70) and explained approximately 12.1, 27.05, 27.05, 27.05, 25.42, 25.42, 20.53, 20.43 and 20.18% of the total phenotypic variation observed for these biomarkers, respectively. F2 plants harbouring the favourable alleles of these effective markers produced higher levels of fragrance. Hence, these rice plants can be used as donor parents to increase the development of fragrance-biofortified tropical rice varieties adapted to growing conditions and consumer preferences, thus contributing to the global rice market. PMID:25865409

  2. EST-based Microsatellite Marker Data Mining and Characterizing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Peanut (Arachis hypogaea L.) is an important crop for oil production. In the recent years, molecular marker technologies have been widely applied to genetic diversity analysis, genetic mapping, molecular marker-assisted breeding, gene tagging and QTLs analysis. However, it is expensive, labor-intens...

  3. Intelligent DNA-based molecular diagnostics using linked genetic markers

    SciTech Connect

    Pathak, D.K.; Perlin, M.W.; Hoffman, E.P.

    1994-12-31

    This paper describes a knowledge-based system for molecular diagnostics, and its application to fully automated diagnosis of X-linked genetic disorders. Molecular diagnostic information is used in clinical practice for determining genetic risks, such as carrier determination and prenatal diagnosis. Initially, blood samples are obtained from related individuals, and PCR amplification is performed. Linkage-based molecular diagnosis then entails three data analysis steps. First, for every individual, the alleles (i.e., DNA composition) are determined at specified chromosomal locations. Second, the flow of genetic material among the individuals is established. Third, the probability that a given individual is either a carrier of the disease or affected by the disease is determined. The current practice is to perform each of these three steps manually, which is costly, time consuming, labor-intensive, and error-prone. As such, the knowledge-intensive data analysis and interpretation supersede the actual experimentation effort as the major bottleneck in molecular diagnostics. By examining the human problem solving for the task, we have designed and implemented a prototype knowledge-based system capable of fully automating linkage-based molecular diagnostics in X-linked genetic disorders, including Duchenne Muscular Dystrophy (DMD). Our system uses knowledge-based interpretation of gel electrophoresis images to determine individual DNA marker labels, a constraint satisfaction search for consistent genetic flow among individuals, and a blackboard-style problem solver for risk assessment. We describe the system`s successful diagnosis of DMD carrier and affected individuals from raw clinical data.

  4. Gabor feature-based registration: accurate alignment without fiducial markers

    NASA Astrophysics Data System (ADS)

    Parra, Nestor A.; Parra, Carlos A.

    2007-03-01

    Accurate registration of diagnosis and treatment images is a critical factor for the success of radiotherapy. This study presents a feature-based image registration algorithm that uses a branch- and-bound method to search the space of possible transformations, as well as a Hausdorff distance metric to evaluate their quality. This distance is computed in the space of responses to a circular Gabor filter, in which, for each point of interest in both reference and subject images, a vector of complex responses to different Gabor kernels is computed. Each kernel is generated using different frequencies and variances of the Gabor function, which determines correspondent regions in the images to be registered, by virtue of its rotation invariance characteristics. Responses to circular Gabor filters have also been reported in literature as a successful tool for image classification; and in this particular application we utilize them for patient positioning in cranial radiotherapy. For test purposes, we use 2D portal images acquired with an electronic portal imaging device (EPID). Our method presents EPID-EPID registrations errors under 0.2 mm for translations and 0.05 deg for rotations (subpixel accuracy). We are using fiducial marker registration as the ground truth for comparisons. Registration times average 2.70 seconds based on 1400 feature points using a 1.4 GHz processor.

  5. Genetic diversity of Greek Aegilops species using different types of nuclear genome markers.

    PubMed

    Thomas, Konstantinos G; Bebeli, Penelope J

    2010-09-01

    Random Amplified Polymorphic DNA (RAPD) and Inter-Simple Sequence Repeat (ISSR) analyses were used to evaluate genetic variability and relationships of Greek Aegilops species. Thirty-eight accessions of seven Greek Aegilops species [Ae. triuncialis (genome UC), Ae. neglecta (UM), Ae. biuncialis (UM), Ae. caudata (C), Ae. comosa (M), Ae. geniculata (MU) and Ae. umbellulata (U)] as well as Triticum accessions were studied. Nineteen RAPD and ten ISSR primers yielded 344 and 170 polymorphic bands, respectively, that were used for the construction of dendrograms. Regardless of the similarity coefficient and marker type used, UPGMA placed 38 Aegilops accessions into one branch while the other branch consisted of wheat species. Within the Aegilops cluster, subgroups were identified that included species that shared the same genome or belonged to the same botanical section. Within the Triticum cluster, two robust subgroups were formed, one including diploid wheat and another including polyploid wheat. In conclusion, results showed that there is genetic diversity in the Greek Aegilops species studied, and clustering based on genetic similarities was in agreement with botanical classifications.

  6. Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants.

    PubMed

    Shirasawa, Kenta; Isobe, Sachiko; Tabata, Satoshi; Hirakawa, Hideki

    2014-09-01

    In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops. PMID:25320561

  7. Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants.

    PubMed

    Shirasawa, Kenta; Isobe, Sachiko; Tabata, Satoshi; Hirakawa, Hideki

    2014-09-01

    In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops.

  8. Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants

    PubMed Central

    Shirasawa, Kenta; Isobe, Sachiko; Tabata, Satoshi; Hirakawa, Hideki

    2014-01-01

    In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops. PMID:25320561

  9. A vision-based automated guided vehicle system with marker recognition for indoor use.

    PubMed

    Lee, Jeisung; Hyun, Chang-Ho; Park, Mignon

    2013-08-07

    We propose an intelligent vision-based Automated Guided Vehicle (AGV) system using fiduciary markers. In this paper, we explore a low-cost, efficient vehicle guiding method using a consumer grade web camera and fiduciary markers. In the proposed method, the system uses fiduciary markers with a capital letter or triangle indicating direction in it. The markers are very easy to produce, manipulate, and maintain. The marker information is used to guide a vehicle. We use hue and saturation values in the image to extract marker candidates. When the known size fiduciary marker is detected by using a bird's eye view and Hough transform, the positional relation between the marker and the vehicle can be calculated. To recognize the character in the marker, a distance transform is used. The probability of feature matching was calculated by using a distance transform, and a feature having high probability is selected as a captured marker. Four directional signals and 10 alphabet features are defined and used as markers. A 98.87% recognition rate was achieved in the testing phase. The experimental results with the fiduciary marker show that the proposed method is a solution for an indoor AGV system.

  10. A Vision-Based Automated Guided Vehicle System with Marker Recognition for Indoor Use

    PubMed Central

    Lee, Jeisung; Hyun, Chang-Ho; Park, Mignon

    2013-01-01

    We propose an intelligent vision-based Automated Guided Vehicle (AGV) system using fiduciary markers. In this paper, we explore a low-cost, efficient vehicle guiding method using a consumer grade web camera and fiduciary markers. In the proposed method, the system uses fiduciary markers with a capital letter or triangle indicating direction in it. The markers are very easy to produce, manipulate, and maintain. The marker information is used to guide a vehicle. We use hue and saturation values in the image to extract marker candidates. When the known size fiduciary marker is detected by using a bird's eye view and Hough transform, the positional relation between the marker and the vehicle can be calculated. To recognize the character in the marker, a distance transform is used. The probability of feature matching was calculated by using a distance transform, and a feature having high probability is selected as a captured marker. Four directional signals and 10 alphabet features are defined and used as markers. A 98.87% recognition rate was achieved in the testing phase. The experimental results with the fiduciary marker show that the proposed method is a solution for an indoor AGV system. PMID:23966180

  11. Development of DArT-based PCR markers for selecting drought-tolerant spring barley.

    PubMed

    Fiust, Anna; Rapacz, Marcin; Wójcik-Jagła, Magdalena; Tyrka, Mirosław

    2015-08-01

    The tolerance of spring barley (Hordeum vulgare L.) cultivars to spring drought is an important agronomic trait affecting crop yield and quality in Poland. Therefore, breeders require new molecular markers to select plants with lower spring drought susceptibility. With the advent of genomic selection technology, simple molecular tools may still be applicable to screen material for markers of the most important traits and in-depth genome scanning. In previous studies, diversity arrays technology (DArT)-based genetic maps were constructed for F2 populations of Polish fodder and malt barley elite breeding lines, and 15 and 18 quantitative trait loci (QTLs) related to spring drought tolerance were identified, respectively. In this paper, we show the results of a conversion of 30 DArT markers corresponding to 11 QTLs into simple sequence repeat (SSR) and sequence tagged site (STS) markers. Twenty-two polymorphic markers were obtained, including 13 DArT-based SSRs. Additionally, 31 SSR markers, located in close proximity to the DArT markers, were selected from the GrainGenes database and tested. Further analyses of 24 advanced breeding lines with different drought tolerances confirmed that five out of the 30 converted markers, as well as three out of the 31 additional SSR markers, were effective in marker-assisted selection for drought tolerance. The possible function of clones related to these markers in drought tolerance is discussed. PMID:25716655

  12. Identification of putative gene based markers of renal toxicity.

    PubMed Central

    Amin, Rupesh P; Vickers, Alison E; Sistare, Frank; Thompson, Karol L; Roman, Richard J; Lawton, Michael; Kramer, Jeffrey; Hamadeh, Hisham K; Collins, Jennifer; Grissom, Sherry; Bennett, Lee; Tucker, C Jeffrey; Wild, Stacie; Kind, Clive; Oreffo, Victor; Davis, John W; Curtiss, Sandra; Naciff, Jorge M; Cunningham, Michael; Tennant, Raymond; Stevens, James; Car, Bruce; Bertram, Timothy A; Afshari, Cynthia A

    2004-01-01

    This study, designed and conducted as part of the International Life Sciences Institute working group on the Application of Genomics and Proteomics, examined the changes in the expression profile of genes associated with the administration of three different nephrotoxicants--cisplatin, gentamicin, and puromycin--to assess the usefulness of microarrays in the understanding of mechanism(s) of nephrotoxicity. Male Sprague-Dawley rats were treated with daily doses of puromycin (5-20 mg/kg/day for 21 days), gentamicin (2-240 mg/kg/day for 7 days), or a single dose of cisplatin (0.1-5 mg/kg). Groups of rats were sacrificed at various times after administration of these compounds for standard clinical chemistry, urine analysis, and histological evaluation of the kidney. RNA was extracted from the kidney for microarray analysis. Principal component analysis and gene expression-based clustering of compound effects confirmed sample separation based on dose, time, and degree of renal toxicity. In addition, analysis of the profile components revealed some novel changes in the expression of genes that appeared to be associated with injury in specific portions of the nephron and reflected the mechanism of action of these various nephrotoxicants. For example, although puromycin is thought to specifically promote injury of the podocytes in the glomerulus, the changes in gene expression after chronic exposure of this compound suggested a pattern similar to the known proximal tubular nephrotoxicants cisplatin and gentamicin; this prediction was confirmed histologically. We conclude that renal gene expression profiling coupled with analysis of classical end points affords promising opportunities to reveal potential new mechanistic markers of renal toxicity. PMID:15033597

  13. Biomedical wellness monitoring system based upon molecular markers

    NASA Astrophysics Data System (ADS)

    Ingram, Whitney

    2012-06-01

    We wish to assist caretakers with a sensor monitoring systems for tracking the physiological changes of homealone patients. One goal is seeking biomarkers and modern imaging sensors like stochastic optical reconstruction microscopy (STORM), which has achieved visible imaging at the nano-scale range. Imaging techniques like STORM can be combined with a fluorescent functional marker in a system to capture the early transformation signs from wellness to illness. By exploiting both microscopic knowledge of genetic pre-disposition and the macroscopic influence of epigenetic factors we hope to target these changes remotely. We adopt dual spectral infrared imaging for blind source separation (BSS) to detect angiogenesis changes and use laser speckle imaging for hypertension blood flow monitoring. Our design hypothesis for the monitoring system is guided by the user-friendly, veteran-preferred "4-Non" principles (noninvasive, non-contact, non-tethered, non-stop-to-measure) and by the NIH's "4Ps" initiatives (predictive, personalized, preemptive, and participatory). We augment the potential storage system with the recent know-how of video Compressive Sampling (CSp) from surveillance cameras. In CSp only major changes are saved, which reduces the manpower cost of caretakers and medical analysts. This CSp algorithm is based on smart associative memory (AM) matrix storage: change features and detailed scenes are written by the outer-product and read by the inner product without the usual Harsh index for image searching. From this approach, we attempt to design an effective household monitoring approach to save healthcare costs and maintain the quality of life of seniors.

  14. Optical detection of sepsis markers using liquid crystal based biosensors

    NASA Astrophysics Data System (ADS)

    McCamley, Maureen K.; Artenstein, Andrew W.; Opal, Steven M.; Crawford, Gregory P.

    2007-02-01

    A liquid crystal based biosensor for the detection and diagnosis of sepsis is currently in development. Sepsis, a major clinical syndrome with a significant public health burden in the US due to a large elderly population, is the systemic response of the body to a localized infection and is defined as the combination of pathologic infection and physiological changes. Bacterial infections are responsible for 90% of cases of sepsis in the US. Currently there is no bedside diagnostic available to positively identify sepsis. The basic detection scheme employed in a liquid crystal biosensor contains attributes that would find value in a clinical setting, especially for the early detection of sepsis. Utilizing the unique properties of liquid crystals, such as birefringence, a bedside diagnostic is in development which will optically report the presence of biomolecules. In a septic patient, an endotoxin known as lipopolysaccharide (LPS) is released from the outer membrane of Gram-negative bacteria and can be found in the blood stream. It is hypothesized that this long chained molecule will cause local disruptions to the open surface of a sensor containing aligned liquid crystal. The bulk liquid crystal ampli.es these local changes at the surface due to the presence of the sepsis marker, providing an optical readout through polarizing microscopy images. Liquid crystal sensors consisting of both square and circular grids, 100-200 μm in size, have been fabricated and filled with a common liquid crystal material, 5CB. Homeotropic alignment was confirmed using polarizing microscopy. The grids were then contacted with either saline only (control), or saline with varying concentrations of LPS. Changes in the con.guration of the nematic director of the liquid crystal were observed through the range of concentrations tested (5mg/mL - 1pg/mL) which have been confirmed by a consulting physician as clinically relevant levels.

  15. Development of marker-based tracking methods for augmented reality applied to NPP maintenance work support and its experimental evaluation

    SciTech Connect

    Ishii, H.; Fujino, H.; Bian, Z.; Sekiyama, T.; Shimoda, H.; Yoshikawa, H.

    2006-07-01

    In this study, two types of marker-based tracking methods for Augmented Reality have been developed. One is a method which employs line-shaped markers and the other is a method which employs circular-shaped markers. These two methods recognize the markers by means of image processing and calculate the relative position and orientation between the markers and the camera in real time. The line-shaped markers are suitable to be pasted in the buildings such as NPPs where many pipes and tanks exist. The circular-shaped markers are suitable for the case that there are many obstacles and it is difficult to use line-shaped markers because the obstacles hide the part of the line-shaped markers. Both methods can extend the maximum distance between the markers and the camera compared to the legacy marker-based tracking methods. (authors)

  16. A new type of model-based Roentgen stereophotogrammetric analysis for solving the occluded marker problem.

    PubMed

    Kaptein, B L; Valstar, E R; Stoel, B C; Rozing, P M; Reiber, J H C

    2005-11-01

    Roentgen stereophotogrammetric analysis (RSA) measures micromotion of an orthopaedic implant with respect to its surrounding bone. A problem in RSA is that the markers are sometimes overprojected by the implant itself. This study describes the so-called Marker Configuration Model-based RSA (MCM-based RSA) that is able to measure the pose of a rigid body in situations where less than three markers could be detected in both images of an RSA radiograph. MCM-based RSA is based on fitting a Marker Configuration model (MC-model) to the projection lines from the marker projection positions in the image to their corresponding Roentgen foci. An MC-model describes the positions of markers relative to each other and is obtained using conventional RSA. We used data from 15 double examinations of a clinical study of total knee prostheses and removed projections of the three tibial component markers, simulating occlusion of markers. The migration of the tibial component with respect to the bone, which should be zero, for the double examination is a measure of the accuracy of algorithm. With the new algorithm, it is possible to estimate the pose of a rigid body of which one or two markers are occluded in one of the images of the RSA radiograph with high accuracy as long as a proper MC-model of the markers in the rigid body is available. The new algorithm makes RSA more robust for occlusion of markers. This improves the results of clinical RSA studies because the number of lost RSA follow-up moments is reduced.

  17. Molecular Identification of Sex in Phoenix dactylifera Using Inter Simple Sequence Repeat Markers

    PubMed Central

    Al-Ameri, Abdulhafed A.; Al-Qurainy, Fahad; Gaafar, Abdel-Rhman Z.; Khan, Salim; Nadeem, M.

    2016-01-01

    Early sex identification of Date Palm (Phoenix dactylifera L.) at seedling stage is an economically desirable objective, which will significantly increase the profits of seed based cultivation. The utilization of molecular markers at this stage for early and rapid identification of sex is important due to the lack of morphological markers. In this study, a total of two hundred Inter Simple Sequence Repeat (ISSR) primers were screened among male and female Date palm plants to identify putative sex-specific marker, out of which only two primers (IS_A02 and IS_A71) were found to be associated with sex. The primer IS_A02 produced a unique band of size 390 bp and was found clearly in all female plants, while it was absent in all male plants. Contrary to this, the primer IS_A71 produced a unique band of size 380 bp and was clearly found in all male plants, whereas it was absent in all the female plants. Subsequently, these specific fragments were excised, purified, and sequenced for the development of sequence specific markers further in future for the implementation on dioecious Date Palm for sex determination. These markers are efficient, highly reliable, and reproducible for sex identification at the early stage of seedling. PMID:27419132

  18. Genetic analysis and marker assisted identification of life phases of red alga Gracilaria corticata (J. Agardh).

    PubMed

    Baghel, Ravi S; Kumari, Puja; Bijo, A J; Gupta, Vishal; Reddy, C R K; Jha, B

    2011-08-01

    The present study firstly reports the cytological and molecular marker assisted differentiation of isomorphic population of Gracilaria corticata (J. Agardh) with inter and intra-phasic genetic diversity analysis using ISSR markers. The genetic diversity of inbreeding population of G. corticata as determined in terms of percentage of polymorphic loci (PPL), average heterozygosity (He) and Shannon's Weaver index (I) were 59.80, 0.59 and 1.21, respectively. The inter-phasic pair-wise average polymorphism were found to be 31.6% between male and female, 24.0% in male and tetrasporophyte and 25.3% in female and tetrasporophyte. The intra-phasic average polymorphisms were calculated as a maximum of 5.5% between females, 4.2% between males and the lowest 2.4% between tetrasporophytes. The primer 10 generated a marker of 800 bp specific to male and 650 bp to female gametophyte, while the primer 17 generated a marker of 2,500 bp specific to tetrasporophyte. Both the UPGMA based dendrogram and PCA analysis clustered all the three life phases differentially as distinct identity. Cytological analysis by chromosome count revealed 24 chromosomes in both haploid male and female gametophytes (N) and 48 for diploid (2 N) tetrasporophyte further confirming their genetic distinctness. The life phase specific markers reported in this study could be of help in breeding programmes where differentiation of life phases at the early developmental stages is crucial.

  19. Effects of genotoxicity and its consequences at the population level in sexual and asexual Artemia assessed by analysis of inter-simple sequence repeats (ISSR).

    PubMed

    Sukumaran, Sandhya; Grant, Alastair

    2013-09-18

    There is considerable evidence that genetic damage in organisms occurs in the environment as a result of exposure to genotoxins and ionising radiation, but we have limited understanding of the extent to which this results in adverse consequences at a population level. We used inter-simple sequence repeat (ISSR) markers to quantify genotoxic effects of the mutagen ethylmethane sulfonate (EMS) on a sexual (Artemia franciscana) and an asexual (Artemia parthenogenetica) species of brine shrimp. The method provides information similar to that obtained with assessment of RAPD (random amplification of polymorphic DNA) but is more robust. Genetic damage was transmitted to the F1 generation in both Artemia species, but the sexual species showed a greater degree of recovery, as shown by higher values of genomic template stability. There was a strong correlation between DNA damage and effects on individual fitness parameters: size, survival, reproduction and population growth. These effects persisted into the F2 generation in A. parthenogenetica, but in the sexual A. franciscana only effects on fecundity continued beyond the exposed generation, even though there were substantial alterations in ISSR patterns in the F1 generation. Genetic biomarkers can thus be indicative of effects at the population level, but sexually reproducing species have a considerable assimilative capacity for the effects of genotoxins. PMID:23872504

  20. Effects of genotoxicity and its consequences at the population level in sexual and asexual Artemia assessed by analysis of inter-simple sequence repeats (ISSR).

    PubMed

    Sukumaran, Sandhya; Grant, Alastair

    2013-09-18

    There is considerable evidence that genetic damage in organisms occurs in the environment as a result of exposure to genotoxins and ionising radiation, but we have limited understanding of the extent to which this results in adverse consequences at a population level. We used inter-simple sequence repeat (ISSR) markers to quantify genotoxic effects of the mutagen ethylmethane sulfonate (EMS) on a sexual (Artemia franciscana) and an asexual (Artemia parthenogenetica) species of brine shrimp. The method provides information similar to that obtained with assessment of RAPD (random amplification of polymorphic DNA) but is more robust. Genetic damage was transmitted to the F1 generation in both Artemia species, but the sexual species showed a greater degree of recovery, as shown by higher values of genomic template stability. There was a strong correlation between DNA damage and effects on individual fitness parameters: size, survival, reproduction and population growth. These effects persisted into the F2 generation in A. parthenogenetica, but in the sexual A. franciscana only effects on fecundity continued beyond the exposed generation, even though there were substantial alterations in ISSR patterns in the F1 generation. Genetic biomarkers can thus be indicative of effects at the population level, but sexually reproducing species have a considerable assimilative capacity for the effects of genotoxins.

  1. Assessment of genetic diversity in indigenous turmeric (Curcuma longa) germplasm from India using molecular markers.

    PubMed

    Verma, Sushma; Singh, Shweta; Sharma, Suresh; Tewari, S K; Roy, R K; Goel, A K; Rana, T S

    2015-04-01

    Curcuma longa L., commonly known as turmeric, is one of the economically and medicinally important plant species. It is predominantly cultivated in the tropical and sub tropical countries. India is the largest producer, and exporter of turmeric in the world, followed by China, Indonesia, Bangladesh and Thailand. In the present study, Directed Amplification of Minisatellite DNA (DAMD) and Inter Simple Sequence Repeats (ISSR), methods were used to estimate the genetic variability in indigenous turmeric germplasm. Cumulative data analysis for DAMD (15) and ISSR (13) markers resulted into 478 fragments, out of which 392 fragments were polymorphic, revealing 82 % polymorphism across the turmeric genotypes. Wide range of pairwise genetic distances (0.03-0.59) across the genotypes revealed that these genotypes are genetically quite diverse. The UPGMA dendrogram generated using cumulative data showed significant relationships amongst the genotypes. All 29 genotypes studied grouped into two clusters irrespective of their geographical affiliations with 100 % bootstrap value except few genotypes, suggesting considerable diversity amongst the genotypes. These results suggested that the current collection of turmeric genotypes preserve the vast majority of natural variations. The results further demonstrate the efficiency and reliability of DAMD and ISSR markers in determining the genetic diversity and relationships among the indigenous turmeric germplasm. DAMD and ISSR profiling have identified diverse turmeric genotypes, which could be further utilized in various genetic improvement programmes including conventional as well as marker assisted breeding towards development of new and desirable turmeric genotypes.

  2. Dynamic light scattering (DLS)-based immunoassay for ultra-sensitive detection of tumor marker protein.

    PubMed

    Li, Chao; Ma, Jiehua; Fan, Qiongxuan; Tao, Yaqin; Li, Genxi

    2016-06-14

    A novel dynamic light scattering (DLS)-based immunoassay that utilizes manganese dioxide nanosheet-modified gold nanoparticles (MnO2-GNPs) as an activatable nanoprobe has been developed to detect tumor markers down to femtomolar levels. PMID:27247980

  3. A novel fully automatic scheme for fiducial marker-based alignment in electron tomography.

    PubMed

    Han, Renmin; Wang, Liansan; Liu, Zhiyong; Sun, Fei; Zhang, Fa

    2015-12-01

    Although the topic of fiducial marker-based alignment in electron tomography (ET) has been widely discussed for decades, alignment without human intervention remains a difficult problem. Specifically, the emergence of subtomogram averaging has increased the demand for batch processing during tomographic reconstruction; fully automatic fiducial marker-based alignment is the main technique in this process. However, the lack of an accurate method for detecting and tracking fiducial markers precludes fully automatic alignment. In this paper, we present a novel, fully automatic alignment scheme for ET. Our scheme has two main contributions: First, we present a series of algorithms to ensure a high recognition rate and precise localization during the detection of fiducial markers. Our proposed solution reduces fiducial marker detection to a sampling and classification problem and further introduces an algorithm to solve the parameter dependence of marker diameter and marker number. Second, we propose a novel algorithm to solve the tracking of fiducial markers by reducing the tracking problem to an incomplete point set registration problem. Because a global optimization of a point set registration occurs, the result of our tracking is independent of the initial image position in the tilt series, allowing for the robust tracking of fiducial markers without pre-alignment. The experimental results indicate that our method can achieve an accurate tracking, almost identical to the current best one in IMOD with half automatic scheme. Furthermore, our scheme is fully automatic, depends on fewer parameters (only requires a gross value of the marker diameter) and does not require any manual interaction, providing the possibility of automatic batch processing of electron tomographic reconstruction.

  4. Development of PCR‐Based Markers to Determine the Sex of Kelps

    PubMed Central

    Lipinska, Agnieszka P.; Ahmed, Sophia; Peters, Akira F.; Faugeron, Sylvain; Cock, J. Mark; Coelho, Susana M.

    2015-01-01

    Sex discriminating genetic markers are commonly used to facilitate breeding programs in economically and ecologically important animal and plant species. However, despite their considerable economic and ecological value, the development of sex markers for kelp species has been very limited. In this study, we used the recently described sequence of the sex determining region (SDR) of the brown algal model Ectocarpus to develop novel DNA-based sex-markers for three commercially relevant kelps: Laminaria digitata, Undaria pinnatifida and Macrocystis pyrifera. Markers were designed within nine protein coding genes of Ectocarpus male and female (U/V) sex chromosomes and tested on gametophytes of the three kelp species. Seven primer pairs corresponding to three loci in the Ectocarpus SDR amplified sex-specific bands in the three kelp species, yielding at least one male and one female marker for each species. Our work has generated the first male sex-specific markers for L. digitata and U. pinnatifida, as well as the first sex markers developed for the genus Macrocystis. The markers and methodology presented here will not only facilitate seaweed breeding programs but also represent useful tools for population and demography studies and provide a means to investigate the evolution of sex determination across this largely understudied eukaryotic group. PMID:26496392

  5. Identification of uterine leiomyoma-specific marker genes based on DNA methylation and their clinical application.

    PubMed

    Sato, Shun; Maekawa, Ryo; Yamagata, Yoshiaki; Tamura, Isao; Lee, Lifa; Okada, Maki; Jozaki, Kosuke; Asada, Hiromi; Tamura, Hiroshi; Sugino, Norihiro

    2016-01-01

    Differential diagnosis of uterine leiomyomas and leiomyosarcomas is needed to determine whether the uterus can be retained. Therefore, biomarkers for uterine leiomyomas, and reliable and objective diagnostic methods have been desired besides the pathological diagnosis. In the present study, we identified 12 genes specific to uterine leiomyomas based on DNA methylation. Using these marker genes specific to uterine leiomyomas, we established a hierarchical clustering system based on the DNA methylation level of the marker genes, which could completely differentiate between uterine leiomyomas and normal myometrium. Furthermore, our hierarchical clustering system completely discriminated uterine cancers and differentiated between uterine leiomyosarcomas and leiomyomas with more than 70% accuracy. In conclusion, this study identified DNA methylation-based marker genes specific to uterine leiomyomas, and our hierarchical clustering system using these marker genes was useful for differential diagnosis of uterine leiomyomas and leiomyosarcomas. PMID:27498619

  6. Identification of uterine leiomyoma-specific marker genes based on DNA methylation and their clinical application

    PubMed Central

    Sato, Shun; Maekawa, Ryo; Yamagata, Yoshiaki; Tamura, Isao; Lee, Lifa; Okada, Maki; Jozaki, Kosuke; Asada, Hiromi; Tamura, Hiroshi; Sugino, Norihiro

    2016-01-01

    Differential diagnosis of uterine leiomyomas and leiomyosarcomas is needed to determine whether the uterus can be retained. Therefore, biomarkers for uterine leiomyomas, and reliable and objective diagnostic methods have been desired besides the pathological diagnosis. In the present study, we identified 12 genes specific to uterine leiomyomas based on DNA methylation. Using these marker genes specific to uterine leiomyomas, we established a hierarchical clustering system based on the DNA methylation level of the marker genes, which could completely differentiate between uterine leiomyomas and normal myometrium. Furthermore, our hierarchical clustering system completely discriminated uterine cancers and differentiated between uterine leiomyosarcomas and leiomyomas with more than 70% accuracy. In conclusion, this study identified DNA methylation-based marker genes specific to uterine leiomyomas, and our hierarchical clustering system using these marker genes was useful for differential diagnosis of uterine leiomyomas and leiomyosarcomas. PMID:27498619

  7. Development of new PCR-based markers specific for chromosome arms of rye (Secale cereale L.).

    PubMed

    Qiu, Ling; Tang, Zong-xiang; Li, Meng; Fu, Shu-lan

    2016-03-01

    PCR-based rye (Secale cereale L.) chromosome-specific markers can contribute to the effective utilization of elite genes of rye in wheat (Triticum aestivum L.) breeding programs. In the present study, 578 new PCR-based rye-specific markers have been developed by using specific length amplified fragment sequencing (SLAF-seq) technology, and 76 markers displayed different polymorphism among rye Kustro, Imperial, and King II. A total of 427 and 387 markers were, respectively, located on individual chromosomes and chromosome arms of Kustro by using a set of wheat-rye monosomic addition lines and 13 monotelosomic addition lines, which were derived from T. aestivum L. 'Mianyang11' × S. cereale L. 'Kustro'. In addition, two sets of wheat-rye disomic addition lines, which were derived from T. aestivum L. var. Chinese Spring × S. cereale L. var. Imperial and T. aestivum L. 'Holdfast' × S. cereale L. var. King II, were used to test the chromosomal specificity of the 427 markers. The chromosomal locations of 281 markers were consistent among the three sets of wheat-rye addition lines. The markers developed in this study can be used to identify a given segment of rye chromosomes in wheat background and accelerate the utilization of elite genes on rye chromosomes in wheat breeding programs.

  8. Marker-Based Hierarchical Segmentation and Classification Approach for Hyperspectral Imagery

    NASA Technical Reports Server (NTRS)

    Tarabalka, Yuliya; Tilton, James C.; Benediktsson, Jon Atli; Chanussot, Jocelyn

    2011-01-01

    The Hierarchical SEGmentation (HSEG) algorithm, which is a combination of hierarchical step-wise optimization and spectral clustering, has given good performances for hyperspectral image analysis. This technique produces at its output a hierarchical set of image segmentations. The automated selection of a single segmentation level is often necessary. We propose and investigate the use of automatically selected markers for this purpose. In this paper, a novel Marker-based HSEG (M-HSEG) method for spectral-spatial classification of hyperspectral images is proposed. First, pixelwise classification is performed and the most reliably classified pixels are selected as markers, with the corresponding class labels. Then, a novel constrained marker-based HSEG algorithm is applied, resulting in a spectral-spatial classification map. The experimental results show that the proposed approach yields accurate segmentation and classification maps, and thus is attractive for hyperspectral image analysis.

  9. Identifying Objective EEG Based Markers of Linear Vection in Depth.

    PubMed

    Palmisano, Stephen; Barry, Robert J; De Blasio, Frances M; Fogarty, Jack S

    2016-01-01

    This proof-of-concept study investigated whether a time-frequency EEG approach could be used to examine vection (i.e., illusions of self-motion). In the main experiment, we compared the event-related spectral perturbation (ERSP) data of 10 observers during and directly after repeated exposures to two different types of optic flow display (each was 35° wide by 29° high and provided 20 s of motion stimulation). Displays consisted of either a vection display (which simulated constant velocity forward self-motion in depth) or a control display (a spatially scrambled version of the vection display). ERSP data were decomposed using time-frequency Principal Components Analysis (t-f PCA). We found an increase in 10 Hz alpha activity, peaking some 14 s after display motion commenced, which was positively associated with stronger vection ratings. This followed decreases in beta activity, and was also followed by a decrease in delta activity; these decreases in EEG amplitudes were negatively related to the intensity of the vection experience. After display motion ceased, a series of increases in the alpha band also correlated with vection intensity, and appear to reflect vection- and/or motion-aftereffects, as well as later cognitive preparation for reporting the strength of the vection experience. Overall, these findings provide support for the notion that EEG can be used to provide objective markers of changes in both vection status (i.e., "vection/no vection") and vection strength. PMID:27559328

  10. Characterization of Anatolian traditional quince cultivars, based on microsatellite markers.

    PubMed

    Yüksel, C; Mutaf, F; Demirtaş, İ; Öztürk, G; Pektaş, M; Ergül, A

    2013-01-01

    We conducted simple sequence repeat (SSR) analyses of 15 traditional quince (Cydonia oblonga) cultivars from Anatolian gene sources for molecular characterization and investigation of genetic relationships. Three pear and two apple cultivars were used as references for SSR locus data analysis and to determine allele profiles between species. Eight SSR loci that were developed from apple and pear were used, and a total of 44 alleles were found among quince cultivars. The CH01F02 locus was found to have the highest identification probability, while the CH04E03 locus had the lowest identification probability. Analysis of similarity ratios between quince cultivars showed that the lowest similarity ratio was 18% (Eşme-Bardacık ± k), while the highest similarity ratio was 87% (Bursa-Osmancık ± k and Osmancık ± k-Viranyadevi). In the phylogenetic dendrogram, Eşme quince showed separate branching from other quince cultivars, and no synonymous accessions were found. These results suggest that SSR markers from pear and apple could be used to determine genetic variation among quince cultivars. These findings can be used to guide future quince breeding and management studies.

  11. Identifying Objective EEG Based Markers of Linear Vection in Depth

    PubMed Central

    Palmisano, Stephen; Barry, Robert J.; De Blasio, Frances M.; Fogarty, Jack S.

    2016-01-01

    This proof-of-concept study investigated whether a time-frequency EEG approach could be used to examine vection (i.e., illusions of self-motion). In the main experiment, we compared the event-related spectral perturbation (ERSP) data of 10 observers during and directly after repeated exposures to two different types of optic flow display (each was 35° wide by 29° high and provided 20 s of motion stimulation). Displays consisted of either a vection display (which simulated constant velocity forward self-motion in depth) or a control display (a spatially scrambled version of the vection display). ERSP data were decomposed using time-frequency Principal Components Analysis (t–f PCA). We found an increase in 10 Hz alpha activity, peaking some 14 s after display motion commenced, which was positively associated with stronger vection ratings. This followed decreases in beta activity, and was also followed by a decrease in delta activity; these decreases in EEG amplitudes were negatively related to the intensity of the vection experience. After display motion ceased, a series of increases in the alpha band also correlated with vection intensity, and appear to reflect vection- and/or motion-aftereffects, as well as later cognitive preparation for reporting the strength of the vection experience. Overall, these findings provide support for the notion that EEG can be used to provide objective markers of changes in both vection status (i.e., “vection/no vection”) and vection strength. PMID:27559328

  12. Genetic diversity analysis of common beans based on molecular markers

    PubMed Central

    Gill-Langarica, Homar R.; Muruaga-Martínez, José S.; Vargas-Vázquez, M.L. Patricia; Rosales-Serna, Rigoberto; Mayek-Pérez, Netzahualcoyotl

    2011-01-01

    A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation. PMID:22215964

  13. Genetic diversity analysis of common beans based on molecular markers.

    PubMed

    Gill-Langarica, Homar R; Muruaga-Martínez, José S; Vargas-Vázquez, M L Patricia; Rosales-Serna, Rigoberto; Mayek-Pérez, Netzahualcoyotl

    2011-10-01

    A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

  14. A Study on Marker Overlapping Control for M2M-Based Augmented Reality Multiple Object Loading Using Bresenham Algorithm

    NASA Astrophysics Data System (ADS)

    Jung, Sungmo; Song, Jae-Gu; Kim, Seoksoo

    The problem of one marker one object loading only available in marker-based augmented reality technology can be solved by PPHT-based augmented reality multiple objects loading technology which detects the same marker in the image and copies at a desirable location. However, since the distance between markers will not be measured in the process of detecting and copying markers, markers can be overlapped and thus the objects would not be augmented. To solve this problem, a circle having the longest radius needs to be created from a focal point of a marker to be copied, so that no object is copied within the confines of the circle. Therefore, a marker overlapping control for M2M-based augmented reality multiple object loading has been studied using Bresenham algorithm.

  15. Infrared marker-based tracking in an indoor unknown environment for augmented reality applications

    NASA Astrophysics Data System (ADS)

    Huang, Yetao; Weng, Dongdong; Liu, Yue; Wang, Yongtian

    2009-11-01

    Marker based tracking requires complicated preparation work that impedes its use in augmented reality applications. This paper presents a novel tracking scheme to be used in an indoor unknown scene by adapting simultaneous localization and mapping (SLAM) algorithms. An infrared (IR) marker system is specifically designed to simplify the feature recognition and tracking in SLAM process. With one initial IR marker, the other markers can be projected randomly onto a large-area environment. The pose of camera can be estimated with a monocular IR camera in real time. Experimental result demonstrates that the proposed system meets the requirements of accuracy for large-area tracking. A prototype system is built to show its feasibility in unknown environment and potential use in applications.

  16. Genetic relationships among populations of Aedes aegypti from Uruguay and northeastern Argentina inferred from ISSR-PCR data.

    PubMed

    Soliani, C; Rondan-Dueñas, J; Chiappero, M B; Martínez, M; Da Rosa, E García; Gardenal, C N

    2010-09-01

    Aedes aegypti (L.) (Diptera: Culicidae), the main vector of yellow fever and dengue viruses, was eradicated from Argentina between 1955 and 1963, but reinvaded the country in 1986. In Uruguay, the species was reintroduced in 1997. In this study we used highly polymorphic inter-simple sequence repeats (ISSR) markers to analyse the genetic structure of Ae. aegypti populations from Uruguay and northeastern Argentina to identify possible colonization patterns of the vector. Overall genetic differentiation among populations was high (F(ST) = 0.106) and showed no correlation with geographic distance, which is consistent with the short time since the reintroduction of the species in the area. Differentiation between pairs of Argentine populations (F(ST) 0.072 to 0.221) was on average higher than between Uruguayan populations (F(ST)-0.044 to 0.116). Bayesian estimation of population structure defined four genetic clusters and most populations were admixtures of two of them: Mercedes and Treinta y Tres (Uruguay) were mixtures of clusters 1 and 3; Salto (Uruguay) and Paraná (Argentina) of clusters 1 and 4; Fray Bentos (Uruguay) of clusters 2 and 3, and Gualeguaychú (Argentina) of clusters 2 and 3. Posadas and Buenos Aires in Argentina were fairly genetically homogeneous. Our results suggest that Ae. aegypti recolonized Uruguay from bordering cities in Argentina via bridges over the Uruguay River and also from Brazil.

  17. Molecular tracing of white muscardine in Asian corn borer using inter-simple sequence repeat (ISSR) analysis.

    PubMed

    Hu, B J; Xu, L N; Zhou, Z Y; Hu, F; Luan, F G; Chen, X; Li, Z Z

    2015-01-01

    Beauveria bassiana is a soil fungus that parasitizes arthropod species, and is used to control the Asian corn borer in Northeast China. In this study, B. bassiana was investigated in Xiaoxian County and Baicheng City, and the results were compared with those of Gongzhuling City, where the fungus was not applied. Using the inter-simple sequence repeat (ISSR) molecular marker technique, 198 isolates were extracted from Asian corn borer and other insect cadavers, and soil and air, and two released strains were analyzed to trace the infection source. In Xiaoxian and Baicheng populations, artificially released B. bassiana subpopulations were more abundant than indigenous fungi, and the released strains were the main cause of disease in those areas. Artificial B. bassiana displayed positive effect on overwintering of Asian corn borers in corn straw stacks in Xiaoxian County. Indigenous populations in Gongzhuling City showed higher genetic variation. In summary, we identified a significant correlation between genetic distance and geographic distance (P < 0.01). PMID:26782522

  18. Comparison between low-cost marker-less and high-end marker-based motion capture systems for the computer-aided assessment of working ergonomics.

    PubMed

    Patrizi, Alfredo; Pennestrì, Ettore; Valentini, Pier Paolo

    2016-01-01

    The paper deals with the comparison between a high-end marker-based acquisition system and a low-cost marker-less methodology for the assessment of the human posture during working tasks. The low-cost methodology is based on the use of a single Microsoft Kinect V1 device. The high-end acquisition system is the BTS SMART that requires the use of reflective markers to be placed on the subject's body. Three practical working activities involving object lifting and displacement have been investigated. The operational risk has been evaluated according to the lifting equation proposed by the American National Institute for Occupational Safety and Health. The results of the study show that the risk multipliers computed from the two acquisition methodologies are very close for all the analysed activities. In agreement to this outcome, the marker-less methodology based on the Microsoft Kinect V1 device seems very promising to promote the dissemination of computer-aided assessment of ergonomics while maintaining good accuracy and affordable costs. PRACTITIONER’S SUMMARY: The study is motivated by the increasing interest for on-site working ergonomics assessment. We compared a low-cost marker-less methodology with a high-end marker-based system. We tested them on three different working tasks, assessing the working risk of lifting loads. The two methodologies showed comparable precision in all the investigations.

  19. Deoxysphingoid bases as plasma markers in Diabetes mellitus

    PubMed Central

    2010-01-01

    Background Sphingoid bases are formed from the precursors L-serine and palmitoyl-CoA-a reaction which is catalyzed by the serine-palmitoyltransferase (SPT). SPT metabolizes, besides palmitoyl-CoA also other acyl-CoAs but shows also variability towards the use of other amino acid substrates. The enzyme is also able to metabolize alanine, which results in the formation of an atypical deoxy-sphingoid base (DSB). This promiscuous activity is greatly increased in the case of the sensory neuropathy HSAN1, and pathologically elevated DSB levels have been identified as the cause of this disease. Clinically, HSAN1 shows a pronounced similarity to the diabetic sensory neuropathy (DSN), which is the most common chronic complication of diabetes mellitus. Since serine and alanine metabolism is functionally linked to carbohydrate metabolism by their precursors 3-phosphoglycerate and pyruvate, we were interested to see whether the levels of certain sphingoid base metabolites are altered in patients with diabetes. Results In a case-control study we compared plasma sphingoid base levels between healthy and diabetic individuals. DSB levels were higher in the diabetic group whereas C16 and C18 sphingoid bases were not significantly different. Plasma serine, but not alanine levels were lower in the diabetic group. A subsequent lipoprotein fractionation showed that the DSBs are primarily present in the LDL and VLDL fraction. Conclusion Our results suggest that DSBs are a novel category of plasma biomarkers in diabetes which reflect functional impairments of carbohydrate metabolism. Furthermore, elevated DSB levels as we see them in diabetic patients might also contribute to the progression of the diabetic sensory neuropathy, the most frequent complication of diabetes. PMID:20712864

  20. Selection of sugar cane full-sib families using mixed models and ISSR markers.

    PubMed

    Almeida, L M; Viana, A P; Gonçalves, G M; Entringer, G C

    2014-01-01

    In 2006, an experiment examining families belonging to the first selection stage of the Sugar Cane Breeding Program of Universidade Federal Rural do Rio de Janeiro/Rede Interuniversitária para o Desenvolvimento do Setor Sucroalcooleiro was conducted. Families and plants within families were evaluated to select superior plants for subsequent stages of the breeding program. The experiment was arranged in a randomized block design, in which progenies were grouped into 4 sets, each with 4 replicates and 100 seedlings per plot. The following traits were evaluated: average stem diameter, total plot weight, number of stems, Brix of the lower stem, and Brix of the upper stem. The study of families used the restricted maximum likelihood/best linear unbiased procedure mixed models. After selection, families were genotyped via inter-simple sequence repeat to assess the genetic distance of genotypes. This approach was found to be efficient for selecting new genotypes. PMID:25501142

  1. Marker-based estimation of genetic parameters in genomics.

    PubMed

    Hu, Zhiqiu; Yang, Rong-Cai

    2014-01-01

    Linear mixed model (LMM) analysis has been recently used extensively for estimating additive genetic variances and narrow-sense heritability in many genomic studies. While the LMM analysis is computationally less intensive than the Bayesian algorithms, it remains infeasible for large-scale genomic data sets. In this paper, we advocate the use of a statistical procedure known as symmetric differences squared (SDS) as it may serve as a viable alternative when the LMM methods have difficulty or fail to work with large datasets. The SDS procedure is a general and computationally simple method based only on the least squares regression analysis. We carry out computer simulations and empirical analyses to compare the SDS procedure with two commonly used LMM-based procedures. Our results show that the SDS method is not as good as the LMM methods for small data sets, but it becomes progressively better and can match well with the precision of estimation by the LMM methods for data sets with large sample sizes. Its major advantage is that with larger and larger samples, it continues to work with the increasing precision of estimation while the commonly used LMM methods are no longer able to work under our current typical computing capacity. Thus, these results suggest that the SDS method can serve as a viable alternative particularly when analyzing 'big' genomic data sets. PMID:25025305

  2. Marker-Based Estimation of Genetic Parameters in Genomics

    PubMed Central

    Hu, Zhiqiu; Yang, Rong-Cai

    2014-01-01

    Linear mixed model (LMM) analysis has been recently used extensively for estimating additive genetic variances and narrow-sense heritability in many genomic studies. While the LMM analysis is computationally less intensive than the Bayesian algorithms, it remains infeasible for large-scale genomic data sets. In this paper, we advocate the use of a statistical procedure known as symmetric differences squared (SDS) as it may serve as a viable alternative when the LMM methods have difficulty or fail to work with large datasets. The SDS procedure is a general and computationally simple method based only on the least squares regression analysis. We carry out computer simulations and empirical analyses to compare the SDS procedure with two commonly used LMM-based procedures. Our results show that the SDS method is not as good as the LMM methods for small data sets, but it becomes progressively better and can match well with the precision of estimation by the LMM methods for data sets with large sample sizes. Its major advantage is that with larger and larger samples, it continues to work with the increasing precision of estimation while the commonly used LMM methods are no longer able to work under our current typical computing capacity. Thus, these results suggest that the SDS method can serve as a viable alternative particularly when analyzing ‘big’ genomic data sets. PMID:25025305

  3. Kernel-Based Aggregation of Marker-Level Genetic Association Tests Involving Copy-Number Variation

    PubMed Central

    Li, Yinglei; Breheny, Patrick

    2013-01-01

    Genetic association tests involving copy-number variants (CNVs) are complicated by the fact that CNVs span multiple markers at which measurements are taken. The power of an association test at a single marker is typically low, and it is desirable to pool information across the markers spanned by the CNV. However, CNV boundaries are not known in advance, and the best way to proceed with this pooling is unclear. In this article, we propose a kernel-based method for aggregation of marker-level tests and explore several aspects of its implementation. In addition, we explore some of the theoretical aspects of marker-level test aggregation, proposing a permutation-based approach that preserves the family-wise error rate of the testing procedure, while demonstrating that several simpler alternatives fail to do so. The empirical power of the approach is studied in a number of simulations constructed from real data involving a pharmacogenomic study of gemcitabine and compares favorably with several competing approaches.

  4. Network-based identification of reliable bio-markers for cancers.

    PubMed

    Deng, Shiguo; Qi, Jingchao; Stephen, Mutua; Qiu, Lu; Yang, Huijie

    2015-10-21

    Finding bio-markers for complex disease from gene expression profiles attracts extensive attentions for its potential use in diagnosis, therapy, and drug design. In this paper we propose a network-based method to seek high-confident bio-markers from candidate genes collected in the literature. The algorithm includes three consequent steps. First, one can collect the proposed bio-markers in literature as being the preliminary candidate; Second, a spanning-tree based threshold can be used to reconstruct gene networks for normal and cancer samples; Third, by jointly using of degree changes and distribution of the candidates in communities, one can filter out the low-confident genes. The survival candidates are high-confident genes. Specially, we consider expression profiles for carcinoma of colon. A total of 34 preliminary bio-markers collected from literature are evaluated and a set of 16 genes are proposed as high confident bio-markers, which behave high performance in distinguishing normal and cancer samples.

  5. Analysis of genetic diversity in earthworms using DNA markers.

    PubMed

    Sharma, Anshul; Sonah, Humira; Deshmukh, Rupesh K; Gupta, Navneet K; Singh, Nagendra K; Sharma, Tilak R

    2011-01-01

    Earthworms are one of the most important and beneficial macrofauna, and are used extensively in organic farming. Earthworms mediate soil biological regulation systems, and produce biogenic structures. They help to maintain soil structure, water infiltration, and regulate the availability of nutrients assimilated by plants. The objectives of this study were to perform morphological and molecular characterizations of 24 earthworm individuals collected from geographically diverse locations to assess the level of genetic variation. For molecular analysis, the effectiveness of RAPD, ISSR, and Universal rice primers (URPs) markers was investigated to identify polymorphism among 24 isolates of earthworms. A total of 62 molecular markers were used for amplification of genomic DNA of earthworms. Of these, 10 RAPD, 10 ISSR, and 10 URPs markers were used for characterization, which showed 95.7%, 96.7% and 98.3% polymorphism, respectively. The dendrogram, generated from the DNA markers by the unweighted pair group method using arithmetic averages, grouped all the isolates into two main clusters. All Eisenia fetida isolates were clustered in group A, whereas group B included three isolates belonging to Eudrilus eugeniae. Molecular markers allowed a rapid assessment of genetic variation among these closely related isolates of earthworms. These results suggest that molecular markers are a good choice for diversity analysis of earthworm individuals. PMID:21186943

  6. An improved consensus linkage map of barley based on flow-sorted chromosomes and SNP markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent advances in high-throughput genotyping have made it easier to combine information from different mapping populations into consensus genetic maps, which provide increased marker density and genome coverage compared to individual maps. Previously, a SNP-based genotyping platform was developed a...

  7. Development of universal genetic markers based on single-copy orthologous (COSII) genes in Poaceae.

    PubMed

    Liu, Hailan; Guo, Xiaoqin; Wu, Jiasheng; Chen, Guo-Bo; Ying, Yeqing

    2013-03-01

    KEY MESSAGE : We develop a set of universal genetic markers based on single-copy orthologous (COSII) genes in Poaceae. Being evolutionary conserved, single-copy orthologous (COSII) genes are particularly useful in comparative mapping and phylogenetic investigation among species. In this study, we identified 2,684 COSII genes based on five sequenced Poaceae genomes including rice, maize, sorghum, foxtail millet, and brachypodium, and then developed 1,072 COSII markers whose transferability and polymorphism among five bamboo species were further evaluated with 46 pairs of randomly selected primers. 91.3 % of the 46 primers obtained clear amplification in at least one bamboo species, and 65.2 % of them produced polymorphism in more than one species. We also used 42 of them to construct the phylogeny for the five bamboo species, and it might reflect more precise evolutionary relationship than the one based on the vegetative morphology. The results indicated a promising prospect of applying these markers to the investigation of genetic diversity and the classification of Poaceae. To ease and facilitate access of the information of common interest to readers, a web-based database of the COSII markers is provided ( http://www.sicau.edu.cn/web/yms/PCOSWeb/PCOS.html ).

  8. Interpreting the clinical utility of a pharmacogenomic marker based on observational association studies.

    PubMed

    Sorich, M J; Coory, M

    2014-02-01

    It is increasingly recognized that the clinical utility of a pharmacogenomic marker is a fundamental characteristic influencing the likelihood of successful clinical translation. Although appropriately designed and executed randomized controlled trials generally provide the most valid evidence for the clinical utility of a pharmacogenomic marker, such evidence may not always be available. Observational pharmacogenomic association studies are a common form of evidence available, but the assessment of clinical utility based on such evidence is often not straightforward. This paper aims to provide insight into this issue using a range of illustrative examples.

  9. Genetic variability in wild genotypes of Passiflora cincinnata based on RAPD markers.

    PubMed

    Cerqueira-Silva, C B M; Conceição, L D H C S; Santos, E S L; Cardoso-Silva, C B; Pereira, A S; Oliveira, A C; Corrêa, R X

    2010-12-21

    The genetic diversity and characteristics of commercial interest of Passiflora species make it useful to characterize wild germplasm, because of their potential use for fruit, ornamental and medicinal purposes. We evaluated genetic diversity, using RAPD markers, of 32 genotypes of Passiflora cincinnata collected from the wild in the region of Vitória da Conquista, Bahia, Brazil. Thirteen primers generated 95 polymorphic markers and only one monomorphic marker. The mean genetic distance between the genotypes estimated by the complement of the Dice index was 0.51 (ranging from 0.20-0.85), and genotype grouping based on the UPGMA algorithm showed wide variability among the genotypes. This type of information contributes to identification and conservation of the biodiversity of this species and for the identification of pairs of divergent individuals for maximum exploitation of existing variability.

  10. Mach-zehnder based optical marker/comb generator for streak camera calibration

    SciTech Connect

    Miller, Edward Kirk

    2015-03-03

    This disclosure is directed to a method and apparatus for generating marker and comb indicia in an optical environment using a Mach-Zehnder (M-Z) modulator. High speed recording devices are configured to record image or other data defining a high speed event. To calibrate and establish time reference, the markers or combs are indicia which serve as timing pulses (markers) or a constant-frequency train of optical pulses (comb) to be imaged on a streak camera for accurate time based calibration and time reference. The system includes a camera, an optic signal generator which provides an optic signal to an M-Z modulator and biasing and modulation signal generators configured to provide input to the M-Z modulator. An optical reference signal is provided to the M-Z modulator. The M-Z modulator modulates the reference signal to a higher frequency optical signal which is output through a fiber coupled link to the streak camera.

  11. The first genetic linkage map of Primulina eburnea (Gesneriaceae) based on EST-derived SNP markers.

    PubMed

    Feng, Chen; Feng, Chao; Kang, Ming

    2016-06-01

    Primulina eburnea is a promising candidate for domestication and floriculture, since it is easy to culture and has beautiful flowers. An F₂ population of 189 individuals was established for the construction of first-generation linkage maps based on expressed sequence tags-derived single-nucleotide polymorphism markers using the massARRAY genotyping platform. Of the 232 screened markers, 215 were assigned to 18 LG according to the haploid number of chromosomes in the species. The linkage map spanned a total of 3774.7 cM with an average distance of 17.6 cM between adjacent markers. This linkage map provides a framework for identification of important genes in breeding programmes. PMID:27350682

  12. Population genetic structure and trait associations in forest savory using molecular, morphological and phytochemical markers.

    PubMed

    Khadivi-Khub, Abdollah; Karimi, Ehsan; Hadian, Javad

    2014-08-10

    In this investigation, morphological, phytochemical and ISSR markers were used to estimate the relationships among and within seven populations of white savory (Satureja mutica), belonging to four provinces in Iran. The individuals were phenotypically diverse, which stamen length, corolla length, corolla diameter, calyx length, bract length, inflorescence length, calyx length and bracteole width were characteristics with the highest variation. Leaf dimensions were in significant correlation with flower and inflorescence characteristics. Chemical compounds of essential oils were found variable in various individuals and all samples were principally composed of phenolic constituents (carvacrol and/or thymol). As a consequence, the plants were classified into two major chemotypes including carvacrol and thymol. A total of 197 band positions were produced by 14 ISSR primers, of which 176 were found polymorphic with 88.91% polymorphism. ISSR genetic similarity values among individuals ranged between 0.45 and 0.94 which was indicative of a high level of genetic variation. Multiple regression analysis (MRA) revealed that phytochemical compositions as dependent variable, showed statistically significant correlation and in association with leaf and flower traits as independent variable, indicating a main role of leaf and flower on production of these compounds. Also, several ISSR fragments were found associated with some morphological traits and phytochemical compositions. The high diversity within and among populations of S. mutica according to different data systems could provide useful information for conservation and selection of cross-parents in breeding programs. PMID:24878369

  13. The use and abuse of genetic marker-based estimates of relatedness and inbreeding

    PubMed Central

    Taylor, Helen R

    2015-01-01

    Genetic marker-based estimators remain a popular tool for measuring relatedness (rxy) and inbreeding (F) coefficients at both the population and individual level. The performance of these estimators fluctuates with the number and variability of markers available, and the relatedness composition and demographic history of a population. Several methods are available to evaluate the reliability of the estimates of rxy and F, some of which are implemented in the program COANCESTRY. I used the simulation module in COANCESTRY since assess the performance of marker-based estimators of rxy and F in a species with very low genetic diversity, New Zealand’s little spotted kiwi (Apteryx owenii). I also conducted a review of published papers that have used COANCESTRY as its release to assess whether and how the reliability of the estimates of rxy and F produced by genetic markers are being measured and reported in published studies. My simulation results show that even when the correlation between true (simulated) and estimated rxy or F is relatively high (Pearson’s r = 0.66–0.72 and 0.81–0.85, respectively) the imprecision of the estimates renders them highly unreliable on an individual basis. The literature review demonstrates that the majority of studies do not report the reliability of marker-based estimates of rxy and F. There is currently no standard practice for selecting the best estimator for a given data set or reporting an estimator’s performance. This could lead to experimental results being interpreted out of context and render the robustness of conclusions based on measures of rxy and F debatable. PMID:26357542

  14. Genetic fidelity of long-term micropropagated shoot cultures of vanilla (Vanilla planifolia Andrews) as assessed by molecular markers.

    PubMed

    Sreedhar, Reddampalli V; Venkatachalam, Lakshmanan; Bhagyalakshmi, Neelwarne

    2007-08-01

    Occurrence of genetic variants during micropropagation is occasionally encountered when the cultures are maintained in vitro for long period. Therefore, the micropropagated multiple shoots of Vanilla planifolia Andrews developed from axillary bud explants established 10 years ago were used to determine somaclonal variation using random amplified polymorphic DNA (RAPD) and intersimple sequence repeats markers (ISSR). One thousand micro-plants were established in soil of which 95 plantlets (consisting of four phenotypes) along with the mother plant were subjected to genetic analyses using RAPD and ISSR markers. Out of the 45 RAPD and 20 ISSR primers screened, 30 RAPD and 7 ISSR primers showed 317 clear, distinct and reproducible band classes resulting in a total of 30 115 bands. However, no difference was observed in banding patterns of any of the samples for a particular primer, indicating the absence of variation among the micropropagated plants. Our results allow us to conclude that the micropropagation protocol that we have used for in vitro proliferation of vanilla plantlets for the last 10 years might be applicable for the production of clonal plants over a considerable period of time.

  15. Cytotype-specific ISSR profiles and karyotypes in the Neotropical genus Eigenmannia (Teleostei: Gymnotiformes).

    PubMed

    Moysés, Cinthia Bachir; Daniel-Silva, Maria de Fatima Zambelli; Lopes, Carlos Eduardo; de Almeida-Toledo, Lurdes Foresti

    2010-02-01

    The genus Eigenmannia (Teleostei: Gymnotiformes), a widely distributed fish genus from the Neotropical region, presents very complex morphological patterns and many taxonomic problems. It is suggested that this genus harbors a species complex that is hard to differentiate using only morphological characteristics. As a result, many species of Eigenmannia may be currently gathered under a common name. With the objective of providing new tools for species characterization in this group, an analysis of the polymorphism of DNA inter-simple sequence repeats (ISSR), obtained by single primer amplification reaction (SPAR), combined with karyotype identification, was carried out in specimens sampled from populations of the Upper Paraná, São Francisco and Amazon river basins (Brazil). Specific ISSR patterns generated by primers (AAGC)(4) and (GGAC)(4) were found to characterize the ten cytotypes analyzed, even though the cytotypes 2n = 38 and 2n = 38 XX:XY, from the Upper Paraná basin, share some ISSR amplification patterns. The geographical distribution of all Eigenmannia specimens sampled was inferred, showing the cytotype 2n = 31/2n = 32 as the most frequent and largely distributed in the Upper Paraná basin. The cytotype 2n = 34 was reported for the first time in the genus Eigenmania, restricted to the São Francisco basin. Polymorphic ISSR patterns were also detected for each cytotype. Considering our results and the data reported previously in the literature, it is suggested that many of the forms of Eigenmannia herein analyzed might be regarded as different species. This work reinforces the importance of employing diverse approaches, such as molecular and cytogenetic characterization, to address taxonomic and evolutionary issues. PMID:19779835

  16. Cytotype-specific ISSR profiles and karyotypes in the Neotropical genus Eigenmannia (Teleostei: Gymnotiformes).

    PubMed

    Moysés, Cinthia Bachir; Daniel-Silva, Maria de Fatima Zambelli; Lopes, Carlos Eduardo; de Almeida-Toledo, Lurdes Foresti

    2010-02-01

    The genus Eigenmannia (Teleostei: Gymnotiformes), a widely distributed fish genus from the Neotropical region, presents very complex morphological patterns and many taxonomic problems. It is suggested that this genus harbors a species complex that is hard to differentiate using only morphological characteristics. As a result, many species of Eigenmannia may be currently gathered under a common name. With the objective of providing new tools for species characterization in this group, an analysis of the polymorphism of DNA inter-simple sequence repeats (ISSR), obtained by single primer amplification reaction (SPAR), combined with karyotype identification, was carried out in specimens sampled from populations of the Upper Paraná, São Francisco and Amazon river basins (Brazil). Specific ISSR patterns generated by primers (AAGC)(4) and (GGAC)(4) were found to characterize the ten cytotypes analyzed, even though the cytotypes 2n = 38 and 2n = 38 XX:XY, from the Upper Paraná basin, share some ISSR amplification patterns. The geographical distribution of all Eigenmannia specimens sampled was inferred, showing the cytotype 2n = 31/2n = 32 as the most frequent and largely distributed in the Upper Paraná basin. The cytotype 2n = 34 was reported for the first time in the genus Eigenmania, restricted to the São Francisco basin. Polymorphic ISSR patterns were also detected for each cytotype. Considering our results and the data reported previously in the literature, it is suggested that many of the forms of Eigenmannia herein analyzed might be regarded as different species. This work reinforces the importance of employing diverse approaches, such as molecular and cytogenetic characterization, to address taxonomic and evolutionary issues.

  17. SNP markers-based map construction and genome-wide linkage analysis in Brassica napus.

    PubMed

    Raman, Harsh; Dalton-Morgan, Jessica; Diffey, Simon; Raman, Rosy; Alamery, Salman; Edwards, David; Batley, Jacqueline

    2014-09-01

    An Illumina Infinium array comprising 5306 single nucleotide polymorphism (SNP) markers was used to genotype 175 individuals of a doubled haploid population derived from a cross between Skipton and Ag-Spectrum, two Australian cultivars of rapeseed (Brassica napus L.). A genetic linkage map based on 613 SNP and 228 non-SNP (DArT, SSR, SRAP and candidate gene markers) covering 2514.8 cM was constructed and further utilized to identify loci associated with flowering time and resistance to blackleg, a disease caused by the fungus Leptosphaeria maculans. Comparison between genetic map positions of SNP markers and the sequenced Brassica rapa (A) and Brassica oleracea (C) genome scaffolds showed several genomic rearrangements in the B. napus genome. A major locus controlling resistance to L. maculans was identified at both seedling and adult plant stages on chromosome A07. QTL analyses revealed that up to 40.2% of genetic variation for flowering time was accounted for by loci having quantitative effects. Comparative mapping showed Arabidopsis and Brassica flowering genes such as Phytochrome A/D, Flowering Locus C and agamous-Like MADS box gene AGL1 map within marker intervals associated with flowering time in a DH population from Skipton/Ag-Spectrum. Genomic regions associated with flowering time and resistance to L. maculans had several SNP markers mapped within 10 cM. Our results suggest that SNP markers will be suitable for various applications such as trait introgression, comparative mapping and high-resolution mapping of loci in B. napus.

  18. A High Density Consensus Map of Rye (Secale cereale L.) Based on DArT Markers

    PubMed Central

    Myśków, Beata; Stojałowski, Stefan; Heller-Uszyńska, Katarzyna; Góralska, Magdalena; Brągoszewski, Piotr; Uszyński, Grzegorz; Kilian, Andrzej; Rakoczy-Trojanowska, Monika

    2011-01-01

    Background Rye (Secale cereale L.) is an economically important crop, exhibiting unique features such as outstanding resistance to biotic and abiotic stresses and high nutrient use efficiency. This species presents a challenge to geneticists and breeders due to its large genome containing a high proportion of repetitive sequences, self incompatibility, severe inbreeding depression and tissue culture recalcitrance. The genomic resources currently available for rye are underdeveloped in comparison with other crops of similar economic importance. The aim of this study was to create a highly saturated, multilocus linkage map of rye via consensus mapping, based on Diversity Arrays Technology (DArT) markers. Methodology/Principal Findings Recombinant inbred lines (RILs) from 5 populations (564 in total) were genotyped using DArT markers and subjected to linkage analysis using Join Map 4.0 and Multipoint Consensus 2.2 software. A consensus map was constructed using a total of 9703 segregating markers. The average chromosome map length ranged from 199.9 cM (2R) to 251.4 cM (4R) and the average map density was 1.1 cM. The integrated map comprised 4048 loci with the number of markers per chromosome ranging from 454 for 7R to 805 for 4R. In comparison with previously published studies on rye, this represents an eight-fold increase in the number of loci placed on a consensus map and a more than two-fold increase in the number of genetically mapped DArT markers. Conclusions/Significance Through the careful choice of marker type, mapping populations and the use of software packages implementing powerful algorithms for map order optimization, we produced a valuable resource for rye and triticale genomics and breeding, which provides an excellent starting point for more in-depth studies on rye genome organization. PMID:22163026

  19. Linkage map of the honey bee, Apis mellifera, based on RAPD markers

    SciTech Connect

    Hunt, G.J.; Page, R.E. Jr.

    1995-03-01

    A linkage map was constructed for the honey bee based on the segregation of 365 random amplified polymorphic DNA (RAPD) markers in haploid male progeny of a single female bee. The X locus for sex determination and genes for black body color and malate dehydrogenase were mapped to separate linkage groups. RAPD markers were very efficient for mapping, with an average of about 2.8 loci mapped for each 10-nucleotide primer that was used in polymerase chain reactions. The mean interval size between markers on the map was 9.1 cM. The map covered 3110 cM of linked markers on 26 linkage groups. We estimate the total genome size to be {approximately}3450 cM. The size of the map indicated a very high recombination rate for the honey bee. The relationship of physical to genetic distance was estimated at 52 kb/cM, suggesting that map-based cloning of genes will be feasible for this species. 71 refs., 6 figs., 1 tab.

  20. Ultrasound-based Measurement of Molecular Marker Concentration in Large Blood Vessels: A Feasibility Study

    PubMed Central

    Wang, Shiying; Mauldin, F. William; Klibanov, Alexander L.; Hossack, John A.

    2014-01-01

    Ultrasound molecular imaging has demonstrated efficacy in pre-clinical studies for cancer and cardiovascular inflammation. However, these techniques often require lengthy protocols due to waiting periods or additional control microbubble injections. Moreover, they are not capable of quantifying molecular marker concentration in human tissue environments that exhibit variable attenuation and propagation path lengths. Our group recently investigated a modulated Acoustic Radiation Force (ARF)-based imaging sequence, which was demonstrated to detect targeted adhesion independent of control measurements. In the present study, this sequence was tested against various experimental parameters to determine feasibility for quantitative measurements of molecular marker concentration. Results demonstrated that measurements obtained from the sequence (residual-to-saturation ratio, Rresid) were independent of acoustic pressure and attenuation (p> 0.13, n = 10)when acoustic pressures were sufficiently low. The Rresid parameter exhibited a linear relationship with measured molecular marker concentration (R2> 0.94). Consequently, feasibility was demonstrated in vitro, for quantification of molecular marker concentration in large vessels using a modulated ARF-based sequence. Moreover, these measurements were independent of absolute acoustic reflection amplitude and used short imaging protocols(3 min) without control measurements. PMID:25308943

  1. Ultrasound-based measurement of molecular marker concentration in large blood vessels: a feasibility study.

    PubMed

    Wang, Shiying; Mauldin, F William; Klibanov, Alexander L; Hossack, John A

    2015-01-01

    Ultrasound molecular imaging has demonstrated efficacy in pre-clinical studies for cancer and cardiovascular inflammation. However, these techniques often require lengthy protocols because of waiting periods or additional control microbubble injections. Moreover, they are not capable of quantifying molecular marker concentration in human tissue environments that exhibit variable attenuation and propagation path lengths. Our group recently investigated a modulated acoustic radiation force-based imaging sequence, which was found to detect targeted adhesion independent of control measurements. In the present study, this sequence was tested against various experimental parameters to determine its feasibility for quantitative measurements of molecular marker concentration. Results indicated that measurements obtained from the sequence (residual-to-saturation ratio, Rresid) were independent of acoustic pressure and attenuation (p > 0.13, n = 10) when acoustic pressures were sufficiently low. The Rresid parameter exhibited a linear relationship with measured molecular marker concentration (R(2) > 0.94). Consequently, feasibility was illustrated in vitro, for quantification of molecular marker concentration in large vessels using a modulated acoustic radiation force-based sequence. Moreover, these measurements were independent of absolute acoustic reflection amplitude and used short imaging protocols (3 min) without control measurements.

  2. Genetic diversity in Capsicum germplasm based on microsatellite and random amplified microsatellite polymorphism markers.

    PubMed

    Rai, Ved Prakash; Kumar, Rajesh; Kumar, Sanjay; Rai, Ashutosh; Kumar, Sanjeet; Singh, Major; Singh, Sheo Pratap; Rai, Awadesh Bahadur; Paliwal, Rajneesh

    2013-10-01

    A sound knowledge of the genetic diversity among germplasm is vital for strategic germplasm collection, maintenance, conservation and utilisation. Genomic simple sequence repeats (SSRs) and random amplified microsatellite polymorphism (RAMPO) markers were used to analyse diversity and relationships among 48 pepper (Capsicum spp.) genotypes originating from nine countries. These genotypes covered 4 species including 13 germplasm accessions, 30 improved lines of 4 domesticated species and 5 landraces derived from natural interspecific crosses. Out of 106 SSR markers, 25 polymorphic SSR markers (24 %) detected a total of 76 alleles (average, 3.04; range, 2-5). The average polymorphic information content (PIC) was 0.69 (range, 0.29-0.92). Seventeen RAMPO markers produced 87 polymorphic fragments with average PIC of 0.63 (range, 0.44-0.81). Dendrograms based on SSRs and RAMPOs generated two clusters. All 38 Capsicum annuum genotypes and an interspecific landrace clustered together, whereas nine non-annuum (three Capsicum frutescens, one Capsicum chinense, one Capsicum baccatum and four interspecific landraces) genotypes clustered separately. Genetic variation within non-annuum genotypes was greater than the C. annuum genotypes. Distinctness of interspecific derivative landraces grown in northeast India was validated; natural crossing between sympatric Capsicum species has been proposed as the mechanism of their origin. PMID:24431527

  3. Marker-based estimates of relatedness and inbreeding coefficients: an assessment of current methods.

    PubMed

    Wang, J

    2014-03-01

    Inbreeding (F) of and relatedness (r) between individuals are now routinely calculated from marker data in studies in the fields of quantitative genetics, conservation genetics, forensics, evolution and ecology. Although definable in terms of either correlation coefficient or probability of identity by descent (IBD) relative to a reference, they are better interpreted as correlations in marker-based analyses because the reference in practice is frequently the current sample or population whose F and r are being estimated. In such situations, negative estimates have a biological meaning, a substantial proportion of the estimates are expected to be negative, and the average estimates are close to zero for r and equivalent to FIS for F. I show that although current r estimators were developed from the IBD-based concept of relatedness, some of them conform to the correlation-based concept of relatedness and some do not. The latter estimators can be modified, however, so that they estimate r as a correlation coefficient. I also show that F and r estimates can be misleading and become biased and marker dependent when a sample containing a high proportion of highly inbred and/or closely related individuals is used as reference. In analyses depending on the comparison between r (or F) estimates and a priori values expected under ideal conditions (e.g. for identifying genealogical relationship), the estimators should be used with caution.

  4. Variability analysis of 'Persian' acid lime tree selections using agronomic and molecular markers.

    PubMed

    Santos, M G; Passos, O S; Soares Filho, W S; Girardi, E A; Gesteira, A S; Ferreira, C F

    2013-01-01

    'Persian' acid lime (PAL) is the most important triploid commercial citrus crop planted in the world. Little is known about the genetic variability of the selections used in Brazil. Therefore, 25 genotypes originating from the PAL, and three control species, Citrus sunki, C. limon, and C. aurantiifolia, were assessed using inter-simple sequence repeat (ISSR) and inter-retrotransposon amplified polymorphism (IRAP) molecular markers and agronomic traits of the fruit. The dendrograms were designed using the mean Euclidean distance for the physicochemical attributes of the fruit (weight, length, diameter, peel color, peel thickness, number of seeds, juice yield, titratable acidity, soluble solids, and ratio) and the Jaccard distances using the data from the ISSR and IRAP molecular markers. In the physicochemical analysis, the genotypes were grouped according to species. The trait that contributed most to the diversity among accessions was the number of seeds. The 17 ISSR primers produced 69 polymorphic bands in the molecular analysis, and the seven IRAP primers generated 30 polymorphic bands. The markers detected polymorphisms within and among the PALs; two groups were formed within the PALs. PMID:24222236

  5. A Usage-Based Approach to Early-Discourse Pragmatic Functions of the Japanese Subject Markers "wa" and "ga"

    ERIC Educational Resources Information Center

    Uno, Mariko

    2016-01-01

    This study investigates the emergence and development of the discourse-pragmatic functions of the Japanese subject markers "wa" and "ga" from a usage-based perspective (Tomasello, 2000). The use of each marker in longitudinal speech data for four Japanese children from 1;0 to 3;1 and their parents available in the CHILDES…

  6. SSR marker-based DNA fingerprinting and cultivar identification of olives (Olea europaea).

    PubMed

    Ercisli, Sezai; Ipek, Ahmet; Barut, Erdogan

    2011-10-01

    Four well-known commercial olive cultivars (Domat, Edremit, Gemlik, and Memecik) and six local cultivars (Ziraat, Isrange, Tuz, Patos, Yag, and Marantelli) from northeastern Turkey were analyzed for genetic diversity and relationships using seven SSR primers (DCA-4, DCA-09, DCA-11, DCA-16, DCA-17, GAPU-89, UDO-14). The number of markers ranged from 3 (DCA-04 and DCA-17) to 6 (DCA-11, DCA-16, GAPU-89), with an average of 4.57 alleles per primer. UPGMA cluster analysis based on a simple matching similarity matrix grouped cultivars into two main clusters. Three pairs of cultivars (Ziraat and Gemlik, Isrange and Tuz, and Patos and Yag) were thought to be different cultivars although they produced identical SSR profiles. The results indicate the efficiency of SSR markers for evaluation of genetic diversity in olives and identification of misnamed individuals of the same genotype.

  7. Automatic Identification of Web-Based Risk Markers for Health Events

    PubMed Central

    Borsa, Diana; Hayward, Andrew C; McKendry, Rachel A; Cox, Ingemar J

    2015-01-01

    Background The escalating cost of global health care is driving the development of new technologies to identify early indicators of an individual’s risk of disease. Traditionally, epidemiologists have identified such risk factors using medical databases and lengthy clinical studies but these are often limited in size and cost and can fail to take full account of diseases where there are social stigmas or to identify transient acute risk factors. Objective Here we report that Web search engine queries coupled with information on Wikipedia access patterns can be used to infer health events associated with an individual user and automatically generate Web-based risk markers for some of the common medical conditions worldwide, from cardiovascular disease to sexually transmitted infections and mental health conditions, as well as pregnancy. Methods Using anonymized datasets, we present methods to first distinguish individuals likely to have experienced specific health events, and classify them into distinct categories. We then use the self-controlled case series method to find the incidence of health events in risk periods directly following a user’s search for a query category, and compare to the incidence during other periods for the same individuals. Results Searches for pet stores were risk markers for allergy. We also identified some possible new risk markers; for example: searching for fast food and theme restaurants was associated with a transient increase in risk of myocardial infarction, suggesting this exposure goes beyond a long-term risk factor but may also act as an acute trigger of myocardial infarction. Dating and adult content websites were risk markers for sexually transmitted infections, such as human immunodeficiency virus (HIV). Conclusions Web-based methods provide a powerful, low-cost approach to automatically identify risk factors, and support more timely and personalized public health efforts to bring human and economic benefits. PMID

  8. DNA-Based Genetic Markers for Rapid Cycling Brassica Rapa (Fast Plants Type) Designed for the Teaching Laboratory.

    PubMed

    Slankster, Eryn E; Chase, Jillian M; Jones, Lauren A; Wendell, Douglas L

    2012-01-01

    We have developed DNA-based genetic markers for rapid cycling Brassica rapa (RCBr), also known as Fast Plants. Although markers for B. rapa already exist, ours were intentionally designed for use in a teaching laboratory environment. The qualities we selected for were robust amplification in PCR, polymorphism in RCBr strains, and alleles that can be easily resolved in simple agarose slab gels. We have developed two single nucleotide polymorphism (SNP) based markers and 14 variable number tandem repeat (VNTR)-type markers spread over four chromosomes. The DNA sequences of these markers represent variation in a wide range of genomic features. Among the VNTR-type markers, there are examples of variation in a non-genic region, variation within an intron, and variation in the coding sequence of a gene. Among the SNP-based markers there are examples of polymorphism in intronic DNA and synonymous substitution in a coding sequence. Thus these markers can serve laboratory exercises in both transmission genetics and molecular biology.

  9. DNA-Based Genetic Markers for Rapid Cycling Brassica Rapa (Fast Plants Type) Designed for the Teaching Laboratory

    PubMed Central

    Slankster, Eryn E.; Chase, Jillian M.; Jones, Lauren A.; Wendell, Douglas L.

    2012-01-01

    We have developed DNA-based genetic markers for rapid cycling Brassica rapa (RCBr), also known as Fast Plants. Although markers for B. rapa already exist, ours were intentionally designed for use in a teaching laboratory environment. The qualities we selected for were robust amplification in PCR, polymorphism in RCBr strains, and alleles that can be easily resolved in simple agarose slab gels. We have developed two single nucleotide polymorphism (SNP) based markers and 14 variable number tandem repeat (VNTR)-type markers spread over four chromosomes. The DNA sequences of these markers represent variation in a wide range of genomic features. Among the VNTR-type markers, there are examples of variation in a non-genic region, variation within an intron, and variation in the coding sequence of a gene. Among the SNP-based markers there are examples of polymorphism in intronic DNA and synonymous substitution in a coding sequence. Thus these markers can serve laboratory exercises in both transmission genetics and molecular biology. PMID:22675329

  10. DNA-Based Genetic Markers for Rapid Cycling Brassica Rapa (Fast Plants Type) Designed for the Teaching Laboratory.

    PubMed

    Slankster, Eryn E; Chase, Jillian M; Jones, Lauren A; Wendell, Douglas L

    2012-01-01

    We have developed DNA-based genetic markers for rapid cycling Brassica rapa (RCBr), also known as Fast Plants. Although markers for B. rapa already exist, ours were intentionally designed for use in a teaching laboratory environment. The qualities we selected for were robust amplification in PCR, polymorphism in RCBr strains, and alleles that can be easily resolved in simple agarose slab gels. We have developed two single nucleotide polymorphism (SNP) based markers and 14 variable number tandem repeat (VNTR)-type markers spread over four chromosomes. The DNA sequences of these markers represent variation in a wide range of genomic features. Among the VNTR-type markers, there are examples of variation in a non-genic region, variation within an intron, and variation in the coding sequence of a gene. Among the SNP-based markers there are examples of polymorphism in intronic DNA and synonymous substitution in a coding sequence. Thus these markers can serve laboratory exercises in both transmission genetics and molecular biology. PMID:22675329

  11. Electrochemiluminescence immunosensor for tumor markers based on biological barcode mode with conductive nanospheres.

    PubMed

    Du, Shuping; Guo, Zhiyong; Chen, Beibei; Sha, Yuhong; Jiang, Xiaohua; Li, Xing; Gan, Ning; Wang, Sui

    2014-03-15

    A novel sandwich-type electrochemiluminescence (ECL) immunosensor was developed for highly sensitive and selective determination of tumor markers based on biological barcode mode. N-(4-aminobutyl)-N-ethylisoluminol (ABEI) and the second antibody (Ab2) were simultaneously immobilized on conductive nanospheres to construct ABEI/Ab2-CNSs probes, which could form sandwich immunocomplex by Ab2 and emit ECL signals by ABEI. The gold layer coated on the surface of the conductive nanospheres could extend the outer Helmholtz plane (OHP) of the ECL immunosensor effectively. Benefited from it, all ABEI molecules immobilized on conductive nanospheres would act as biological barcode to give in-situ ECL signals without interfering with the activity of the second antibody. In such a case, the sensitivity of the ECL immunosensor would be greatly improved because an antigen molecule would correspond to ECL signals of thousands of ABEI molecules. Using prostate specific antigen (PSA) as a model tumor marker, the ECL intensity was found to increase with the logarithm of PSA concentration with a wide linear range from 0.04 to 10 fg/mL. In addition, specificity, stability, reproducibility, regeneration and application were satisfactory. Therefore, this developed ECL immunosensor has a potential for practical detection of disease-related proteins besides tumor markers in the clinical diagnostics.

  12. Variability of Marker-Based Rectal Dose Evaluation in HDR Cervical Brachytherapy

    SciTech Connect

    Wang Zhou; Jaggernauth, Wainwright; Malhotra, Harish K.; Podgorsak, Matthew B.

    2010-01-01

    In film-based intracavitary brachytherapy for cervical cancer, position of the rectal markers may not accurately represent the anterior rectal wall. This study was aimed at analyzing the variability of rectal dose estimation as a result of interfractional variation of marker placement. A cohort of five patients treated with multiple-fraction tandem and ovoid high-dose-rate (HDR) brachytherapy was studied. The cervical os point and the orientation of the applicators were matched among all fractional plans for each patient. Rectal points obtained from all fractions were then input into each clinical treated plan. New fractional rectal doses were obtained and a new cumulative rectal dose for each patient was calculated. The maximum interfractional variation of distances between rectal dose points and the closest source positions was 1.1 cm. The corresponding maximum variability of fractional rectal dose was 65.5%. The percentage difference in cumulative rectal dose estimation for each patient was 5.4%, 19.6%, 34.6%, 23.4%, and 13.9%, respectively. In conclusion, care should be taken when using rectal markers as reference points for estimating rectal dose in HDR cervical brachytherapy. The best estimate of true rectal dose for each fraction should be determined by the most anterior point among all fractions.

  13. Comparison of similarity coefficients used for cluster analysis based on RAPD markers in wild olives.

    PubMed

    Sesli, M; Yegenoglu, E D

    2010-11-16

    Five different similarity coefficients (Jaccard, Sorensen-Dice, simple matching, Rogers and Tanimoto, and Russel and Rao) were evaluated and 10 wild olives analyzed with RAPD markers. The influence of the similarity coefficients on wild olives clustering was investigated. Forty-five primers were used on samples from 10 wild olives (Wild 1 and 2 obtained from Mugla province; Wild 3, 4, 5, 6, 7, and 8 from Manisa province and Wild 9 and 10 from Izmir province of Turkey). The similarity matrices obtained from RAPD markers were compared by the Mantel test. Cluster analysis was made with UPGMA dendrograms, and the consensus fork indexes between all pairs of dendrograms were calculated. The Jaccard and Sorensen-Dice coefficients gave the same results, due to the fact that both exclude negative co-occurrences. The dendrograms using the simple matching and Rogers and Tanimoto coefficients were similar; Wild 4 (Akhisar, Manisa) and Wild 9 (Bornova, Izmir) olives had the closest genetic similarities. This occurred because these coefficients include negative co-occurrences. The Russel and Rao coefficients produced different results, because they include negative co-occurrences in the denominator. We concluded that the coefficients that do not include negative co-occurrences are more efficient for studies of wild olives clustering based on RAPD markers.

  14. Sequence-based marker development in wheat: advances and applications to breeding.

    PubMed

    Paux, Etienne; Sourdille, Pierre; Mackay, Ian; Feuillet, Catherine

    2012-01-01

    In the past two decades, the wheat community has made remarkable progress in developing molecular resources for breeding. A wide variety of molecular tools has been established to accelerate genetic and physical mapping for facilitating the efficient identification of molecular markers linked to genes and QTL of agronomic interest. Already, wheat breeders are benefiting from a wide range of techniques to follow the introgression of the most favorable alleles in elite material and develop improved varieties. Breeders soon will be able to take advantage of new technological developments based on Next Generation Sequencing. In this paper, we review the molecular toolbox available to wheat scientists and breeders for performing fundamental genomic studies and breeding. Special emphasis is given on the production and detection of single nucleotide polymorphisms (SNPs) that should enable a step change in saturating the wheat genome for more efficient genetic studies and for the development of new selection methods. The perspectives offered by the access to an ordered full genome sequence for further marker development and enhanced precision breeding is also discussed. Finally, we discuss the advantages and limitations of marker-assisted selection for supporting wheat improvement.

  15. Effects of Simulated Marker Placement Deviations on Running Kinematics and Evaluation of a Morphometric-Based Placement Feedback Method

    PubMed Central

    Osis, Sean T.; Hettinga, Blayne A.; Macdonald, Shari; Ferber, Reed

    2016-01-01

    In order to provide effective test-retest and pooling of information from clinical gait analyses, it is critical to ensure that the data produced are as reliable as possible. Furthermore, it has been shown that anatomical marker placement is the largest source of inter-examiner variance in gait analyses. However, the effects of specific, known deviations in marker placement on calculated kinematic variables are unclear, and there is currently no mechanism to provide location-based feedback regarding placement consistency. The current study addresses these disparities by: applying a simulation of marker placement deviations to a large (n = 411) database of runners; evaluating a recently published method of morphometric-based deviation detection; and pilot-testing a system of location-based feedback for marker placements. Anatomical markers from a standing neutral trial were moved virtually by up to 30 mm to simulate deviations. Kinematic variables during running were then calculated using the original, and altered static trials. Results indicate that transverse plane angles at the knee and ankle are most sensitive to deviations in marker placement (7.59 degrees of change for every 10 mm of marker error), followed by frontal plane knee angles (5.17 degrees for every 10 mm). Evaluation of the deviation detection method demonstrated accuracies of up to 82% in classifying placements as deviant. Finally, pilot testing of a new methodology for providing location-based feedback demonstrated reductions of up to 80% in the deviation of outcome kinematics. PMID:26765846

  16. A Delay Vector Variance based Marker for an Output-Only Assessment of Structural Changes in Tension Leg Platforms

    NASA Astrophysics Data System (ADS)

    Jaksic, V.; Wright, C.; Mandic, D. P.; Murphy, J.; Pakrashi, V.

    2015-07-01

    Although aspects of power generation of many offshore renewable devices are well understood, their dynamic responses under high wind and wave conditions are still to be investigated to a great detail. Output only statistical markers are important for these offshore devices, since access to the device is limited and information about the exposure conditions and the true behaviour of the devices are generally partial, limited, and vague or even absent. The markers can summarise and characterise the behaviour of these devices from their dynamic response available as time series data. The behaviour may be linear or nonlinear and consequently a marker that can track the changes in structural situations can be quite important. These markers can then be helpful in assessing the current condition of the structure and can indicate possible intervention, monitoring or assessment. This paper considers a Delay Vector Variance based marker for changes in a tension leg platform tested in an ocean wave basin for structural changes brought about by single column dampers. The approach is based on dynamic outputs of the device alone and is based on the estimation of the nonlinearity of the output signal. The advantages of the selected marker and its response with changing structural properties are discussed. The marker is observed to be important for monitoring the as- deployed structural condition and is sensitive to changes in such conditions. Influence of exposure conditions of wave loading is also discussed in this study based only on experimental data.

  17. Prognostic value of inflammation-based markers in patients with pancreatic cancer administered gemcitabine and erlotinib

    PubMed Central

    Lee, Jae Min; Lee, Hong Sik; Hyun, Jong Jin; Choi, Hyuk Soon; Kim, Eun Sun; Keum, Bora; Seo, Yeon Seok; Jeen, Yoon Tae; Chun, Hoon Jai; Um, Soon Ho; Kim, Chang Duck

    2016-01-01

    AIM: To evaluate the value of systemic inflammation-based markers as prognostic factors for advanced pancreatic cancer (PC). METHODS: Data from 82 patients who underwent combination chemotherapy with gemcitabine and erlotinib for PC from 2011 to 2014 were collected retrospectively. Data that included the neutrophil-to-lymphocyte ratio (NLR), the platelet-to-lymphocyte ratio, and the C-reactive protein (CRP)-to-albumin (CRP/Alb) ratio were analyzed. Kaplan-Meier curves, and univariate and multivariate Cox proportional hazards regression analyses were used to identify the prognostic factors associated with progression-free survival (PFS) and overall survival (OS). RESULTS: The univariate analysis demonstrated the prognostic value of the NLR (P = 0.049) and the CRP/Alb ratio (P = 0.047) in relation to PFS, and a positive relationship between an increase in inflammation-based markers and a poor prognosis in relation to OS. The multivariate analysis determined that an increased NLR (hazard ratio = 2.76, 95%CI: 1.33-5.75, P = 0.007) is an independent prognostic factor for poor OS. There was no association between the PLR and the patients’ prognoses in those who had received chemotherapy that comprised gemcitabine and erlotinib in combination. The Kaplan-Meier method and the log-rank test determined significantly worse outcomes in relation to PFS and OS in patients with an NLR > 5 or a CRP/Alb ratio > 5. CONCLUSION: Systemic inflammation-based markers, including increases in the NLR and the CRP/Alb ratio, may be useful for predicting PC prognoses. PMID:27559435

  18. Data on phylogenetic analyses of gazelles (genus Gazella) based on mitochondrial and nuclear intron markers

    PubMed Central

    Lerp, Hannes; Klaus, Sebastian; Allgöwer, Stefanie; Wronski, Torsten; Pfenninger, Markus; Plath, Martin

    2016-01-01

    The data provided is related to the article “Phylogenetic analyses of gazelles reveal repeated transitions of key ecological traits and provide novel insights into the origin of the genus Gazella” [1]. The data is based on 48 tissue samples of all nine extant species of the genus Gazella, namely Gazella gazella, Gazella arabica, Gazella bennettii, Gazella cuvieri, Gazella dorcas, Gazella leptoceros, Gazella marica, Gazella spekei, and Gazella subgutturosa and four related taxa (Saiga tatarica, Antidorcas marsupialis, Antilope cervicapra and Eudorcas rufifrons). It comprises alignments of sequences of a cytochrome b data set and of six nuclear intron markers. For the latter new primers were designed based on cattle and sheep genomes. Based on these alignments phylogenetic trees were inferred using Bayesian Inference and Maximum Likelihood methods. Furthermore, ancestral character states (inferred with BayesTraits 1.0) and ancestral ranges based on a Dispersal-Extinction-Cladogenesis model were estimated and results׳ files were stored within this article. PMID:27054158

  19. Data on phylogenetic analyses of gazelles (genus Gazella) based on mitochondrial and nuclear intron markers.

    PubMed

    Lerp, Hannes; Klaus, Sebastian; Allgöwer, Stefanie; Wronski, Torsten; Pfenninger, Markus; Plath, Martin

    2016-06-01

    The data provided is related to the article "Phylogenetic analyses of gazelles reveal repeated transitions of key ecological traits and provide novel insights into the origin of the genus Gazella" [1]. The data is based on 48 tissue samples of all nine extant species of the genus Gazella, namely Gazella gazella, Gazella arabica, Gazella bennettii, Gazella cuvieri, Gazella dorcas, Gazella leptoceros, Gazella marica, Gazella spekei, and Gazella subgutturosa and four related taxa (Saiga tatarica, Antidorcas marsupialis, Antilope cervicapra and Eudorcas rufifrons). It comprises alignments of sequences of a cytochrome b data set and of six nuclear intron markers. For the latter new primers were designed based on cattle and sheep genomes. Based on these alignments phylogenetic trees were inferred using Bayesian Inference and Maximum Likelihood methods. Furthermore, ancestral character states (inferred with BayesTraits 1.0) and ancestral ranges based on a Dispersal-Extinction-Cladogenesis model were estimated and results׳ files were stored within this article. PMID:27054158

  20. [Differentiation of two hemp nettle species (Galeopsis bifida Boenn. and G. tetrahit L.) inferred from morphological characters and DNA markers].

    PubMed

    Maslova, E V

    2008-03-01

    Two species of the genus Galeopsis L., G. tetrahit L. and G. bifida (family Lamiaceae), are problematic to distinguish often wrongly recognized, and treated by some taxonomists as a single species. Morphological diagnostical characters of these species are variable and partly overlap. Species independence of G. tetrahit and G. bifida was evaluated and their diagnostic characters verified using ISSR and RAPD markers. A total of 57 ISSR and 28 RAPD fragments were obtained providing distinct subdivision of the accessions examined into two groups. Analysis of molecular data using the neighbor-joining method showed that the accessions studied fell into two clades in the same way as demonstrated by the analysis of 20 morphological characters using single linkage method. The morphological characters were found to be more variable compared to the molecular markers, although the combined of these characters provided differentiation of the species.

  1. Organic composition and source apportionment of fine aerosol at Monterrey, Mexico, based on organic markers

    NASA Astrophysics Data System (ADS)

    Mancilla, Y.; Mendoza, A.; Fraser, M. P.; Herckes, P.

    2016-01-01

    attribution results obtained using the CMB (chemical mass balance) model indicate that emissions from motor vehicle exhausts are the most important, accounting for the 64 % of the PM2.5, followed by meat-cooking operations with 31 % The vegetative detritus and biomass burning had the smallest contribution (2.2 % of the PM2.5). To our knowledge, this is only the second study to explore the organic composition and source apportionment of fine organic aerosol based on molecular markers in Mexico and the first for the MMA. Particularly molecular marker were quantified by solvent extraction with dichloromethane, derivatization, and gas chromatography with mass spectrometry (GC/MS).

  2. A set of GFP-based organelle marker lines combined with DsRed-based gateway vectors for subcellular localization study in rice (Oryza sativa L.).

    PubMed

    Wu, Tsung-Meng; Lin, Ke-Chun; Liau, Wei-Shiang; Chao, Yun-Yang; Yang, Ling-Hung; Chen, Szu-Yun; Lu, Chung-An; Hong, Chwan-Yang

    2016-01-01

    In the post-genomic era, many useful tools have been developed to accelerate the investigation of gene functions. Fluorescent proteins have been widely used as protein tags for studying the subcellular localization of proteins in plants. Several fluorescent organelle marker lines have been generated in dicot plants; however, useful and reliable fluorescent organelle marker lines are lacking in the monocot model rice. Here, we developed eight different GFP-based organelle markers in transgenic rice and created a set of DsRed-based gateway vectors for combining with the marker lines. Two mitochondrial-localized rice ascorbate peroxidase genes fused to DsRed and successfully co-localized with mitochondrial-targeted marker lines verified the practical use of this system. The co-localization of GFP-fusion marker lines and DsRed-fusion proteins provide a convenient platform for in vivo or in vitro analysis of subcellular localization of rice proteins.

  3. A whole-genome DNA marker map for cotton based on the D-genome sequence of Gossypium raimondii L.

    PubMed

    Wang, Zining; Zhang, Dong; Wang, Xiyin; Tan, Xu; Guo, Hui; Paterson, Andrew H

    2013-10-03

    We constructed a very-high-density, whole-genome marker map (WGMM) for cotton by using 18,597 DNA markers corresponding to 48,958 loci that were aligned to both a consensus genetic map and a reference genome sequence. The WGMM has a density of one locus per 15.6 kb, or an average of 1.3 loci per gene. The WGMM was anchored by the use of colinear markers to a detailed genetic map, providing recombinational information. Mapped markers occurred at relatively greater physical densities in distal chromosomal regions and lower physical densities in the central regions, with all 1 Mb bins having at least nine markers. Hotspots for quantitative trait loci and resistance gene analog clusters were aligned to the map and DNA markers identified for targeting of these regions of high practical importance. Based on the cotton D genome reference sequence, the locations of chromosome structural rearrangements plotted on the map facilitate its translation to other Gossypium genome types. The WGMM is a versatile genetic map for marker assisted breeding, fine mapping and cloning of genes and quantitative trait loci, developing new genetic markers and maps, genome-wide association mapping, and genome evolution studies.

  4. Identification of Single-Locus PCR-Based Markers Linked to Shell Background Color in the Pacific Oyster (Crassostrea gigas).

    PubMed

    Ge, Jianlong; Li, Qi; Yu, Hong; Kong, Lingfeng

    2015-10-01

    A number of Pacific oyster (Crassostrea gigas) with golden shell background color were obtained which show great potential to develop a niche market. To improve the selective breeding progress of true-breeding strains with complete golden oysters, research was conducted to identify genetic markers linked to the shell color locus. An F1-segregating population was obtained by crossing two oysters with golden shell and white shell. Genomic DNA from eight progenies with golden shell and eight progenies with white shell were equally pooled for amplified fragment length polymorphism (AFLP) screening. In bulked segregant analysis, six out of 225 selective primer pair combinations produced seven polymorphic fragments tightly linked to shell color across the segregating population. The seven AFLP markers were all derived from the golden dam and mapped onto a single linkage group flanking the shell color locus. In conversion of the AFLPs into single-locus PCR-based markers, a sequence-characterized amplified region (SCAR) marker, named SCARJ8-2, a single nucleotide polymorphism (SNP) marker, named SNPL2-4, and a simple sequence repeat (SSR) marker, named SSRO11-2, were obtained. These markers obtained in this study will be useful for marker-assisted selection of the Pacific oyster.

  5. Risk factor correlates of platelet and leukocyte markers assessed by flow cytometry in a population-based sample

    PubMed Central

    Folsom, Aaron R.; Aleksic, Nena; Sanhueza, Antonio; Boerwinkle, Eric

    2008-01-01

    Background Platelet and leukocyte products are involved in atherothrombosis. However, the determinants of of platelet and leukocyte markers assessed by flow cytometry have not been documented in a population-based sample. Methods and results We performed flow cytometry on blood from participants (n=1,894) in the Atherosclerosis Risk in Communities (ARIC) Carotid MRI Study. Cellular aggregates and multiple platelet and leukocyte markers, such as myeloperoxidase in granulocytes and toll-like receptor-4, CD14, and CD45 in monocytes, were quantified. Their cross-sectional associations with demographic and risk factors were assessed using multiple linear regression. Mean values of most cellular markers and aggregates were considerably higher in blacks than whites (p<0.01). There were some differences in cellular markers between men and women, but little association with age. LDL-cholesterol was associated positively with several markers (toll-like receptor-4 and myeloperoxidase in granulocytes and CD162 in lymphocytes). Lipid lowering therapy tended to show opposite associations. Smokers had much higher granulocyte myeloperoxidase than nonsmokers. However, most other correlations between risk factors and cellular markers were nonsignificant. Conclusions Race/ethnicity, sex, and to a lesser degree LDL-cholesterol and lipid-lowering therapy, but few other risk factors, were correlated with markers of cellular activation in this population-based study. PMID:19124123

  6. Kalman smoothing improves the estimation of joint kinematics and kinetics in marker-based human gait analysis.

    PubMed

    De Groote, F; De Laet, T; Jonkers, I; De Schutter, J

    2008-12-01

    We developed a Kalman smoothing algorithm to improve estimates of joint kinematics from measured marker trajectories during motion analysis. Kalman smoothing estimates are based on complete marker trajectories. This is an improvement over other techniques, such as the global optimisation method (GOM), Kalman filtering, and local marker estimation (LME), where the estimate at each time instant is only based on part of the marker trajectories. We applied GOM, Kalman filtering, LME, and Kalman smoothing to marker trajectories from both simulated and experimental gait motion, to estimate the joint kinematics of a ten segment biomechanical model, with 21 degrees of freedom. Three simulated marker trajectories were studied: without errors, with instrumental errors, and with soft tissue artefacts (STA). Two modelling errors were studied: increased thigh length and hip centre dislocation. We calculated estimation errors from the known joint kinematics in the simulation study. Compared with other techniques, Kalman smoothing reduced the estimation errors for the joint positions, by more than 50% for the simulated marker trajectories without errors and with instrumental errors. Compared with GOM, Kalman smoothing reduced the estimation errors for the joint moments by more than 35%. Compared with Kalman filtering and LME, Kalman smoothing reduced the estimation errors for the joint accelerations by at least 50%. Our simulation results show that the use of Kalman smoothing substantially improves the estimates of joint kinematics and kinetics compared with previously proposed techniques (GOM, Kalman filtering, and LME) for both simulated, with and without modelling errors, and experimentally measured gait motion.

  7. The use of lacZ marker in enumeration of Azotobacter chroococcum in carrier based inoculants.

    PubMed

    Solanki, Manu; Garg, Faquir C

    2014-01-01

    A transconjugant of Azotobacter chroococcum Mac 27 tagged with lac Z(A. chroococcum Mac27 L) was found to possess high levels of β-galactosidase activity constitutively. Further, the lac Z marker was found to be stably integrated into the chromosome of the A. chroococcum Mac 27 and did not have any adverse effect on growth, nitrogen fixation and excretion of ammonia. A quick method to determine the viable cell number in broth culture and carrier based inoculants has been developed on the basis of β-galactosidase assay. It was found that there was a direct relationship between the number of cell as determined by standard plate count and intensity of colour that developed upon degradation of ONPG due to β-galactosidase activity. The method was found to be sensitive enough to determine 1.7 × 10(6) CFU mL(-1) in broth culture as well as carrier based Azotobacter inoculants. Further, it was observed that when A. chroococcum Mac27 L was inoculated on Brassica campestris, it could be detected in the presence of other bacteria capable of growing on Burks agar medium containing X-gal on the basis of lac Z genetic marker.

  8. Vehicle Position Estimation Based on Magnetic Markers: Enhanced Accuracy by Compensation of Time Delays

    PubMed Central

    Byun, Yeun-Sub; Jeong, Rag-Gyo; Kang, Seok-Won

    2015-01-01

    The real-time recognition of absolute (or relative) position and orientation on a network of roads is a core technology for fully automated or driving-assisted vehicles. This paper presents an empirical investigation of the design, implementation, and evaluation of a self-positioning system based on a magnetic marker reference sensing method for an autonomous vehicle. Specifically, the estimation accuracy of the magnetic sensing ruler (MSR) in the up-to-date estimation of the actual position was successfully enhanced by compensating for time delays in signal processing when detecting the vertical magnetic field (VMF) in an array of signals. In this study, the signal processing scheme was developed to minimize the effects of the distortion of measured signals when estimating the relative positional information based on magnetic signals obtained using the MSR. In other words, the center point in a 2D magnetic field contour plot corresponding to the actual position of magnetic markers was estimated by tracking the errors between pre-defined reference models and measured magnetic signals. The algorithm proposed in this study was validated by experimental measurements using a test vehicle on a pilot network of roads. From the results, the positioning error was found to be less than 0.04 m on average in an operational test. PMID:26580622

  9. The use of lacZ marker in enumeration of Azotobacter chroococcum in carrier based inoculants

    PubMed Central

    Solanki, Manu; Garg, Faquir C.

    2014-01-01

    A transconjugant of Azotobacter chroococcum Mac 27 tagged with lac Z(A. chroococcum Mac27 L) was found to possess high levels of β-galactosidase activity constitutively. Further, the lac Z marker was found to be stably integrated into the chromosome of the A. chroococcum Mac 27 and did not have any adverse effect on growth, nitrogen fixation and excretion of ammonia. A quick method to determine the viable cell number in broth culture and carrier based inoculants has been developed on the basis of β-galactosidase assay. It was found that there was a direct relationship between the number of cell as determined by standard plate count and intensity of colour that developed upon degradation of ONPG due to β-galactosidase activity. The method was found to be sensitive enough to determine 1.7 × 106 CFU mL−1 in broth culture as well as carrier based Azotobacter inoculants. Further, it was observed that when A. chroococcum Mac27 L was inoculated on Brassica campestris, it could be detected in the presence of other bacteria capable of growing on Burks agar medium containing X-gal on the basis of lac Z genetic marker. PMID:25242946

  10. Vehicle Position Estimation Based on Magnetic Markers: Enhanced Accuracy by Compensation of Time Delays.

    PubMed

    Byun, Yeun-Sub; Jeong, Rag-Gyo; Kang, Seok-Won

    2015-01-01

    The real-time recognition of absolute (or relative) position and orientation on a network of roads is a core technology for fully automated or driving-assisted vehicles. This paper presents an empirical investigation of the design, implementation, and evaluation of a self-positioning system based on a magnetic marker reference sensing method for an autonomous vehicle. Specifically, the estimation accuracy of the magnetic sensing ruler (MSR) in the up-to-date estimation of the actual position was successfully enhanced by compensating for time delays in signal processing when detecting the vertical magnetic field (VMF) in an array of signals. In this study, the signal processing scheme was developed to minimize the effects of the distortion of measured signals when estimating the relative positional information based on magnetic signals obtained using the MSR. In other words, the center point in a 2D magnetic field contour plot corresponding to the actual position of magnetic markers was estimated by tracking the errors between pre-defined reference models and measured magnetic signals. The algorithm proposed in this study was validated by experimental measurements using a test vehicle on a pilot network of roads. From the results, the positioning error was found to be less than 0.04 m on average in an operational test. PMID:26580622

  11. Diversity of black Aspergilli isolated from raisins in Argentina: Polyphasic approach to species identification and development of SCAR markers for Aspergillus ibericus.

    PubMed

    Giaj Merlera, G; Muñoz, S; Coelho, I; Cavaglieri, L R; Torres, A M; Reynoso, M M

    2015-10-01

    Aspergillus section Nigri is a heterogeneous fungal group including some ochratoxin A producer species that usually contaminate raisins. The section contains the Series Carbonaria which includes the toxigenic species Aspergillus carbonarius and nontoxigenic Aspergillus ibericus that are phenotypically undistinguishable. The aim of this study was to examine the diversity of black aspergilli isolated from raisins and to develop a specific genetic marker to distinguish A. ibericus from A. carbonarius. The species most frequently found in raisins in this study were Aspergillus tubingensis (35.4%) and A. carbonarius (32.3%), followed by Aspergillus luchuensis (10.7%), Aspergillus japonicus (7.7%), Aspergillus niger (6.2%), Aspergillus welwitschiae (4.6%) and A. ibericus (3.1%). Based on inter-simple sequence repeat (ISSR) fingerprinting profiles of major Aspergillus section Nigri members, a sequence-characterized amplified region (SCAR) marker was identified. Primers were designed based on the conserved regions of the SCAR marker and were utilized in a PCR for simultaneous identification of A. carbonarius and A. ibericus. The detection level of the SCAR-PCR was found to be 0.01 ng of purified DNA. The present SCAR-PCR is rapid and less cumbersome than conventional identification techniques and could be a supplementary strategy and a reliable tool for high-throughput sample analysis.

  12. Accuracy of an infrared marker-based patient positioning system (ExacTrac®) for stereotactic body radiotherapy in localizing the planned isocenter using fiducial markers

    NASA Astrophysics Data System (ADS)

    Montes-Rodríguez, María de los Ángeles; Hernández-Bojórquez, Mariana; Martínez-Gómez, Alma Angélica; Contreras-Pérez, Agustín; Negrete-Hernández, Ingrid Mireya; Hernández-Oviedo, Jorge Omar; Mitsoura, Eleni; Santiago-Concha, Bernardino Gabriel

    2014-11-01

    Stereotactic Body Radiation Therapy (SBRT) requires a controlled immobilization and position monitoring of patient and target. The purpose of this work is to analyze the performance of the imaging system ExacTrac® (ETX) using infrared and fiducial markers. Materials and methods: In order to assure the accuracy of isocenter localization, a Quality Assurance procedure was applied using an infrared marker-based positioning system. Scans were acquired of an inhouse-agar gel and solid water phantom with infrared spheres. In the inner part of the phantom, three reference markers were delineated as reference and one pellet was place internally; which was assigned as the isocenter. The iPlan® RT Dose treatment planning system. Images were exported to the ETX console. Images were acquired with the ETX to check the correctness of the isocenter placement. Adjustments were made in 6D the reference markers were used to fuse the images. Couch shifts were registered. The procedure was repeated for verification purposes. Results: The data recorded of the verifications in translational and rotational movements showed averaged 3D spatial uncertainties of 0.31 ± 0.42 mm respectively 0.82° ± 0.46° in the phantom and the first correction of these uncertainties were of 1.51 ± 1.14 mm respectively and 1.37° ± 0.61°. Conclusions: This study shows a high accuracy and repeatability in positioning the selected isocenter. The ETX-system for verifying the treatment isocenter position has the ability to monitor the tracing position of interest, making it possible to be used for SBRT positioning within uncertainty ≤1mm.

  13. Accuracy of an infrared marker-based patient positioning system (ExacTrac®) for stereotactic body radiotherapy in localizing the planned isocenter using fiducial markers

    SciTech Connect

    Montes-Rodríguez, María de los Ángeles Mitsoura, Eleni; Hernández-Bojórquez, Mariana; Martínez-Gómez, Alma Angélica; Contreras-Pérez, Agustín; Negrete-Hernández, Ingrid Mireya; Hernández-Oviedo, Jorge Omar; Santiago-Concha, Bernardino Gabriel

    2014-11-07

    Stereotactic Body Radiation Therapy (SBRT) requires a controlled immobilization and position monitoring of patient and target. The purpose of this work is to analyze the performance of the imaging system ExacTrac® (ETX) using infrared and fiducial markers. Materials and methods: In order to assure the accuracy of isocenter localization, a Quality Assurance procedure was applied using an infrared marker-based positioning system. Scans were acquired of an inhouse-agar gel and solid water phantom with infrared spheres. In the inner part of the phantom, three reference markers were delineated as reference and one pellet was place internally; which was assigned as the isocenter. The iPlan® RT Dose treatment planning system. Images were exported to the ETX console. Images were acquired with the ETX to check the correctness of the isocenter placement. Adjustments were made in 6D the reference markers were used to fuse the images. Couch shifts were registered. The procedure was repeated for verification purposes. Results: The data recorded of the verifications in translational and rotational movements showed averaged 3D spatial uncertainties of 0.31 ± 0.42 mm respectively 0.82° ± 0.46° in the phantom and the first correction of these uncertainties were of 1.51 ± 1.14 mm respectively and 1.37° ± 0.61°. Conclusions: This study shows a high accuracy and repeatability in positioning the selected isocenter. The ETX-system for verifying the treatment isocenter position has the ability to monitor the tracing position of interest, making it possible to be used for SBRT positioning within uncertainty ≤1mm.

  14. Genetic diversity analysis with ISSR PCR on green algae Chlorella vulgaris and Chlorella pyrenoidosa

    NASA Astrophysics Data System (ADS)

    Shen, Songdong

    2008-11-01

    In the present study, genetic polymorphism and diversity in unicellular clones of Chlorella vulgaris Beijerinck and Chlorella pyrenoidosa Chick were studied with Inter Simple Sequence Repeats PCR (ISSR PCR). Samples including four clones of C. vulgaris and three clones of C. pyrenoidosa were purified by single-clone-choice method. For four C. vulgaris unicellular clones, the total number of the bands scored for 18 primers was 298; and the number of the polymorphic bands was 118, of which 39.6% were polymorphic. The size of PCR products ranged from 200 to 2 500 bp. The total number of bands scored for 18 primers, the number of polymorphic bands and the percentage of three C. pyrenoidosa unicellular clones was 194.83 and 30.8%, respectively. POPGENE analysis show that the average Nei genetic diversity (h*) and Shannon index of diversity (I*) in the four C. vulgaris unicellular clones was 0.2181 and 0.3208, respectively, which is slightly higher than those of the three C. pyrenoidosa unicellular clones (0.190 3 and 0.274 8), which agreed with the percentage of polymorphic bands in the mixed samples of the two species. The results suggest that ISSR is a useful method to Chlorella for intraspecies genetic analysis.

  15. Comparison of marker types and map assumptions using Markov chain Monte Carlo-based linkage analysis of COGA data

    PubMed Central

    Sieh, Weiva; Basu, Saonli; Fu, Audrey Q; Rothstein, Joseph H; Scheet, Paul A; Stewart, William CL; Sung, Yun J; Thompson, Elizabeth A; Wijsman, Ellen M

    2005-01-01

    We performed multipoint linkage analysis of the electrophysiological trait ECB21 on chromosome 4 in the full pedigrees provided by the Collaborative Study on the Genetics of Alcoholism (COGA). Three Markov chain Monte Carlo (MCMC)-based approaches were applied to the provided and re-estimated genetic maps and to five different marker panels consisting of microsatellite (STRP) and/or SNP markers at various densities. We found evidence of linkage near the GABRB1 STRP using all methods, maps, and marker panels. Difficulties encountered with SNP panels included convergence problems and demanding computations. PMID:16451566

  16. Genetic Variability among Lucerne Cultivars Based on Biochemical (SDS-PAGE) and Morphological Markers

    NASA Astrophysics Data System (ADS)

    Farshadfar, M.; Farshadfar, E.

    The present research was conducted to determine the genetic variability of 18 Lucerne cultivars, based on morphological and biochemical markers. The traits studied were plant height, tiller number, biomass, dry yield, dry yield/biomass, dry leaf/dry yield, macro and micro elements, crude protein, dry matter, crude fiber and ash percentage and SDS- PAGE in seed and leaf samples. Field experiments included 18 plots of two meter rows. Data based on morphological, chemical and SDS-PAGE markers were analyzed using SPSSWIN soft ware and the multivariate statistical procedures: cluster analysis (UPGMA), principal component. Analysis of analysis of variance and mean comparison for morphological traits reflected significant differences among genotypes. Genotype 13 and 15 had the greatest values for most traits. The Genotypic Coefficient of Variation (GCV), Phenotypic Coefficient of Variation (PCV) and Heritability (Hb) parameters for different characters raged from 12.49 to 26.58% for PCV, hence the GCV ranged from 6.84 to 18.84%. The greatest value of Hb was 0.94 for stem number. Lucerne genotypes could be classified, based on morphological traits, into four clusters and 94% of the variance among the genotypes was explained by two PCAs: Based on chemical traits they were classified into five groups and 73.492% of variance was explained by four principal components: Dry matter, protein, fiber, P, K, Na, Mg and Zn had higher variance. Genotypes based on the SDS-PAGE patterns all genotypes were classified into three clusters. The greatest genetic distance was between cultivar 10 and others, therefore they would be suitable parent in a breeding program.

  17. Efficient Software for Multi-marker, Region-Based Analysis of GWAS Data

    PubMed Central

    Sanjak, Jaleal S.; Long, Anthony D.; Thornton, Kevin R.

    2016-01-01

    Genome-wide association studies (GWAS) have associated many single variants with complex disease, yet the better part of heritable complex disease risk remains unexplained. Analytical tools designed to work under specific population genetic models are needed. Rare variants are increasingly shown to be important in human complex disease, but most existing GWAS data do not cover rare variants. Explicit population genetic models predict that genes contributing to complex traits and experiencing recurrent, unconditionally deleterious, mutation will harbor multiple rare, causative mutations of subtle effect. It is difficult to identify genes harboring rare variants of large effect that contribute to complex disease risk via the single marker association tests typically used in GWAS. Gene/region-based association tests may have the power detect associations by combining information from multiple markers, but have yielded limited success in practice. This is partially because many methods have not been widely applied. Here, we empirically demonstrate the utility of a procedure based on the rank truncated product (RTP) method, filtered to reduce the effects of linkage disequilibrium. We apply the procedure to the Wellcome Trust Case Control Consortium (WTCCC) data set, and uncover previously unidentified associations, some of which have been replicated in much larger studies. We show that, in the absence of significant rare variant coverage, RTP based methods still have the power to detect associated genes. We recommend that RTP-based methods be applied to all existing GWAS data to maximize the usefulness of those data. For this, we provide efficient software implementing our procedure. PMID:26865700

  18. Error analysis of marker-based object localization using a single-plane XRII

    SciTech Connect

    Habets, Damiaan F.; Pollmann, Steven I.; Yuan, Xunhua; Peters, Terry M.; Holdsworth, David W.

    2009-01-15

    The role of imaging and image guidance is increasing in surgery and therapy, including treatment planning and follow-up. Fluoroscopy is used for two-dimensional (2D) guidance or localization; however, many procedures would benefit from three-dimensional (3D) guidance or localization. Three-dimensional computed tomography (CT) using a C-arm mounted x-ray image intensifier (XRII) can provide high-quality 3D images; however, patient dose and the required acquisition time restrict the number of 3D images that can be obtained. C-arm based 3D CT is therefore limited in applications for x-ray based image guidance or dynamic evaluations. 2D-3D model-based registration, using a single-plane 2D digital radiographic system, does allow for rapid 3D localization. It is our goal to investigate - over a clinically practical range - the impact of x-ray exposure on the resulting range of 3D localization precision. In this paper it is assumed that the tracked instrument incorporates a rigidly attached 3D object with a known configuration of markers. A 2D image is obtained by a digital fluoroscopic x-ray system and corrected for XRII distortions ({+-}0.035 mm) and mechanical C-arm shift ({+-}0.080 mm). A least-square projection-Procrustes analysis is then used to calculate the 3D position using the measured 2D marker locations. The effect of x-ray exposure on the precision of 2D marker localization and on 3D object localization was investigated using numerical simulations and x-ray experiments. The results show a nearly linear relationship between 2D marker localization precision and the 3D localization precision. However, a significant amplification of error, nonuniformly distributed among the three major axes, occurs, and that is demonstrated. To obtain a 3D localization error of less than {+-}1.0 mm for an object with 20 mm marker spacing, the 2D localization precision must be better than {+-}0.07 mm. This requirement was met for all investigated nominal x-ray exposures at 28 cm

  19. Performance comparison of genetic markers for high-throughput sequencing-based biodiversity assessment in complex communities.

    PubMed

    Zhan, Aibin; Bailey, Sarah A; Heath, Daniel D; Macisaac, Hugh J

    2014-09-01

    Metabarcode surveys of DNA extracted from environmental samples are increasingly popular for biodiversity assessment in natural communities. Such surveys rely heavily on robust genetic markers. Therefore, analysis of PCR efficiency and subsequent biodiversity estimation for different types of genetic markers and their corresponding primers is important. Here, we test the PCR efficiency and biodiversity recovery potential of three commonly used genetic markers - nuclear small subunit ribosomal DNA (18S), mitochondrial cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (mt16S) - using 454 pyrosequencing of a zooplankton community collected from Hamilton Harbour, Ontario. We found that biodiversity detection power and PCR efficiency varied widely among these markers. All tested primers for COI failed to provide high-quality PCR products for pyrosequencing, but newly designed primers for 18S and 16S passed all tests. Furthermore, multiple analyses based on large-scale pyrosequencing (i.e. 1/2 PicoTiter plate for each marker) showed that primers for 18S recover more (38 orders) groups than 16S (10 orders) across all taxa, and four vs. two orders and nine vs. six families for Crustacea. Our results showed that 18S, using newly designed primers, is an efficient and powerful tool for profiling biodiversity in largely unexplored communities, especially when amplification difficulties exist for mitochondrial markers such as COI. Universal primers for higher resolution markers such as COI are still needed to address the possible low resolution of 18S for species-level identification.

  20. Evaluation of Psoriasis Genetic Risk Based on Five Susceptibility Markers in a Population from Northern Poland

    PubMed Central

    Stawczyk-Macieja, Marta; Rębała, Krzysztof; Szczerkowska-Dobosz, Aneta; Wysocka, Joanna; Cybulska, Lidia; Kapińska, Ewa; Haraś, Agnieszka; Miniszewska, Paulina; Nowicki, Roman

    2016-01-01

    Psoriasis genetic background depends on polygenic and multifactorial mode of inheritance. As in other complex disorders, the estimation of the disease risk based on individual genetic variants is impossible. For this reason, recent investigations have been focused on combinations of known psoriasis susceptibility markers in order to improve the disease risk evaluation. Our aim was to compare psoriasis genetic risk score (GRS) for five susceptibility loci involved in the immunological response (HLA-C, ERAP1, ZAP70) and in the skin barrier function (LCE3, CSTA) between patients with chronic plaque psoriasis (n = 148) and the control group (n = 146). A significantly higher number of predisposing alleles was observed in patients with psoriasis in comparison to healthy individuals (6.1 vs. 5.2, respectively; P = 8.8×10−7). The statistical significance was even more profound when GRS weighted by logarithm odds ratios was evaluated (P = 9.9×10−14). Our results demonstrate the developed panel of five susceptibility loci to be more efficient in predicting psoriasis risk in the Polish population and to possess higher sensitivity and specificity for the disease than any of the markers analyzed separately, including the most informative HLA-C*06 allele. PMID:27658291

  1. Marker-based monitoring of seated spinal posture using a calibrated single-variable threshold model.

    PubMed

    Walsh, Pauline; Dunne, Lucy E; Caulfield, Brian; Smyth, Barry

    2006-01-01

    This work, as part of a larger project developing wearable posture monitors for the work environment, seeks to monitor and model seated posture during computer use. A non-wearable marker-based optoelectronic motion capture system was used to monitor seated posture for ten healthy subjects during a calibration exercise and a typing task. Machine learning techniques were used to select overall spinal sagittal flexion as the best indicator of posture from a set of marker and vector variables. Overall flexion data from the calibration exercise were used to define a threshold model designed to classify posture for each subject, which was then applied to the typing task data. Results of the model were analysed visually by qualified physiotherapists with experience in ergonomics and posture analysis to confirm the accuracy of the calibration. The calibration formula was found to be accurate on 100% subjects. This process will be used as a comparative measure in the evaluation of several wearable posture sensors, and to inform the design of the wearable system. PMID:17946301

  2. Development of a cassava core collection based on single nucleotide polymorphism markers.

    PubMed

    Oliveira, E J; Ferreira, C F; Santos, V S; Oliveira, G A F

    2014-08-25

    Single nucleotide polymorphism (SNP) markers were used in the largest cassava (Manihot esculenta Crantz) germplasm collection from Brazil to develop core collections based on the maximization strategy. Subsets with 61, 64, 84, 128, 256, and 384 cassava accessions were selected and named PoHEU, MST64, PoRAN, MST128, MST256, and MST384, respectively. All the 798 alleles identified by 402 SNP markers in the entire collection were captured in all core collections. Only small alterations in the diversity parameters were observed for the different core collections compared with the complete collection. Because of the optimal adjustment of the validation parameters representative of the complete collection, the absence of genotypes with high genetic similarity and the maximization of the genetic distances between accessions of the PoHEU core collection, which contained 4.7% of the accessions of the complete collection, maximized the genetic conservation of this important cassava collection. Furthermore, the development of this core collection will allow concentrated efforts toward future characterization and agronomic evaluation of accessions to maximize the diversity and genetic gains in cassava breeding programs.

  3. Development of a core collection for ramie by heuristic search based on SSR markers

    PubMed Central

    Luan, Ming-Bao; Zou, Zi-Zheng; Zhu, Juan-Juan; Wang, Xiao-Fei; Xu, Ying; Ma, Qing-Hua; Sun, Zhi-Min; Chen, Jian-Hua

    2014-01-01

    There are more than 2000 ramie germplasms in the National Ramie Germplasm Nursery affiliated with the Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science, China. As it is difficult to perform effective conservation, management, evaluation, and utilization of redundant genetic resources, it is necessary to construct a core collection by using molecular markers. In this study, a core collection of ramie consisting of 22 germplasms was constructed from 108 accessions by heuristic search based on 21 Simple Sequence Repeat (SSR) marker combinations. The results showed that there is a poor relationship between the core collection and the geographic distribution. The number of amplification bands for the core collection was the same as that for the entire collection. Shannon's index for three of the SSR primers (14%) and Nei's index for nine of the SSR primers (19%) were lower in the core collection than in the entire collection. The true core collection had wider genetic diversity compared with the random core collection. Collectively, the core collection constructed in this study is reliable and represents the genetic diversity of all the 108 accessions. PMID:26019563

  4. Development and application of EST-based markers specific for chromosome arms of rye (Secale cereale L.).

    PubMed

    Xu, H; Yin, D; Li, L; Wang, Q; Li, X; Yang, X; Liu, W; An, D

    2012-01-01

    To develop a set of molecular markers specific for the chromosome arms of rye, a total of 1,098 and 93 primer pairs derived from the expressed sequence tag (EST) sequences distributed on all 21 wheat chromosomes and 7 rye chromosomes, respectively, were initially screened on common wheat 'Chinese Spring' and rye cultivar 'Imperial'. Four hundred and fourteen EST-based markers were specific for the rye genome. Seven disomic chromosome addition lines, 10 telosomic addition lines and 1 translocation line of 'Chinese Spring-Imperial' were confirmed by genomic in situ hybridization and fluorescencein situ hybridization, and used to screen the rye-specific markers. Thirty-one of the 414 markers produced stable specific amplicons in 'Imperial', as well as individual addition lines and were assigned to 13 chromosome arms of rye except for 6RS. Six rye cultivars, wheat cultivar 'Xiaoyan 6' and accessions of 4 wheat relatives were then used to test the specificity of the 31 EST-based markers. To confirm the specificity, 4 wheat-rye derivatives of 'Xiaoyan 6 × German White', with chromosomes 1RS, 2R and 4R, were amplified by some of the EST-based markers. The results indicated that they can effectively be used to detect corresponding rye chromosomes or chromosome arms introgressed into a wheat background, and hence to accelerate the utilization of rye genes in wheat breeding.

  5. Use of SSR and retrotransposon-based markers to interpret the population structure of native grapevines from southern Italy.

    PubMed

    Villano, Clizia; Carputo, Domenico; Frusciante, Luigi; Santoro, Xenia; Aversano, Riccardo

    2014-11-01

    Native grapevines are the quintessential elements of Southern Italy winemaking, and genomic characterization plays a role of primary importance for preservation and sustainable use of these unexploited genetic resources. Among the various molecular techniques available, SSR and retrotransposons-based markers result to be the most valuable for cultivars and biotypes distinctiveness. A total of 62 accessions including 38 local grape cultivars were analyzed with 30 SSR, four REMAP and one IRAP markers to assess their genetic diversity and obtain a complete genomic profiling. The use of VrZAG79, VrZAG112, VVS2, VVMD25 and VVMD5 combined with retrotransposon-based markers proved to be the most discriminating and polymorphic markers for the rapid and unambiguous identification of minority grapevines from Campania region, which is considered one of the most appreciated Italian districts for wine production. Results revealed 58 SSR marker-specific alleles, 22 genotype-specific SSR alleles, and four REMAP and IRAP private bands. Cases of synonymy and homonymy were discovered. In conclusion, we provided evidences that the integrating SSR and retrotransposon-based markers is an effective strategy to assess the genetic diversity of autochthonous grapes, allowing their easy identification.

  6. Use of SSR and retrotransposon-based markers to interpret the population structure of native grapevines from southern Italy.

    PubMed

    Villano, Clizia; Carputo, Domenico; Frusciante, Luigi; Santoro, Xenia; Aversano, Riccardo

    2014-11-01

    Native grapevines are the quintessential elements of Southern Italy winemaking, and genomic characterization plays a role of primary importance for preservation and sustainable use of these unexploited genetic resources. Among the various molecular techniques available, SSR and retrotransposons-based markers result to be the most valuable for cultivars and biotypes distinctiveness. A total of 62 accessions including 38 local grape cultivars were analyzed with 30 SSR, four REMAP and one IRAP markers to assess their genetic diversity and obtain a complete genomic profiling. The use of VrZAG79, VrZAG112, VVS2, VVMD25 and VVMD5 combined with retrotransposon-based markers proved to be the most discriminating and polymorphic markers for the rapid and unambiguous identification of minority grapevines from Campania region, which is considered one of the most appreciated Italian districts for wine production. Results revealed 58 SSR marker-specific alleles, 22 genotype-specific SSR alleles, and four REMAP and IRAP private bands. Cases of synonymy and homonymy were discovered. In conclusion, we provided evidences that the integrating SSR and retrotransposon-based markers is an effective strategy to assess the genetic diversity of autochthonous grapes, allowing their easy identification. PMID:24973024

  7. Multiple template-based fluoroscopic tracking of lung tumor mass without implanted fiducial markers

    NASA Astrophysics Data System (ADS)

    Cui, Ying; Dy, Jennifer G.; Sharp, Gregory C.; Alexander, Brian; Jiang, Steve B.

    2007-10-01

    Precise lung tumor localization in real time is particularly important for some motion management techniques, such as respiratory gating or beam tracking with a dynamic multi-leaf collimator, due to the reduced clinical tumor volume (CTV) to planning target volume (PTV) margin and/or the escalated dose. There might be large uncertainties in deriving tumor position from external respiratory surrogates. While tracking implanted fiducial markers has sufficient accuracy, this procedure may not be widely accepted due to the risk of pneumothorax. Previously, we have developed a technique to generate gating signals from fluoroscopic images without implanted fiducial markers using a template matching method (Berbeco et al 2005 Phys. Med. Biol. 50 4481-90, Cui et al 2007 Phys. Med. Biol. 52 741-55). In this paper, we present an extension of this method to multiple-template matching for directly tracking the lung tumor mass in fluoroscopy video. The basic idea is as follows: (i) during the patient setup session, a pair of orthogonal fluoroscopic image sequences are taken and processed off-line to generate a set of reference templates that correspond to different breathing phases and tumor positions; (ii) during treatment delivery, fluoroscopic images are continuously acquired and processed; (iii) the similarity between each reference template and the processed incoming image is calculated; (iv) the tumor position in the incoming image is then estimated by combining the tumor centroid coordinates in reference templates with proper weights based on the measured similarities. With different handling of image processing and similarity calculation, two such multiple-template tracking techniques have been developed: one based on motion-enhanced templates and Pearson's correlation score while the other based on eigen templates and mean-squared error. The developed techniques have been tested on six sequences of fluoroscopic images from six lung cancer patients against the reference

  8. Multiple template-based fluoroscopic tracking of lung tumor mass without implanted fiducial markers.

    PubMed

    Cui, Ying; Dy, Jennifer G; Sharp, Gregory C; Alexander, Brian; Jiang, Steve B

    2007-10-21

    Precise lung tumor localization in real time is particularly important for some motion management techniques, such as respiratory gating or beam tracking with a dynamic multi-leaf collimator, due to the reduced clinical tumor volume (CTV) to planning target volume (PTV) margin and/or the escalated dose. There might be large uncertainties in deriving tumor position from external respiratory surrogates. While tracking implanted fiducial markers has sufficient accuracy, this procedure may not be widely accepted due to the risk of pneumothorax. Previously, we have developed a technique to generate gating signals from fluoroscopic images without implanted fiducial markers using a template matching method (Berbeco et al 2005 Phys. Med. Biol. 50 4481-90, Cui et al 2007 Phys. Med. Biol. 52 741-55). In this paper, we present an extension of this method to multiple-template matching for directly tracking the lung tumor mass in fluoroscopy video. The basic idea is as follows: (i) during the patient setup session, a pair of orthogonal fluoroscopic image sequences are taken and processed off-line to generate a set of reference templates that correspond to different breathing phases and tumor positions; (ii) during treatment delivery, fluoroscopic images are continuously acquired and processed; (iii) the similarity between each reference template and the processed incoming image is calculated; (iv) the tumor position in the incoming image is then estimated by combining the tumor centroid coordinates in reference templates with proper weights based on the measured similarities. With different handling of image processing and similarity calculation, two such multiple-template tracking techniques have been developed: one based on motion-enhanced templates and Pearson's correlation score while the other based on eigen templates and mean-squared error. The developed techniques have been tested on six sequences of fluoroscopic images from six lung cancer patients against the reference

  9. Establishment of a simple model for hepatitis B virus infection status based on trait marker from quantitative measurement of serum markers.

    PubMed

    Ningyu, Zhang; Ying, Zhang; Hui, Liu

    2015-06-01

    The objectives of this study were to establish a simple model based on quantitative serum markers of hepatitis B virus (HBV) infection to understand the complex immune response to HBV. Patients samples were obtained from individuals with active HBV infection (alanine transaminase [ALT]-positive, aspartate aminotransferase [AST]-positive and HBsAg-positive), or patients who had recovered from infection (ALT-negative, AST-negative, anti-HBs-positive and either HBsAg, HBeAg, anti-HBe or anti-HBc positive). HBV quantitative markers, including HBsAg, anti-HBs, HBeAg, anti-HBe, and anti-HBc, were measured using a chemiluminescent microparticle immunoassay. Based on cut-off values, anti-HBs levels were converted to a ratio (sample value/cut-off value, RV). Anti-HBe and anti-HBc levels were determined using a competition method, resulting in the use of a ratio (cut-off value/sample value, RV) for determination of anti-HBe and anti-HBc values. The greater RV value in a patient was considered as a trait marker for HBV infection (TMHB) of this patient. Patients with TMHB including HBsAg or HBeAg were defined as TMHB-Ag; and patients with TMHB including anti-HBs, anti-HBe, or anti-HBc TMHB were defined as TMHB-Ab. The percentage of patients determined to be TMHB-Ag was 96.3% in the HBV group. The percentage of patients determined to be TMHB-Ab was 94.7% in recovery group. TMHBs could be used to analyze different status of HBV infection.

  10. Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding.

    PubMed

    Fan, Wei; Zong, Jie; Luo, Zhijing; Chen, Mingjiao; Zhao, Xiangxiang; Zhang, Dabing; Qi, Yiping; Yuan, Zheng

    2016-01-01

    Rapid and accurate genome-wide marker detection is essential to the marker-assisted breeding and functional genomics studies. In this work, we developed an integrated software, AgroMarker Finder (AMF: http://erp.novelbio.com/AMF), for providing graphical user interface (GUI) to facilitate the recently developed restriction-site associated DNA (RAD) sequencing data analysis in rice. By application of AMF, a total of 90,743 high-quality markers (82,878 SNPs and 7,865 InDels) were detected between rice varieties JP69 and Jiaoyuan5A. The density of the identified markers is 0.2 per Kb for SNP markers, and 0.02 per Kb for InDel markers. Sequencing validation revealed that the accuracy of genome-wide marker detection by AMF is 93%. In addition, a validated subset of 82 SNPs and 31 InDels were found to be closely linked to 117 important agronomic trait genes, providing a basis for subsequent marker-assisted selection (MAS) and variety identification. Furthermore, we selected 12 markers from 31 validated InDel markers to identify seed authenticity of variety Jiaoyuanyou69, and we also identified 10 markers closely linked to the fragrant gene BADH2 to minimize linkage drag for Wuxiang075 (BADH2 donor)/Jiachang1 recombinants selection. Therefore, this software provides an efficient approach for marker identification from RAD-seq data, and it would be a valuable tool for plant MAS and variety protection. PMID:26799713

  11. Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding

    PubMed Central

    Luo, Zhijing; Chen, Mingjiao; Zhao, Xiangxiang; Zhang, Dabing; Qi, Yiping; Yuan, Zheng

    2016-01-01

    Rapid and accurate genome-wide marker detection is essential to the marker-assisted breeding and functional genomics studies. In this work, we developed an integrated software, AgroMarker Finder (AMF: http://erp.novelbio.com/AMF), for providing graphical user interface (GUI) to facilitate the recently developed restriction-site associated DNA (RAD) sequencing data analysis in rice. By application of AMF, a total of 90,743 high-quality markers (82,878 SNPs and 7,865 InDels) were detected between rice varieties JP69 and Jiaoyuan5A. The density of the identified markers is 0.2 per Kb for SNP markers, and 0.02 per Kb for InDel markers. Sequencing validation revealed that the accuracy of genome-wide marker detection by AMF is 93%. In addition, a validated subset of 82 SNPs and 31 InDels were found to be closely linked to 117 important agronomic trait genes, providing a basis for subsequent marker-assisted selection (MAS) and variety identification. Furthermore, we selected 12 markers from 31 validated InDel markers to identify seed authenticity of variety Jiaoyuanyou69, and we also identified 10 markers closely linked to the fragrant gene BADH2 to minimize linkage drag for Wuxiang075 (BADH2 donor)/Jiachang1 recombinants selection. Therefore, this software provides an efficient approach for marker identification from RAD-seq data, and it would be a valuable tool for plant MAS and variety protection. PMID:26799713

  12. Dynamic markers based on blood perfusion fluctuations for selecting skin melanocytic lesions for biopsy

    NASA Astrophysics Data System (ADS)

    Lancaster, Gemma; Stefanovska, Aneta; Pesce, Margherita; Marco Vezzoni, Gian; Loggini, Barbara; Pingitore, Raffaele; Ghiara, Fabrizio; Barachini, Paolo; Cervadoro, Gregorio; Romanelli, Marco; Rossi, Marco

    2015-08-01

    Skin malignant melanoma is a highly angiogenic cancer, necessitating early diagnosis for positive prognosis. The current diagnostic standard of biopsy and histological examination inevitably leads to many unnecessary invasive excisions. Here, we propose a non-invasive method of identification of melanoma based on blood flow dynamics. We consider a wide frequency range from 0.005-2 Hz associated with both local vascular regulation and effects of cardiac pulsation. Combining uniquely the power of oscillations associated with individual physiological processes we obtain a marker which distinguishes between melanoma and atypical nevi with sensitivity of 100% and specificity of 90.9%. The method reveals valuable functional information about the melanoma microenvironment. It also provides the means for simple, accurate, in vivo distinction between malignant melanoma and atypical nevi, and may lead to a substantial reduction in the number of biopsies currently undertaken.

  13. Development of polymorphic microsatellite markers based on expressed sequence tags in Populus cathayana (Salicaceae).

    PubMed

    Tian, Z Z; Zhang, F Q; Cai, Z Y; Chen, S L

    2016-01-01

    Populus cathayana occupies a large area within the northern, central, and southwestern regions of China, and is considered to be an important reforestation species in western China. In order to investigate the population genetic structure of this species, 10 polymorphic microsatellite loci were identified based on expressed sequence tags from de novo sequencing on the Illumina HiSeq 2000 platform. All microsatellite primers were tested on 48 P. cathayana individuals from four locations on the Qinghai-Tibet Plateau. The observed heterozygosity ranged from 0.000 to 1.000, and the null-allele frequency ranged from 0.000 to 0.904. These microsatellite markers may be a useful tool in genetic studies on P. cathayana and closely related species.

  14. Dynamic markers based on blood perfusion fluctuations for selecting skin melanocytic lesions for biopsy.

    PubMed

    Lancaster, Gemma; Stefanovska, Aneta; Pesce, Margherita; Marco Vezzoni, Gian; Loggini, Barbara; Pingitore, Raffaele; Ghiara, Fabrizio; Barachini, Paolo; Cervadoro, Gregorio; Romanelli, Marco; Rossi, Marco

    2015-08-11

    Skin malignant melanoma is a highly angiogenic cancer, necessitating early diagnosis for positive prognosis. The current diagnostic standard of biopsy and histological examination inevitably leads to many unnecessary invasive excisions. Here, we propose a non-invasive method of identification of melanoma based on blood flow dynamics. We consider a wide frequency range from 0.005-2 Hz associated with both local vascular regulation and effects of cardiac pulsation. Combining uniquely the power of oscillations associated with individual physiological processes we obtain a marker which distinguishes between melanoma and atypical nevi with sensitivity of 100% and specificity of 90.9%. The method reveals valuable functional information about the melanoma microenvironment. It also provides the means for simple, accurate, in vivo distinction between malignant melanoma and atypical nevi, and may lead to a substantial reduction in the number of biopsies currently undertaken.

  15. Development of polymorphic microsatellite markers based on expressed sequence tags in Populus cathayana (Salicaceae).

    PubMed

    Tian, Z Z; Zhang, F Q; Cai, Z Y; Chen, S L

    2016-01-01

    Populus cathayana occupies a large area within the northern, central, and southwestern regions of China, and is considered to be an important reforestation species in western China. In order to investigate the population genetic structure of this species, 10 polymorphic microsatellite loci were identified based on expressed sequence tags from de novo sequencing on the Illumina HiSeq 2000 platform. All microsatellite primers were tested on 48 P. cathayana individuals from four locations on the Qinghai-Tibet Plateau. The observed heterozygosity ranged from 0.000 to 1.000, and the null-allele frequency ranged from 0.000 to 0.904. These microsatellite markers may be a useful tool in genetic studies on P. cathayana and closely related species. PMID:27525845

  16. Development of Randomly Amplified Polymorphic DNA Based SCAR Marker for Identification of Ipomoea mauritiana Jacq (Convolvulaceae)

    PubMed Central

    Devaiah, Kambiranda; Balasubramani, Subramani Paranthaman; Venkatasubramanian, Padma

    2011-01-01

    Vidari is an Ayurvedic herbal drug used as aphrodisiac, galactagogue and is also used in the preparation of Chyavanaprash. Tubers of Ipomoea mauritiana Jacq. (Convolvulaceae), Pueraria tuberosa (Roxb. ex Willd.) DC (Fabaceae), Adenia hondala (Gaertn.) de Wilde (Passifloraceae) and pith of Cycas circinalis L. (Cycadaceae) are all traded in the name of Vidari, creating issues of botanical authenticity of the Ayurvedic raw drug. DNA-based markers have been developed to distinguish I. mauritiana from the other Vidari candidates. A putative 600-bp polymorphic sequence, specific to I. mauritiana was identified using randomly amplified polymorphic DNA (RAPD) technique. Furthermore, sequence characterized amplified region (SCAR) primers (IM1F and IM1R) were designed from the unique RAPD amplicon. The SCAR primers produced a specific 323-bp amplicon in authentic I. mauritiana and not in the allied species. PMID:21738554

  17. Development of Randomly Amplified Polymorphic DNA Based SCAR Marker for Identification of Ipomoea mauritiana Jacq (Convolvulaceae).

    PubMed

    Devaiah, Kambiranda; Balasubramani, Subramani Paranthaman; Venkatasubramanian, Padma

    2011-01-01

    Vidari is an Ayurvedic herbal drug used as aphrodisiac, galactagogue and is also used in the preparation of Chyavanaprash. Tubers of Ipomoea mauritiana Jacq. (Convolvulaceae), Pueraria tuberosa (Roxb. ex Willd.) DC (Fabaceae), Adenia hondala (Gaertn.) de Wilde (Passifloraceae) and pith of Cycas circinalis L. (Cycadaceae) are all traded in the name of Vidari, creating issues of botanical authenticity of the Ayurvedic raw drug. DNA-based markers have been developed to distinguish I. mauritiana from the other Vidari candidates. A putative 600-bp polymorphic sequence, specific to I. mauritiana was identified using randomly amplified polymorphic DNA (RAPD) technique. Furthermore, sequence characterized amplified region (SCAR) primers (IM1F and IM1R) were designed from the unique RAPD amplicon. The SCAR primers produced a specific 323-bp amplicon in authentic I. mauritiana and not in the allied species.

  18. Subdivisions of the adult zebrafish pallium based on molecular marker analysis

    PubMed Central

    Ganz, Julia; Kroehne, Volker; Freudenreich, Dorian; Machate, Anja; Geffarth, Michaela; Braasch, Ingo; Kaslin, Jan; Brand, Michael

    2015-01-01

    Background: The telencephalon shows a remarkable structural diversity among vertebrates. In particular, the everted telencephalon of ray-finned fishes has a markedly different morphology compared to the evaginated telencephalon of all other vertebrates. This difference in development has hampered the comparison between different areas of the pallium of ray-finned fishes and the pallial nuclei of all other vertebrates. Various models of homology between pallial subdivisions in ray-finned fishes and the pallial nuclei in tetrapods have been proposed based on connectional, neurochemical, gene expression and functional data. However, no consensus has been reached so far. In recent years, the analysis of conserved developmental marker genes has assisted the identification of homologies for different parts of the telencephalon among several tetrapod species. Results: We have investigated the gene expression pattern of conserved marker genes in the adult zebrafish ( Danio rerio) pallium to identify pallial subdivisions and their homology to pallial nuclei in tetrapods. Combinatorial expression analysis of ascl1a, eomesa, emx1, emx2, emx3, and Prox1 identifies four main divisions in the adult zebrafish pallium. Within these subdivisions, we propose that Dm is homologous to the pallial amygdala in tetrapods and that the dorsal subdivision of Dl is homologous to part of the hippocampal formation in mouse. We have complemented this analysis be examining the gene expression of emx1, emx2 and emx3 in the zebrafish larval brain. Conclusions: Based on our gene expression data, we propose a new model of subdivisions in the adult zebrafish pallium and their putative homologies to pallial nuclei in tetrapods. Pallial nuclei control sensory, motor, and cognitive functions, like memory, learning and emotion. The identification of pallial subdivisions in the adult zebrafish and their homologies to pallial nuclei in tetrapods will contribute to the use of the zebrafish system as a model

  19. Construction of an SSR and RAD-Marker Based Molecular Linkage Map of Vigna vexillata (L.) A. Rich.

    PubMed

    Marubodee, Rusama; Ogiso-Tanaka, Eri; Isemura, Takehisa; Chankaew, Sompong; Kaga, Akito; Naito, Ken; Ehara, Hiroshi; Tomooka, Norihiko

    2015-01-01

    Vigna vexillata (L.) A. Rich. (tuber cowpea) is an underutilized crop for consuming its tuber and mature seeds. Wild form of V. vexillata is a pan-tropical perennial herbaceous plant which has been used by local people as a food. Wild V. vexillata has also been considered as useful gene(s) source for V. unguiculata (cowpea), since it was reported to have various resistance gene(s) for insects and diseases of cowpea. To exploit the potential of V. vexillata, an SSR-based linkage map of V. vexillata was developed. A total of 874 SSR markers successfully amplified single DNA fragment in V. vexillata among 1,336 SSR markers developed from Vigna angularis (azuki bean), V. unguiculata and Phaseolus vulgaris (common bean). An F2 population of 300 plants derived from a cross between salt resistant (V1) and susceptible (V5) accessions was used for mapping. A genetic linkage map was constructed using 82 polymorphic SSR markers loci, which could be assigned to 11 linkage groups spanning 511.5 cM in length with a mean distance of 7.2 cM between adjacent markers. To develop higher density molecular linkage map and to confirm SSR markers position in a linkage map, RAD markers were developed and a combined SSR and RAD markers linkage map of V. vexillata was constructed. A total of 559 (84 SSR and 475 RAD) markers loci could be assigned to 11 linkage groups spanning 973.9 cM in length with a mean distance of 1.8 cM between adjacent markers. Linkage and genetic position of all SSR markers in an SSR linkage map were confirmed. When an SSR genetic linkage map of V. vexillata was compared with those of V. radiata and V. unguiculata, it was suggested that the structure of V. vexillata chromosome was considerably differentiated. This map is the first SSR and RAD marker-based V. vexillata linkage map which can be used for the mapping of useful traits. PMID:26398819

  20. Construction of an SSR and RAD-Marker Based Molecular Linkage Map of Vigna vexillata (L.) A. Rich

    PubMed Central

    Chankaew, Sompong; Kaga, Akito; Naito, Ken; Ehara, Hiroshi; Tomooka, Norihiko

    2015-01-01

    Vigna vexillata (L.) A. Rich. (tuber cowpea) is an underutilized crop for consuming its tuber and mature seeds. Wild form of V. vexillata is a pan-tropical perennial herbaceous plant which has been used by local people as a food. Wild V. vexillata has also been considered as useful gene(s) source for V. unguiculata (cowpea), since it was reported to have various resistance gene(s) for insects and diseases of cowpea. To exploit the potential of V. vexillata, an SSR-based linkage map of V. vexillata was developed. A total of 874 SSR markers successfully amplified single DNA fragment in V. vexillata among 1,336 SSR markers developed from Vigna angularis (azuki bean), V. unguiculata and Phaseolus vulgaris (common bean). An F2 population of 300 plants derived from a cross between salt resistant (V1) and susceptible (V5) accessions was used for mapping. A genetic linkage map was constructed using 82 polymorphic SSR markers loci, which could be assigned to 11 linkage groups spanning 511.5 cM in length with a mean distance of 7.2 cM between adjacent markers. To develop higher density molecular linkage map and to confirm SSR markers position in a linkage map, RAD markers were developed and a combined SSR and RAD markers linkage map of V. vexillata was constructed. A total of 559 (84 SSR and 475 RAD) markers loci could be assigned to 11 linkage groups spanning 973.9 cM in length with a mean distance of 1.8 cM between adjacent markers. Linkage and genetic position of all SSR markers in an SSR linkage map were confirmed. When an SSR genetic linkage map of V. vexillata was compared with those of V. radiata and V. unguiculata, it was suggested that the structure of V. vexillata chromosome was considerably differentiated. This map is the first SSR and RAD marker-based V. vexillata linkage map which can be used for the mapping of useful traits. PMID:26398819

  1. Construction of an SSR and RAD-Marker Based Molecular Linkage Map of Vigna vexillata (L.) A. Rich.

    PubMed

    Marubodee, Rusama; Ogiso-Tanaka, Eri; Isemura, Takehisa; Chankaew, Sompong; Kaga, Akito; Naito, Ken; Ehara, Hiroshi; Tomooka, Norihiko

    2015-01-01

    Vigna vexillata (L.) A. Rich. (tuber cowpea) is an underutilized crop for consuming its tuber and mature seeds. Wild form of V. vexillata is a pan-tropical perennial herbaceous plant which has been used by local people as a food. Wild V. vexillata has also been considered as useful gene(s) source for V. unguiculata (cowpea), since it was reported to have various resistance gene(s) for insects and diseases of cowpea. To exploit the potential of V. vexillata, an SSR-based linkage map of V. vexillata was developed. A total of 874 SSR markers successfully amplified single DNA fragment in V. vexillata among 1,336 SSR markers developed from Vigna angularis (azuki bean), V. unguiculata and Phaseolus vulgaris (common bean). An F2 population of 300 plants derived from a cross between salt resistant (V1) and susceptible (V5) accessions was used for mapping. A genetic linkage map was constructed using 82 polymorphic SSR markers loci, which could be assigned to 11 linkage groups spanning 511.5 cM in length with a mean distance of 7.2 cM between adjacent markers. To develop higher density molecular linkage map and to confirm SSR markers position in a linkage map, RAD markers were developed and a combined SSR and RAD markers linkage map of V. vexillata was constructed. A total of 559 (84 SSR and 475 RAD) markers loci could be assigned to 11 linkage groups spanning 973.9 cM in length with a mean distance of 1.8 cM between adjacent markers. Linkage and genetic position of all SSR markers in an SSR linkage map were confirmed. When an SSR genetic linkage map of V. vexillata was compared with those of V. radiata and V. unguiculata, it was suggested that the structure of V. vexillata chromosome was considerably differentiated. This map is the first SSR and RAD marker-based V. vexillata linkage map which can be used for the mapping of useful traits.

  2. Genetic diversity and relatedness of sweet cherry (prunus avium L.) cultivars based on single nucleotide polymorphic markers.

    PubMed

    Fernandez I Marti, Angel; Athanson, Blessing; Koepke, Tyson; Font I Forcada, Carolina; Dhingra, Amit; Oraguzie, Nnadozie

    2012-01-01

    Most previous studies on genetic fingerprinting and cultivar relatedness in sweet cherry were based on isoenzyme, RAPD, and simple sequence repeat (SSR) markers. This study was carried out to assess the utility of single nucleotide polymorphism (SNP) markers generated from 3' untranslated regions (UTR) for genetic fingerprinting in sweet cherry. A total of 114 sweet cherry germplasm representing advanced selections, commercial cultivars, and old cultivars imported from different parts of the world were screened with seven SSR markers developed from other Prunus species and with 40 SNPs obtained from 3' UTR sequences of Rainier and Bing sweet cherry cultivars. Both types of marker study had 99 accessions in common. The SSR data was used to validate the SNP results. Results showed that the average number of alleles per locus, mean observed heterozygosity, expected heterozygosity, and polymorphic information content values were higher in SSRs than in SNPs although both set of markers were similar in their grouping of the sweet cherry accessions as shown in the dendrogram. SNPs were able to distinguish sport mutants from their wild type germplasm. For example, "Stella" was separated from "Compact Stella." This demonstrates the greater power of SNPs for discriminating mutants from their original parents than SSRs. In addition, SNP markers confirmed parentage and also determined relationships of the accessions in a manner consistent with their pedigree relationships. We would recommend the use of 3' UTR SNPs for genetic fingerprinting, parentage verification, gene mapping, and study of genetic diversity in sweet cherry.

  3. A new phylogeny of the Cephalaspidea (Gastropoda: Heterobranchia) based on expanded taxon sampling and gene markers.

    PubMed

    Oskars, Trond R; Bouchet, Philippe; Malaquias, Manuel António E

    2015-08-01

    The Cephalaspidea is a diverse marine clade of euthyneuran gastropods with many groups still known largely from shells or scant anatomical data. The definition of the group and the relationships between members has been hampered by the difficulty of establishing sound synapomorphies, but the advent of molecular phylogenetics is helping to change significantly this situation. Yet, because of limited taxon sampling and few genetic markers employed in previous studies, many questions about the sister relationships and monophyletic status of several families remained open. In this study 109 species of Cephalaspidea were included covering 100% of traditional family-level diversity (12 families) and 50% of all genera (33 genera). Bayesian and maximum likelihood phylogenetics analyses based on two mitochondrial (COI, 16S rRNA) and two nuclear gene markers (28S rRNA and Histone-3) were used to infer the relationships of Cephalaspidea. The monophyly of the Cephalaspidea was confirmed. The families Cylichnidae, Diaphanidae, Haminoeidae, Philinidae, and Retusidae were found non-monophyletic. This result suggests that the family level taxonomy of the Cephalaspidea warrants a profound revision and several new family and genus names are required to reflect the new phylogenetic hypothesis presented here. We propose a new classification of the Cephalaspidea including five new families (Alacuppidae, Colinatydidae, Colpodaspididae, Mnestiidae, Philinorbidae) and one new genus (Alacuppa). Two family names (Acteocinidae, Laonidae) and two genera (Laona, Philinorbis) are reinstated as valid. An additional lineage with family rank (Philinidae "Clade 4") was unravelled, but no genus and species names are available to reflect the phylogeny and formal description will take place elsewhere. PMID:25916189

  4. Benchmark Dose for Urinary Cadmium based on a Marker of Renal Dysfunction: A Meta-Analysis

    PubMed Central

    Woo, Hae Dong; Chiu, Weihsueh A.; Jo, Seongil; Kim, Jeongseon

    2015-01-01

    Background Low doses of cadmium can cause adverse health effects. Benchmark dose (BMD) and the one-sided 95% lower confidence limit of BMD (BMDL) to derive points of departure for urinary cadmium exposure have been estimated in several previous studies, but the methods to derive BMD and the estimated BMDs differ. Objectives We aimed to find the associated factors that affect BMD calculation in the general population, and to estimate the summary BMD for urinary cadmium using reported BMDs. Methods A meta-regression was performed and the pooled BMD/BMDL was estimated using studies reporting a BMD and BMDL, weighted by sample size, that were calculated from individual data based on markers of renal dysfunction. Results BMDs were highly heterogeneous across studies. Meta-regression analysis showed that a significant predictor of BMD was the cut-off point which denotes an abnormal level. Using the 95th percentile as a cut off, BMD5/BMDL5 estimates for 5% benchmark responses (BMR) of β2-microglobulinuria (β2-MG) estimated was 6.18/4.88 μg/g creatinine in conventional quantal analysis and 3.56/3.13 μg/g creatinine in the hybrid approach, and BMD5/BMDL5 estimates for 5% BMR of N-acetyl-β-d-glucosaminidase (NAG) was 10.31/7.61 μg/g creatinine in quantal analysis and 3.21/2.24 g/g creatinine in the hybrid approach. However, the meta-regression showed that BMD and BMDL were significantly associated with the cut-off point, but BMD calculation method did not significantly affect the results. The urinary cadmium BMDL5 of β2-MG was 1.9 μg/g creatinine in the lowest cut-off point group. Conclusion The BMD was significantly associated with the cut-off point defining the abnormal level of renal dysfunction markers. PMID:25970611

  5. a Marker-Based Eulerian-Lagrangian Method for Multiphase Flow with Supersonic Combustion Applications

    NASA Astrophysics Data System (ADS)

    Fan, Xiaofeng; Wang, Jiangfeng

    2016-06-01

    The atomization of liquid fuel is a kind of intricate dynamic process from continuous phase to discrete phase. Procedures of fuel spray in supersonic flow are modeled with an Eulerian-Lagrangian computational fluid dynamics methodology. The method combines two distinct techniques and develops an integrated numerical simulation method to simulate the atomization processes. The traditional finite volume method based on stationary (Eulerian) Cartesian grid is used to resolve the flow field, and multi-component Navier-Stokes equations are adopted in present work, with accounting for the mass exchange and heat transfer occupied by vaporization process. The marker-based moving (Lagrangian) grid is utilized to depict the behavior of atomized liquid sprays injected into a gaseous environment, and discrete droplet model 13 is adopted. To verify the current approach, the proposed method is applied to simulate processes of liquid atomization in supersonic cross flow. Three classic breakup models, TAB model, wave model and K-H/R-T hybrid model, are discussed. The numerical results are compared with multiple perspectives quantitatively, including spray penetration height and droplet size distribution. In addition, the complex flow field structures induced by the presence of liquid spray are illustrated and discussed. It is validated that the maker-based Eulerian-Lagrangian method is effective and reliable.

  6. Genome-wide development of transposable elements-based markers in foxtail millet and construction of an integrated database.

    PubMed

    Yadav, Chandra Bhan; Bonthala, Venkata Suresh; Muthamilarasan, Mehanathan; Pandey, Garima; Khan, Yusuf; Prasad, Manoj

    2015-02-01

    Transposable elements (TEs) are major components of plant genome and are reported to play significant roles in functional genome diversity and phenotypic variations. Several TEs are highly polymorphic for insert location in the genome and this facilitates development of TE-based markers for various genotyping purposes. Considering this, a genome-wide analysis was performed in the model plant foxtail millet. A total of 30,706 TEs were identified and classified as DNA transposons (24,386), full-length Copia type (1,038), partial or solo Copia type (10,118), full-length Gypsy type (1,570), partial or solo Gypsy type (23,293) and Long- and Short-Interspersed Nuclear Elements (3,659 and 53, respectively). Further, 20,278 TE-based markers were developed, namely Retrotransposon-Based Insertion Polymorphisms (4,801, ∼24%), Inter-Retrotransposon Amplified Polymorphisms (3,239, ∼16%), Repeat Junction Markers (4,451, ∼22%), Repeat Junction-Junction Markers (329, ∼2%), Insertion-Site-Based Polymorphisms (7,401, ∼36%) and Retrotransposon-Microsatellite Amplified Polymorphisms (57, 0.2%). A total of 134 Repeat Junction Markers were screened in 96 accessions of Setaria italica and 3 wild Setaria accessions of which 30 showed polymorphism. Moreover, an open access database for these developed resources was constructed (Foxtail millet Transposable Elements-based Marker Database; http://59.163.192.83/ltrdb/index.html). Taken together, this study would serve as a valuable resource for large-scale genotyping applications in foxtail millet and related grass species.

  7. Genetic diversity of Poa pratensis L. depending on geographical origin and compared with genetic markers

    PubMed Central

    Śmietana, Przemysław; Stępień, Edyta

    2016-01-01

    Background Poa pratensis is one of the most common species of meadow grass in Europe. Most cultivars of the species found in Poland were originally derived from its ecotypes. We compared the effectiveness of the RAPD and ISSR methods in assessing the genetic diversity of the selected populations of P. pratensis. We examined whether these methods could be useful for detecting a possible link between the geographical origin of a given population and its assessed genetic variation. Methods The molecular markers RAPD and ISSR were used and their efficiency compared using, inter alia, statistical multivariate methods (UPGMA and PCA). Results The low value of Dice’s coefficient (0.369) along with the significantly high percentage of polymorphic products indicates a substantial degree of genetic diversity among the studied populations. Our results found a correlation between the geographical origin of the studied populations and their genetic variations. For ISSR, which proved to be the more effective method in that respect, we selected primers with the greatest differentiating powers correlating to geographical origin. Discussion The populations evaluated in this study were characterized by a high genetic diversity. This seems to confirm the hypothesis that ecotypes of P. pratensis originating from different regions of Central Europe with different terrain structures and habitat conditions can be a source of great genetic variability. PMID:27703847

  8. A Site-Specific Recombinase-Based Method to Produce Antibiotic Selectable Marker Free Transgenic Cattle

    PubMed Central

    Tong, Qi; Liu, Xu; Su, Feng; Quan, Fusheng; Guo, Zekun; Zhang, Yong

    2013-01-01

    Antibiotic selectable marker genes have been widely used to generate transgenic animals. Once transgenic animals have been obtained, the selectable marker is no longer necessary but raises public concerns regarding biological safety. The aim of this study was to prepare competent antibiotic selectable marker free transgenic cells for somatic cell nuclear transfer (SCNT). PhiC31 intergrase was used to insert a transgene cassette into a “safe harbor” in the bovine genome. Then, Cre recombinase was employed to excise the selectable marker under the monitoring of a fluorescent double reporter. By visually tracking the phenotypic switch from red to green fluorescence, antibiotic selectable marker free cells were easily detected and sorted by fluorescence-activated cell sorting. For safety, we used phiC31 mRNA and cell-permeant Cre protein in this study. When used as donor nuclei for SCNT, these safe harbor integrated marker-free transgenic cells supported a similar developmental competence of SCNT embryos compared with that of non-transgenic cells. After embryo transfer, antibiotic selectable marker free transgenic cattle were generated and anti-bacterial recombinant human β-defensin-3 in milk was detected during their lactation period. Thus, this approach offers a rapid and safe alternative to produce antibiotic selectable marker free transgenic farm animals, thereby making it a valuable tool to promote the healthy development and welfare of transgenic farm animals. PMID:23658729

  9. A site-specific recombinase-based method to produce antibiotic selectable marker free transgenic cattle.

    PubMed

    Yu, Yuan; Wang, Yongsheng; Tong, Qi; Liu, Xu; Su, Feng; Quan, Fusheng; Guo, Zekun; Zhang, Yong

    2013-01-01

    Antibiotic selectable marker genes have been widely used to generate transgenic animals. Once transgenic animals have been obtained, the selectable marker is no longer necessary but raises public concerns regarding biological safety. The aim of this study was to prepare competent antibiotic selectable marker free transgenic cells for somatic cell nuclear transfer (SCNT). PhiC31 intergrase was used to insert a transgene cassette into a "safe harbor" in the bovine genome. Then, Cre recombinase was employed to excise the selectable marker under the monitoring of a fluorescent double reporter. By visually tracking the phenotypic switch from red to green fluorescence, antibiotic selectable marker free cells were easily detected and sorted by fluorescence-activated cell sorting. For safety, we used phiC31 mRNA and cell-permeant Cre protein in this study. When used as donor nuclei for SCNT, these safe harbor integrated marker-free transgenic cells supported a similar developmental competence of SCNT embryos compared with that of non-transgenic cells. After embryo transfer, antibiotic selectable marker free transgenic cattle were generated and anti-bacterial recombinant human β-defensin-3 in milk was detected during their lactation period. Thus, this approach offers a rapid and safe alternative to produce antibiotic selectable marker free transgenic farm animals, thereby making it a valuable tool to promote the healthy development and welfare of transgenic farm animals.

  10. A composite genetic map of the parasitoid wasp Trichogramma brassicae based on RAPD markers.

    PubMed Central

    Laurent, V; Wajnberg, E; Mangin, B; Schiex, T; Gaspin, C; Vanlerberghe-Masutti, F

    1998-01-01

    Three linkage maps of the genome of the microhymenopteran Trichogramma brassicae were constructed from the analysis of segregation of random amplified polymorphic DNA markers in three F2 populations. These populations were composed of the haploid male progeny of several virgin F1 females, which resulted from the breeding of four parental lines that were nearly fixed for different random amplified polymorphic DNA markers and that were polymorphic for longevity and fecundity characters. As the order of markers common to the three mapping populations was found to be well conserved, a composite linkage map was constructed. Eighty-four markers were organized into five linkage groups and two pairs. The mean interval between two markers was 17.7 cM, and the map spanned 1330 cM. PMID:9725846

  11. Genetic diversity of Cercospora kikuchii isolates from soybean cultured in Argentina as revealed by molecular markers and cercosporin production.

    PubMed

    Lurá, María Cristina; Latorre Rapela, María Gabriela; Vaccari, María Celia; Maumary, Roxana; Soldano, Anabel; Mattio, Mónica; González, Ana María

    2011-05-01

    Leaf blight and purple seed, caused by the fungal pathogen Cercospora kikuchii (Matsumoto & Tomoyasu) M. W. Gardner are very important diseases of soybean (Glycine max L. Merr.) in Argentina. The aims of this work were: (a) to confirm and to assess the genetic variability among C. kikuchii isolates collected from different soybean growing areas in Santa Fe province using inter simple sequence repeats (ISSR) markers and sequence information from the internal transcribed spacer (ITS) region of rDNA and (b) to analyze the cercosporin production of the regional C. kikuchi isolates in order to assess whether there was any relationship between the molecular profiles and the toxin production. Isolates from different regions in Santa Fe province were studied. The sequence of the ITS regions showed high similarity (99-100%) to the GenBank sequences of C. kikuchii BRCK179 (accession number AY633838). The ISSR markers clustered all the isolates into many groups and cercosporin content was highly variable among isolates. No relationship was observed between ITS region, ISSR groups and origin or cercosporin content. The high degree of genetic variability and cercosporin production among isolates compared in this study characterizes a diverse population of C. kikuchii in the region.

  12. Fluorescence-based AFLPs occur as the most suitable marker system for oilseed rape cultivar identification.

    PubMed

    Sobotka, Roman; Dolanská, Lenka; Curn, Vladislav; Ovesná, Jaroslava

    2004-01-01

    Three different types of molecular markers, RAPD, SSR and fluorescence-based AFLP, were evaluated and compared for their ability to identify oilseed rape cultivars. The direct comparison of RAPD, SSR and AFLP approaches in cultivar identification showed that the AFLP methodology detected polymorphisms more efficiently than either RAPD or SSR methods. For the characterisation of six oilseed rape cultivars, 60 RAPD primers were tested and only eight of them (14%) detected sufficient levels of polymorphism. Five microsatellites out of fifteen tested were polymorphic, but in all loci, except one, only two different alleles were detected. This result indicated the limited degree of polymorphism found in Brassica napus. Each of the six tested AFLP combinations detected polymorphisms, the best combination (M-CAA/E-ACT) had 26% polymorphic peaks from a total of 90 peaks and could distinguish the analysed cultivars and 4 out of 5 core lines of cultivars. The results presented show that florescence-based AFLP is, for the purposes of oilseed rape cultivar fingerprinting, a more suitable approach than either RAPD or SSR.

  13. Evaluation of genetic diversity in jackfruit (Artocarpus heterophyllus Lam.) based on amplified fragment length polymorphism markers.

    PubMed

    Shyamalamma, S; Chandra, S B C; Hegde, M; Naryanswamy, P

    2008-01-01

    Artocarpus heterophyllus Lam., commonly called jackfruit, is a medium-sized evergreen tree that bears high yields of the largest known edible fruit. Yet, it has been little explored commercially due to wide variation in fruit quality. The genetic diversity and genetic relatedness of 50 jackfruit accessions were studied using amplified fragment length polymorphism markers. Of 16 primer pairs evaluated, eight were selected for screening of genotypes based on the number and quality of polymorphic fragments produced. These primer combinations produced 5976 bands, 1267 (22%) of which were polymorphic. Among the jackfruit accessions, the similarity coefficient ranged from 0.137 to 0.978; the accessions also shared a large number of monomorphic fragments (78%). Cluster analysis and principal component analysis grouped all jackfruit genotypes into three major clusters. Cluster I included the genotypes grown in a jackfruit region of Karnataka, called Tamaka, with very dry conditions; cluster II contained the genotypes collected from locations having medium to heavy rainfall in Karnataka; cluster III grouped the genotypes in distant locations with different environmental conditions. Strong coincidence of these amplified fragment length polymorphism-based groupings with geographical localities as well as morphological characters was observed. We found moderate genetic diversity in these jackfruit accessions. This information should be useful for tree breeding programs, as part of our effort to popularize jackfruit as a commercial crop.

  14. Evaluation of genetic diversity in jackfruit (Artocarpus heterophyllus Lam.) based on amplified fragment length polymorphism markers.

    PubMed

    Shyamalamma, S; Chandra, S B C; Hegde, M; Naryanswamy, P

    2008-01-01

    Artocarpus heterophyllus Lam., commonly called jackfruit, is a medium-sized evergreen tree that bears high yields of the largest known edible fruit. Yet, it has been little explored commercially due to wide variation in fruit quality. The genetic diversity and genetic relatedness of 50 jackfruit accessions were studied using amplified fragment length polymorphism markers. Of 16 primer pairs evaluated, eight were selected for screening of genotypes based on the number and quality of polymorphic fragments produced. These primer combinations produced 5976 bands, 1267 (22%) of which were polymorphic. Among the jackfruit accessions, the similarity coefficient ranged from 0.137 to 0.978; the accessions also shared a large number of monomorphic fragments (78%). Cluster analysis and principal component analysis grouped all jackfruit genotypes into three major clusters. Cluster I included the genotypes grown in a jackfruit region of Karnataka, called Tamaka, with very dry conditions; cluster II contained the genotypes collected from locations having medium to heavy rainfall in Karnataka; cluster III grouped the genotypes in distant locations with different environmental conditions. Strong coincidence of these amplified fragment length polymorphism-based groupings with geographical localities as well as morphological characters was observed. We found moderate genetic diversity in these jackfruit accessions. This information should be useful for tree breeding programs, as part of our effort to popularize jackfruit as a commercial crop. PMID:18752192

  15. Iterative h-minima-based marker-controlled watershed for cell nucleus segmentation.

    PubMed

    Koyuncu, Can Fahrettin; Akhan, Ece; Ersahin, Tulin; Cetin-Atalay, Rengul; Gunduz-Demir, Cigdem

    2016-04-01

    Automated microscopy imaging systems facilitate high-throughput screening in molecular cellular biology research. The first step of these systems is cell nucleus segmentation, which has a great impact on the success of the overall system. The marker-controlled watershed is a technique commonly used by the previous studies for nucleus segmentation. These studies define their markers finding regional minima on the intensity/gradient and/or distance transform maps. They typically use the h-minima transform beforehand to suppress noise on these maps. The selection of the h value is critical; unnecessarily small values do not sufficiently suppress the noise, resulting in false and oversegmented markers, and unnecessarily large ones suppress too many pixels, causing missing and undersegmented markers. Because cell nuclei show different characteristics within an image, the same h value may not work to define correct markers for all the nuclei. To address this issue, in this work, we propose a new watershed algorithm that iteratively identifies its markers, considering a set of different h values. In each iteration, the proposed algorithm defines a set of candidates using a particular h value and selects the markers from those candidates provided that they fulfill the size requirement. Working with widefield fluorescence microscopy images, our experiments reveal that the use of multiple h values in our iterative algorithm leads to better segmentation results, compared to its counterparts. © 2016 International Society for Advancement of Cytometry.

  16. A first linkage map of pecan cultivars based on RAPD and AFLP markers.

    PubMed

    Beedanagari, Sudheer R; Dove, Sue K; Wood, Bruce W; Conner, Patrick J

    2005-04-01

    We report here the first genetic linkage maps of pecan [Carya illinoinensis (Wangenh.) K. Koch], using random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers. Independent maps were constructed for the cultivars 'Pawnee' and 'Elliot' using the double pseudo-testcross mapping strategy and 120 F1 seedlings from a full-sib family. A total of 477 markers, including 217 RAPD, 258 AFLP, and two morphological markers were used in linkage analysis. The 'Pawnee' linkage map has 218 markers, comprising 176 testcross and 42 intercross markers placed in 16 major and 13 minor (doublets and triplets) linkage groups. The 'Pawnee' linkage map covered 2,227 cM with an average map distance of 12.7 cM between adjacent markers. The 'Elliot' linkage map has 174 markers comprising 150 testcross and 22 intercross markers placed in 17 major and nine minor linkage groups. The 'Elliot' map covered 1,698 cM with an average map distance of 11.2 cM between adjacent markers. Segregation ratios for dichogamy type and stigma color were not significantly different from 1:1, suggesting that both traits are controlled by single loci with protogyny and green stigmas dominant to protandry and red stigmas. These loci were tightly linked (1.9 cM) and were placed in 'Elliot' linkage group 16. These linkage maps are an important first step towards the detection of genes controlling horticulturally important traits such as nut size, nut maturity date, kernel quality, and disease resistance. PMID:15782296

  17. A PCR based SNPs marker for specific characterization of English walnut (Juglans regia L.) cultivars.

    PubMed

    Ciarmiello, Loredana F; Piccirillo, Pasquale; Pontecorvo, Giovanni; De Luca, Antonio; Kafantaris, Ioannis; Woodrow, Pasqualina

    2011-02-01

    English walnut (Juglans regia L.) is the most economically important species from all the 21 species belonging to the genus Juglans and is an important and healthy food as well as base material for timber industry. The aim of this study was to develop a simple technique for specific characterization of English walnut using DNA method. The first and second internal transcribed spacers (ITS1 and ITS2) as well as the intervening 5.8S coding region of the rRNA gene for 18 cultivars of J. regia L. isolated from different geographic origins were characterized. The size of the spacers sequences ranged from 257 to 263 bases for ITS1 and from 217 to 219 bases for ITS2. Variation of GC contents has also been observed and scored as 55-56.7 and 57.1-58.9% for ITS1 and ITS2, respectively. This data exhibited the presence of polymorphism among cultivars. Alignment of the ITS1-5.8S-ITS2 sequences from 18 walnut cultivars showed that there were 244 single nucleotide polymorphisms (SNPs) and 1 short insertion-deletion (indel) at 5' end ITS1. Amplification refractory mutation system strategy was successfully applied to the SNP markers of the ITS1 and ITS2 sequences for the fingerprinting analysis of 17 on 18 walnut cultivars. The prediction of ITS1 and ITS2 RNA secondary structure from each cultivar was improved by detecting key functional elements shared by all sequences in the alignments. Phylogenetic analysis of the ITS1-5.8S-ITS2 region clearly separated the isolated sequences into two clusters. The results showed that ITS1 and ITS2 region could be used to discriminate these walnut cultivars.

  18. Genetic diversity in South African Nguni cattle ecotypes based on microsatellite markers.

    PubMed

    Sanarana, Yandisiwe; Visser, Carina; Bosman, Lydia; Nephawe, Khathutshelo; Maiwashe, Azwihangwisi; van Marle-Köster, Este

    2016-02-01

    The Nguni cattle breed is a landrace breed adapted to different ecological regions of South Africa. A number of ecotypes are recognised based on phenotype within the breed, but it is not known if they are genetically distinct. In this study, molecular characterisation was performed on Makhathini (MAK), Pedi (PED), Shangaan (SHA) and Venda (VEN) Nguni cattle ecotypes. Two Nguni cattle populations, not kept as separate ecotypes, from the University of Fort Hare (UFH) and Agricultural Research Council Loskop South farm (LOS) were also included. Genotypic data was generated for 189 unrelated Nguni cattle selected based on pedigree records using 22 microsatellite markers. The expected heterozygosity values varied from 69 % (UFH) to 72 % (PED) with a mean number of alleles ranging from 6.0 to 6.9. The F ST estimate demonstrated that 4.8 % of the total genetic variation was due to the genetic differentiation between the populations and 92.2 % accounted for differences within the populations. The genetic distances and structure analysis revealed the closest relationship between MAK, PEDI and SHA ecotypes, followed by SHA and VEN. The UFH population clustered with the MAK ecotype, indicating that they are more genetically similar, while the LOS cattle grouped as a distinct cluster. Results suggest that the genetic differentiation between the PED and SHA ecotypes is low and can be regarded as one ecotype based on limited genetic differences. The results of this study can be applied as a point of reference for further genetic studies towards conservation of Nguni cattle ecotypes.

  19. New insights into family relationships within the avian superfamily Sylvioidea (Passeriformes) based on seven molecular markers

    PubMed Central

    2012-01-01

    Background The circumscription of the avian superfamily Sylvioidea is a matter of long ongoing debate. While the overall inclusiveness has now been mostly agreed on and 20 families recognised, the phylogenetic relationships among the families are largely unknown. We here present a phylogenetic hypothesis for Sylvioidea based on one mitochondrial and six nuclear markers, in total ~6.3 kbp, for 79 ingroup species representing all currently recognised families and some species with uncertain affinities, making this the most comprehensive analysis of this taxon. Results The resolution, especially of the deeper nodes, is much improved compared to previous studies. However, many relationships among families remain uncertain and are in need of verification. Most families themselves are very well supported based on the total data set and also by indels. Our data do not support the inclusion of Hylia in Cettiidae, but do not strongly reject a close relationship with Cettiidae either. The genera Scotocerca and Erythrocercus are closely related to Cettiidae, but separated by relatively long internodes. The families Paridae, Remizidae and Stenostiridae clustered among the outgroup taxa and not within Sylvioidea. Conclusions Although the phylogenetic position of Hylia is uncertain, we tentatively support the recognition of the family Hyliidae Bannerman, 1923 for this genus and Pholidornis. We propose new family names for the genera Scotocerca and Erythrocercus, Scotocercidae and Erythrocercidae, respectively, rather than including these in Cettiidae, and we formally propose the name Macrosphenidae, which has been in informal use for some time. We recommend that Paridae, Remizidae and Stenostiridae are not included in Sylvioidea. We also briefly discuss the problems of providing a morphological diagnosis when proposing a new family-group name (or genus-group name) based on a clade. PMID:22920688

  20. Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and whole-genome-based data.

    PubMed

    Edwards, J D; Baldo, A M; Mueller, L A

    2016-01-01

    Ricebase (http://ricebase.org) is an integrative genomic database for rice (Oryza sativa) with an emphasis on combining datasets in a way that maintains the key links between past and current genetic studies. Ricebase includes DNA sequence data, gene annotations, nucleotide variation data and molecular marker fragment size data. Rice research has benefited from early adoption and extensive use of simple sequence repeat (SSR) markers; however, the majority of rice SSR markers were developed prior to the latest rice pseudomolecule assembly. Interpretation of new research using SNPs in the context of literature citing SSRs requires a common coordinate system. A new pipeline, using a stepwise relaxation of stringency, was used to map SSR primers onto the latest rice pseudomolecule assembly. The SSR markers and experimentally assayed amplicon sizes are presented in a relational database with a web-based front end, and are available as a track loaded in a genome browser with links connecting the browser and database. The combined capabilities of Ricebase link genetic markers, genome context, allele states across rice germplasm and potentially user curated phenotypic interpretations as a community resource for genetic discovery and breeding in rice. PMID:27515824

  1. Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and whole-genome-based data

    PubMed Central

    Edwards, J. D.; Baldo, A. M.; Mueller, L. A.

    2016-01-01

    Ricebase (http://ricebase.org) is an integrative genomic database for rice (Oryza sativa) with an emphasis on combining datasets in a way that maintains the key links between past and current genetic studies. Ricebase includes DNA sequence data, gene annotations, nucleotide variation data and molecular marker fragment size data. Rice research has benefited from early adoption and extensive use of simple sequence repeat (SSR) markers; however, the majority of rice SSR markers were developed prior to the latest rice pseudomolecule assembly. Interpretation of new research using SNPs in the context of literature citing SSRs requires a common coordinate system. A new pipeline, using a stepwise relaxation of stringency, was used to map SSR primers onto the latest rice pseudomolecule assembly. The SSR markers and experimentally assayed amplicon sizes are presented in a relational database with a web-based front end, and are available as a track loaded in a genome browser with links connecting the browser and database. The combined capabilities of Ricebase link genetic markers, genome context, allele states across rice germplasm and potentially user curated phenotypic interpretations as a community resource for genetic discovery and breeding in rice. PMID:27515824

  2. [Evaluation of genetic diversity and population structure of Bletilla striata based on SRAP markers].

    PubMed

    Sun, Yu-long; Hou, Bei-wei; Geng, Li-xia; Niu, Zhi-tao; Yan, Wen-jin; Xue, Qing-yun; Ding, Xiao-yu

    2016-01-01

    Bletilla striata has been used as traditional Chinese medicine for several centuries. In recent years, the quality and quantity of wild B. striata plants have declined sharply due to habitat deterioration and human over-exploitation. Therefore, it is of great urgency to evaluate and protect B. striata wild plant resource. In this study, sequence-related amplified polymorphism (SRAP) markers were applied to assess the level and pattern of genetic diversity in twelve populations of B. striata. The results showed a high level of genetic diversity (PPB = 90.48%, H = 0.349 4, I = 0.509 6) and moderate genetic differentiation among populations (G(st) = 0.260 9). Based on the unweighted pair-group method with arithmetic average (UPGMA), twelve populations gathered in three clusters. The cluster 1 included four populations. There are Nanjing, Zhenjiang, Xuancheng and Hangzhou. The seven populations which come from Hubei Province, Hunan Province, Jiangxi Province and Guizhou Province belonged to the cluster 2. The cluster 3 only contained Wenshan population. Moreover, Mantel test revealed significant positive correlation between genetic distances and geographic distances (r = 0.632 9; P < 0.000 1). According to the results, we proposed a series of conservation consideration for B. striata. PMID:27405177

  3. Evolutionary changes of the importance of olfaction in cetaceans based on the olfactory marker protein gene.

    PubMed

    Kishida, Takushi; Thewissen, J G M

    2012-01-25

    Odontocetes and mysticetes are two extant suborders of cetaceans. It is reported that the former have no sense of olfaction, while the latter can smell in air. To explain the ecological reason why mysticetes still retain their sense of smell, two hypotheses have been proposed - the echolocation-priority hypothesis, which assumes that the acquisition of echolocation causes the reduction of the importance of olfaction, and the filter-feeder hypothesis, which assumes that olfactory ability is important for filter-feeders to locate their prey because clouds of plankton give off a peculiar odor. The olfactory marker protein (OMP) is almost exclusively expressed in vertebrate olfactory receptor neurons, and is considered to play important roles in olfactory systems. In this study, full-length open reading frames of OMP genes were identified in 6 cetacean species and we analyzed the nonsynonymous to synonymous substitution rate ratio based on the maximum likelihood method. The evolutionary changes of the selective pressures on OMP genes did fit better to the filter-feeder hypothesis than to the echolocation-priority hypothesis. In addition, no pseudogenization mutations are found in all five odontocetes OMP genes investigated in this study. It may suggest that OMP retains some function even in 'anosmic' odontocetes.

  4. Decision support framework for Parkinson's disease based on novel handwriting markers.

    PubMed

    Drotár, Peter; Mekyska, Jiří; Rektorová, Irena; Masarová, Lucia; Smékal, Zdeněk; Faundez-Zanuy, Marcos

    2015-05-01

    Parkinson's disease (PD) is a neurodegenerative disorder which impairs motor skills, speech, and other functions such as behavior, mood, and cognitive processes. One of the most typical clinical hallmarks of PD is handwriting deterioration, usually the first manifestation of PD. The aim of this study is twofold: (a) to find a subset of handwriting features suitable for identifying subjects with PD and (b) to build a predictive model to efficiently diagnose PD. We collected handwriting samples from 37 medicated PD patients and 38 age- and sex-matched controls. The handwriting samples were collected during seven tasks such as writing a syllable, word, or sentence. Every sample was used to extract the handwriting measures. In addition to conventional kinematic and spatio-temporal handwriting measures, we also computed novel handwriting measures based on entropy, signal energy, and empirical mode decomposition of the handwriting signals. The selected features were fed to the support vector machine classifier with radial Gaussian kernel for automated diagnosis. The accuracy of the classification of PD was as high as 88.13%, with the highest values of sensitivity and specificity equal to 89.47% and 91.89%, respectively. Handwriting may be a valuable marker as a diagnostic and screening tool. PMID:25265632

  5. Lectin-based glycoproteomics to explore and analyze hepatocellular carcinoma-related glycoprotein markers.

    PubMed

    Dai, Zhi; Zhou, Jian; Qiu, Shuang-Jian; Liu, Yin-Kun; Fan, Jia

    2009-09-01

    More and more new diagnostic biomarkers of hepatocellular carcinoma (HCC) have been found in association with advances in the standardization of 2-DE coupled with MS analysis. However, the diagnosis of HCC is still detected in the late stages of the disease, when treatment options are limited and prognosis is poor. The glycosylation of proteins is known to change in tumor cells during the development of HCC as the result of alterations in the levels of glycosyltransferases, such as increased fucosylation of Golgi Protein 73 and alpha-fetoprotein. These structural changes can influence the function or physiochemical properties of a protein, resulting in abnormal cancer cell behavior. Therefore, identification of HCC-related glycoprotein markers and analysis of glycan structural alterations might assist in the early detection of HCC. Here, we summarize lectin-based glycoproteomic strategies for the discovery of relevant biomarkers of HCC. The carbohydrate-binding specificities of different lectins offer a biological affinity approach that complements existing MS capabilities. These strategies involve the enrichment of glycoproteins or glycopeptides by lectins, followed by releasing carbohydrates with peptide-N-glycosidase F or reductive beta-elimination. The obtained glycopeptides are then identified by automated MS/MS and structural analysis of glycans is performed through modern methods such as quadrupole IT-TOF, MALDI-TOF/TOF and lectin microarray. These strategies will lead to faster and more clinically adaptable tests with greater sensitivity and specificity.

  6. Emergence of biological markers of musicianship with school-based music instruction.

    PubMed

    Kraus, Nina; Strait, Dana L

    2015-03-01

    Musician children and adults demonstrate biological distinctions in auditory processing relative to nonmusicians. For example, musician children and adults have more robust neural encoding of speech harmonics, more adaptive sound processing, and more precise neural encoding of acoustically similar sounds; these enhancements may contribute to musicians' linguistic advantages, such as for hearing speech in noise and reading. Such findings have inspired proposals that the auditory and cognitive stimulation induced by musical practice renders musicians enhanced according to biological metrics germane to communication. Cross-sectional methodologies comparing musicians with nonmusicians, however, are limited by the inability to disentangle training-related effects from demographic and innate qualities that may predistinguish musicians. Over the past several years, our laboratory has addressed this problem by examining the emergence of neural markers of musicianship in children and adolescents using longitudinal approaches to track the development of biological indices of speech processing. This work was conducted in partnership with successful community-based music programs, thus avoiding reliance on a synthetic program for the purposes of laboratory study. Outcomes indicate that many of musicians' auditory-related biological enhancements emerge with training and may promote the acquisition of language skills, including in at-risk populations.

  7. The relationship between inflammatory markers and voxel-based gray matter volumes in nondemented older adults.

    PubMed

    Zhang, Haobo; Sachdev, Perminder S; Wen, Wei; Crawford, John D; Brodaty, Henry; Baune, Bernard T; Kochan, Nicole A; Slavin, Melissa J; Reppermund, Simone; Kang, Kristan; Trollor, Julian N

    2016-01-01

    Ageing is characterized by chronically elevated inflammatory markers (IMs). Peripheral IM levels have been found in negative correlations with brain structural measures including global and lobar volumes and the hippocampus. This study investigated the relationship between 10 peripheral IMs and voxel-based gray matter (GM) volumes in nondemented older adults (n = 463). Two proinflammatory cytokines (tumor necrosis factor-α [TNF-α] and interleukin-1β) and 2 vascular IMs (vascular cellular adhesion molecule-1 and plasminogen activator inhibitor-1) were negatively correlated with regional GM volumes. TNF-α and interleukin-1β were both significantly correlated with GM volumes in the left occipitotemporal area, left superior occipital gyrus, and left inferior parietal lobule; TNF-α was also significantly correlated with the bilateral medial prefrontal cortices and approached significance for the correlations with the bilateral hippocampi. Significant GM correlations with vascular cellular adhesion molecule-1 were located in the bilateral anterior cingulate cortices, and with plasminogen activator inhibitor-1 in the cerebellum and right hippocampus. The neuroanatomical correlation patterns of 2 proinflammatory cytokines and 2 vascular IMs might be reflective of the effects of neurodegenerative and vascular pathological processes in the ageing brain.

  8. Retrotransposon-Based Molecular Markers for Analysis of Genetic Diversity within the Genus Linum

    PubMed Central

    Melnikova, Nataliya V.; Kudryavtseva, Anna V.; Zelenin, Alexander V.; Lakunina, Valentina A.; Yurkevich, Olga Yu.; Speranskaya, Anna S.; Dmitriev, Alexey A.; Krinitsina, Anastasia A.; Belenikin, Maxim S.; Uroshlev, Leonid A.; Snezhkina, Anastasiya V.; Sadritdinova, Asiya F.; Koroban, Nadezda V.; Amosova, Alexandra V.; Samatadze, Tatiana E.; Guzenko, Elena V.; Lemesh, Valentina A.; Savilova, Anastasya M.; Rachinskaia, Olga A.; Kishlyan, Natalya V.; Rozhmina, Tatiana A.; Bolsheva, Nadezhda L.; Muravenko, Olga V.

    2014-01-01

    SSAP method was used to study the genetic diversity of 22 Linum species from sections Linum, Adenolinum, Dasylinum, Stellerolinum, and 46 flax cultivars. All the studied flax varieties were distinguished using SSAP for retrotransposons FL9 and FL11. Thus, the validity of SSAP method was demonstrated for flax marking, identification of accessions in genebank collections, and control during propagation of flax varieties. Polymorphism of Fl1a, Fl1b, and Cassandra insertions were very low in flax varieties, but these retrotransposons were successfully used for the investigation of Linum species. Species clusterization based on SSAP markers was in concordance with their taxonomic division into sections Dasylinum, Stellerolinum, Adenolinum, and Linum. All species of sect. Adenolinum clustered apart from species of sect. Linum. The data confirmed the accuracy of the separation in these sections. Members of section Linum are not as closely related as members of other sections, so taxonomic revision of this section is desirable. L. usitatissimum accessions genetically distant from modern flax cultivars were revealed in our work. These accessions are of utmost interest for flax breeding and introduction of new useful traits into flax cultivars. The chromosome localization of Cassandra retrotransposon in Linum species was determined. PMID:25243121

  9. Microsatellite marker-based assessment of the biodiversity of native bioethanol yeast strains.

    PubMed

    Antonangelo, Ana Teresa B F; Alonso, Diego P; Ribolla, Paulo E M; Colombi, Débora

    2013-08-01

    Although many Brazilian sugar mills initiate the fermentation process by inoculating selected commercial Saccharomyces cerevisiae strains, the unsterile conditions of the industrial sugar cane ethanol fermentation process permit the constant entry of native yeast strains. Certain of those native strains are better adapted and tend to predominate over the initial strain, which may cause problems during fermentation. In the industrial fermentation process, yeast cells are often exposed to stressful environmental conditions, including prolonged cell recycling, ethanol toxicity and osmotic, oxidative or temperature stress. Little is known about these S. cerevisiae strains, although recent studies have demonstrated that heterogeneous genome architecture is exhibited by some selected well-adapted Brazilian indigenous yeast strains that display high performance in bioethanol fermentation. In this study, 11 microsatellite markers were used to assess the genetic diversity and population structure of the native autochthonous S. cerevisiae strains in various Brazilian sugar mills. The resulting multilocus data were used to build a similarity-based phenetic tree and to perform a Bayesian population structure analysis. The tree revealed the presence of great genetic diversity among the strains, which were arranged according to the place of origin and the collection year. The population structure analysis revealed genotypic differences among populations; in certain populations, these genotypic differences are combined to yield notably genotypically diverse individuals. The high yeast diversity observed among native S. cerevisiae strains provides new insights on the use of autochthonous high-fitness strains with industrial characteristics as starter cultures at bioethanol plants. PMID:23765797

  10. Genetic diversity and population structure in Harpadon nehereus based on sequence-related amplified polymorphism markers.

    PubMed

    Zhu, Z H; Li, H Y; Qin, Y; Wang, R X

    2014-01-01

    In this study, the genetic diversity among ten populations of the Bombay duck was studied on the basis of sequence-related amplified polymorphism (SRAP). The ten populations were collected from the East China Sea and South China Sea areas. A total of 98 loci were obtained from 292 individuals using eight SRAP primers. The average proportion of polymorphic loci, genetic diversity (H), and Shannon's information index were 75.20%, 0.2478, and 0.3735, respectively. Nei's genetic distance and Shannon's information index between the ten populations ranged from 0.0410 to 0.3841 and from 0.2396 to 0.4506, and the averages Nei's gene diversity index (H = 0.2478) and Shannon's information index (I = 0.3735) at the population level were high. AMOVA showed that most of the variation was within populations (71.74%), and only 28.26% of the variation was between populations. The neighbor-joining tree based on genetic distance revealed that significant genealogical structure existed throughout the examined range of the Bombay duck. The results demonstrated that SRAP marker was an effective tool for the assessment of genetic diversity in the Bombay duck. The results could be used for further protection of the germplasm resource of the Bombay duck.

  11. Study of Aided Diagnosis of Hepatic Carcinoma Based on Artificial Neural Network Combined with Tumor Marker Group

    NASA Astrophysics Data System (ADS)

    Tan, Shanjuan; Feng, Feifei; Wu, Yongjun; Wu, Yiming

    To develop a computer-aided diagnostic scheme by using an artificial neural network (ANN) combined with tumor markers for diagnosis of hepatic carcinoma (HCC) as a clinical assistant method. 140 serum samples (50 malignant, 40 benign and 50 normal) were analyzed for α-fetoprotein (AFP), carbohydrate antigen 125 (CA125), carcinoembryonic antigen (CEA), sialic acid (SA) and calcium (Ca). The five tumor marker values were then used as ANN inputs data. The result of ANN was compared with that of discriminant analysis by receiver operating characteristic (ROC) curve (AUC) analysis. The diagnostic accuracy of ANN and discriminant analysis among all samples of the test group was 95.5% and 79.3%, respectively. Analysis of multiple tumor markers based on ANN may be a better choice than the traditional statistical methods for differentiating HCC from benign or normal.

  12. Screening for simple sequence repeat markers in Puccinia striiformis tritici based on genomic sequence.

    PubMed

    Zhan, Gang-ming; Wang, Fu-ping; Luo, Huai-yong; Jiang, Shu-chang; Zheng, Wen-ming; Huang, Li-li; Kang, Zhen-sheng

    2015-08-01

    Puccinia striiformis f. sp. tritici (Pst) is the obligate biotrophic fungus responsible for stripe rust wheat. In this study, we developed and characterized 20 polymorphic microsatellite markers from the genomic sequence of an isolate of Chinese Pst race CY32. Polymorphism at each simple sequence repeat (SSR) locus was determined using 32 Pst isolates from 7 countries. The number of alleles varied from 2 to 7 across isolates, and the observed and expected heterozygosities ranged from 0.33 to 0.97 (mean 0.62) and 0.23 to 0.73 (mean 0.51), respectively. As expected the genomic SSR markers were more polymorphic than the expressed sequence tag (EST)-SSR markers developed previously. These markers will be more useful for population genetics and molecular genetics studies in Pst.

  13. SSR and SRAP marker-based linkage map of Vitis vinifera L.

    PubMed Central

    Guo, Yinshan; Lin, Hong; Liu, Zhendong; Zhao, Yuhui; Guo, Xiuwu; Li, Kun

    2014-01-01

    An F1 population was created by the cross ‘87-1’ × ‘9-22’. The female parent ‘87-1’ was an extremely early maturing cultivar with strong flavour. The male parent was an excellent breeding line producing large berries maturing late. The mapping population included 149 randomly chosen individuals. Molecular genetic map for each parent and the consensus map were constructed using simple sequence repeat and sequence-related amplified polymorphism markers by software JoinMap 3.0. The ‘87-1’ map covers a total length of 1272.9 cM distributed in 21 linkage groups and consists of 163 molecular markers with an average distance between adjacent markers of 8.9 cM. The ‘9-22’ map covers a total length of 1267.4 cM distributed in 20 linkage groups and consists of 158 molecular markers with an average distance between adjacent markers of 9.1 cM. The consensus map covers a total length of 1537.1 cM distributed in 21 linkage groups and one doublet and consists of 217 molecular markers with an average distance of 7.8 cM between adjacent markers. The length of the linkage groups is 69.8 cM on average. The map covers the 19 chromosomes of the Vitis genome and can lay a solid foundation for further studies such as quantative trait loci (QTL) mapping of correlated traits and marker-assisted selection. PMID:26019507

  14. Genetic diversity of Brazilian and introduced olive germplasms based on microsatellite markers.

    PubMed

    do Val, A D B; Ferreira, J L; Vieira Neto, J; Pasqual, M; de Oliveira, A F; Borém, A; Cançado, G M A

    2012-01-01

    Olive trees have been grown since the beginning of civilization, and the consumption of olives and olive products is increasing worldwide, due to their health benefits and organoleptic qualities. To meet the growing market for olives, commercial cultivation of this species is expanding from traditional areas to new regions. Although the Brazilian olive industry has just begun to be established, breeding programs are already developing cultivars that are more adapted to local conditions. We used 12 microsatellite markers to evaluate 60 olive accessions, including several cultivars that were developed in Brazil. The analyses identified 72 distinct alleles; the largest number of alleles per locus were at the markers GAPU 101 and GAPU 71B, which contained 10 and 9 alleles, respectively. The largest allelic diversity and polymorphic information contents were also found at the GAPU 101 and GAPU 71B markers, with values of 0.8399/0.8203 and 0.8117/0.7863, respectively. Additionally, the 12 microsatellite markers generated a cumulative identity probability of 1.51 x 10(-10), indicating a high level of accuracy of accession identification. The set of markers that we used allowed the identification of 52 of the 60 olive genotypes, in addition to the recognition of several varietal synonyms. The components of a two-dimensional principal coordinate analysis explained 48.6% of the total genetic variation. The results obtained from the microsatellite markers showed a substantial degree of genetic diversity in the olive tree accessions used in Brazil.

  15. A Marker-Based Approach for the Automated Selection of a Single Segmentation from a Hierarchical Set of Image Segmentations

    NASA Technical Reports Server (NTRS)

    Tarabalka, Y.; Tilton, J. C.; Benediktsson, J. A.; Chanussot, J.

    2012-01-01

    The Hierarchical SEGmentation (HSEG) algorithm, which combines region object finding with region object clustering, has given good performances for multi- and hyperspectral image analysis. This technique produces at its output a hierarchical set of image segmentations. The automated selection of a single segmentation level is often necessary. We propose and investigate the use of automatically selected markers for this purpose. In this paper, a novel Marker-based HSEG (M-HSEG) method for spectral-spatial classification of hyperspectral images is proposed. Two classification-based approaches for automatic marker selection are adapted and compared for this purpose. Then, a novel constrained marker-based HSEG algorithm is applied, resulting in a spectral-spatial classification map. Three different implementations of the M-HSEG method are proposed and their performances in terms of classification accuracies are compared. The experimental results, presented for three hyperspectral airborne images, demonstrate that the proposed approach yields accurate segmentation and classification maps, and thus is attractive for remote sensing image analysis.

  16. Development of sequence-characterized amplified region (SCAR) markers as a quality standard of inoculants based on Azospirillum.

    PubMed

    Reddy Priya, Pasupuleti; Selastin Antony, Raju; Gopalaswamy, Ganesan; Balachandar, Dananjeyan

    2016-04-01

    An attempt was made in this work to develop a strain-level molecular marker for unambiguous authentication of two Azospirillum inoculants, viz. A. lipoferum (strain Az204) and A. brasilense (strain Sp7). The sequence-characterized amplified region (SCAR) markers obtained from DNA fingerprints were designed for discrete detection of the strains. The SCAR primers could successfully amplify the target strain without cross-reaction with other Azospirillum strains, native isolates and other inoculants. The detection limit of SCAR primer for Az204 was 8.00 pg of DNA (approximately 10(5) cells per mL), and for Sp7, it was 0.49 pg of DNA (equal to 10(4) cells per mL). A simplified Sephadex G100-based crude DNA extraction protocol developed in this study was found suitable for SCAR marker-based strain authentication. Further, SCAR primers were assessed for simultaneous authentication as well as quantification of commercially prepared Azospirillum inoculants by quantitative real-time PCR (RT-PCR) and most-probable-number PCR (MPN-PCR). The RT-PCR assay can be able to quantify the commercial formulations as equal to culturable MPN method, while MPN-PCR failed for Az204. The SCAR marker-based strain authentication and presumptive quantification developed in the present work can contribute to improving the quality standard of commercial inoculants. PMID:26792777

  17. Marker development

    SciTech Connect

    Adams, M.R.

    1987-05-01

    This report is to discuss the marker development for radioactive waste disposal sites. The markers must be designed to last 10,000 years, and place no undue burdens on the future generations. Barriers cannot be constructed that preclude human intrusion. Design specifications for surface markers will be discussed, also marker pictograms will also be covered.

  18. [Genetic diversity of Camellia sinensis germplasm in Guangdong Province based on morphological parameters and SRAP markers].

    PubMed

    Shen, Cheng-Wen; Ning, Zheng-Xiang; Huang, Jian-An; Chen, Dong; Li, Jia-Xian

    2009-07-01

    By the methods of phenotypic identification and SRAP makers amplification, the genetic diversity of twenty-five local tea cultivars in Guangdong Province and five contrastive cultivars from other regions was assessed and classified, and the phenotypic traits of the cultivars were clustered by Pearson correlation and Farthest neighbor methods. The coefficient of variation of the phenotypic traits was averagely 32.15%. Fine-hair had the highest coefficient of variation (42.41%), while the growth period of bud leaves had the smallest one (18.52%). Based on the cluster analysis of phenotypic traits, the test 30 tea cultivars could be clustered into 4 groups, 17 cultivars in the first group, 10 cultivars in the second group, 2 contrastive cultivars Yunnan-dayezhong and Lingyun-baimaocha in the third group, and 1 contrastive cultivar Hainan-dayezhong in the fourth group. After the amplification with 21 SRAP primers, a total of 127 fragments were detected, among which, 114 fragments were polymorphic, accounting for 88.67% of the total. The amplified fragments and polymorphic fragments per primer combination were averagely 6.05 and 5.43, respectively. At the genetic distance of 0.39 cm, the tea cultivars could be classified into three groups A, B and C, and 83.33% of the cultivars were belonged to group A. At the genetic distance of 0.31 cm, group A could be further classified into three sub-groups I , II and III, 13 cultivars in subgroup I, 2 cultivars in subgroup II, and 10 cultivars in subgroup III. It was not exactly the same between the clustering based on SRAP markers amplification and the performance of phenotypic traits.

  19. Epigenetic and inflammatory marker profiles associated with depression in a community-based epidemiologic sample

    PubMed Central

    Uddin, M.; Koenen, K. C.; Aiello, A. E.; Wildman, D. E.; de los Santos, R.; Galea, S.

    2011-01-01

    Background Recent work suggests that epigenetic differences may be associated with psychiatric disorders. Here we investigate, in a community-based sample, whether methylation profiles distinguish between individuals with and without lifetime depression. We also investigate the physiologic consequences that may be associated with these profiles. Method Using whole blood-derived genomic DNA from a subset of participants in the Detroit Neighborhood Health Study (DNHS), we applied methylation microarrays to assess genome-wide methylation profiles for over 14 000 genes in 33 persons who reported a lifetime history of depression and 67 non-depressed adults. Bioinformatic functional analyses were performed on the genes uniquely methylated and unmethylated in each group, and inflammatory biomarkers [interleukin (IL)-6 and C-reactive protein (CRP)] were measured to investigate the possible functional significance of the methylation profiles observed. Results Uniquely unmethylated gene sets distinguished between those with versus without lifetime depression. In particular, some processes (e.g. brain development, tryptophan metabolism) showed patterns suggestive of increased methylation among individuals with depression whereas others (e.g. lipoprotein) showed patterns suggestive of decreased methylation among individuals with depression. IL-6 and CRP levels were elevated among those with lifetime depression and, among those with depression only, IL-6 methylation showed an inverse correlation with circulating IL-6 and CRP. Conclusions Genome-wide methylation profiles distinguish individuals with versus without lifetime depression in a community-based setting, and show coordinated signals with pathophysiological mechanisms previously implicated in the etiology of this disorder. Examining epigenetic mechanisms in concert with other dynamic markers of physiologic functioning should improve our understanding of the neurobiology of depression. PMID:20836906

  20. A second-generation genetic linkage map for bighead carp (Aristichthys nobilis) based on microsatellite markers.

    PubMed

    Zhu, C; Tong, J; Yu, X; Guo, W; Wang, X; Liu, H; Feng, X; Sun, Y; Liu, L; Fu, B

    2014-10-01

    Bighead carp (Aristichthys nobilis) is an important aquaculture fish worldwide. Genetic linkage maps for the species were previously reported, but map resolution remained to be improved. In this study, a second-generation genetic linkage map was constructed for bighead carp through a pseudo-testcross strategy using interspecific hybrids between bighead carp and silver carp. Of the 754 microsatellites genotyped in two interspecific mapping families (with 77 progenies for each family), 659 markers were assigned to 24 linkage groups, which were equal to the chromosome numbers of the haploid genome. The consensus map spanned 1917.3 cM covering 92.8% of the estimated bighead carp genome with an average marker interval of 2.9 cM. The length of linkage groups ranged from 52.2 to 133.5 cM with an average of 79.9 cM. The number of markers per linkage group varied from 11 to 55 with an average of 27.5 per linkage group. Normality tests on interval distances of the map showed a non-normal marker distribution; however, significant correlation was found between the length of linkage group and the number of markers below the 0.01 significance level (two-tailed). The length of the female map was 1.12 times that of the male map, and the average recombination ratio of female to male was 1.10:1. Visual inspection showed that distorted markers gathered in some linkage groups and in certain regions of the male and female maps. This well-defined genetic linkage map will provide a basic framework for further genome mapping of quantitative traits, comparative mapping and marker-assisted breeding in bighead carp. PMID:25040196

  1. A second-generation genetic linkage map for bighead carp (Aristichthys nobilis) based on microsatellite markers.

    PubMed

    Zhu, C; Tong, J; Yu, X; Guo, W; Wang, X; Liu, H; Feng, X; Sun, Y; Liu, L; Fu, B

    2014-10-01

    Bighead carp (Aristichthys nobilis) is an important aquaculture fish worldwide. Genetic linkage maps for the species were previously reported, but map resolution remained to be improved. In this study, a second-generation genetic linkage map was constructed for bighead carp through a pseudo-testcross strategy using interspecific hybrids between bighead carp and silver carp. Of the 754 microsatellites genotyped in two interspecific mapping families (with 77 progenies for each family), 659 markers were assigned to 24 linkage groups, which were equal to the chromosome numbers of the haploid genome. The consensus map spanned 1917.3 cM covering 92.8% of the estimated bighead carp genome with an average marker interval of 2.9 cM. The length of linkage groups ranged from 52.2 to 133.5 cM with an average of 79.9 cM. The number of markers per linkage group varied from 11 to 55 with an average of 27.5 per linkage group. Normality tests on interval distances of the map showed a non-normal marker distribution; however, significant correlation was found between the length of linkage group and the number of markers below the 0.01 significance level (two-tailed). The length of the female map was 1.12 times that of the male map, and the average recombination ratio of female to male was 1.10:1. Visual inspection showed that distorted markers gathered in some linkage groups and in certain regions of the male and female maps. This well-defined genetic linkage map will provide a basic framework for further genome mapping of quantitative traits, comparative mapping and marker-assisted breeding in bighead carp.

  2. Makorin Ring Finger Protein 1 as Adjunctive Marker in Liquid-based Cervical Cytology

    PubMed Central

    Lee, Maria; Chang, Min Young; Shin, Ha-Yeon; Shin, Eunah; Hong, Sun Won; Kim, Kyung-Mi; Chay, Doo Byung; Cho, Hanbyoul; Kim, Jae-Hoon

    2016-01-01

    Abstract To assess the utility of makorin ring finger protein 1 (MKRN1) as a marker of cervical pathology. A PROspective specimen collection and retrospective Blinded Evaluation study was conducted. Liquid-based cytology samples were collected from 187 women, embedding all residuals as cell blocks for immunohistochemical staining of MKRN1 and P16 INK4a. Results of liquid-based cervical cytology, immunostained cell block sections, and human papillomavirus (HPV) hybrid capture (with real-time polymerase chain reaction) were analyzed. Clinical outcomes were analyzed overall and in subsets of specimens yielding atypical squamous cells of undetermined significance or low-grade squamous intraepithelial lesions. Makorin ring finger protein 1 positivity and grades (1–3) of cervical intraepithelial neoplasia (CIN) increased in tandem (CIN1, 32.4%; CIN2, 60.0%; and CIN3, 80.0%), reaching 92.3% in invasive cancer. Sensitivity, specificity, positive predictive value, and negative predictive value in detecting CIN2+ via MKRN1 were 73.8%, 76.8%, 75.6%, and 75.0%, respectively. The performance of liquid-based cytology was poorer by comparison (61.3%, 69.5%, 66.2%, and 64.8%, respectively), and HPV assay (versus MKRN1 immunohistochemical staining) displayed lower specificity (67.7%). Combined HPV + MKRN1 testing proved highest in sensitivity, specificity, positive predictive value, and negative predictive value (71.8%, 85.5%, 82.3%, and 76.5%, respectively), whereas corresponding values for cytology + HPV (60.6%, 81.8%, 75.4%, and 69.2%) and cytology + MKRN1 (58.8%, 84.1%, 78.3%, and 67.7%) were all similar. In instances of atypical squamous cells of undetermined significance or low-grade squamous intraepithelial lesions, the HPV + MKRN1 combination performed best by above measures (100%, 72.7%, 73.9%, and 100%), followed by cytology + MKRN1 (100%, 50.0%, 60.7%, and 100%). Makorin ring finger protein 1 displayed greater sensitivity and specificity than liquid-based

  3. Genetic Diversity and Relatedness of Sweet Cherry (Prunus Avium L.) Cultivars Based on Single Nucleotide Polymorphic Markers

    PubMed Central

    Fernandez i Marti, Angel; Athanson, Blessing; Koepke, Tyson; Font i Forcada, Carolina; Dhingra, Amit; Oraguzie, Nnadozie

    2012-01-01

    Most previous studies on genetic fingerprinting and cultivar relatedness in sweet cherry were based on isoenzyme, RAPD, and simple sequence repeat (SSR) markers. This study was carried out to assess the utility of single nucleotide polymorphism (SNP) markers generated from 3′ untranslated regions (UTR) for genetic fingerprinting in sweet cherry. A total of 114 sweet cherry germplasm representing advanced selections, commercial cultivars, and old cultivars imported from different parts of the world were screened with seven SSR markers developed from other Prunus species and with 40 SNPs obtained from 3′ UTR sequences of Rainier and Bing sweet cherry cultivars. Both types of marker study had 99 accessions in common. The SSR data was used to validate the SNP results. Results showed that the average number of alleles per locus, mean observed heterozygosity, expected heterozygosity, and polymorphic information content values were higher in SSRs than in SNPs although both set of markers were similar in their grouping of the sweet cherry accessions as shown in the dendrogram. SNPs were able to distinguish sport mutants from their wild type germplasm. For example, “Stella” was separated from “Compact Stella.” This demonstrates the greater power of SNPs for discriminating mutants from their original parents than SSRs. In addition, SNP markers confirmed parentage and also determined relationships of the accessions in a manner consistent with their pedigree relationships. We would recommend the use of 3′ UTR SNPs for genetic fingerprinting, parentage verification, gene mapping, and study of genetic diversity in sweet cherry. PMID:22737155

  4. Breeding of a target genotype variety based on identified chalkiness marker-QTL associations in rice (Oryza sativa L.).

    PubMed

    Liu, X; Du, Y R; Li, X H; Li, X L; Yang, W Q; Wang, Y

    2015-10-21

    The aim of this study was to breed a target genotype variety based on the identified chalkiness marker-QTL (quantitative trait locus) associations in rice. First, a permanent mapping population of rice that consisted of 525 recombinant inbred lines (RILs), which were derived from Zhenshan 97/Minghui 63, was used to identify QTLs with additive effects for rice quantitative traits and percentage of grain chalkiness (PGC). Subsequently, based on the identified QTLs in rice, the molecular marker 68923-PGC was selected to screen the low chalkiness rice line. Then, using the integration of molecular marker breeding and traditional breeding, we analyzed the genotype and phenotype of inbred lines from 525 RILs; we identified one rice variety with particularly high yields, good taste, and broad adaptability. The new variety was temporarily named RIL10, which was a high quality, high yield, and broadly adaptable variety, and it is predominantly a feature that has contributed to its geographical adaptability, which would be planted from 35°E to 18°E in Chinain China, where 2/3 of rice production occurs. RIL10 was a marker-assisted selection breeding achievement for producing a high quality, high yield, and broadly adaptable rice variety.

  5. Development of retrotransposon-based markers IRAP and REMAP for cassava (Manihot esculenta).

    PubMed

    Kuhn, B C; Mangolin, C A; Souto, E R; Vicient, C M; Machado, M F P S

    2016-01-01

    Retrotransposons are abundant in the genomes of plants. In the present study, inter-retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphism (REMAP) markers were developed for the cassava genome (Manihot esculenta Crantz). Four cassava cultivars (Fécula Branca, IPR-União, Olho Junto, and Tamboara, two samples per cultivar) were used to obtain IRAP and REMAP fingerprints. Twelve designed primers were amplified alone and in combinations. The 42 IRAP/REMAP primer combinations amplified 431 DNA segments (bands; markers) of which 36 (8.36%) were polymorphic. The largest number of informative markers (16) was detected using the primers AYF2 and AYF2xAYF4. The number of bands for each primer varied from 3 to 16, with an average of 10.26 amplified segments per primer. The size of the amplified products ranged between 100 and 7000 bp. The AYF2 primer generated the highest number of amplified segments and showed the highest number of polymorphic bands (68.75%). Two samples of each cassava cultivar were used to illustrate the usefulness and the polymorphism of IRAP/REMAP markers. IRAP and REMAP markers produced a high number of reproducible bands, and might be informative and reliable for investigation of genetic diversity and relationships among cassava cultivars. PMID:27173210

  6. Development of retrotransposon-based markers IRAP and REMAP for cassava (Manihot esculenta).

    PubMed

    Kuhn, B C; Mangolin, C A; Souto, E R; Vicient, C M; Machado, M F P S

    2016-04-07

    Retrotransposons are abundant in the genomes of plants. In the present study, inter-retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphism (REMAP) markers were developed for the cassava genome (Manihot esculenta Crantz). Four cassava cultivars (Fécula Branca, IPR-União, Olho Junto, and Tamboara, two samples per cultivar) were used to obtain IRAP and REMAP fingerprints. Twelve designed primers were amplified alone and in combinations. The 42 IRAP/REMAP primer combinations amplified 431 DNA segments (bands; markers) of which 36 (8.36%) were polymorphic. The largest number of informative markers (16) was detected using the primers AYF2 and AYF2xAYF4. The number of bands for each primer varied from 3 to 16, with an average of 10.26 amplified segments per primer. The size of the amplified products ranged between 100 and 7000 bp. The AYF2 primer generated the highest number of amplified segments and showed the highest number of polymorphic bands (68.75%). Two samples of each cassava cultivar were used to illustrate the usefulness and the polymorphism of IRAP/REMAP markers. IRAP and REMAP markers produced a high number of reproducible bands, and might be informative and reliable for investigation of genetic diversity and relationships among cassava cultivars.

  7. Development of INDEL Markers for Genetic Mapping Based on Whole Genome Resequencing in Soybean

    PubMed Central

    Song, Xiaofeng; Wei, Haichao; Cheng, Wen; Yang, Suxin; Zhao, Yanxiu; Li, Xuan; Luo, Da; Zhang, Hui; Feng, Xianzhong

    2015-01-01

    Soybean [Glycine max (L.) Merrill] is an important crop worldwide. In this study, a Chinese local soybean cultivar, Hedou 12, was resequenced by next generation sequencing technology to develop INsertion/DELetion (INDEL) markers for genetic mapping. 49,276 INDEL polymorphisms and 242,059 single nucleotide polymorphisms were detected between Hedou 12 and the Williams 82 reference sequence. Of these, 243 candidate INDEL markers ranging from 5–50 bp in length were chosen for validation, and 165 (68%) of them revealed polymorphisms between Hedou 12 and Williams 82. The validated INDEL markers were also tested in 12 other soybean cultivars. The number of polymorphisms in the pairwise comparisons of 14 soybean cultivars varied from 27 to 165. To test the utility of these INDEL markers, they were used to perform genetic mapping of a crinkly leaf mutant, and the CRINKLY LEAF locus was successfully mapped to a 360 kb region on chromosome 7. This research shows that high-throughput sequencing technologies can facilitate the development of genome-wide molecular markers for genetic mapping in soybean. PMID:26483012

  8. Development of INDEL Markers for Genetic Mapping Based on Whole Genome Resequencing in Soybean.

    PubMed

    Song, Xiaofeng; Wei, Haichao; Cheng, Wen; Yang, Suxin; Zhao, Yanxiu; Li, Xuan; Luo, Da; Zhang, Hui; Feng, Xianzhong

    2015-10-19

    Soybean [Glycine max (L.) Merrill] is an important crop worldwide. In this study, a Chinese local soybean cultivar, Hedou 12, was resequenced by next generation sequencing technology to develop INsertion/DELetion (INDEL) markers for genetic mapping. 49,276 INDEL polymorphisms and 242,059 single nucleotide polymorphisms were detected between Hedou 12 and the Williams 82 reference sequence. Of these, 243 candidate INDEL markers ranging from 5-50 bp in length were chosen for validation, and 165 (68%) of them revealed polymorphisms between Hedou 12 and Williams 82. The validated INDEL markers were also tested in 12 other soybean cultivars. The number of polymorphisms in the pairwise comparisons of 14 soybean cultivars varied from 27 to 165. To test the utility of these INDEL markers, they were used to perform genetic mapping of a crinkly leaf mutant, and the CRINKLY LEAF locus was successfully mapped to a 360 kb region on chromosome 7. This research shows that high-throughput sequencing technologies can facilitate the development of genome-wide molecular markers for genetic mapping in soybean.

  9. A comparative analysis of genetic diversity in bitter gourd (Momordica charantia L.) genotypes using RAPD and ISSR markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bitter gourd (Momordica charantia L.) or bitter melon is a cucurbit of major economic importance where it is widely cultivated (India, China, Africa, and South America). The morphology (i.e., growth habit, maturity, and fruit shape, size, colour and surface texture) of Indian M. charantia germplasm...

  10. Estimation of the Genetic Diversity in Tetraploid Alfalfa Populations Based on RAPD Markers for Breeding Purposes

    PubMed Central

    Nagl, Nevena; Taski-Ajdukovic, Ksenija; Barac, Goran; Baburski, Aleksandar; Seccareccia, Ivana; Milic, Dragan; Katic, Slobodan

    2011-01-01

    Alfalfa is an autotetraploid, allogamous and heterozygous forage legume, whose varieties are synthetic populations. Due to the complex nature of the species, information about genetic diversity of germplasm used in any alfalfa breeding program is most beneficial. The genetic diversity of five alfalfa varieties, involved in progeny tests at Institute of Field and Vegetable Crops, was characterized based on RAPD markers. A total of 60 primers were screened, out of which 17 were selected for the analysis of genetic diversity. A total of 156 polymorphic bands were generated, with 10.6 bands per primer. Number and percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon’s information index were used to estimate genetic variation. Variety Zuzana had the highest values for all tested parameters, exhibiting the highest level of variation, whereas variety RSI 20 exhibited the lowest. Analysis of molecular variance (AMOVA) showed that 88.39% of the total genetic variation was attributed to intra-varietal variance. The cluster analysis for individual samples and varieties revealed differences in their population structures: variety Zuzana showed a very high level of genetic variation, Banat and Ghareh were divided in subpopulations, while Pecy and RSI 20 were relatively uniform. Ways of exploiting the investigated germplasm in the breeding programs are suggested in this paper, depending on their population structure and diversity. The RAPD analysis shows potential to be applied in analysis of parental populations in semi-hybrid alfalfa breeding program in both, development of new homogenous germplasm, and identification of promising, complementary germplasm. PMID:21954370

  11. Detection of chloroquine and artemisinin resistance molecular markers in Plasmodium falciparum: A hospital based study

    PubMed Central

    Ramani, S; Parija, Subhash Chandra; Mandal, Jharna; Hamide, Abdoul; Bhat, Vishnu

    2016-01-01

    Introduction: Emergence of chloroquine (CQ) resistance in Plasmodium falciparum has increased the morbidity and mortality of falciparum malaria worldwide. Artemisinin-based combination therapies are now recommended by the World Health Organization as the first line treatment for falciparum malaria. Numerous molecular markers have been implicated in the CQ and artemisinin resistance. Materials and Methods: A total of 26 confirmed cases of falciparum malaria (by giemsa stained thick and thin smear, quantitative buffy coat, immunochromatographic test, or polymerase chain reaction [PCR]) were included in the study. About 5 ml of ethylenediaminetetraacetic acid blood sample was collected and stored at −20°C till use. Plasmodium DNA was extracted using QIAamp whole blood DNA extraction kit. PCR was done to amplify pfcrt, pfmdr1, pfserca, and pfmrp1 genes and the amplicons obtained were sequenced by Macrogen, Inc., Korea. Single nucleotide polymorphism (SNP) analysis was done using Bio-Edit Sequence Alignment Editor. Results: Out of the four genes targeted, we noted a SNP in the pfcrt gene alone. This SNP (G > T) was noted in the 658th position of the gene, which was seen in 13 patients. The pfmdr1 and pfserca genes were present in 9 and 14 patients respectively. But we could not find any SNPs in these genes. This SNP in pfcrt gene was not significantly associated with any adverse outcome and neither altered disease progression. Conclusion: Presence of a single SNP may not be associated with any adverse clinical outcome. As the sample size was small, we may have not been able to detect any other known or unknown polymorphisms. PMID:26998436

  12. Molecular characterization of Brazilian equid herpesvirus type 1 strains based on neuropathogenicity markers

    PubMed Central

    Mori, Enio; Lara, Maria do Carmo C.S.H.; Cunha, Elenice M.S.; Villalobos, Eliana M.C.; Mori, Claudia M.C.; Soares, Rodrigo M.; Brandão, Paulo E.; Fernandes, Wilson R.; Richtzenhain, Leonardo J.

    2015-01-01

    Partial nucleotide sequences of ORF72 (glycoprotein D, gD), ORF64 (infected cell protein 4, ICP4) and ORF30 (DNA polymerase) genes were compared with corresponding sequences of EHV-1 reference strains to characterize the molecular variability of Brazilian strains. Virus isolation assays were applied to 74 samples including visceral tissue, total blood, cerebrospinal fluid (CSF) and nasal swabs of specimens from a total of 64 animals. Only one CSF sample (Iso07/05 strain) was positive by virus isolation in cell culture. EHV-1 Iso07/05 neurologic strain and two abortion visceral tissues samples (Iso11/06 and Iso33/06) were PCR-positive for ORF33 (glycoprotein B, gB) gene of EHV-1. A sequence analysis of the ORF72, ORF64 and ORF30 genes from three EHV-1 archival strains (A3/97, A4/72, A9/92) and three clinical samples (Iso07/05, Iso11/06 and Iso33/06) suggested that among Brazilian EHV-1 strains, the amplified region of the gD gene sequence is highly conserved. Additionally, the analysis of ICP4 gene showed high nucleotide and amino acid identities when compared with genotype P strains, suggesting that the EHV-1 Brazilian strains belonged to the same group. All the EHV-1 Brazilian strains were classified as non-neuropathogenic variants (N752) based on the ORF30 analysis. These findings indicate a high conservation of the gD-, ICP4- and ORF30-encoding sequences. Different pathotypes of the EHV-1 strain might share identical genes with no specific markers, and tissue tropism is not completely dependent on the gD envelope, immediate-early ICP4 and DNA polymerase proteins. PMID:26273275

  13. Genome-Wide Analysis of Microsatellite Markers Based on Sequenced Database in Chinese Spring Wheat (Triticum aestivum L.).

    PubMed

    Han, Bin; Wang, Changbiao; Tang, Zhaohui; Ren, Yongkang; Li, Yali; Zhang, Dayong; Dong, Yanhui; Zhao, Xinghua

    2015-01-01

    Microsatellites or simple sequence repeats (SSRs) are distributed across both prokaryotic and eukaryotic genomes and have been widely used for genetic studies and molecular marker-assisted breeding in crops. Though an ordered draft sequence of hexaploid bread wheat have been announced, the researches about systemic analysis of SSRs for wheat still have not been reported so far. In the present study, we identified 364,347 SSRs from among 10,603,760 sequences of the Chinese spring wheat (CSW) genome, which were present at a density of 36.68 SSR/Mb. In total, we detected 488 types of motifs ranging from di- to hexanucleotides, among which dinucleotide repeats dominated, accounting for approximately 42.52% of the genome. The density of tri- to hexanucleotide repeats was 24.97%, 4.62%, 3.25% and 24.65%, respectively. AG/CT, AAG/CTT, AGAT/ATCT, AAAAG/CTTTT and AAAATT/AATTTT were the most frequent repeats among di- to hexanucleotide repeats. Among the 21 chromosomes of CSW, the density of repeats was highest on chromosome 2D and lowest on chromosome 3A. The proportions of di-, tri-, tetra-, penta- and hexanucleotide repeats on each chromosome, and even on the whole genome, were almost identical. In addition, 295,267 SSR markers were successfully developed from the 21 chromosomes of CSW, which cover the entire genome at a density of 29.73 per Mb. All of the SSR markers were validated by reverse electronic-Polymerase Chain Reaction (re-PCR); 70,564 (23.9%) were found to be monomorphic and 224,703 (76.1%) were found to be polymorphic. A total of 45 monomorphic markers were selected randomly for validation purposes; 24 (53.3%) amplified one locus, 8 (17.8%) amplified multiple identical loci, and 13 (28.9%) did not amplify any fragments from the genomic DNA of CSW. Then a dendrogram was generated based on the 24 monomorphic SSR markers among 20 wheat cultivars and three species of its diploid ancestors showing that monomorphic SSR markers represented a promising source to

  14. Imaging of moving fiducial markers during radiotherapy using a fast, efficient active pixel sensor based EPID

    SciTech Connect

    Osmond, John P. F.; Zin, Hafiz M.; Harris, Emma J.; Lupica, Giovanni; Allinson, Nigel M.; Evans, Philip M.

    2011-11-15

    Purpose: The purpose of this work was to investigate the use of an experimental complementary metal-oxide-semiconductor (CMOS) active pixel sensor (APS) for tracking of moving fiducial markers during radiotherapy. Methods: The APS has an active area of 5.4 x 5.4 cm and maximum full frame read-out rate of 20 frame s{sup -1}, with the option to read out a region-of-interest (ROI) at an increased rate. It was coupled to a 4 mm thick ZnWO4 scintillator which provided a quantum efficiency (QE) of 8% for a 6 MV x-ray treatment beam. The APS was compared with a standard iViewGT flat panel amorphous Silicon (a-Si) electronic portal imaging device (EPID), with a QE of 0.34% and a frame-rate of 2.5 frame s{sup -1}. To investigate the ability of the two systems to image markers, four gold cylinders of length 8 mm and diameter 0.8, 1.2, 1.6, and 2 mm were placed on a motion-platform. Images of the stationary markers were acquired using the APS at a frame-rate of 20 frame s{sup -1}, and a dose-rate of 143 MU min{sup -1} to avoid saturation. EPID images were acquired at the maximum frame-rate of 2.5 frame s{sup -1}, and a reduced dose-rate of 19 MU min{sup -1} to provide a similar dose per frame to the APS. Signal-to-noise ratio (SNR) of the background signal and contrast-to-noise ratio (CNR) of the marker signal relative to the background were evaluated for both imagers at doses of 0.125 to 2 MU. Results: Image quality and marker visibility was found to be greater in the APS with SNR {approx}5 times greater than in the EPID and CNR up to an order of magnitude greater for all four markers. To investigate the ability to image and track moving markers the motion-platform was moved to simulate a breathing cycle with period 6 s, amplitude 20 mm and maximum speed 13.2 mm s{sup -1}. At the minimum integration time of 50 ms a tracking algorithm applied to the APS data found all four markers with a success rate of {>=}92% and positional error {<=}90 {mu}m. At an integration time of 400

  15. Development of ITS sequence based molecular marker to distinguish, Tribulus terrestris L. (Zygophyllaceae) from its adulterants.

    PubMed

    Balasubramani, Subramani Paranthaman; Murugan, Ramar; Ravikumar, Kaliamoorthy; Venkatasubramanian, Padma

    2010-09-01

    Tribulus terrestris L. (Zygophyllaceae) is one of the highly traded raw drugs and also used as a stimulative food additive in Europe and USA. While, Ayurvedic Pharmacopoeia of India recognizes T. terrestris as Goksura, Tribulus lanuginosus and T. subramanyamii are also traded by the same name raising issues of quality control. The nuclear ribosomal RNA genes and ITS (internal transcribed spacer) sequence were used to develop species-specific DNA markers. The species-specific markers efficiently amplified 295bp for T. terrestris (TT1F and TT1R), 300bp for T. lanuginosus (TL1F and TL1R) and 214bp for T. subramanyamii (TS1F and TS1R). These DNA markers can be used to distinguish T. terrestris from its adulterants.

  16. Molecular characterization and marker based chemotaxonomic studies of Podophyllum hexandrum Royle.

    PubMed

    Sultan, Phalisteen; Shawl, A S; Rehman, Suriya; Ahmed, S Fayaz; Ramteke, P W

    2010-06-01

    Detailed chemical studies and RAPD analysis were done in different populations of Podophyllum hexandrum collected from high altitude regions of North Western Himalayas. Random amplified polymorphic DNA (RAPD) analysis revealed a high degree of genetic diversity among the 12 collected accessions, attributed to their geographical and climatic conditions. HPLC analysis also revealed variation in the concentration of two major marker compounds which lead to the identification of a chemotype. The study demonstrated that RAPD and chemical markers are very useful tools to compare the genetic relationship and pattern of variation among such prioritized and endangered medicinal plants.

  17. First genetic linkage map of Taraxacum koksaghyz Rodin based on AFLP, SSR, COS and EST-SSR markers.

    PubMed

    Arias, Marina; Hernandez, Monica; Remondegui, Naroa; Huvenaars, Koen; van Dijk, Peter; Ritter, Enrique

    2016-01-01

    Taraxacum koksaghyz Rodin (TKS) has been studied in many occasions as a possible alternative source for natural rubber production of good quality and for inulin production. Some tire companies are already testing TKS tire prototypes. There are also many investigations on the production of bio-fuels from inulin and inulin applications for health improvement and in the food industry. A limited amount of genomic resources exist for TKS and particularly no genetic linkage map is available in this species. We have constructed the first TKS genetic linkage map based on AFLP, COS, SSR and EST-SSR markers. The integrated linkage map with eight linkage groups (LG), representing the eight chromosomes of Russian dandelion, has 185 individual AFLP markers from parent 1, 188 individual AFLP markers from parent 2, 75 common AFLP markers and 6 COS, 1 SSR and 63 EST-SSR loci. Blasting the EST-SSR sequences against known sequences from lettuce allowed a partial alignment of our TKS map with a lettuce map. Blast searches against plant gene databases revealed some homologies with useful genes for downstream applications in the future. PMID:27488242

  18. First genetic linkage map of Taraxacum koksaghyz Rodin based on AFLP, SSR, COS and EST-SSR markers

    PubMed Central

    Arias, Marina; Hernandez, Monica; Remondegui, Naroa; Huvenaars, Koen; van Dijk, Peter; Ritter, Enrique

    2016-01-01

    Taraxacum koksaghyz Rodin (TKS) has been studied in many occasions as a possible alternative source for natural rubber production of good quality and for inulin production. Some tire companies are already testing TKS tire prototypes. There are also many investigations on the production of bio-fuels from inulin and inulin applications for health improvement and in the food industry. A limited amount of genomic resources exist for TKS and particularly no genetic linkage map is available in this species. We have constructed the first TKS genetic linkage map based on AFLP, COS, SSR and EST-SSR markers. The integrated linkage map with eight linkage groups (LG), representing the eight chromosomes of Russian dandelion, has 185 individual AFLP markers from parent 1, 188 individual AFLP markers from parent 2, 75 common AFLP markers and 6 COS, 1 SSR and 63 EST-SSR loci. Blasting the EST-SSR sequences against known sequences from lettuce allowed a partial alignment of our TKS map with a lettuce map. Blast searches against plant gene databases revealed some homologies with useful genes for downstream applications in the future. PMID:27488242

  19. First genetic linkage map of Taraxacum koksaghyz Rodin based on AFLP, SSR, COS and EST-SSR markers.

    PubMed

    Arias, Marina; Hernandez, Monica; Remondegui, Naroa; Huvenaars, Koen; van Dijk, Peter; Ritter, Enrique

    2016-08-04

    Taraxacum koksaghyz Rodin (TKS) has been studied in many occasions as a possible alternative source for natural rubber production of good quality and for inulin production. Some tire companies are already testing TKS tire prototypes. There are also many investigations on the production of bio-fuels from inulin and inulin applications for health improvement and in the food industry. A limited amount of genomic resources exist for TKS and particularly no genetic linkage map is available in this species. We have constructed the first TKS genetic linkage map based on AFLP, COS, SSR and EST-SSR markers. The integrated linkage map with eight linkage groups (LG), representing the eight chromosomes of Russian dandelion, has 185 individual AFLP markers from parent 1, 188 individual AFLP markers from parent 2, 75 common AFLP markers and 6 COS, 1 SSR and 63 EST-SSR loci. Blasting the EST-SSR sequences against known sequences from lettuce allowed a partial alignment of our TKS map with a lettuce map. Blast searches against plant gene databases revealed some homologies with useful genes for downstream applications in the future.

  20. Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis.

    PubMed

    Alland, David; Whittam, Thomas S; Murray, Megan B; Cave, M Donald; Hazbon, Manzour H; Dix, Kim; Kokoris, Mark; Duesterhoeft, Andreas; Eisen, Jonathan A; Fraser, Claire M; Fleischmann, Robert D

    2003-06-01

    The comparative-genomic sequencing of two Mycobacterium tuberculosis strains enabled us to identify single nucleotide polymorphism (SNP) markers for studies of evolution, pathogenesis, and epidemiology in clinical M. tuberculosis. Phylogenetic analysis using these "comparative-genome markers" (CGMs) produced a highly unusual phylogeny with a complete absence of secondary branches. To investigate CGM-based phylogenies, we devised computer models to simulate sequence evolution and calculate new phylogenies based on an SNP format. We found that CGMs represent a distinct class of phylogenetic markers that depend critically on the genetic distances between compared "reference strains." Properly distanced reference strains generate CGMs that accurately depict evolutionary relationships, distorted only by branch collapse. Improperly distanced reference strains generate CGMs that distort and reroot outgroups. Applying this understanding to the CGM-based phylogeny of M. tuberculosis, we found evidence to suggest that this species is highly clonal without detectable lateral gene exchange. We noted indications of evolutionary bottlenecks, including one at the level of the PHRI "C" strain previously associated with particular virulence characteristics. Our evidence also suggests that loss of IS6110 to fewer than seven elements per genome is uncommon. Finally, we present population-based evidence that KasA, an important component of mycolic acid biosynthesis, develops G312S polymorphisms under selective pressure. PMID:12754238

  1. Linguistic Markers of Stance in Early and Advanced Academic Writing: A Corpus-Based Comparison

    ERIC Educational Resources Information Center

    Aull, Laura L.; Lancaster, Zak

    2014-01-01

    This article uses corpus methods to examine linguistic expressions of stance in over 4,000 argumentative essays written by incoming first-year university students in comparison with the writing of upper-level undergraduate students and published academics. The findings reveal linguistic stance markers shared across the first-year essays despite…

  2. Bone Markers

    MedlinePlus

    ... Alkaline Phosphatase; Osteocalcin; P1NP; Procollagen Type 1 N-Terminal Propeptide Formal name: Biochemical Markers of Bone Remodeling ... tests for evaluating bone turnover: C-telopeptide (C-terminal telopeptide of type 1 collagen (CTx)) – a marker ...

  3. Exogenous Visual Orienting Is Associated with Specific Neurotransmitter Genetic Markers: A Population-Based Genetic Association Study

    PubMed Central

    Lundwall, Rebecca A.; Guo, Dong-Chuan; Dannemiller, James L.

    2012-01-01

    Background Currently, there is a sense that the spatial orienting of attention is related to genotypic variations in cholinergic genes but not to variations in dopaminergic genes. However, reexamination of associations with both cholinergic and dopaminergic genes is warranted because previous studies used endogenous rather than exogenous cues and costs and benefits were not analyzed separately. Examining costs (increases in response time following an invalid pre-cue) and benefits (decreases in response time following a valid pre-cue) separately could be important if dopaminergic genes (implicated in disorders such as attention deficit disorder) independently influence the different processes of orienting (e.g., disengage, move, engage). Methodology/Principal Findings We tested normal subjects (N = 161) between 18 and 61 years. Participants completed a computer task in which pre-cues preceded the presence of a target. Subjects responded (with a key press) to the location of the target (right versus left of fixation). The cues could be valid (i.e., appear where the target would appear) or invalid (appear contralateral to where the target would appear). DNA sequencing assays were performed on buccal cells to genotype known genetic markers and these were examined for association with task scores. Here we show significant associations between visual orienting and genetic markers (on COMT, DAT1, and APOE; R2s from 4% to 9%). Conclusions/Significance One measure in particular – the response time cost of a single dim, invalid cue – was associated with dopaminergic markers on COMT and DAT1. Additionally, variations of APOE genotypes based on the ε2/ε3/ε4 alleles were also associated with response time differences produced by simultaneous cues with unequal luminances. We conclude that individual differences in visual orienting are related to several dopaminergic markers as well as to a cholinergic marker. These results challenge the view that orienting is not

  4. The development of chlorophyll-based markers in poultry diets to aid detection of fluorescent fecal contamination.

    PubMed

    Lee, M R F; Leemans, D; Theobald, V J; Fleming, H R; Gay, A P

    2013-12-01

    Incidents of foodborne illness associated with consuming undercooked or raw chicken are often linked to 2 causative pathogens: Campylobacter spp. or Salmonella spp. Numerous studies have shown that contamination of carcasses results when pathogens are transferred from the intestinal tract or fecal material on feet and feathers to the dressed carcass. Ultraviolet spectral imaging to detect surface fecal and ingesta contamination on poultry carcasses may provide a solution to aid detection. However, poultry diets do not provide sufficiently high levels of natural fluorophores for this system to be reliable. This study investigated the potential of chlorophyll-based feed additives to improve fluorescence of the feces and narrow the excitation and emission wavelengths to aid in the development of a simple visualization system. Twenty-four hens (Gallus gallus domesticus) were allocated at random to 1 of 4 treatments: control (C, no marker), Zn chlorophyllin, Mg chlorophyllin, or Fe chlorophyllin. All markers were incorporated into mash before pelleting at a rate of 1 g/kg of DM. The experiment consisted of two 4 × 4 Latin squares with each period consisting of 2 wk. Feces were collected and extracted in acetone:water (50:50; vol/vol) with fecal fluorescence emission spectra determined using a Jasco FP-6200 Spectrofluorometer with excitation at 382 nm. A main peak evolved at wavelength 670 nm with the total area under the peak used as fluorescence intensity. Following 7 d of marker supplementation, the 3 markers improved the fluorescence intensity by ×14.8, 12.8, and 6.9 for Fe, Mg, and Zn chlorophyllin, respectively, compared with the control. The addition of feces containing Mg chlorophyllin to chicken carcass increased detection of the feces compared with feces with no marker. Also, due to the plain background of chicken skin, a simple image at 675 nm with appropriate thresholds would allow detection of contaminated carcasses at the current slaughter line speed

  5. Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers

    PubMed Central

    2012-01-01

    Background Pinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS) through the identification of Quantitative Trait Loci and selection of allelic variants of interest in breeding populations. In this study, we report annotated genetic linkage maps for two individuals (C14 and C15) belonging to a breeding program aiming to increase resin production. We use different types of DNA markers, including last-generation molecular markers. Results We obtained 13 and 14 linkage groups for C14 and C15 maps, respectively. A total of 211 and 215 markers were positioned on each map and estimated genome length was between 1,870 and 2,166 cM respectively, which represents near 65% of genome coverage. Comparative mapping with previously developed genetic linkage maps for P. pinaster based on about 60 common markers enabled aligning linkage groups to this reference map. The comparison of our annotated linkage maps and linkage maps reporting QTL information revealed 11 annotated SNPs in candidate genes that co-localized with previously reported QTLs for wood properties and water use efficiency. Conclusions This study provides genetic linkage maps from a Spanish population that shows high levels of genetic divergence with French populations from which segregating progenies have been previously mapped. These genetic maps will be of interest to construct a reliable consensus linkage map for the species. The importance of developing functional genetic linkage maps is highlighted, especially when working with breeding populations for its future application in MAS for traits of interest. PMID:23036012

  6. Molecular markers based on LTR retrotransposons BARE-1 and Jeli uncover different strata of evolutionary relationships in diploid wheats.

    PubMed

    Konovalov, Fedor A; Goncharov, Nikolay P; Goryunova, Svetlana; Shaturova, Aleksandra; Proshlyakova, Tatyana; Kudryavtsev, Alexander

    2010-06-01

    Molecular markers based on retrotransposon insertions are widely used for various applications including phylogenetic analysis. Multiple cases were described where retrotransposon-based markers, namely sequence-specific amplification polymorphism (SSAP), were superior to other marker types in resolving the phylogenetic relationships due to their higher variability and informativeness. However, the patterns of evolutionary relationships revealed by SSAP may be dependent on the underlying retrotransposon activity in different periods of time. Hence, the proper choice of retrotransposon family is essential for obtaining significant results. We compared the phylogenetic trees for a diverse set of diploid A-genome wheat species (Triticum boeoticum, T. urartu and T. monococcum) based on two unrelated retrotransposon families, BARE-1 and Jeli. BARE-1 belongs to Copia class and has a uniform distribution between common wheat (T. aestivum) genomes of different origin (A, B and D), indicating similar activity in the respective diploid genome donors. Gypsy-class family Jeli was found by us to be an A-genome retrotransposon with >70% copies residing in A genome of hexaploid common wheat, suggesting a burst of transposition in the history of A-genome progenitors. The results indicate that a higher Jeli transpositional activity was associated with T. urartu versus T. boeoticum speciation, while BARE-1 produced more polymorphic insertions during subsequent intraspecific diversification; as an outcome, each retrotransposon provides more informative markers at the corresponding level of phylogenetic relationships. We conclude that multiple retroelement families should be analyzed for an image of evolutionary relationships to be solid and comprehensive. PMID:20407790

  7. Mapping QTLs for root morphological traits in Brassica rapa L. based on AFLP and RAPD markers.

    PubMed

    Lu, Gang; Cao, Jiashu; Yu, Xiaolin; Xiang, Xun; Chen, Hang

    2008-01-01

    Root growth and thickening plays a key role in the final productivity and even the quality of storage roots in root crops. This study was conducted to identify and map quantitative trait loci (QTLs) affecting root morphological traits in Brassica rapa by using molecular markers. An F2 population was developed from a cross between Chinese cabbage (Brassica rapa ssp. chinensis) and turnip (B. rapa ssp. rapifera), which differed greatly in root characters. A genetic map covering 1837.1 cM, with 192 marker loci and 11 linkage groups, was constructed by using this F2 population. The F3 families derived from F2 plants were grown in the field and evaluated for taproot traits (thickness, length, and weight). QTL analysis via simple interval mapping detected 18 QTLs for the 3 root traits, including 7 QTLs for taproot thickness, 5 QTLs for taproot length, and 6 QTLs for taproot weight. Individually, the QTLs accounted for 8.4-27.4% of the phenotypic variation. The 2 major QTLs, qTRT4b for taproot thickness and qTRW4 for taproot weight, explained 27.4% and 24.8% of the total phenotypic variance, respectively. The QTLs for root traits, firstly detected in Brassica crops, may provide a basis for marker-assisted selection to improve productivity in root-crop breeding.

  8. Phylogenetic relationships between four Salix L. species based on DArT markers.

    PubMed

    Przyborowski, Jerzy A; Sulima, Paweł; Kuszewska, Anna; Załuski, Dariusz; Kilian, Andrzej

    2013-12-11

    The objectives of this study were to evaluate the usefulness of DArT markers in genotypic identification of willow species and describe genetic relationships between four willow species: Salix viminalis, S. purpurea, S. alba and S. triandra. The experimental plant material comprised 53 willow genotypes of these four species, which are popularly grown in Poland. DArT markers seem to identify Salix species with a high degree of accuracy. As a result, the examined species were divided into four distinct groups which corresponded to the four analyzed species. In our study, we observed that S. triandra was very different genetically from the other species, including S. alba which is generally classified into the same subgenus of Salix. The above corroborates the findings of other authors who relied on molecular methods to reveal that the classification of S. triandra to the subgenus Salix was erroneous. The Principal Coordinate Analysis (PCoA) and the neighbor-joining dendrogram also confirmed the clear division of the studied willow genotypes into four clusters corresponding to individual species. This confirmed the usefulness of DArT markers in taxonomic analyses and identification of willow species.

  9. Phylogeny of Rosa sections Chinenses and Synstylae (Rosaceae) based on chloroplast and nuclear markers.

    PubMed

    Zhu, Zhang-Ming; Gao, Xin-Fen; Fougère-Danezan, Marie

    2015-06-01

    Rosa sections Chinenses and Synstylae contain approximately 39 wild species mainly distributed in East Asia and are closely related according to previous studies. But the specific relationships within these two sections were still obscure due to limited sampling, low genetic variation of molecular markers, and complex evolutionary histories. In this study, we used four chloroplast (ndhC-trnV, ndhF-rpl32, ndhJ-trnF and psbJ-petA) and two nuclear (ribosomal ITS and GAPDH) markers with an extensive geographic and taxonomic sampling to explore their evolutionary history. Our phylogenetic analyses suggested that Rosa sections Chinenses and Synstylae defined in traditional taxonomic system are not monophyletic and close to sections Caninae and Gallicanae. Additionally, our results showed incongruence between chloroplast and nuclear markers, and the patterns of incongruence might be due to ancient hybridization (genetic introgression). One putative hybrid species and three samples identified as interspecific hybrids are further discussed in terms of topological incongruence, biological characters and distribution patterns.

  10. Mining and gene ontology based annotation of SSR markers from expressed sequence tags of Humulus lupulus.

    PubMed

    Singh, Swati; Gupta, Sanchita; Mani, Ashutosh; Chaturvedi, Anoop

    2012-01-01

    Humulus lupulus is commonly known as hops, a member of the family moraceae. Currently many projects are underway leading to the accumulation of voluminous genomic and expressed sequence tag sequences in public databases. The genetically characterized domains in these databases are limited due to non-availability of reliable molecular markers. The large data of EST sequences are available in hops. The simple sequence repeat markers extracted from EST data are used as molecular markers for genetic characterization, in the present study. 25,495 EST sequences were examined and assembled to get full-length sequences. Maximum frequency distribution was shown by mononucleotide SSR motifs i.e. 60.44% in contig and 62.16% in singleton where as minimum frequency are observed for hexanucleotide SSR in contig (0.09%) and pentanucleotide SSR in singletons (0.12%). Maximum trinucleotide motifs code for Glutamic acid (GAA) while AT/TA were the most frequent repeat of dinucleotide SSRs. Flanking primer pairs were designed in-silico for the SSR containing sequences. Functional categorization of SSRs containing sequences was done through gene ontology terms like biological process, cellular component and molecular function.

  11. Simultaneous quantitative detection of multiple tumor markers with a rapid and sensitive multicolor quantum dots based immunochromatographic test strip.

    PubMed

    Wang, Chunying; Hou, Fei; Ma, Yicai

    2015-06-15

    A novel multicolor quantum dots (QDs) based immunochromatographic test strip (ICTS) was developed for simultaneous quantitative detection of multiple tumor markers, by utilizing alpha fetoprotein (AFP) and carcinoembryonic antigen (CEA) as models. The immunosensor could realize simultaneous quantitative detection of tumor markers with only one test line and one control line on the nitrocellulose membrane (NC membrane) due to the introduction of multicolor QDs. In this method, a mixture of mouse anti-AFP McAb and mouse anti-CEA McAb was coated on NC membrane as test line and goat anti-mouse IgG antibody was coated as control line. Anti-AFP McAb-QDs546 conjugates and anti-CEA McAb-QDs620 conjugates were mixed and applied to the conjugate pad. Simultaneous quantitative detection of multiple tumor markers was achieved by detecting the fluorescence intensity of captured QDs labels on test line and control line using a test strip reader. Under the optimum conditions, AFP and CEA could be detected as low as 3 ng/mL and 2 ng/mL in 15 min with a sample volume of 80 μL, and no obvious cross-reactivity was observed. The immunosensor was validated with 130 clinical samples and in which it exhibited high sensitivity (93% for AFP and 87% for CEA) and specificity (94% for AFP and 97% for CEA). The immunosensor also demonstrated high recoveries (87.5-113% for AFP and 90-97.3% for CEA) and low relative standard deviations (RSDs) (2.8-6.2% for AFP and 4.9-9.6% for CEA) when testing spiked human serum. This novel multicolor QDs based ICTS provides an easy and rapid, simultaneous quantitative detecting strategy for point-of-care testing of tumor markers. PMID:25562743

  12. A new species of Docosia Winnertz from Central Europe, with DNA barcoding based on four gene markers (Diptera, Mycetophilidae)

    PubMed Central

    Ševčík, Jan; Kaspřák, David; Rulik, Björn

    2016-01-01

    Abstract A new species of Docosia Winnertz, Docosia dentata sp. n., is described and illustrated, based on a single male specimen collected in Muránska planina National Park in Central Slovakia. DNA sequences (COI, COII, CytB, and ITS2) are included and compared for 13 species of Docosia. There was found only little congruence between the molecular results and previous scarce data about interspecific relationships based on morphology. The COI and CytB gene markers showed the highest interspecific gene distances while ITS2 showed the lowest ones. An updated key to the 23 Central European species of Docosia is also presented. PMID:26843833

  13. Assessment of genetic diversity among Indian potato (Solanum tuberosum L.) collection using microsatellite and retrotransposon based marker systems.

    PubMed

    Sharma, Vishakha; Nandineni, Madhusudan R

    2014-04-01

    Potato (Solanum tuberosum) is an important non-cereal crop throughout the world and is highly recommended for ensuring global food security. Owing to the complexities in genetics and inheritance pattern of potato, the conventional method of cross breeding for developing improved varieties has been difficult. Identification and tagging of desirable traits with informative molecular markers would aid in the development of improved varieties. Insertional polymorphism of copia-like and gypsy-like long terminal repeat retrotransposons (RTN) were investigated among 47 potato varieties from India using Inter-Retrotransposon Amplified Polymorphism (IRAP) and Retrotransposon Microsatellite Amplified Polymorphism (REMAP) marker techniques and were compared with the DNA profiles obtained with simple sequence repeats (SSRs). The genetic polymorphism, efficiency of polymorphism and effectiveness of marker systems were evaluated to assess the extent of genetic diversity among Indian potato varieties. A total of 139 polymorphic SSR alleles, 270 IRAP and 98 REMAP polymorphic bands, showing polymorphism of 100%, 87.9% and 68.5%, respectively, were used for detailed characterization of the genetic relationships among potato varieties by using cluster analysis and principal coordinate analysis (PCoA). IRAP analysis resulted in the highest number of polymorphic bands with an average of 15 polymorphic bands per assay unit when compared to the other two marker systems. Based on pair-wise comparison, the genetic similarity was calculated using Dice similarity coefficient. The SSRs showed a wide range in genetic similarity values (0.485-0.971) as compared to IRAP (0.69-0.911) and REMAP (0.713-0.947). A Mantel's matrix correspondence test showed a high positive correlation (r=0.6) between IRAP and REMAP, an intermediate value (r=0.58) for IRAP and SSR and the lowest value (r=0.17) for SSR and REMAP. Statistically significant cophenetic correlation coefficient values, of 0.961, 0.941 and 0

  14. Assessment of genetic diversity among Indian potato (Solanum tuberosum L.) collection using microsatellite and retrotransposon based marker systems.

    PubMed

    Sharma, Vishakha; Nandineni, Madhusudan R

    2014-04-01

    Potato (Solanum tuberosum) is an important non-cereal crop throughout the world and is highly recommended for ensuring global food security. Owing to the complexities in genetics and inheritance pattern of potato, the conventional method of cross breeding for developing improved varieties has been difficult. Identification and tagging of desirable traits with informative molecular markers would aid in the development of improved varieties. Insertional polymorphism of copia-like and gypsy-like long terminal repeat retrotransposons (RTN) were investigated among 47 potato varieties from India using Inter-Retrotransposon Amplified Polymorphism (IRAP) and Retrotransposon Microsatellite Amplified Polymorphism (REMAP) marker techniques and were compared with the DNA profiles obtained with simple sequence repeats (SSRs). The genetic polymorphism, efficiency of polymorphism and effectiveness of marker systems were evaluated to assess the extent of genetic diversity among Indian potato varieties. A total of 139 polymorphic SSR alleles, 270 IRAP and 98 REMAP polymorphic bands, showing polymorphism of 100%, 87.9% and 68.5%, respectively, were used for detailed characterization of the genetic relationships among potato varieties by using cluster analysis and principal coordinate analysis (PCoA). IRAP analysis resulted in the highest number of polymorphic bands with an average of 15 polymorphic bands per assay unit when compared to the other two marker systems. Based on pair-wise comparison, the genetic similarity was calculated using Dice similarity coefficient. The SSRs showed a wide range in genetic similarity values (0.485-0.971) as compared to IRAP (0.69-0.911) and REMAP (0.713-0.947). A Mantel's matrix correspondence test showed a high positive correlation (r=0.6) between IRAP and REMAP, an intermediate value (r=0.58) for IRAP and SSR and the lowest value (r=0.17) for SSR and REMAP. Statistically significant cophenetic correlation coefficient values, of 0.961, 0.941 and 0

  15. Allele-specific CAPS markers based on point mutations in resistance alleles at the pvr1 locus encoding eIF4E in Capsicum.

    PubMed

    Yeam, Inhwa; Kang, Byoung-Cheorl; Lindeman, Wouter; Frantz, James D; Faber, Nanne; Jahn, Molly M

    2005-12-01

    Marker-assisted selection has been widely implemented in crop breeding and can be especially useful in cases where the traits of interest show recessive or polygenic inheritance and/or are difficult or impossible to select directly. Most indirect selection is based on DNA polymorphism linked to the target trait, resulting in error when the polymorphism recombines away from the mutation responsible for the trait and/or when the linkage between the mutation and the polymorphism is not conserved in all relevant genetic backgrounds. In this paper, we report the generation and use of molecular markers that define loci for selection using cleaved amplified polymorphic sequences (CAPS). These CAPS markers are based on nucleotide polymorphisms in the resistance gene that are perfectly correlated with disease resistance, the trait of interest. As a consequence, the possibility that the marker will not be linked to the trait in all backgrounds or that the marker will recombine away from the trait is eliminated. We have generated CAPS markers for three recessive viral resistance alleles used widely in pepper breeding, pvr1, pvr1 (1), and pvr1 (2). These markers are based on single nucleotide polymorphisms (SNPs) within the coding region of the pvr1 locus encoding an eIF4E homolog on chromosome 3. These three markers define a system of indirect selection for potyvirus resistance in Capsicum based on genomic sequence. We demonstrate the utility of this marker system using commercially significant germplasm representing two Capsicum species. Application of these markers to Capsicum improvement is discussed.

  16. A multiplexed marker-based algorithm for diagnosis of carcinoma of unknown primary using circulating tumor cells.

    PubMed

    Matthew, Elizabeth M; Zhou, Lanlan; Yang, Zhaohai; Dicker, David T; Holder, Sheldon L; Lim, Bora; Harouaka, Ramdane; Zheng, Si-Yang; Drabick, Joseph J; Lamparella, Nicholas E; Truica, Cristina I; El-Deiry, Wafik S

    2016-01-26

    Real-time, single-cell multiplex immunophenotyping of circulating tumor cells (CTCs) is hypothesized to inform diagnosis of tissue of origin in patients with carcinoma of unknown primary (CUP). In 20 to 50% of CUP patients, the primary site remains unidentified, presenting a challenge for clinicians in diagnosis and treatment. We developed a post-CellSearch CTC assay using multiplexed Q-dot or DyLight conjugated antibodies with the goal of detecting multiple markers in single cells within a CTC population. We adapted our approach to size-based CTC enrichment protocols for capturing CTCs and subsequent immunofluorescence (IF) using a minimal set of markers to predict the primary sites for common metastatic tumors. The carcinomas are characterized with cytokeratin 7 (CK7), cytokeratin 20 (CK20), thyroid transcription factor 1 (TTF-1), estrogen receptor (ER) or prostate-specific antigen (PSA. IF has been optimized in cultured tumor cells with individual antibodies, then with conjugated antibodies to form a multiplex antibody set. With IF, we evaluated antibodies specific to these 5 markers in lung, breast, colorectal, and prostate cancer cell lines and blood from metastatic prostate and breast cancer patients. This advanced technology provides a noninvasive, diagnostic blood test as an adjunct to routine tissue biopsy. Its further implementation requires prospective clinical testing.

  17. A multiplexed marker-based algorithm for diagnosis of carcinoma of unknown primary using circulating tumor cells

    PubMed Central

    Yang, Zhaohai; Dicker, David T.; Holder, Sheldon L.; Lim, Bora; Harouaka, Ramdane; Zheng, Si-Yang; Drabick, Joseph J.; Lamparella, Nicholas E.; Truica, Cristina I.; El-Deiry, Wafik S.

    2016-01-01

    Real-time, single-cell multiplex immunophenotyping of circulating tumor cells (CTCs) is hypothesized to inform diagnosis of tissue of origin in patients with carcinoma of unknown primary (CUP). In 20 to 50% of CUP patients, the primary site remains unidentified, presenting a challenge for clinicians in diagnosis and treatment. We developed a post-CellSearch CTC assay using multiplexed Q-dot or DyLight conjugated antibodies with the goal of detecting multiple markers in single cells within a CTC population. We adapted our approach to size-based CTC enrichment protocols for capturing CTCs and subsequent immunofluorescence (IF) using a minimal set of markers to predict the primary sites for common metastatic tumors. The carcinomas are characterized with cytokeratin 7 (CK7), cytokeratin 20 (CK20), thyroid transcription factor 1 (TTF-1), estrogen receptor (ER) or prostate-specific antigen (PSA. IF has been optimized in cultured tumor cells with individual antibodies, then with conjugated antibodies to form a multiplex antibody set. With IF, we evaluated antibodies specific to these 5 markers in lung, breast, colorectal, and prostate cancer cell lines and blood from metastatic prostate and breast cancer patients. This advanced technology provides a noninvasive, diagnostic blood test as an adjunct to routine tissue biopsy. Its further implementation requires prospective clinical testing. PMID:26695546

  18. Quality Assurance and Commissioning of an Infrared Marker-Based Patient Positioning System for Frameless Extracranial Stereotactic Radiotherapy

    PubMed Central

    Gupta, Tejpal; Phurailatpam, Reena; Ajay, Mishra; Rajeshri, Pai; Pranshu, Mohindra; Supriya, Chopra

    2007-01-01

    Rapid advancements in imaging technology have led to remarkable improvements in identification and localization of tumors, ushering the era of high-precision techniques in contemporary radiotherapy practice. However, uncertainties in patient set-up and organ motion during a course of fractionated radiotherapy can compromise precision of radiation therapy. Excellent accuracy has been achieved with invasive and non-invasive fixation systems for stereotactic radiotherapy. This report describes the commissioning procedure and Quality Assurance studies done to evaluate the accuracy of isocenter localization by an infrared marker-based positioning system (ExacTrac). The ExacTrac has two infrared cameras that emit and detect infrared rays from reflective markers and construct three-dimensional coordinates of each marker. It detects the difference of the actual isocenter position from the planned isocenter coordinates in three translational (lateral, longitudinal, vertical, or x,y,z axes) and three rotational axes (six degree of freedom). This study performed on a flat and static phantom shows excellent accuracy achieved by the ExacTrac system. The positioning accuracy of ExacTrac (± 1 mm translational displacement and ± 1° rotational errors) can be a valuable tool in implementing frameless extracranial stereotactic radiotherapy. Nevertheless, it needs to be further evaluated on patients with inherent motion and greater positional uncertainty before being adopted in clinical practice. PMID:23675057

  19. Long-range transport of biomass burning emissions based on organic molecular markers and carbonaceous thermal distribution.

    PubMed

    Bae, Min-Suk; Shin, Ju-Seon; Lee, Kwang-Yul; Lee, Kwon-Ho; Kim, Young J

    2014-01-01

    Semi-continuous organic carbon (OC), elemental carbon (EC), and organic molecular markers were analyzed using the thermal optical transmittance method at the Gosan supersite (on Jeju Island, Korea), which has been widely used as a regional background site for East Asia. The Carbonaceous Thermal Distribution (CTD) method, which can provide detailed carbon signature characteristics relative to analytical temperature, was used to improve the carbon fractionation of the analytical method. Ground-based measurements were conducted from October 25 to November 5, 2010. During the sampling period, one high OC concentration event and two characteristic periods were observed. Considering the thermal distribution patterns, the relationship between the EC and black carbon (BC) by optical measurements, the backward trajectories, the aerosol optical thickness, the PM10 concentrations from the 316 PM-network sites that were operated by the Ministry of Environment in Korea, and the organic molecular markers, such as levoglucosan, PAHs, and organic acids, we concluded that the event was influenced by long-range transport from biomass burning emissions. This study discusses the CTD analysis with organic molecular marker concentrations, extracts and interprets additional carbon fractions from a semi-continuous data set, and provides knowledge regarding the origin of carbon sources and their behaviors. PMID:23892024

  20. Associations between serum 25-hydroxyvitamin D and bone turnover markers in a population based sample of German children.

    PubMed

    Thiering, E; Brüske, I; Kratzsch, J; Hofbauer, L C; Berdel, D; von Berg, A; Lehmann, I; Hoffmann, B; Bauer, C P; Koletzko, S; Heinrich, J

    2015-01-01

    Severe vitamin D deficiency is known to cause rickets, however epidemiological studies and RCTs did not reveal conclusive associations for other parameters of bone health. In our study, we aimed to investigate the association between serum levels of 25(OH) vitamin D and bone turnover markers in a population-based sample of children. 25(OH)D, calcium (Ca), osteocalcin (OC), and β-Crosslaps (β-CTx) were measured in 2798 ten-year-old children from the German birth cohorts GINIplus and LISAplus. Linear regression was used to determine the association between bone turnover markers and 25(OH)D levels. 25(OH)D, OC, and β-CTx showed a clear seasonal variation. A 10 nmol/l increase in 25(OH)D was significantly associated with a 10.5 ng/l decrease (p < 0.001) in β-CTx after adjustment for design, sex, fasting status, time of blood drawn, BMI, growth rate, and detectable testosterone/estradiol. For OC alone no significant association with 25(OH)D was observed, whereas the β-CTx-to-OC ratio was inversely associated with 25(OH)D (-1.7% change, p < 0.001). When stratifying the analyses by serum calcium levels, associations were stronger in children with Ca levels below the median. This study in school-aged children showed a seasonal variation of 25(OH)D and the bone turnover markers OC and β-CTx. Furthermore a negative association between 25(OH)D and the bone resorption marker β-CTx was observed. PMID:26667774

  1. Seroprevalence of infectious markers & their trends in blood donors in a hospital based blood bank in north india

    PubMed Central

    Makroo, R.N.; Hegde, Vikas; Chowdhry, Mohit; Bhatia, Aakanksha; Rosamma, N.L.

    2015-01-01

    Background & objectives: Hepatitis B virus (HBV), human immunodeficiency virus (HIV), hepatitis C virus (HCV) and syphilis infections pose a great threat to blood safety. This study was undertaken to investigate the seroprevalence of serologic markers for transfusion transmitted infections (TTIs) among blood donors at a hospital based blood centre in north India over a period of nine years. Methods: The results of serologic markers for TTIs (HBsAg, anti-HCV, anti-HIV and syphilis) of all blood donations (both voluntary and replacement) at our hospital from January 2005 to December 2013 were screened. Additional analysis was conducted to examine the prevalence trends associated with each of the positive marker. Results: The data of 180,477 donors [173,019 (95.86%) males and 7,458 (4.13%) females] were analyzed. Replacement donations [174,939 (96.93%)] represented the majority whereas, only 5,538 (3.06%) donations were from the voluntary donors. The risk of blood being reactive was three times higher in male donors when compared with the female donors. The risk of blood being reactive for one or more infectious markers was 2.1 times higher in replacement donors when compared with the voluntary donors. Seropositivity of HIV, HBsAg, HBcAb, syphilis showed a significant decreasing trend (P<0.05) while there was an increasing trend in HCV infection which was insignificant. Interpretation & conclusions: This study reflects that the risk of TTIs has been decreased over time with respect to HIV, HBV and syphilis, but the trends for HCV remains almost the same in blood donors. Blood transfusion remains a risk factor for the spread of blood-borne infections. Therefore, improvements are needed to strengthen both safety and availability of blood. PMID:26458348

  2. Plant genetic transformation efficiency of selected Malaysian rice based on selectable marker gene (hptII).

    PubMed

    Htwe, Nwe Nwe; Ling, Ho Chai; Zaman, Faridah Qamaruz; Maziah, Mahmood

    2014-04-01

    Rice is one of the most important cereal crops with great potential for biotechnology progress. In transformation method, antibiotic resistance genes are routinely used as powerful markers for selecting transformed cells from surrounding non-transformed cells. In this study, the toxicity level of hygromycin was optimized for two selected mutant rice lines, MR219 line 4 and line 9. The mature embryos were isolated and cultured on an MS medium with different hygromycin concentrations (0, 20, 40, 60, 80 and 100 mg L(-1)). Evidently, above 60 mg L(-1) was effective for callus formation and observed completely dead. Further there were tested for specific concentration (0-60). Although, 21.28% calli survived on the medium containing 45 mg L(-1) hygromycin, it seemed suitable for the identification of putative transformants. These findings indicated that a system for rice transformation in a relatively high frequency and the transgenes are stably expressed in the transgenic plants. Green shoots were regenerated from the explant under hygromycin stress. RT-PCR using hptII and gus sequence specific primer and Southern blot analysis were used to confirm the presence of the transgene and to determine the transformation efficiency for their stable integration in regenerated plants. This study demonstrated that the hygromycin resistance can be used as an effective marker for rice transformation.

  3. Development of a SCAR marker for male gametophyte of Gracilariopsis lemaneiformis based on AFLP technique

    NASA Astrophysics Data System (ADS)

    Zhou, Wei; Ding, Hongye; Sui, Zhenghong; Wang, Zhongxia; Wang, Jinguo

    2014-05-01

    The red alga Gracilariopsis lemaneiformis (Bory) is an economically valuable macroalgae. As a means to identify the sex of immature Gracilariopsis lemaneiformis, the amplified fragment length polymorphism (AFLP) technique was used to search for possible sex- or phase-related markers in male gametophytes, female gametophytes, and tetrasporophytes, respectively. Seven AFLP selective amplification primers were used in this study. The primer combination E-TG/M-CCA detected a specific band linked to male gametophytes. The DNA fragment was recovered and a 402-bp fragment was sequenced. However, no DNA sequence match was found in public databases. Sequence characterized amplified region (SCAR) primers were designed from the sequence to test the repeatability of the relationship to the sex, using 69 male gametophytes, 139 female gametophytes, and 47 tetrasporophytes. The test results demonstrate a good linkage and repeatability of the SCAR marker to sex. The SCAR primers developed in this study could reduce the time required for sex identification of Gracilariopsis lemaneiformis by four to six months. This can reduce both the time investment and number of specimens required in breeding experiments.

  4. Ancestry informative markers for distinguishing between Thai populations based on genome-wide association datasets.

    PubMed

    Vongpaisarnsin, Kornkiat; Listman, Jennifer Beth; Malison, Robert T; Gelernter, Joel

    2015-07-01

    The main purpose of this work was to identify a set of AIMs that stratify the genetic structure and diversity of the Thai population from a high-throughput autosomal genome-wide association study. In this study, more than one million SNPs from the international HapMap database and the Thai depression genome-wide association study have been examined to identify ancestry informative markers (AIMs) that distinguish between Thai populations. An efficient strategy is proposed to identify and characterize such SNPs and to test high-resolution SNP data from international HapMap populations. The best AIMs are identified to stratify the population and to infer genetic ancestry structure. A total of 124 AIMs were clearly clustered geographically across the continent, whereas only 89 AIMs stratified the Thai population from East Asian populations. Finally, a set of 273 AIMs was able to distinguish northern from southern Thai subpopulations. These markers will be of particular value in identifying the ethnic origins in regions where matching by self-reports is unavailable or unreliable, which usually occurs in real forensic cases.

  5. Genetic relationship of cowpea (Vigna unguiculata) varieties from Senegal based on SSR markers.

    PubMed

    Badiane, F A; Gowda, B S; Cissé, N; Diouf, D; Sadio, O; Timko, M P

    2012-02-08

    Genetic diversity and phylogenetic relationships among 22 local cowpea (Vigna unguiculata) varieties and inbred lines collected throughout Senegal were evaluated using simple sequence repeat molecular markers. A set of 49 primer combinations were developed from cowpea genomic/expressed sequence tags and evaluated for their ability to detect polymorphisms among the various cowpea genotypes. Forty-four primer combinations detected polymorphisms, with the remaining five primer sets failing to yield PCR amplification products. From one to 16 alleles were found among the informative primer combinations; their frequencies ranged from 0.60 to 0.95 (mean = 0.79). The genetic diversity of the sample varied from 0.08 to 0.42 (mean = 0.28). The polymorphic information content ranged from 0.08 to 0.33 (mean = 0.23). The local varieties clustered in the same group, except 53-3, 58-53, and 58-57; while Ndoute yellow pods, Ndoute violet pods and Baye Ngagne were in the second group. The photosensitive varieties (Ndoute yellow pods and Ndoute violet pods) were closely clustered in the second group and so were inbred line Mouride and local cultivar 58-57, which is also one of the parents for inbred line Mouride. These molecular markers could be used for selection and identification of elite varieties for cowpea improvement and germplasm management in Senegal.

  6. Using quantitative PCR with retrotransposon-based insertion polymorphisms as markers in sugarcane

    PubMed Central

    Metcalfe, Cushla J.; Oliveira, Sarah G.; Gaiarsa, Jonas W.; Aitken, Karen S.; Carneiro, Monalisa S.; Zatti, Fernanda; Van Sluys, Marie-Anne

    2015-01-01

    Sugarcane is the main source of the world’s sugar and is becoming increasingly important as a source of biofuel. The highly polyploid and heterozygous nature of the sugarcane genome has meant that characterization of the genome has lagged behind that of other important crops. Here we developed a method using a combination of quantitative PCR with a transposable marker system to score the relative number of alleles with a transposable element (TE) present at a particular locus. We screened two genera closely related to Saccharum (Miscanthus and Erianthus), wild Saccharum, traditional cultivars, and 127 modern cultivars from Brazilian and Australian breeding programmes. We showed how this method could be used in various ways. First, we showed that the method could be extended to be used as part of a genotyping system. Secondly, the history of insertion and timing of the three TEs examined supports our current understanding of the evolution of the Saccharum complex. Thirdly, all three TEs were found in only one of the two main lineages leading to the modern sugarcane cultivars and are therefore the first TEs identified that could potentially be used as markers for Saccharum spontaneum. PMID:26093024

  7. Using quantitative PCR with retrotransposon-based insertion polymorphisms as markers in sugarcane.

    PubMed

    Metcalfe, Cushla J; Oliveira, Sarah G; Gaiarsa, Jonas W; Aitken, Karen S; Carneiro, Monalisa S; Zatti, Fernanda; Van Sluys, Marie-Anne

    2015-07-01

    Sugarcane is the main source of the world's sugar and is becoming increasingly important as a source of biofuel. The highly polyploid and heterozygous nature of the sugarcane genome has meant that characterization of the genome has lagged behind that of other important crops. Here we developed a method using a combination of quantitative PCR with a transposable marker system to score the relative number of alleles with a transposable element (TE) present at a particular locus. We screened two genera closely related to Saccharum (Miscanthus and Erianthus), wild Saccharum, traditional cultivars, and 127 modern cultivars from Brazilian and Australian breeding programmes. We showed how this method could be used in various ways. First, we showed that the method could be extended to be used as part of a genotyping system. Secondly, the history of insertion and timing of the three TEs examined supports our current understanding of the evolution of the Saccharum complex. Thirdly, all three TEs were found in only one of the two main lineages leading to the modern sugarcane cultivars and are therefore the first TEs identified that could potentially be used as markers for Saccharum spontaneum.

  8. Time markers for Drosophila morphogenesis based on cell-pattern topology.

    NASA Astrophysics Data System (ADS)

    Zallen, Richard; Zallen, Jennifer A.

    2007-03-01

    Recent work on convergent extension in Drosophila has shown that the accumulation of actin-myosin networks at specific cell interfaces initiates planar polarity and the formation of multicellular rosette structures that contribute to elongation of the body axis [1]. This cell-rearrangement process takes place within a one-cell-thick layer, and the changing two-dimensional cell pattern can be characterized using topological measures such as cell-shape statistics [2]. We find that the timeline for the process contains a well-defined marker corresponding to a sharp increase in the slope of the time dependence of the variance of the cell-shape (number-of-sides) distribution. A rosette in this context is a cluster of cells enclosing high-order vertices at which 4 or 5 or more cells meet. While the cell-shape variance climbs steadily during axis elongation, the frequency of high-order vertices and large rosettes plateaus after 10 and 13 minutes, respectively. These time markers calibrate the conventional timeline descriptors referred to as stages 7 and 8 of embryonic development [3]. [1] J.T. Blankenship et al., Developmental Cell 11, 459 (2006); [2] J.A. Zallen and R. Zallen, J. Phys.: Condensed Matter 16, S5073 (2004); [3] J.A. Campos-Ortega and V. Hartenstein, The embryonic development of Drosophila melanogaster (1985).

  9. A tribal level phylogeny of Lake Tanganyika cichlid fishes based on a genomic multi-marker approach.

    PubMed

    Meyer, Britta S; Matschiner, Michael; Salzburger, Walter

    2015-02-01

    The species-flocks of cichlid fishes in the East African Great Lakes Victoria, Malawi and Tanganyika constitute the most diverse extant adaptive radiations in vertebrates. Lake Tanganyika, the oldest of the lakes, harbors the morphologically and genetically most diverse assemblage of cichlids and contains the highest number of endemic cichlid genera of all African lakes. Based on morphological grounds, the Tanganyikan cichlid species have been grouped into 12-16 distinct lineages, so-called tribes. While the monophyly of most of the tribes is well established, the phylogenetic relationships among the tribes remain largely elusive. Here, we present a new tribal level phylogenetic hypothesis for the cichlid fishes of Lake Tanganyika that is based on the so far largest set of nuclear markers and a total alignment length of close to 18kb. Using next-generation amplicon sequencing with the 454 pyrosequencing technology, we compiled a dataset consisting of 42 nuclear loci in 45 East African cichlid species, which we subjected to maximum likelihood and Bayesian inference phylogenetic analyses. We analyzed the entire concatenated dataset and each marker individually, and performed a Bayesian concordance analysis and gene tree discordance tests. Overall, we find strong support for a position of the Oreochromini, Boulengerochromini, Bathybatini and Trematocarini outside of a clade combining the substrate spawning Lamprologini and the mouthbrooding tribes of the 'H-lineage', which are both strongly supported to be monophyletic. The Eretmodini are firmly placed within the 'H-lineage', as sister-group to the most species-rich tribe of cichlids, the Haplochromini. The phylogenetic relationships at the base of the 'H-lineage' received less support, which is likely due to high speciation rates in the early phase of the radiation. Discordance among gene trees and marker sets further suggests the occurrence of past hybridization and/or incomplete lineage sorting in the cichlid

  10. THE USE OF INTER SIMPLE SEQUENCE REPEATS (ISSR) IN DISTINGUISHING NEIGHBORING DOUGLAS-FIR TREES AS A MEANS TO IDENTIFYING TREE ROOTS WITH ABOVE-GROUND BIOMASS

    EPA Science Inventory

    We are attempting to identify specific root fragments from soil cores with individual trees. We successfully used Inter Simple Sequence Repeats (ISSR) to distinguish neighboring old-growth Douglas-fir trees from one another, while maintaining identity among each tree's parts. W...

  11. Genetic distances between popcorn populations based on molecular markers and correlations with heterosis estimates made by diallel analysis of hybrids.

    PubMed

    Munhoz, R E F; Prioli, A J; Amaral, A T; Scapim, C A; Simon, G A

    2009-01-01

    Diallel analysis was used to obtain information on combining ability, heterosis, estimates of genetic distances by random amplified polymorphic DNA (RAPD) and on their correlations with heterosis, for the popcorn varieties RS 20, UNB2, CMS 43, CMS 42, Zélia, UEM J1, UEM M2, Beija-Flor, and Viçosa, which were crossed to obtain all possible combinations, without reciprocals. The genitors and the 36 F(1) hybrids were evaluated in field trials in Maringá during two growing seasons in a randomized complete block design with three replications. Based on the results, strategies for further studies were developed, including the construction of composites by joining varieties with high general combining ability for grain yield (UNB2 and CMS 42) with those with high general combining ability for popping expansion (Zélia, RS 20 and UEM M2). Based on the RAPD markers, UEM J1 and Zélia were the most genetically distant and RS 20 and UNB2 were the most similar. The low correlation between heterosis and genetic distances may be explained by the random dispersion of the RAPD markers, which were insufficient for the exploitation of the popcorn genome. We concluded that an association between genetic dissimilarity and heterosis based only on genetic distance is not expected without considering the effect of dominant loci. PMID:19731196

  12. [Markers for Immunofluorescence Analysis Based on Europium Complex with Fluorinated β-Diketones Carbazole Series].

    PubMed

    Kostryukova, T S; Ivanovskaya, N P; Zatonsky, G V; Osin, N S; Vasilev, N V

    2015-01-01

    In order to develop new markers for immunofluorescence time-resolved luminescence analysis tetraketodiester carbazole series was obtained. Compound contains methoxycarbonyl reactive groups, separated from the 1,3-dicarbonyl chelating fragment by difluoromethylene spacers (CF2)4. Complexes of this compound with the ions Eu3+ are stable in aqueous solution and possess a long-living intensive luminescence with the main peaks: emission--in the area of 615 nm and excitation--in the 380-390 nm, that distinguishes them from most used analogues. Conjugate of streptavidin to compound was obtained and its fluorescent spectral characteristics allow to use it as a universal reagent for various schemes of biological microanalysis.

  13. Genetic variability in three native Iranian chicken populations of the Khorasan province based on microsatellite markers.

    PubMed

    MohammadabadiM, R; Nikbakhti, M; Mirzaee, H R; Shandi, M A; Saghi, D A; Romanov, M N; Moiseyeva, I G

    2010-04-01

    This paper represents the results of a study on the genetic diversity in three native chicken populations (Barred, Brown and Black) of Khorasan, a province in northeastern Iran, by using four microsatellite markers (MCW0005, MCW0016, MCW0018 and MCW0034). Average number of alleles was found to be 5.25 per locus across all populations. The examined populations were characterized by a high level of genetic variability as assessed by computing the expected and observed heterozygosities, and polymorphism information content. The authors consider the results of this investigation as an accumulation of data in a research program concerning genetic characteristics of the native chicken populations of Iran that have not been surveyed yet.

  14. Laser-guidance based cell detection for identifying malignant cancerous cells without any fluorescent markers.

    PubMed

    Ma, Zhen; Gao, Bruce Z

    2011-09-01

    Laser guidance technique employs the optical forces generated from a focused Gaussian laser beam incident on a biological cell to trap and guide the cell along the laser propagation direction. The optical force, which determines the guidance speed, is dependent on the cellular characteristics of the cell being guided, such as size, shape, composition and morphology. Different cell populations or subpopulations can be detected without any fluorescent markers by measuring their guidance speeds. We found that cell guidance speeds were sensitive enough to monitor the subtle changes during the progression of mouse fibroblast cells from normal to cancerous phenotype. The results also demonstrated that this technique can effectively distinguish mouse mammary cancerous cells with different metastatic competence. Laser guidance technique can be used as a label-free cell detection method for basic cell biological investigation and cancer diagnosis.

  15. Tumor Hypoxia: Causative Mechanisms, Microregional Heterogeneities, and the Role of Tissue-Based Hypoxia Markers.

    PubMed

    Vaupel, Peter; Mayer, Arnulf

    2016-01-01

    Tumor hypoxia is a hallmark of solid malignant tumor growth, profoundly influences malignant progression and contributes to the development of therapeutic resistance. Pathogenesis of tumor hypoxia is multifactorial, with contributions from both acute and chronic factors. Spatial distribution of hypoxia within tumors is markedly heterogeneous and often changes over time, e.g., during a course of radiotherapy. Substantial changes in the oxygenation status can occur within the distance of a few cell layers, explaining the inability of currently used molecular imaging techniques to adequately assess this crucial trait. Due to the possible importance of tumor hypoxia for clinical decision-making, there is a great demand for molecular tools which may provide the necessary resolution down to the single cell level. Exogenous and endogenous markers of tumor hypoxia have been investigated for this purpose. Their potential use may be greatly enhanced by multiparametric in situ methods in experimental and human tumor tissue. PMID:27526128

  16. Design and recognition of three dimensional calibration target based on coded marker

    NASA Astrophysics Data System (ADS)

    Zhai, You; Xiong, Wei; Zeng, Luan; Gu, Dalong

    2015-08-01

    Traditional three-dimensional (3D) calibration targets consist of two or three mutual orthogonal planes (each of the planes contains several control points constituted by corners or circular points) that cannot be captured simultaneously by cameras in front view. Therefore, large perspective distortions exist in the images of the calibration targets resulting in inaccurate image coordinate detection of the control points. Besides, in order to eliminate mismatches, recognition of the control points usually needs manual intervention consuming large amount of time. A new design of 3D calibration target is presented for automatic and accurate camera calibration. The target employs two parallel planes instead of orthogonal planes to reduce perspective distortion, which can be captured simultaneously by cameras in front view. Control points of the target are constituted by carefully designed circular coded markers, which can be used to realize automatic recognition without manual intervention. Due to perspective projection, projections of the circular coded markers' centers deviate from the centers of their corresponding imaging ellipses. Colinearity of the control points is used to correct perspective distortions of the imaging ellipses. Experiment results show that the calibration target can be automatically and correctly recognized under large illumination and viewpoint change. The image extraction errors of the control points are under 0.1 pixels. When applied to binocular cameras calibration, the mean reprojection errors are less than 0.15 pixels and the 3D measurement errors are less than 0.2mm in x and y axis and 0.5mm in z axis respectively.

  17. Entropy-based adaptive nuclear texture features are independent prognostic markers in a total population of uterine sarcomas.

    PubMed

    Nielsen, Birgitte; Hveem, Tarjei Sveinsgjerd; Kildal, Wanja; Abeler, Vera M; Kristensen, Gunnar B; Albregtsen, Fritz; Danielsen, Håvard E

    2015-04-01

    Nuclear texture analysis measures the spatial arrangement of the pixel gray levels in a digitized microscopic nuclear image and is a promising quantitative tool for prognosis of cancer. The aim of this study was to evaluate the prognostic value of entropy-based adaptive nuclear texture features in a total population of 354 uterine sarcomas. Isolated nuclei (monolayers) were prepared from 50 µm tissue sections and stained with Feulgen-Schiff. Local gray level entropy was measured within small windows of each nuclear image and stored in gray level entropy matrices, and two superior adaptive texture features were calculated from each matrix. The 5-year crude survival was significantly higher (P < 0.001) for patients with high texture feature values (72%) than for patients with low feature values (36%). When combining DNA ploidy classification (diploid/nondiploid) and texture (high/low feature value), the patients could be stratified into three risk groups with 5-year crude survival of 77, 57, and 34% (Hazard Ratios (HR) of 1, 2.3, and 4.1, P < 0.001). Entropy-based adaptive nuclear texture was an independent prognostic marker for crude survival in multivariate analysis including relevant clinicopathological features (HR = 2.1, P = 0.001), and should therefore be considered as a potential prognostic marker in uterine sarcomas.

  18. In situ marker-based assessment of leaf trait evolutionary potential in a marginal European beech population.

    PubMed

    Bontemps, A; Lefèvre, F; Davi, H; Oddou-Muratorio, S

    2016-03-01

    Evolutionary processes are expected to be crucial for the adaptation of natural populations to environmental changes. In particular, the capacity of rear edge populations to evolve in response to the species limiting conditions remains a major issue that requires to address their evolutionary potential. In situ quantitative genetic studies based on molecular markers offer the possibility to estimate evolutionary potentials manipulating neither the environment nor the individuals on which phenotypes are measured. The goal of this study was to estimate heritability and genetic correlations of a suite of leaf functional traits involved in climate adaptation for a natural population of the tree Fagus sylvatica, growing at the rear edge of the species range. Using two marker-based quantitative genetics approaches, we obtained consistent and significant estimates of heritability for leaf phenological (phenology of leaf flush), morphological (mass, area, ratio mass/area) and physiological (δ(13)C, nitrogen content) traits. Moreover, we found only one significant positive genetic correlation between leaf area and leaf mass, which likely reflected mechanical constraints. We conclude first that the studied population has considerable genetic diversity for important ecophysiological traits regarding drought adaptation and, second, that genetic correlations are not likely to impose strong genetic constraints to future population evolution. Our results bring important insights into the question of the capacity of rear edge populations to evolve. PMID:26679342

  19. NOTE: Fluoroscopic gating without implanted fiducial markers for lung cancer radiotherapy based on support vector machines

    NASA Astrophysics Data System (ADS)

    Cui, Ying; Dy, Jennifer G.; Alexander, Brian; Jiang, Steve B.

    2008-08-01

    Various problems with the current state-of-the-art techniques for gated radiotherapy have prevented this new treatment modality from being widely implemented in clinical routine. These problems are caused mainly by applying various external respiratory surrogates. There might be large uncertainties in deriving the tumor position from external respiratory surrogates. While tracking implanted fiducial markers has sufficient accuracy, this procedure may not be widely accepted due to the risk of pneumothorax. Previously, we have developed a technique to generate gating signals from fluoroscopic images without implanted fiducial markers using template matching methods (Berbeco et al 2005 Phys. Med. Biol. 50 4481-90, Cui et al 2007b Phys. Med. Biol. 52 741-55). In this note, our main contribution is to provide a totally different new view of the gating problem by recasting it as a classification problem. Then, we solve this classification problem by a well-studied powerful classification method called a support vector machine (SVM). Note that the goal of an automated gating tool is to decide when to turn the beam ON or OFF. We treat ON and OFF as the two classes in our classification problem. We create our labeled training data during the patient setup session by utilizing the reference gating signal, manually determined by a radiation oncologist. We then pre-process these labeled training images and build our SVM prediction model. During treatment delivery, fluoroscopic images are continuously acquired, pre-processed and sent as an input to the SVM. Finally, our SVM model will output the predicted labels as gating signals. We test the proposed technique on five sequences of fluoroscopic images from five lung cancer patients against the reference gating signal as ground truth. We compare the performance of the SVM to our previous template matching method (Cui et al 2007b Phys. Med. Biol. 52 741-55). We find that the SVM is slightly more accurate on average (1-3%) than

  20. Development of InDel markers for Brassica rapa based on whole-genome re-sequencing.

    PubMed

    Liu, Bo; Wang, Yan; Zhai, Wen; Deng, Jie; Wang, Hui; Cui, Yang; Cheng, Feng; Wang, Xiaowu; Wu, Jian

    2013-01-01

    Genome-wide detection of short insertion/deletion length polymorphisms (InDels, <5 bp) in Brassica rapa (named the A genome) was performed by comparing whole-genome re-sequencing data from two B. rapa accessions, L144 and Z16, to the reference genome sequence of Chiifu-401-42. In total, we identified 108,558 InDel polymorphisms between Chiifu-401-42 and L144, 26,795 InDels between Z16 and Chiifu-401-42, and 26,693 InDels between L144 and Z16. From these, 639 InDel polymorphisms of 3-5 bp in length between L144 and Z16 were selected for experimental validation; 491 (77%) yielded single PCR fragments and showed polymorphisms, 7 (1%) did not amplify a product, and 141 (22%) showed no polymorphism. For further validation of these intra-specific InDel polymorphisms, 503 candidates, randomly selected from the 639 InDels, were screened across seven accessions representing different B. rapa cultivar groups. Of these assayed markers, 387 (77%) were polymorphic, 111 (22%) were not polymorphic and 5 (1%) did not amplify a PCR product. Furthermore, we randomly selected 518 InDel markers to validate their polymorphism in B. napus (the AC genome) and B. juncea (the AB genome), of which more than 90% amplified a PCR product; 132 (25%) showed polymorphism between the two B. napus accessions and 41 (8%) between the two B. juncea accessions. This set of novel PCR-based InDel markers will be a valuable resource for genetic studies and breeding programs in B. rapa.

  1. Development of InDel markers for Brassica rapa based on whole-genome re-sequencing.

    PubMed

    Liu, Bo; Wang, Yan; Zhai, Wen; Deng, Jie; Wang, Hui; Cui, Yang; Cheng, Feng; Wang, Xiaowu; Wu, Jian

    2013-01-01

    Genome-wide detection of short insertion/deletion length polymorphisms (InDels, <5 bp) in Brassica rapa (named the A genome) was performed by comparing whole-genome re-sequencing data from two B. rapa accessions, L144 and Z16, to the reference genome sequence of Chiifu-401-42. In total, we identified 108,558 InDel polymorphisms between Chiifu-401-42 and L144, 26,795 InDels between Z16 and Chiifu-401-42, and 26,693 InDels between L144 and Z16. From these, 639 InDel polymorphisms of 3-5 bp in length between L144 and Z16 were selected for experimental validation; 491 (77%) yielded single PCR fragments and showed polymorphisms, 7 (1%) did not amplify a product, and 141 (22%) showed no polymorphism. For further validation of these intra-specific InDel polymorphisms, 503 candidates, randomly selected from the 639 InDels, were screened across seven accessions representing different B. rapa cultivar groups. Of these assayed markers, 387 (77%) were polymorphic, 111 (22%) were not polymorphic and 5 (1%) did not amplify a PCR product. Furthermore, we randomly selected 518 InDel markers to validate their polymorphism in B. napus (the AC genome) and B. juncea (the AB genome), of which more than 90% amplified a PCR product; 132 (25%) showed polymorphism between the two B. napus accessions and 41 (8%) between the two B. juncea accessions. This set of novel PCR-based InDel markers will be a valuable resource for genetic studies and breeding programs in B. rapa. PMID:22972202

  2. [Development of a genetic transformation system for Candida tropicalis based on a reusable selection marker of URA3 gene].

    PubMed

    Xiang, Zheng; Chen, Xianzhong; Zhang, Lihua; Shen, Wei; Fan, You; Lu, Maolin

    2014-10-01

    Candida tropicalis, a diploid asporogenic yeast, is frequently utilized in industrial applications and research studies. However, the low efficiency of genetic transformation limits the strain improvement by metabolic engineering. A reliable transformation and efficient deletion of target gene are prerequisite for molecular improvement of C. tropicalis. In this study, an efficient approach for genetic transformation of C. tropicalis was developed based on the URA3 gene as a reusable selection marker and both of PDC allele genes encoding pyruvate decarboxylase were successfully deleted by this approach. Firstly, an auxotrophic mutant strain of C. tropicalis XZX which is defective in orotidine-5'-phosphate decarboxylase (URA3) was isolated by chemical mutagenesis combined with nystatin enrichment selection and 5-fluoro-orotic acid (5-FOA) resistance selection using C. tropicalis ATCC 20336 as the parent strain. Then, the first PDC deletion cassette PDC1-hisG-URA3-hisG- PDC1 (PHUHP) which contains a 1.6 kb URA3 marker gene, two copies of 1.1 kb Salmonella hisG fragments and homologous arms of target gene was constructed and transformed into C. tropicalis XZX cells. Transformants with a single copy of PDC deleted were isolated and identified by PCR and DNA sequencing, which was designated as C.tropicalis XZX02. The C.tropicalis XZX02 cells were spread on the minimal medium containing 5-FOA to generate mutant C. tropicalis XZX03 in which URA3 marker gene was excised from PHUHP fragment integrated into the PDC gene site. The second PDC gene deletion cassette PDCm-URA3-PDCm (MUM) was constructed and transformed into C. tropicalis XZX03 to generate C.tropicalis XZX04 in which both of PDC allele genes were deleted. All strains were confirmed by PCR and DNA sequencing. This efficient genetic transformation approach laid a foundation for further metabolic engineering of C. tropicalis.

  3. Distinctively variable sequence-based nuclear DNA markers for multilocus phylogeography of the soybean- and rice-infecting fungal pathogen Rhizoctonia solani AG-1 IA

    PubMed Central

    2009-01-01

    A series of multilocus sequence-based nuclear DNA markers was developed to infer the phylogeographical history of the Basidiomycetous fungal pathogen Rhizoctonia solani AG-1 IA infecting rice and soybean worldwide. The strategy was based on sequencing of cloned genomic DNA fragments (previously used as RFLP probes) and subsequent screening of fungal isolates to detect single nucleotide polymorphisms (SNPs). Ten primer pairs were designed based on these sequences, which resulted in PCR amplification of 200-320 bp size products and polymorphic sequences in all markers analyzed. By direct sequencing we identified both homokaryon and heterokaryon (i.e. dikaryon) isolates at each marker. Cloning the PCR products effectively estimated the allelic phase from heterokaryotic isolates. Information content varied among markers from 0.5 to 5.9 mutations per 100 bp. Thus, the former RFLP codominant probes were successfully converted into six distinctively variable sequence-based nuclear DNA markers. Rather than discarding low polymorphism loci, the combination of these distinctively variable anonymous nuclear markers would constitute an asset for the unbiased estimate of the phylogeographical parameters such as population sizes and divergent times, providing a more reliable species history that shaped the current population structure of R. solani AG-1 IA. PMID:21637462

  4. Genetic differentiation between natural and hatchery populations of Manila clam (Ruditapes philippinarum) based on microsatellite markers.

    PubMed

    Xing, K; Gao, M L; Li, H J

    2014-01-17

    Manila clam (Ruditapes philippinarum) is one of the major aquaculture species around the world and supports an important segment of the aquaculture industry in China. In this study, we used ten microsatellite markers to detect genetic diversity within six R. philippinarum populations and genetic differentiation between them. A total of 109 alleles were detected across all loci. Compared to wild populations (N(A) = 8.4-9.1 alleles/locus, H(E) = 0.75-0.77, H(O) = 0.67-0.73), hatchery stocks showed less genetic variation as revealed in lower number of alleles and lower heterozygosity (N(A) = 7.4-7.5 alleles/locus, H(E) = 0.72-0.75, H(O) = 0.68-0.70), indicating that a bottleneck effect has occurred in hatchery history. Significant genetic differentiation was observed between cultured stocks (P < 0.05), and between cultured and wild populations (P < 0.05). Phylogenetic analysis showed a clear separation of the northern three populations and the southern three populations, suggesting that geographically separated populations of R. philippinarum could be genetically differentiated with limited genetic information exchanged between them. The information obtained in this study indicates that the northern and southern populations of R. philippinarum should be managed separately in hatchery practices for the preservation of genetic diversity in wild populations.

  5. A simple PCR-based marker to determine sex in aspen.

    PubMed

    Pakull, B; Kersten, B; Lüneburg, J; Fladung, M

    2015-01-01

    The genus Populus features a genetically controlled sex determination system, located on chromosome 19. However, different Populus species vary in the position of the sex-linked region on the respective chromosome and the apparent heterogametic sex, and the precise mechanism of sex determination in Populus is still unknown. Using next generation sequencing of pooled samples of male and female aspens, we identified the aspen homologue of the P. trichocarpa gene Potri.019G047300 ('TOZ19') to be male-specific. While in P. tremuloides, the complete gene is missing in the genome of female plants, a short fragment of the 3'-part of the gene is still present in P. tremula females. The male-specific presence and transcription of TOZ19 was further verified using PCR in various different aspen individuals and RT-PCR expression analysis. TOZ19 is potentially involved in early steps of flower development, and represents an interesting candidate gene for involvement in sex determination in aspen. Regardless of its role as candidate gene, TOZ19 represents an ideal marker for determination of the sex of non-flowering aspen individuals or seedlings.

  6. Ancestry informative marker panels for African Americans based on subsets of commercially available SNP arrays.

    PubMed

    Tandon, Arti; Patterson, Nick; Reich, David

    2011-01-01

    Admixture mapping is a widely used method for localizing disease genes in African Americans. Most current methods for inferring ancestry at each locus in the genome use a few thousand single nucleotide polymorphisms (SNPs) that are very different in frequency between West Africans and European Americans, and that are required to not be in linkage disequilibrium in the ancestral populations. Modern SNP arrays provide data on hundreds of thousands of SNPs per sample, and to use these to infer ancestry, using many of the standard methods, it is necessary to choose subsets of the SNPs for analysis. Here we present panels of about 4,300 ancestry informative markers (AIMs) that are subsets respectively of SNPs on the Illumina 1 M, Illumina 650, Illumina 610, Affymetrix 6.0 and Affymetrix 5.0 arrays. To validate the usefulness of these panels, we applied them to samples that are different from the ones used to select the SNPs. The panels provide about 80% of the maximum information about African or European ancestry, even with up to 10% missing data.

  7. Comparison of maize similarity and dissimilarity genetic coefficients based on microsatellite markers.

    PubMed

    Balestre, M; Von Pinho, R G; Souza, J C; Lima, J L

    2008-01-01

    The present study compared different similarity and dissimilarity coefficients and their influence in maize inbred line clustering. Ninety maize S0:1 inbred lines were used and genotyped with 25 microsatellite markers (simple sequence repeat). The simple matching, Rogers and Tanimoto, Russel and Rao, Hamann, Jaccard, Sorensen-Dice, Ochiai, and Roger's modified distance coefficients were compared by consensus index, projection efficiency in a two-dimensional space and by Spearman's correlation. Changes were found in high genetic similarity groupings with different coefficients using the consensus index. Russel and Rao and Jaccard coefficients had the greatest stress values with 75.67 and 40.16%, respectively, indicating that these coefficients should not be used. Genotype ranking changed, mainly in the comparison of the Roger's modified distance in relation to some coefficients (rs = 0.75). Russel and Rao's and Jaccard's coefficients should be avoided for their low accuracy. Moreover, genotype clustering by different similarly coefficients, without a close consideration of these coefficients could affect the research results. PMID:18752197

  8. Serum ferritin as prognostic marker in classical Hodgkin lymphoma treated with ABVD-based therapy.

    PubMed

    Fernandez-Alvarez, Ruben; Gonzalez-Rodriguez, Ana P; Gonzalez, M Esther; Rubio-Castro, Arturo; Dominguez-Iglesias, Francisco; Solano, Jackeline; Alonso-Nogues, Eva; Fernandez-Alvarez, Carmen; Zanabili, Yahya; Alonso, Jose Manuel; Payer, Angel Ramirez; Vicente, Jose Maria; Medina, Jesus; Sancho, Juan M

    2015-01-01

    Ferritin levels might correlate with disease activity in classical Hodgkin lymphoma (cHL). We analyzed the prognostic significance of the ferritin value at diagnosis in 173 cHL patients treated with ABVD between 2003 and 2013. The 5-year overall survival (OS) and progression-free survival (PFS) probabilities were 80% and 64%, respectively. Patients with ferritin ≥ 350 μg/l [high ferritin group (HF), n = 62] were more likely to have advanced stage disease, B-symptoms and higher International Prognostic Score (IPS) compared with patients with ferritin < 350 μg/l [low ferritin group (LF), n = 111]. The complete remission (CR) rate and 5-year PFS and OS probabilities were lower in HF vs. LF patients (69% vs. 89%, p = 0.025; 40% vs. 78%, p < 0.001; 61% vs. 90%, p = 0.001; respectively). Multivariate analysis revealed that advanced stage (p = 0.001) and ferritin levels ≥ 350 μg/l (p = 0.002) were independent predictors for PFS. In conclusion, the ferritin level at diagnosis is a useful prognostic marker for cHL.

  9. Microsatellite marker-based genetic analysis of relatedness between commercial and heritage turkeys (Meleagris gallopavo).

    PubMed

    Kamara, D; Gyenai, K B; Geng, T; Hammade, H; Smith, E J

    2007-01-01

    The turkey is second only to the chicken in importance as an agriculturally important poultry species. Unlike the chicken, however, genetic studies of the turkey continue to be limited. For example, to date, many genomic investigations have been conducted to characterize genetic relationships between commercial (CO) and non-CO chicken breeds, whereas the nature of the genetic relatedness between CO and heritage turkeys remains unknown. The objective of the current research was to use microsatellites to analyze the genetic relatedness between CO and heritage domestic turkeys including Narragansett, Bourbon Red, Blue Slate, Spanish Black, and Royal Palm. Primer pairs specific for 10 previously described turkey microsatellite markers were used. The phylogenetic analysis showed that the Blue Slate, Bourbon Red, and Narragansett were genetically closely related to the CO strain, with a Nei distance of 0.30, and the Royal Palm and Spanish Black were the least related to the CO strain, with Nei distances of 0.41 and 0.40, respectively. The present work provides a foundation for the basis of using heritage turkeys to genetically improve CO populations by introgression.

  10. Current breast cancer proliferative markers correlate variably based on decoupled duration of cell cycle phases

    PubMed Central

    Lee, Lik Hang; Yang, Hua; Bigras, Gilbert

    2014-01-01

    Mitotic count, PhH3, and MIB-1 are used as measures of the proportion of proliferating malignant cells in surgical pathology. They highlight different stages of the cell cycle, but little is known about how this affects their counts. This study assesses the strength of their correlations and attempts to determine the relationship between them. Proliferation counts for forty-nine consecutive cases of invasive breast carcinomas were analyzed, with the same tumor area on each stain counted using digital image analysis. The integrated optical density (IOD) of nuclei was measured as an approximation of nuclear DNA content. PhH3 strongly correlated with mitotic count (r = 0.94). Weaker correlations were found between MIB-1 versus PhH3 (r = 0.79) and mitotic count (r = 0.83). Nuclear IOD showed stronger correlation with MIB-1 (r = 0.37) than to mitotic count (r = 0.23) and PhH3 (r = 0.34). With evidence from a literature review, it is suggested that the weaker correlations with MIB-1 are not explained by count imprecision or error, but relies on temporal decorrelation between cell cycle phases. Consequences on correlation between these proliferative markers are illustrated by mathematical models. PMID:24874299

  11. Tumor Heterogeneity: Mechanisms and Bases for a Reliable Application of Molecular Marker Design

    PubMed Central

    Diaz-Cano, Salvador J.

    2012-01-01

    Tumor heterogeneity is a confusing finding in the assessment of neoplasms, potentially resulting in inaccurate diagnostic, prognostic and predictive tests. This tumor heterogeneity is not always a random and unpredictable phenomenon, whose knowledge helps designing better tests. The biologic reasons for this intratumoral heterogeneity would then be important to understand both the natural history of neoplasms and the selection of test samples for reliable analysis. The main factors contributing to intratumoral heterogeneity inducing gene abnormalities or modifying its expression include: the gradient ischemic level within neoplasms, the action of tumor microenvironment (bidirectional interaction between tumor cells and stroma), mechanisms of intercellular transference of genetic information (exosomes), and differential mechanisms of sequence-independent modifications of genetic material and proteins. The intratumoral heterogeneity is at the origin of tumor progression and it is also the byproduct of the selection process during progression. Any analysis of heterogeneity mechanisms must be integrated within the process of segregation of genetic changes in tumor cells during the clonal expansion and progression of neoplasms. The evaluation of these mechanisms must also consider the redundancy and pleiotropism of molecular pathways, for which appropriate surrogate markers would support the presence or not of heterogeneous genetics and the main mechanisms responsible. This knowledge would constitute a solid scientific background for future therapeutic planning. PMID:22408433

  12. Diversity analysis in Cannabis sativa based on large-scale development of expressed sequence tag-derived simple sequence repeat markers.

    PubMed

    Gao, Chunsheng; Xin, Pengfei; Cheng, Chaohua; Tang, Qing; Chen, Ping; Wang, Changbiao; Zang, Gonggu; Zhao, Lining

    2014-01-01

    Cannabis sativa L. is an important economic plant for the production of food, fiber, oils, and intoxicants. However, lack of sufficient simple sequence repeat (SSR) markers has limited the development of cannabis genetic research. Here, large-scale development of expressed sequence tag simple sequence repeat (EST-SSR) markers was performed to obtain more informative genetic markers, and to assess genetic diversity in cannabis (Cannabis sativa L.). Based on the cannabis transcriptome, 4,577 SSRs were identified from 3,624 ESTs. From there, a total of 3,442 complementary primer pairs were designed as SSR markers. Among these markers, trinucleotide repeat motifs (50.99%) were the most abundant, followed by hexanucleotide (25.13%), dinucleotide (16.34%), tetranucloetide (3.8%), and pentanucleotide (3.74%) repeat motifs, respectively. The AAG/CTT trinucleotide repeat (17.96%) was the most abundant motif detected in the SSRs. One hundred and seventeen EST-SSR markers were randomly selected to evaluate primer quality in 24 cannabis varieties. Among these 117 markers, 108 (92.31%) were successfully amplified and 87 (74.36%) were polymorphic. Forty-five polymorphic primer pairs were selected to evaluate genetic diversity and relatedness among the 115 cannabis genotypes. The results showed that 115 varieties could be divided into 4 groups primarily based on geography: Northern China, Europe, Central China, and Southern China. Moreover, the coefficient of similarity when comparing cannabis from Northern China with the European group cannabis was higher than that when comparing with cannabis from the other two groups, owing to a similar climate. This study outlines the first large-scale development of SSR markers for cannabis. These data may serve as a foundation for the development of genetic linkage, quantitative trait loci mapping, and marker-assisted breeding of cannabis.

  13. Diversity analysis in Cannabis sativa based on large-scale development of expressed sequence tag-derived simple sequence repeat markers.

    PubMed

    Gao, Chunsheng; Xin, Pengfei; Cheng, Chaohua; Tang, Qing; Chen, Ping; Wang, Changbiao; Zang, Gonggu; Zhao, Lining

    2014-01-01

    Cannabis sativa L. is an important economic plant for the production of food, fiber, oils, and intoxicants. However, lack of sufficient simple sequence repeat (SSR) markers has limited the development of cannabis genetic research. Here, large-scale development of expressed sequence tag simple sequence repeat (EST-SSR) markers was performed to obtain more informative genetic markers, and to assess genetic diversity in cannabis (Cannabis sativa L.). Based on the cannabis transcriptome, 4,577 SSRs were identified from 3,624 ESTs. From there, a total of 3,442 complementary primer pairs were designed as SSR markers. Among these markers, trinucleotide repeat motifs (50.99%) were the most abundant, followed by hexanucleotide (25.13%), dinucleotide (16.34%), tetranucloetide (3.8%), and pentanucleotide (3.74%) repeat motifs, respectively. The AAG/CTT trinucleotide repeat (17.96%) was the most abundant motif detected in the SSRs. One hundred and seventeen EST-SSR markers were randomly selected to evaluate primer quality in 24 cannabis varieties. Among these 117 markers, 108 (92.31%) were successfully amplified and 87 (74.36%) were polymorphic. Forty-five polymorphic primer pairs were selected to evaluate genetic diversity and relatedness among the 115 cannabis genotypes. The results showed that 115 varieties could be divided into 4 groups primarily based on geography: Northern China, Europe, Central China, and Southern China. Moreover, the coefficient of similarity when comparing cannabis from Northern China with the European group cannabis was higher than that when comparing with cannabis from the other two groups, owing to a similar climate. This study outlines the first large-scale development of SSR markers for cannabis. These data may serve as a foundation for the development of genetic linkage, quantitative trait loci mapping, and marker-assisted breeding of cannabis. PMID:25329551

  14. Grave Markers.

    ERIC Educational Resources Information Center

    DeMuro, Ted

    1985-01-01

    Junior high school students studied the cultural uses, symbolic meanings, and general physical forms of tombs and tombstones and then used basic slab building techniques to construct large clay grave markers. (RM)

  15. Markers and mapping revisited: finding your gene.

    PubMed

    Jones, Neil; Ougham, Helen; Thomas, Howard; Pasakinskiene, Izolda

    2009-01-01

    This paper is an update of our earlier review (Jones et al., 1997, Markers and mapping: we are all geneticists now. New Phytologist 137: 165-177), which dealt with the genetics of mapping, in terms of recombination as the basis of the procedure, and covered some of the first generation of markers, including restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPDs), simple sequence repeats (SSRs) and quantitative trait loci (QTLs). In the intervening decade there have been numerous developments in marker science with many new systems becoming available, which are herein described: cleavage amplification polymorphism (CAP), sequence-specific amplification polymorphism (S-SAP), inter-simple sequence repeat (ISSR), sequence tagged site (STS), sequence characterized amplification region (SCAR), selective amplification of microsatellite polymorphic loci (SAMPL), single nucleotide polymorphism (SNP), expressed sequence tag (EST), sequence-related amplified polymorphism (SRAP), target region amplification polymorphism (TRAP), microarrays, diversity arrays technology (DArT), single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE) and methylation-sensitive PCR. In addition there has been an explosion of knowledge and databases in the area of genomics and bioinformatics. The number of flowering plant ESTs is c. 19 million and counting, with all the opportunity that this provides for gene-hunting, while the survey of bioinformatics and computer resources points to a rapid growth point for future activities in unravelling and applying the burst of new information on plant genomes. A case study is presented on tracking down a specific gene (stay-green (SGR), a post-transcriptional senescence regulator) using the full suite of mapping tools and comparative mapping resources. We end with a brief speculation on how genome analysis may progress into the future of

  16. Blu-ray Technology-Based Quantitative Assays for Cardiac Markers: From Disc Activation to Multiplex Detection.

    PubMed

    Weng, Samuel; Li, Xiaochun; Niu, Michelle; Ge, Bixia; Yu, Hua-Zhong

    2016-07-01

    Acute myocardial infarction (AMI) is the leading cause of mortality and morbidity globally. To reduce the number of mortalities, reliable and rapid point-of-care (POC) diagnosis of AMI is extremely critical. We herein present a Blu-ray technology-based assay platform for multiplex cardiac biomarker detection; not only off-the-shelf Blu-ray discs (BDs) were adapted as substrates to prepare standard immunoassays and DNA aptamer/antibody hybrid assays for the three key cardiac marker proteins (myoglobin, troponin I, and C-creative protein) but also an unmodified optical drive was directly employed to read the assay results digitally. In particular, we have shown that all three cardiac markers can be quantitated in their respective physiological ranges of interest, and the detection limits achieved are comparable with conventional enzyme-linked immunosorbent assay (ELISA) kits. The Blu-ray assay platform was further validated by measuring real-world samples and establishing a linear correlation with the simultaneously obtained ELISA data. Without the need to modify either the hardware (Blu-ray discs and optical drives) or the software driver, this assay-on-a-BD technique promises to be a low-cost user-friendly quantitative tool for on-site chemical analysis and POC medical diagnosis.

  17. Revisiting the phylogeography and demography of European badgers (Meles meles) based on broad sampling, multiple markers and simulations.

    PubMed

    Frantz, A C; McDevitt, A D; Pope, L C; Kochan, J; Davison, J; Clements, C F; Elmeros, M; Molina-Vacas, G; Ruiz-Gonzalez, A; Balestrieri, A; Van Den Berge, K; Breyne, P; Do Linh San, E; Agren, E O; Suchentrunk, F; Schley, L; Kowalczyk, R; Kostka, B I; Cirović, D; Sprem, N; Colyn, M; Ghirardi, M; Racheva, V; Braun, C; Oliveira, R; Lanszki, J; Stubbe, A; Stubbe, M; Stier, N; Burke, T

    2014-11-01

    Although the phylogeography of European mammals has been extensively investigated since the 1990s, many studies were limited in terms of sampling distribution, the number of molecular markers used and the analytical techniques employed, frequently leading to incomplete postglacial recolonisation scenarios. The broad-scale genetic structure of the European badger (Meles meles) is of interest as it may result from historic restriction to glacial refugia and/or recent anthropogenic impact. However, previous studies were based mostly on samples from western Europe, making it difficult to draw robust conclusions about the location of refugia, patterns of postglacial expansion and recent demography. In the present study, continent-wide sampling and analyses with multiple markers provided evidence for two glacial refugia (Iberia and southeast Europe) that contributed to the genetic variation observed in badgers in Europe today. Approximate Bayesian computation provided support for a colonisation of Scandinavia from both Iberian and southeastern refugia. In the whole of Europe, we observed a decline in genetic diversity with increasing latitude, suggesting that the reduced diversity in the peripheral populations resulted from a postglacial expansion processes. Although MSVAR v.1.3 also provided evidence for recent genetic bottlenecks in some of these peripheral populations, the simulations performed to estimate the method's power to correctly infer the past demography of our empirical populations suggested that the timing and severity of bottlenecks could not be established with certainty. We urge caution against trying to relate demographic declines inferred using MSVAR with particular historic or climatological events. PMID:24781805

  18. Molecular Phylogeny of a tick, Ixodes granulatus (Acari: Ixodidae) based on cytochrome oxidase subunit I (COI) marker

    NASA Astrophysics Data System (ADS)

    Lah, Ernieenor Faraliana Che; Yaakop, Salmah; Ahamad, Mariana; George, Ernna; Nor, Shukor Md

    2014-09-01

    Identification of a local species of tick, Ixodes granulatus from the family Ixodidae is essential because it has potential to be vector for spotted fever group (SFG) rickettsia and tick thypus. The aim of this study is to portray the relationships among several populations of I. granulatus collected from different species of animal hosts and localities in Peninsular Malaysia. Polymerase Chain Reaction was conducted by amplifying mitochondrial DNA marker, namely cytochrome oxidase subunit I (COI) sequences from 15 individual ticks that attached to five different hosts caught from three different localities. Confirmation of the species identity was accomplished using BLAST program. Neighbor-joining (NJ) and Maximum Parsimony (MP) tree based on COI sequences were constructed by using PAUP 4.0b10 to identify the relationship among species. The result of this study showed a high genetic heterogeneity between I. granulatus and other species of the same genus (7.2-23.7%). Furthermore, a low intraspecific variation was observed among the species of I. granulatus collected from different localities (0-3.7%). This study produced the first establishment of molecular marker for clarifying genetic species variation and diversity of local I. granulatus tick which contribute to the control of tick-borne infections.

  19. Blu-ray Technology-Based Quantitative Assays for Cardiac Markers: From Disc Activation to Multiplex Detection.

    PubMed

    Weng, Samuel; Li, Xiaochun; Niu, Michelle; Ge, Bixia; Yu, Hua-Zhong

    2016-07-01

    Acute myocardial infarction (AMI) is the leading cause of mortality and morbidity globally. To reduce the number of mortalities, reliable and rapid point-of-care (POC) diagnosis of AMI is extremely critical. We herein present a Blu-ray technology-based assay platform for multiplex cardiac biomarker detection; not only off-the-shelf Blu-ray discs (BDs) were adapted as substrates to prepare standard immunoassays and DNA aptamer/antibody hybrid assays for the three key cardiac marker proteins (myoglobin, troponin I, and C-creative protein) but also an unmodified optical drive was directly employed to read the assay results digitally. In particular, we have shown that all three cardiac markers can be quantitated in their respective physiological ranges of interest, and the detection limits achieved are comparable with conventional enzyme-linked immunosorbent assay (ELISA) kits. The Blu-ray assay platform was further validated by measuring real-world samples and establishing a linear correlation with the simultaneously obtained ELISA data. Without the need to modify either the hardware (Blu-ray discs and optical drives) or the software driver, this assay-on-a-BD technique promises to be a low-cost user-friendly quantitative tool for on-site chemical analysis and POC medical diagnosis. PMID:27268387

  20. Revisiting the phylogeography and demography of European badgers (Meles meles) based on broad sampling, multiple markers and simulations

    PubMed Central

    Frantz, A C; McDevitt, A D; Pope, L C; Kochan, J; Davison, J; Clements, C F; Elmeros, M; Molina-Vacas, G; Ruiz-Gonzalez, A; Balestrieri, A; Van Den Berge, K; Breyne, P; Do Linh San, E; Ågren, E O; Suchentrunk, F; Schley, L; Kowalczyk, R; Kostka, B I; Ćirović, D; Šprem, N; Colyn, M; Ghirardi, M; Racheva, V; Braun, C; Oliveira, R; Lanszki, J; Stubbe, A; Stubbe, M; Stier, N; Burke, T

    2014-01-01

    Although the phylogeography of European mammals has been extensively investigated since the 1990s, many studies were limited in terms of sampling distribution, the number of molecular markers used and the analytical techniques employed, frequently leading to incomplete postglacial recolonisation scenarios. The broad-scale genetic structure of the European badger (Meles meles) is of interest as it may result from historic restriction to glacial refugia and/or recent anthropogenic impact. However, previous studies were based mostly on samples from western Europe, making it difficult to draw robust conclusions about the location of refugia, patterns of postglacial expansion and recent demography. In the present study, continent-wide sampling and analyses with multiple markers provided evidence for two glacial refugia (Iberia and southeast Europe) that contributed to the genetic variation observed in badgers in Europe today. Approximate Bayesian computation provided support for a colonisation of Scandinavia from both Iberian and southeastern refugia. In the whole of Europe, we observed a decline in genetic diversity with increasing latitude, suggesting that the reduced diversity in the peripheral populations resulted from a postglacial expansion processes. Although MSVAR v.1.3 also provided evidence for recent genetic bottlenecks in some of these peripheral populations, the simulations performed to estimate the method's power to correctly infer the past demography of our empirical populations suggested that the timing and severity of bottlenecks could not be established with certainty. We urge caution against trying to relate demographic declines inferred using MSVAR with particular historic or climatological events. PMID:24781805

  1. Revisiting the phylogeography and demography of European badgers (Meles meles) based on broad sampling, multiple markers and simulations.

    PubMed

    Frantz, A C; McDevitt, A D; Pope, L C; Kochan, J; Davison, J; Clements, C F; Elmeros, M; Molina-Vacas, G; Ruiz-Gonzalez, A; Balestrieri, A; Van Den Berge, K; Breyne, P; Do Linh San, E; Agren, E O; Suchentrunk, F; Schley, L; Kowalczyk, R; Kostka, B I; Cirović, D; Sprem, N; Colyn, M; Ghirardi, M; Racheva, V; Braun, C; Oliveira, R; Lanszki, J; Stubbe, A; Stubbe, M; Stier, N; Burke, T

    2014-11-01

    Although the phylogeography of European mammals has been extensively investigated since the 1990s, many studies were limited in terms of sampling distribution, the number of molecular markers used and the analytical techniques employed, frequently leading to incomplete postglacial recolonisation scenarios. The broad-scale genetic structure of the European badger (Meles meles) is of interest as it may result from historic restriction to glacial refugia and/or recent anthropogenic impact. However, previous studies were based mostly on samples from western Europe, making it difficult to draw robust conclusions about the location of refugia, patterns of postglacial expansion and recent demography. In the present study, continent-wide sampling and analyses with multiple markers provided evidence for two glacial refugia (Iberia and southeast Europe) that contributed to the genetic variation observed in badgers in Europe today. Approximate Bayesian computation provided support for a colonisation of Scandinavia from both Iberian and southeastern refugia. In the whole of Europe, we observed a decline in genetic diversity with increasing latitude, suggesting that the reduced diversity in the peripheral populations resulted from a postglacial expansion processes. Although MSVAR v.1.3 also provided evidence for recent genetic bottlenecks in some of these peripheral populations, the simulations performed to estimate the method's power to correctly infer the past demography of our empirical populations suggested that the timing and severity of bottlenecks could not be established with certainty. We urge caution against trying to relate demographic declines inferred using MSVAR with particular historic or climatological events.

  2. Genetic Structure of Lutzomyia longipalpis Populations in Mato Grosso Do Sul, Brazil, Based on Microsatellite Markers

    PubMed Central

    Santos, Mirella F. C.; Ribolla, Paulo E. M.; Alonso, Diego P.; Andrade-Filho, José D.; Casaril, Aline E.; Ferreira, Alda M. T.; Fernandes, Carlos E. S.; Brazil, Reginaldo P.; Oliveira, Alessandra G.

    2013-01-01

    Background Lutzomyialongipalpis (Diptera: Psychodidae) is the major vector of Leishmania (Leishmania) infantum and thus plays a crucial role in the epidemiology of American visceral leishmaniasis (AVL). This vector is the best studied species of sand fly in the Neotropical region. Many studies claim that this vector is in fact a species complex; however there is still no consensus regarding the number of species that belong into this complex or the geographical distribution of sibling species. The aim of the present study was to analyze the genetic relationships within Lu. longipalpis populations in the state of Mato Grosso do Sul (MS), Brazil. Methodology/Principal Findings We collected 30 Lu. longipalpis (15 females and 15 males) from five localities (Campo Grande, Três Lagoas, Aquidauana, Miranda and Bonito) and 30 Lu. Cruzi from Corumbá, totaling 180 sandflies from MS, and 30 Lu. longipalpis from Estrela de Alagoas, state of Alagoas (AL), Northeast Brazil. We show that eight previously described microsatellite loci were sufficient in distinguishing Lu. longipalpis from Lu. Cruzi, which is a closely related species, and in differentiating between Lu. longipalpis collected in MS versus Estrela de Alagoas. Analyses of the genotypes revealed introgression between sympatric Lu. longipalpis and Lu. Cruzi. Conclusions/Significance Our findings support the hypothesis of cryptic species within the Lu. longipalpis complex. Furthermore, our data revealed introgression between Lu. longipalpis and Lu. cruzi. This phenomenon should be further investigated to determine the level and incidence of hybridization between these two species. We also demonstrated that microsatellite markers are a powerful tool for differentiating sand fly populations and species. The present study has elucidated the population structure of Lu. longipalpis in MS and, by extension, the Neotropical Lu. longipalpis complex itself. PMID:24066129

  3. Development of SSR Markers Linked to Low Hydrocyanic Acid Content in Sorghum-Sudan Grass Hybrid Based on BSA Method.

    PubMed

    Xiao-Xia, Yu; Zhi-Hua, Liu; Zhuo, Yu; Yue, Shi; Xiao-Yu, Li

    2016-01-01

    Sorghum-Sudan grass hybrid containing high hydrocyanic acid content can cause hydrocyanic acid poisoning to the livestock and limit the popularization of this forage crop. Molecular markers associated with low hydrocyanic acid content can speed up the process of identification of genotypes with low hydrocyanic acid content. In the present study, 11 polymorphic SSR primers were screened and used for bulked segregant analysis and single marker analysis. Three SSR markers Xtxp7230, Xtxp7375 and Bnlg667960 associated with low hydrocyanic acid content were rapidly identified by BSA. In single marker analysis, six markers Xtxp7230, Xtxp7375, Bnlg667960, Xtxp67-11, Xtxp295-7 and Xtxp12-9 were linked to low hydrocyanic acid content, which explained the proportion of phenotypic variation from 7.6 % to 41.2 %. The markers identified by BSA were also verified by single marker analysis. The three SSR marker bands were then cloned and sequenced for sequence homology analysis in NCBI. It is the first report on the development of molecular markers associated with low hydrocyanic acid content in sorghum- Sudan grass hybrid. These markers will be useful for genetic improvement of low hydrocyanic acid sorghum-Sudan grass hybrid by marker-assisted breeding. PMID:27001403

  4. Development of SSR Markers Linked to Low Hydrocyanic Acid Content in Sorghum-Sudan Grass Hybrid Based on BSA Method.

    PubMed

    Xiao-Xia, Yu; Zhi-Hua, Liu; Zhuo, Yu; Yue, Shi; Xiao-Yu, Li

    2016-01-01

    Sorghum-Sudan grass hybrid containing high hydrocyanic acid content can cause hydrocyanic acid poisoning to the livestock and limit the popularization of this forage crop. Molecular markers associated with low hydrocyanic acid content can speed up the process of identification of genotypes with low hydrocyanic acid content. In the present study, 11 polymorphic SSR primers were screened and used for bulked segregant analysis and single marker analysis. Three SSR markers Xtxp7230, Xtxp7375 and Bnlg667960 associated with low hydrocyanic acid content were rapidly identified by BSA. In single marker analysis, six markers Xtxp7230, Xtxp7375, Bnlg667960, Xtxp67-11, Xtxp295-7 and Xtxp12-9 were linked to low hydrocyanic acid content, which explained the proportion of phenotypic variation from 7.6 % to 41.2 %. The markers identified by BSA were also verified by single marker analysis. The three SSR marker bands were then cloned and sequenced for sequence homology analysis in NCBI. It is the first report on the development of molecular markers associated with low hydrocyanic acid content in sorghum- Sudan grass hybrid. These markers will be useful for genetic improvement of low hydrocyanic acid sorghum-Sudan grass hybrid by marker-assisted breeding.

  5. Residual Seminal Vesicle Displacement in Marker-Based Image-Guided Radiotherapy for Prostate Cancer and the Impact on Margin Design

    SciTech Connect

    Smitsmans, Monique H.P.; Bois, Josien de; Sonke, Jan-Jakob; Catton, Charles N.; Jaffray, David A.; Lebesque, Joos V.; Herk, Marcel van

    2011-06-01

    Purpose: The objectives of this study were to quantify residual interfraction displacement of seminal vesicles (SV) and investigate the efficacy of rotation correction on SV displacement in marker-based prostate image-guided radiotherapy (IGRT). We also determined the effect of marker registration on the measured SV displacement and its impact on margin design. Methods and Materials: SV displacement was determined relative to marker registration by using 296 cone beam computed tomography scans of 13 prostate cancer patients with implanted markers. SV were individually registered in the transverse plane, based on gray-value information. The target registration error (TRE) for the SV due to marker registration inaccuracies was estimated. Correlations between prostate gland rotations and SV displacement and between individual SV displacements were determined. Results: The SV registration success rate was 99%. Displacement amounts of both SVs were comparable. Systematic and random residual SV displacements were 1.6 mm and 2.0 mm in the left-right direction, respectively, and 2.8 mm and 3.1 mm in the anteroposterior (AP) direction, respectively. Rotation correction did not reduce residual SV displacement. Prostate gland rotation around the left-right axis correlated with SV AP displacement (R{sup 2} = 42%); a correlation existed between both SVs for AP displacement (R{sup 2} = 62%); considerable correlation existed between random errors of SV displacement and TRE (R{sup 2} = 34%). Conclusions: Considerable residual SV displacement exists in marker-based IGRT. Rotation correction barely reduced SV displacement, rather, a larger SV displacement was shown relative to the prostate gland that was not captured by the marker position. Marker registration error partly explains SV displacement when correcting for rotations. Correcting for rotations, therefore, is not advisable when SV are part of the target volume. Margin design for SVs should take these uncertainties into

  6. SU-E-J-39: Dosimetric Benefit of Implanted Marker-Based CBCT Setup for Definitive Prostatic Radiotherapy

    SciTech Connect

    Zhen, H; Wu, Z; Bluemenfeld, P; Chu, J; Wang, D

    2015-06-15

    Purpose Daily setup for definitive prostatic radiotherapy is challenged by suboptimal visibility of the prostate boundary and daily variation of rectum shape and position. For patients with improved bowel preparation, we conducted a dosimetric comparison between prostate implanted marker (IM)-based daily setup and anterior rectal wall (ARW)-based setup, with the hypothesis that the former leads to adequate target coverage with better rectal sparing. Methods Five IMRT/VMAT prostate cases with implanted markers were selected for analysis. Daily CBCT showed improvement of the rectal volume compared to planning CT. For each patient, the prostate and rectum were contoured on three CBCT images (fraction 5/15/25) with subsequent physician review. The CBCTs were then registered to a planning CT using IM-based registration. The deviation of ARW positions from planning CT to CBCT were analyzed at various sup-inf levels (−1.8 cm to 1.8 cm from level of prostate center). To estimate the potential dosimetric impact from ARW-based setup, the treatment plans were recalculated using A-P shifts ranging from −1mm to +6mm. Clinically important rectum DVH values including Dmax, D3cc and Dmean were computed. Results For the studied patients, we observed on average 32% rectum volume reduction from planning CT to CBCT. As a Results, the ARW on average shifts posteriorly by −1mm to +5mm, depending on the sup-inf level of observation, with larger shifts observed at more superior levels. Recalculation shows that when ARW shifts 1mm posteriorly, ARW-based CBCT setup leads to a 1.0%, 4.2%, and 3.2% increase in rectum Dmax, D3cc, and Dmean, respectively, compared to IM-based setup. The dosimetric deviations increase to 4.7%, 25.8% and 24.7% when ARW shifts 6mm posteriorly. No significant prostate-only dose difference was observed. Conclusion For patients with improved bowel preparation, IM-based CBCT setup leads to accurate prostate coverage along with significantly lower rectal dose

  7. Can venous base excess replace arterial base excess as a marker of early shock and a predictor of survival in trauma?

    PubMed Central

    Wijaya, Ramesh; Ng, Jia Hui; Ong, Lester; Wong, Andrew Siang Yih

    2016-01-01

    INTRODUCTION Arterial base excess is an established marker of shock and predictor of survival in trauma patients. However, venous blood is more quickly and easily obtained. This study aimed to determine if venous base excess could replace arterial base excess as a marker in trauma patients at presentation and if venous base excess is predictive of survival at 24 hours and one week. METHODS This was a prospective study of 394 trauma patients presenting to the emergency department of a tertiary hospital over a 17-month period. Data on base excess at presentation, vital signs, shock index (SI), injury severity score (ISS), and mortality at 24 hours and one week was collected and analysed. RESULTS Arterial and venous blood gas tests were performed on 260 and 134 patients, respectively. Patients were stratified into groups based on their SI and ISS for analysis. There was no statistical difference between mean venous blood gas and arterial blood gas levels at presentation when SI > 0.7, regardless of ISS (p > 0.05). The mortality rate was 4.57%. Both venous and arterial base excess was lower in nonsurvivors compared to survivors (p < 0.05). However, at 24 hours and one week, the difference in base excess values at presentation between survivors and nonsurvivors was greater when using venous base excess compared to arterial base excess (11.53 vs. 4.28 and 11.41 vs. 2.66, respectively). CONCLUSION In conclusion, venous base excess can replace arterial base excess in trauma patients as a means of identifying and prognosticating early shock. PMID:26892937

  8. An apricot (Prunus armeniaca L.) F2 progeny linkage map based on SSR and AFLP markers, mapping plum pox virus resistance and self-incompatibility traits.

    PubMed

    Vilanova, S; Romero, C; Abbott, A G; Llácer, G; Badenes, M L

    2003-07-01

    A genetic linkage map of apricot ( Prunus armeniaca L.) was constructed using AFLP and SSR markers. The map is based on an F(2) population (76 individuals) derived from self-pollination of an F(1) individual ('Lito') originated from a cross between 'Stark Early Orange' and 'Tyrinthos'. This family, designated as 'Lito' x 'Lito', segregated for two important agronomical traits: plum pox virus resistance (PPV) and self-incompatibility. A total of 211 markers (180 AFLPs, 29 SSRs and two agronomic traits) were assigned to 11 linkage groups covering 602 cM of the apricot genome. The average distance (cM/marker) between adjacent markers is 3.84 cM. The PPV resistance trait was mapped on linkage group G1 and the self-incompatibility trait was mapped on linkage group G6. Twenty two loci held in common with other Prunus maps allowed us to compare and establish homologies among the respective linkage groups.

  9. A Brassica rapa linkage map of EST-based SNP markers for identification of candidate genes controlling flowering time and leaf morphological traits.

    PubMed

    Li, Feng; Kitashiba, Hiroyasu; Inaba, Kiyofumi; Nishio, Takeshi

    2009-12-01

    For identification of genes responsible for varietal differences in flowering time and leaf morphological traits, we constructed a linkage map of Brassica rapa DNA markers including 170 EST-based markers, 12 SSR markers, and 59 BAC sequence-based markers, of which 151 are single nucleotide polymorphism (SNP) markers. By BLASTN, 223 markers were shown to have homologous regions in Arabidopsis thaliana, and these homologous loci covered nearly the whole genome of A. thaliana. Synteny analysis between B. rapa and A. thaliana revealed 33 large syntenic regions. Three quantitative trait loci (QTLs) for flowering time were detected. BrFLC1 and BrFLC2 were linked to the QTLs for bolting time, budding time, and flowering time. Three SNPs in the promoter, which may be the cause of low expression of BrFLC2 in the early-flowering parental line, were identified. For leaf lobe depth and leaf hairiness, one major QTL corresponding to a syntenic region containing GIBBERELLIN 20 OXIDASE 3 and one major QTL containing BrGL1, respectively, were detected. Analysis of nucleotide sequences and expression of these genes suggested possible involvement of these genes in leaf morphological traits.

  10. A Brassica rapa Linkage Map of EST-based SNP Markers for Identification of Candidate Genes Controlling Flowering Time and Leaf Morphological Traits

    PubMed Central

    Li, Feng; Kitashiba, Hiroyasu; Inaba, Kiyofumi; Nishio, Takeshi

    2009-01-01

    For identification of genes responsible for varietal differences in flowering time and leaf morphological traits, we constructed a linkage map of Brassica rapa DNA markers including 170 EST-based markers, 12 SSR markers, and 59 BAC sequence-based markers, of which 151 are single nucleotide polymorphism (SNP) markers. By BLASTN, 223 markers were shown to have homologous regions in Arabidopsis thaliana, and these homologous loci covered nearly the whole genome of A. thaliana. Synteny analysis between B. rapa and A. thaliana revealed 33 large syntenic regions. Three quantitative trait loci (QTLs) for flowering time were detected. BrFLC1 and BrFLC2 were linked to the QTLs for bolting time, budding time, and flowering time. Three SNPs in the promoter, which may be the cause of low expression of BrFLC2 in the early-flowering parental line, were identified. For leaf lobe depth and leaf hairiness, one major QTL corresponding to a syntenic region containing GIBBERELLIN 20 OXIDASE 3 and one major QTL containing BrGL1, respectively, were detected. Analysis of nucleotide sequences and expression of these genes suggested possible involvement of these genes in leaf morphological traits. PMID:19884167

  11. Restricted Gene Flow for Gadus macrocephalus from Yellow Sea Based on Microsatellite Markers: Geographic Block of Tsushima Current

    PubMed Central

    Song, Na; Liu, Ming; Yanagimoto, Takashi; Sakurai, Yasunori; Han, Zhi-Qiang; Gao, Tian-Xiang

    2016-01-01

    The Pacific cod Gadus macrocephalus is a demersal, economically important fish in the family Gadidae. Population genetic differentiation of Pacific cod was examined across its northwestern Pacific range by screening variation of eight microsatellite loci in the present study. All four populations exhibited high genetic diversity. Pairwise fixation index (Fst) suggested a moderate to high level of genetic differentiation among populations. Population of the Yellow Sea (YS) showed higher genetic difference compared to the other three populations based on the results of pairwise Fst, three-dimensional factorial correspondence analysis (3D-FCA) and STRUCTURE, which implied restricted gene flow among them. Wilcoxon signed rank tests suggested no significant heterozygosity excess and no recent genetic bottleneck events were detected. Microsatellite DNA is an effective molecular marker for detecting the phylogeographic pattern of Pacific cod, and these Pacific cod populations should be three management units. PMID:27043534

  12. Are implicit motives revealed in mere words? Testing the marker-word hypothesis with computer-based text analysis

    PubMed Central

    Schultheiss, Oliver C.

    2013-01-01

    Traditionally, implicit motives (i.e., non-conscious preferences for specific classes of incentives) are assessed through semantic coding of imaginative stories. The present research tested the marker-word hypothesis, which states that implicit motives are reflected in the frequencies of specific words. Using Linguistic Inquiry and Word Count (LIWC; Pennebaker et al., 2001), Study 1 identified word categories that converged with a content-coding measure of the implicit motives for power, achievement, and affiliation in picture stories collected in German and US student samples, showed discriminant validity with self-reported motives, and predicted well-validated criteria of implicit motives (gender difference for the affiliation motive; in interaction with personal-goal progress: emotional well-being). Study 2 demonstrated LIWC-based motive scores' causal validity by documenting their sensitivity to motive arousal. PMID:24137149

  13. Vitamin D-rich marine Inuit diet and markers of inflammation - a population-based survey in Greenland.

    PubMed

    Schæbel, L K; Bonefeld-Jørgensen, E C; Laurberg, P; Vestergaard, H; Andersen, S

    2015-01-01

    The traditional Inuit diet in Greenland consists mainly of fish and marine mammals, rich in vitamin D. Vitamin D has anti-inflammatory capacity but markers of inflammation have been found to be high in Inuit living on a marine diet. Yet, the effect of vitamin D on inflammation in Inuit remains unsettled. This led us to investigate the association between vitamin D and markers of inflammation in a population with a high intake of a marine diet. We studied 535 Inuit and non-Inuit living in West and East Greenland. Information concerning dietary habits was obtained by interview-based FFQ. Blood samples were drawn for analysis of 25-hydroxyvitamin D, high-sensitivity C-reactive protein (hsCRP) and chitinase-3-like protein 1(YKL-40). Participants were divided into three groups based on degree of intake of the traditional Inuit diet. The diet groups (Inuit diet/mixed diet/imported foods) were associated with vitamin D levels in serum (74·2, 69·8 and 52·9 nm; P < 0·001), hsCRP (1·6, 1·4 and 1·3 mg/l; P = 0·002) and YKL-40 (130, 95 and 61 ng/ml; P < 0·001), respectively. YKL-40 level decreased with rising vitamin D level in Inuit (Inuit diet P = 0·002; mixed diet P = 0·011). YKL-40 was lower in groups with higher vitamin D levels after adjusting for other factors known to influence inflammation (P < 0·001). This was not seen for hsCRP. In conclusion, vitamin D and markers of inflammation vary in parallel with the intake of the marine Inuit diet. Vitamin D levels were inversely associated with YKL-40 levels, but no association with hsCRP was found. The hypothesised anti-inflammatory effect of vitamin D was not supported. Other factors in the marine diet may be speculated to influence inflammation.

  14. Development of Gene-Based SSR Markers in Rice Bean (Vigna umbellata L.) Based on Transcriptome Data

    PubMed Central

    Chen, Honglin; Chen, Xin; Tian, Jing; Yang, Yong; Liu, Zhenxing; Hao, Xiyu; Wang, Lixia; Wang, Suhua; Liang, Jie; Zhang, Liya; Yin, Fengxiang; Cheng, Xuzhen

    2016-01-01

    Rice bean (Vigna umbellata (Thunb.) Ohwi & Ohashi) is a warm season annual legume mainly grown in East Asia. Only scarce genomic resources are currently available for this legume crop species and no simple sequence repeat (SSR) markers have been specifically developed for rice bean yet. In this study, approximately 26 million high quality cDNA sequence reads were obtained from rice bean using Illumina paired-end sequencing technology and assembled into 71,929 unigenes with an average length of 986 bp. Of these unigenes, 38,840 (33.2%) showed significant similarity to proteins in the NCBI non-redundant protein and nucleotide sequence databases. Furthermore, 30,170 (76.3%) could be classified into gene ontology categories, 25,451 (64.4%) into Swiss-Prot categories and 21,982 (55.6%) into KOG database categories (E-value < 1.0E-5). A total of 9,301 (23.5%) were mapped onto 118 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway database. A total of 3,011 genic SSRs were identified as potential molecular markers. AG/CT (30.3%), AAG/CTT (8.1%) and AGAA/TTCT (20.0%) are the three main repeat motifs. A total of 300 SSR loci were randomly selected for validation by using PCR amplification. Of these loci, 23 primer pairs were polymorphic among 32 rice bean accessions. A UPGMA dendrogram revealed three major clusters among 32 rice bean accessions. The large number of SSR-containing sequences and genic SSRs in this study will be valuable for the construction of high-resolution genetic linkage maps, association or comparative mapping and genetic analyses of various Vigna species. PMID:26950544

  15. Development of Gene-Based SSR Markers in Rice Bean (Vigna umbellata L.) Based on Transcriptome Data.

    PubMed

    Chen, Honglin; Chen, Xin; Tian, Jing; Yang, Yong; Liu, Zhenxing; Hao, Xiyu; Wang, Lixia; Wang, Suhua; Liang, Jie; Zhang, Liya; Yin, Fengxiang; Cheng, Xuzhen

    2016-01-01

    Rice bean (Vigna umbellata (Thunb.) Ohwi & Ohashi) is a warm season annual legume mainly grown in East Asia. Only scarce genomic resources are currently available for this legume crop species and no simple sequence repeat (SSR) markers have been specifically developed for rice bean yet. In this study, approximately 26 million high quality cDNA sequence reads were obtained from rice bean using Illumina paired-end sequencing technology and assembled into 71,929 unigenes with an average length of 986 bp. Of these unigenes, 38,840 (33.2%) showed significant similarity to proteins in the NCBI non-redundant protein and nucleotide sequence databases. Furthermore, 30,170 (76.3%) could be classified into gene ontology categories, 25,451 (64.4%) into Swiss-Prot categories and 21,982 (55.6%) into KOG database categories (E-value < 1.0E-5). A total of 9,301 (23.5%) were mapped onto 118 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway database. A total of 3,011 genic SSRs were identified as potential molecular markers. AG/CT (30.3%), AAG/CTT (8.1%) and AGAA/TTCT (20.0%) are the three main repeat motifs. A total of 300 SSR loci were randomly selected for validation by using PCR amplification. Of these loci, 23 primer pairs were polymorphic among 32 rice bean accessions. A UPGMA dendrogram revealed three major clusters among 32 rice bean accessions. The large number of SSR-containing sequences and genic SSRs in this study will be valuable for the construction of high-resolution genetic linkage maps, association or comparative mapping and genetic analyses of various Vigna species.

  16. PNA-based microbial pathogen identification and resistance marker detection: an accurate, isothermal rapid assay based on genome-specific features

    PubMed Central

    Smolina, Irina; Miller, Nancy S.; Frank-Kamenetskii, Maxim

    2010-01-01

    With the rapidly growing availability of the entire genome sequences of microbial pathogens, there is unmet need for increasingly sensitive systems to monitor the gene-specific markers for diagnosis of bacteremia that enables an earlier detection of causative agent and determination of drug resistance. To address these challenges, a novel FISH-type genomic sequence-based molecular technique is proposed that can identify bacteria and simultaneously detect antibiotic resistance markers for rapid and accurate testing of pathogens. The approach is based on a synergistic combination of advanced Peptide Nucleic Acid (PNA)-based technology and signal-enhancing Rolling Circle Amplification (RCA) reaction to achieve a highly specific and sensitive assay. A specific PNA-DNA construct serves as an exceedingly selective and very effective biomarker, while RCA enhances detection sensitivity and provide with a highly multiplexed assay system. Distinct-color fluorescent decorator probes are used to identify about 20-nucleotide-long signature sequences in bacterial genomic DNA and/or key genetic markers of drug resistance in order to identify and characterize various pathogens. The technique's potential and its utility for clinical diagnostics are illustrated by identification of S. aureus with simultaneous discrimination of methicillin-sensitive (MSSA) versus methicillin-resistant (MRSA) strains. Overall these promising results hint to the adoption of PNA-based rapid sensitive detection for diagnosis of other clinically relevant organisms. Thereby, new assay enables significantly earlier administration of appropriate antimicrobial therapy and may, thus have a positive impact on the outcome of the patient. PMID:20953307

  17. An annotated genetic map of loblolly pine based on microsatellite and cDNA markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Previous loblolly pine (Pinus taeda L.) genetic linkage maps have been based on a variety of DNA polymorphisms, such as AFLPs, RAPDs, RFLPs, and ESTPs, but only a few SSRs (simple sequence repeats), also known as simple tandem repeats or microsatellites, have been mapped in P. taeda. The objective o...

  18. OCOD-CTTP Integrated Science: School Based Assessment Marker/Tutor Handbook.

    ERIC Educational Resources Information Center

    King, Winston, Ed.; And Others

    This manual informs tutors/evaluators and students about the Caribbean Examinations Council's (CXC) school based assessment (SBA) of integrated science skills. It includes directions for the teacher/evaluator and a student activity package. The SBA is done in agricultural science, biology, chemistry, integrated science, and social studies and is…

  19. Cancer Markers Selection Using Network-Based Cox Regression: A Methodological and Computational Practice

    PubMed Central

    Iuliano, Antonella; Occhipinti, Annalisa; Angelini, Claudia; De Feis, Italia; Lió, Pietro

    2016-01-01

    International initiatives such as the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) are collecting multiple datasets at different genome-scales with the aim of identifying novel cancer biomarkers and predicting survival of patients. To analyze such data, several statistical methods have been applied, among them Cox regression models. Although these models provide a good statistical framework to analyze omic data, there is still a lack of studies that illustrate advantages and drawbacks in integrating biological information and selecting groups of biomarkers. In fact, classical Cox regression algorithms focus on the selection of a single biomarker, without taking into account the strong correlation between genes. Even though network-based Cox regression algorithms overcome such drawbacks, such network-based approaches are less widely used within the life science community. In this article, we aim to provide a clear methodological framework on the use of such approaches in order to turn cancer research results into clinical applications. Therefore, we first discuss the rationale and the practical usage of three recently proposed network-based Cox regression algorithms (i.e., Net-Cox, AdaLnet, and fastcox). Then, we show how to combine existing biological knowledge and available data with such algorithms to identify networks of cancer biomarkers and to estimate survival of patients. Finally, we describe in detail a new permutation-based approach to better validate the significance of the selection in terms of cancer gene signatures and pathway/networks identification. We illustrate the proposed methodology by means of both simulations and real case studies. Overall, the aim of our work is two-fold. Firstly, to show how network-based Cox regression models can be used to integrate biological knowledge (e.g., multi-omics data) for the analysis of survival data. Secondly, to provide a clear methodological and computational approach for

  20. Oral cancer diagnostics based on infrared spectral markers and wax physisorption kinetics.

    PubMed

    Chiu, Li-Fang; Huang, Pei-Yu; Chiang, Wei-Fan; Wong, Tung-Yiu; Lin, Sheng-Hsiang; Lee, Yao-Chang; Shieh, Dar-Bin

    2013-02-01

    Infrared microspectroscopy is an emerging approach for disease analysis owing to its capability for in situ chemical characterization of pathological processes. Synchrotron-based infrared microspectroscopy (SR-IMS) provides ultra-high spatial resolution for profiling biochemical events associated with disease progression. Spectral alterations were observed in cultured oral cells derived from healthy, precancerous, primary, and metastatic cancers. An innovative wax-physisorption-based kinetic FTIR imaging method for the detection of oral precancer and cancer was demonstrated successfully. The approach is based on determining the residual amount of paraffin wax (C(25)H(52)) or beeswax (C(46)H(92)O(2)) on a sample surface after xylene washing. This amount is used as a signpost of the degree of physisorption that altered during malignant transformation. The results of linear discriminant analysis (LDA) of oral cell lines indicated that the methylene (CH(2)) and methyl group (CH(3)) stretching vibrations in the range of 3,000-2,800 cm(-1) have the highest accuracy rate (89.6 %) to discriminate the healthy keratinocytes (NHOK) from cancer cells. The results of wax-physisorption-based FTIR imaging showed a stronger physisorption with beeswax in oral precancerous and cancer cells as compared with that of NHOK, which showed a strong capability with paraffin wax. The infrared kinetic study of oral cavity tissue showed a consistency in the wax physisorption of the cell lines. On the basis of our findings, these results show the potential use of wax-physisorption-based kinetic FTIR imaging for the early screening of oral cancer lesions and the chemical changes during oral carcinogenesis.

  1. Transcriptome sequencing of different narrow-leafed lupin tissue types provides a comprehensive uni-gene assembly and extensive gene-based molecular markers.

    PubMed

    Kamphuis, Lars G; Hane, James K; Nelson, Matthew N; Gao, Lingling; Atkins, Craig A; Singh, Karam B

    2015-01-01

    Narrow-leafed lupin (NLL; Lupinus angustifolius L.) is an important grain legume crop that is valuable for sustainable farming and is becoming recognized as a human health food. NLL breeding is directed at improving grain production, disease resistance, drought tolerance and health benefits. However, genetic and genomic studies have been hindered by a lack of extensive genomic resources for the species. Here, the generation, de novo assembly and annotation of transcriptome datasets derived from five different NLL tissue types of the reference accession cv. Tanjil are described. The Tanjil transcriptome was compared to transcriptomes of an early domesticated cv. Unicrop, a wild accession P27255, as well as accession 83A:476, together being the founding parents of two recombinant inbred line (RIL) populations. In silico predictions for transcriptome-derived gene-based length and SNP polymorphic markers were conducted and corroborated using a survey assembly sequence for NLL cv. Tanjil. This yielded extensive indel and SNP polymorphic markers for the two RIL populations. A total of 335 transcriptome-derived markers and 66 BAC-end sequence-derived markers were evaluated, and 275 polymorphic markers were selected to genotype the reference NLL 83A:476 × P27255 RIL population. This significantly improved the completeness, marker density and quality of the reference NLL genetic map.

  2. Improved sensitivity in the diagnosis of gastro-intestinal tumors by fuzzy logic-based tumor marker profiles including the tumor M2-PK.

    PubMed

    Schneider, Joachim; Bitterlich, Norman; Schulze, Guntram

    2005-01-01

    The aim of this study was to improve diagnostic efficiency in the detection of gastro-intestinal cancers by using fuzzy logic modeling in combination with a tumor marker panel (CEA, CA72-4, CA19-9) including Tumor M2-PK. In this prospective study histologically confirmed colorectal (n=247), esophageal (n=86) and gastric cancer (n=122) patients were investigated and compared to control (n=53) persons without any malignant diseases. Tumor M2-PK was measured in plasma with an ELISA (ScheBoBiotech, Germany); all other markers were measured in sera (Roche, Germany). At 95% specificity, tumor detection was possible by the best single marker in colorectal cancer patients in 48% (Tumor M2-PK), in gastric cancers in 61% (CA72-4) and in esophageal cancers in 56% (Tumor M2-PK). A fuzzy logic rule-based system employing a tumor marker panel increased sensitivity significantly in colorectal cancers (p<0. 001) to 63% (Tumor M2-PK and CEA), in gastric cancers (p<0.001) to 81% (Tumor M2-PK and CA 72-4) and in esophageal cancers (p<0.02) to 74% (Tumor M2-PK and CA72-4). Adding a third marker further improved the sensitivity only marginally. Fuzzy logic analysis has proven to be more powerful than measurement of single markers alone or combinations using multiple logistic regression analysis of the markers. Therefore, with the fuzzy logic method and a tumor marker panel (including Tumor M2-PK), a new diagnostic tool for the detection of gastro-intestinal cancers is available.

  3. Insights into the phylogeny of sporadotrichid ciliates (Protozoa, Ciliophora: Hypotricha) based on genealogical analyses of multiple molecular markers

    NASA Astrophysics Data System (ADS)

    Hu, Xiaoyan; Hu, Xiaozhong; Al-Rasheid, Khaled A. S.; Al-Farraj, Saleh A.; Song, Weibo

    2011-01-01

    The sporadotrichid ciliates are an especially diverse group. A number of investigators have studied the morphological, morphogenetic, and molecular relationships among members of this group. Despite this, a consistent classification is still lacking and several important questions about the phylogenetic relationships within this group remain unsolved. To improve our understanding of these relationships, we constructed phylogenetic trees using the nucleotide sequences of the small-subunit rRNA (SSrRNA) gene and amino acid sequences of actin I and α-tubulin. Analyses of SSrRNA gene sequences indicated that: 1) the Sporadotrichida sensu Lynn (2008) and the Oxytrichidae are polyphyletic; 2) the Uroleptus species, which are classified to urostylids, formed a sister group with the oxytrichids; 3) Halteria grandinella, which is grouped morphologically with oligotrich species, clustered within the oxytrichids. These results are congruent with previous studies based on SSrRNA gene sequences. However, the amino acid sequences of actin I and α-tubulin yielded different topologies. The main results are: 1) in all phylogenetic trees, the genus Oxytricha was paraphyletic; 2) Uroleptus was sister to a subset of Urostyla and Holosticha, albeit with low supporting values; 3) Halteria grandinella was separated distantly from the Oxytrichidae in trees inferred from actin I amino acid sequences but clustered with oligotrichids in the α-tubulin analysis. The inconsistency among the trees inferred from these different molecular markers may be caused by rapidly accumulated genetic characterizations of ciliates. Further studies with additional molecular markers and sampling of more taxa are expected to better address the relationships among sporadotrichids.

  4. Phylogeny reconstruction in the Caesalpinieae grade (Leguminosae) based on duplicated copies of the sucrose synthase gene and plastid markers.

    PubMed

    Manzanilla, Vincent; Bruneau, Anne

    2012-10-01

    The Caesalpinieae grade (Leguminosae) forms a morphologically and ecologically diverse group of mostly tropical tree species with a complex evolutionary history. This grade comprises several distinct lineages, but the exact delimitation of the group relative to subfamily Mimosoideae and other members of subfamily Caesalpinioideae, as well as phylogenetic relationships among the lineages are uncertain. With the aim of better resolving phylogenetic relationships within the Caesalpinieae grade, we investigated the utility of several nuclear markers developed from genomic studies in the Papilionoideae. We cloned and sequenced the low copy nuclear gene sucrose synthase (SUSY) and combined the data with plastid trnL and matK sequences. SUSY has two paralogs in the Caesalpinieae grade and in the Mimosoideae, but occurs as a single copy in all other legumes tested. Bayesian and maximum likelihood phylogenetic analyses suggest the two nuclear markers are congruent with plastid DNA data. The Caesalpinieae grade is divided into four well-supported clades (Cassia, Caesalpinia, Tachigali and Peltophorum clades), a poorly supported clade of Dimorphandra Group genera, and two paraphyletic groups, one with other Dimorphandra Group genera and the other comprising genera previously recognized as the Umtiza clade. A selection analysis of the paralogs, using selection models from PAML, suggests that SUSY genes are subjected to a purifying selection. One of the SUSY paralogs, under slightly stronger positive selection, may be undergoing subfunctionalization. The low copy SUSY gene is useful for phylogeny reconstruction in the Caesalpinieae despite the presence of duplicate copies. This study confirms that the Caesalpinieae grade is an artificial group, and highlights the need for further analyses of lineages at the base of the Mimosoideae. PMID:22699157

  5. Immunoassay for tumor markers in human serum based on Si nanoparticles and SiC@Ag SERS-active substrate.

    PubMed

    Zhou, Lu; Zhou, Jun; Feng, Zhao; Wang, Fuyan; Xie, Shushen; Bu, Shizhong

    2016-04-21

    Based on a sandwich structure consisting of nano-Si immune probes and a SiC@Ag SERS-active immune substrate, a kind of ultra-sensitive immunoassay protocol is presented to detect tumor markers in human serum. The nano-Si immune probes were prepared by immobilizing the detecting antibodies onto the surfaces of SiO2-coated Si nanoparticles (NPs) which were modified with 3-(aminopropyl)trimethoxysilane, and the SiC@Ag SERS-active immune substrates were prepared by immobilizing the captured antibodies on Ag film sputtered on SiC sandpaper. To the best of our knowledge, it is the first time that Si NPs are directly used as Raman tags in an immunoassay strategy. And, the SiC@Ag SERS-active substrates exhibit excellent surface enhanced Raman scattering (SERS) performances with an enhancement factor of ∼10(5), owing to the plasmonic effect of the Ag film on the rough surface of the SiC sandpaper. In our experiments, the sandwich immunoassay structure has been successfully applied to detect prostate specific antigen (PSA), α-fetoprotein (AFP) and carbohydrate antigen 19-9 (CA19-9) in a human serum sample and the limit of detections are as low as 1.79 fg mL(-1), 0.46 fg mL(-1) and 1.3 × 10(-3) U mL(-1), respectively. It reveals that the proposed immunoassay protocol has demonstrated a high sensitivity for tumor markers in human serum and a potential practicability in biosensing and clinical diagnostics. PMID:27003871

  6. Phylogeny reconstruction in the Caesalpinieae grade (Leguminosae) based on duplicated copies of the sucrose synthase gene and plastid markers.

    PubMed

    Manzanilla, Vincent; Bruneau, Anne

    2012-10-01

    The Caesalpinieae grade (Leguminosae) forms a morphologically and ecologically diverse group of mostly tropical tree species with a complex evolutionary history. This grade comprises several distinct lineages, but the exact delimitation of the group relative to subfamily Mimosoideae and other members of subfamily Caesalpinioideae, as well as phylogenetic relationships among the lineages are uncertain. With the aim of better resolving phylogenetic relationships within the Caesalpinieae grade, we investigated the utility of several nuclear markers developed from genomic studies in the Papilionoideae. We cloned and sequenced the low copy nuclear gene sucrose synthase (SUSY) and combined the data with plastid trnL and matK sequences. SUSY has two paralogs in the Caesalpinieae grade and in the Mimosoideae, but occurs as a single copy in all other legumes tested. Bayesian and maximum likelihood phylogenetic analyses suggest the two nuclear markers are congruent with plastid DNA data. The Caesalpinieae grade is divided into four well-supported clades (Cassia, Caesalpinia, Tachigali and Peltophorum clades), a poorly supported clade of Dimorphandra Group genera, and two paraphyletic groups, one with other Dimorphandra Group genera and the other comprising genera previously recognized as the Umtiza clade. A selection analysis of the paralogs, using selection models from PAML, suggests that SUSY genes are subjected to a purifying selection. One of the SUSY paralogs, under slightly stronger positive selection, may be undergoing subfunctionalization. The low copy SUSY gene is useful for phylogeny reconstruction in the Caesalpinieae despite the presence of duplicate copies. This study confirms that the Caesalpinieae grade is an artificial group, and highlights the need for further analyses of lineages at the base of the Mimosoideae.

  7. Genetic markers for rapid PCR-based identification of gull, Canada goose, duck, and chicken fecal contamination in water.

    PubMed

    Green, Hyatt C; Dick, Linda K; Gilpin, Brent; Samadpour, Mansour; Field, Katharine G

    2012-01-01

    Avian feces contaminate waterways but contribute fewer human pathogens than human sources. Rapid identification and quantification of avian contamination would therefore be useful to prevent overestimation of human health risk. We used subtractive hybridization of PCR-amplified gull fecal 16S RNA genes to identify avian-specific fecal rRNA gene sequences. The subtracters were rRNA genes amplified from human, dog, cat, cow, and pig feces. Recovered sequences were related to Enterobacteriaceae (47%), Helicobacter (26%), Catellicoccus (11%), Fusobacterium (11%), and Campylobacter (5%). Three PCR assays, designated GFB, GFC, and GFD, were based on recovered sequence fragments. Quantitative PCR assays for GFC and GFD were developed using SYBR green. GFC detected down to 0.1 mg gull feces/100 ml (corresponding to 2 gull enterococci most probable number [MPN]/100 ml). GFD detected down to 0.1 mg chicken feces/100 ml (corresponding to 13 Escherichia coli MPN/100 ml). GFB and GFC were 97% and 94% specific to gulls, respectively. GFC cross-reacted with 35% of sheep samples but occurred at about 100,000 times lower concentrations in sheep. GFD was 100% avian specific and occurred in gulls, geese, chickens, and ducks. In the United States, Canada, and New Zealand, the three markers differed in their geographic distributions but were found across the range tested. These assays detected four important bird groups contributing to fecal contamination of waterways: gulls, geese, ducks, and chickens. Marker distributions across North America and in New Zealand suggest that they will have broad applicability in other parts of the world as well. PMID:22081573

  8. Cell-based Models for Discovery of Pharmacogenomic Markers of Anticancer Agent Toxicity

    PubMed Central

    Zhang, Wei; Huang, R. Stephanie; Dolan, M. Eileen

    2009-01-01

    The field of pharmacogenomics is challenging because of the multigenic nature of drug response and toxicity. The candidate gene approach has been traditionally utilized to determine the contribution of genetic variation to a particular phenotype; however, the sequencing of the human genome and the genetic resource provided by the International HapMap Project has allowed researchers to perform genome-wide studies without a priori knowledge. Recent work has demonstrated the usefulness of cell-based models for pharmacogenomic discovery using the HapMap samples, which are a panel of well-genotyped, human lymphoblastoid cell lines (LCLs) derived from 90 Utah residents with ancestry from northern and western Europe (CEU), 90 Yoruba in Ibadan, Nigeria (YRI), 45 Japanese in Tokyo, Japan (JPT) and 45 Han Chinese in Beijing, China (CHB). Using these cell-based models, investigators are able to study not only individual variation in drug response, but also population differences in drug response. Finally, besides single nucleotide polymorphisms (SNPs) and gene expression, these cell-based models can also be used to investigate other genetic (e.g. copy number variants, CNVs), epigenetic or environmental factors responsible for drug response. PMID:21499559

  9. Improved sandwich-hybridization assay for an electrical DNA-chip-based monitoring of bioprocess-relevant marker genes.

    PubMed

    Pioch, Daniel; Jürgen, Britta; Evers, Stefan; Maurer, Karl-Heinz; Hecker, Michael; Schweder, Thomas

    2008-03-01

    Recently, it was shown that electrical DNA-chips in connection with a magnetic bead-based sandwich-hybridization assay can be a suitable alternative for the analysis of gene expression by monitoring the respective mRNA levels. In this study, we established an improved assay which allowed for a significantly shortened but sensitive detection of specific mRNAs. These improvements include the change to a solution-based sandwich-hybridization and the rearrangement of the used oligonucleotide probes. The introduction of a second labeled detection probe further increased the hybridization signals and, in turn, leads to a substantial time reduction of the detection protocol. The presented solution-based sandwich-hybridization protocol for the electrochemical detection of specific mRNAs requires about 60 min and the whole procedure, including sampling, cell disruption, and RNA isolation, approx. 80 min. The assay of this study was verified by nutrient-limited growth experiments and the analysis of selected starvation marker genes of the industrial host Bacillus licheniformis. The expression profiles determined with the electrical chip and the optimized protocol were, in most cases, comparable with the profiles determined by real-time RT-PCR measurements.

  10. Development of simple sequence repeat (SSR) markers for discrimination among isolates of Fusarium proliferatum.

    PubMed

    Moncrief, I; Garzon, C; Marek, S; Stack, J; Gamliel, A; Garrido, P; Proaño, F; Gard, M; Dehne, H; Fletcher, J

    2016-07-01

    The plant pathogen Fusarium proliferatum has a wide host range and occurs worldwide. Many isolates of the fungus produce mycotoxins in plant tissues, which, if ingested, can cause harm to animals and humans. In 2008, an outbreak of salmon blotch of onions, caused by F. proliferatum, was detected in southern Israel. The source and distribution of the fungus in Israel were unknown. Inter-simple sequence repeats (ISSR) were used to identify repetitive motifs present in seven isolates of F. proliferatum from Israel, Germany and Austria. ISSR repeat motifs were, used to develop 17 simple sequence repeat (SSR) loci. Six of these SSR markers were polymorphic in and consistently amplified from ten isolates collected in Israel, Germany, Austria and North America, from cucumber, onion, garlic, maize, and asparagus. These six polymorphic SSR alleles included 5 to 12 copies of di-, tri, and pentanucleotide motifs and yielded six to 9 alleles each. Sixteen of the SSR loci were amplified at least one of the seven Fusarium species, F. verticillioides, F. thapsinum, F. subglutinans, F. andiyazi, F. globosum, F. fujikoroi and F. oxysporum. The data demonstrate that these SSRs can be used for characterization of F. proliferatum isolates from diverse hosts and geographic locations and that they are transferable to other species of Fusarium. PMID:27021663

  11. Development of simple sequence repeat (SSR) markers for discrimination among isolates of Fusarium proliferatum.

    PubMed

    Moncrief, I; Garzon, C; Marek, S; Stack, J; Gamliel, A; Garrido, P; Proaño, F; Gard, M; Dehne, H; Fletcher, J

    2016-07-01

    The plant pathogen Fusarium proliferatum has a wide host range and occurs worldwide. Many isolates of the fungus produce mycotoxins in plant tissues, which, if ingested, can cause harm to animals and humans. In 2008, an outbreak of salmon blotch of onions, caused by F. proliferatum, was detected in southern Israel. The source and distribution of the fungus in Israel were unknown. Inter-simple sequence repeats (ISSR) were used to identify repetitive motifs present in seven isolates of F. proliferatum from Israel, Germany and Austria. ISSR repeat motifs were, used to develop 17 simple sequence repeat (SSR) loci. Six of these SSR markers were polymorphic in and consistently amplified from ten isolates collected in Israel, Germany, Austria and North America, from cucumber, onion, garlic, maize, and asparagus. These six polymorphic SSR alleles included 5 to 12 copies of di-, tri, and pentanucleotide motifs and yielded six to 9 alleles each. Sixteen of the SSR loci were amplified at least one of the seven Fusarium species, F. verticillioides, F. thapsinum, F. subglutinans, F. andiyazi, F. globosum, F. fujikoroi and F. oxysporum. The data demonstrate that these SSRs can be used for characterization of F. proliferatum isolates from diverse hosts and geographic locations and that they are transferable to other species of Fusarium.

  12. Ovarian Cancer: In Search of Better Marker Systems Based on DNA Repair Defects

    PubMed Central

    Varga, Dominic; Deniz, Miriam; Schwentner, Lukas; Wiesmüller, Lisa

    2013-01-01

    Ovarian cancer is the fifth most common female cancer in the Western world, and the deadliest gynecological malignancy. The overall poor prognosis for ovarian cancer patients is a consequence of aggressive biological behavior and a lack of adequate diagnostic tools for early detection. In fact, approximately 70% of all patients with epithelial ovarian cancer are diagnosed at advanced tumor stages. These facts highlight a significant clinical need for reliable and accurate detection methods for ovarian cancer, especially for patients at high risk. Because CA125 has not achieved satisfactory sensitivity and specificity in detecting ovarian cancer, numerous efforts, including those based on single and combined molecule detection and “omics” approaches, have been made to identify new biomarkers. Intriguingly, more than 10% of all ovarian cancer cases are of familial origin. BRCA1 and BRCA2 germline mutations are the most common genetic defects underlying hereditary ovarian cancer, which is why ovarian cancer risk assessment in developed countries, aside from pedigree analysis, relies on genetic testing of BRCA1 and BRCA2. Because not only BRCA1 and BRCA2 but also other susceptibility genes are tightly linked with ovarian cancer-specific DNA repair defects, another possible approach for defining susceptibility might be patient cell-based functional testing, a concept for which support came from a recent case-control study. This principle would be applicable to risk assessment and the prediction of responsiveness to conventional regimens involving platinum-based drugs and targeted therapies involving poly (ADP-ribose) polymerase (PARP) inhibitors. PMID:23344037

  13. Identification of associated SSR markers for yield component and fiber quality traits based on frame map and Upland cotton collections.

    PubMed

    Qin, Hongde; Chen, Min; Yi, Xianda; Bie, Shu; Zhang, Cheng; Zhang, Youchang; Lan, Jiayang; Meng, Yanyan; Yuan, Youlu; Jiao, Chunhai

    2015-01-01

    Detecting QTLs (quantitative trait loci) that enhance cotton yield and fiber quality traits and accelerate breeding has been the focus of many cotton breeders. In the present study, 359 SSR (simple sequence repeat) markers were used for the association mapping of 241 Upland cotton collections. A total of 333 markers, representing 733 polymorphic loci, were detected. The average linkage disequilibrium (LD) decay distances were 8.58 cM (r2 > 0.1) and 5.76 cM (r2 > 0.2). 241 collections were arranged into two subgroups using STRUCTURE software. Mixed linear modeling (MLM) methods (with population structure (Q) and relative kinship matrix (K)) were applied to analyze four phenotypic datasets obtained from four environments (two different locations and two years). Forty-six markers associated with the number of bolls per plant (NB), boll weight (BW), lint percentage (LP), fiber length (FL), fiber strength (FS) and fiber micornaire value (FM) were repeatedly detected in at least two environments. Of 46 associated markers, 32 were identified as new association markers, and 14 had been previously reported in the literature. Nine association markers were near QTLs (at a distance of less than 1-2 LD decay on the reference map) that had been previously described. These results provide new useful markers for marker-assisted selection in breeding programs and new insights for understanding the genetic basis of Upland cotton yields and fiber quality traits at the whole-genome level.

  14. EXPANSION OF PCR-BASED MARKER RESOURCES IN OAT BY SURVEYING GENOMIC-DERIVED SSRs FROM BARLEY AND WHEAT

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Identifying simple sequence repeat (SSR) regions in crop genomes and amplifying them with specific primer sets have provided a relatively new generation of molecular markers for mapping projects. SSRs are advantageous to most of other markers because they are present in large numbers, are evenly d...

  15. Single strand conformation polymorphism based SNP and Indel markers for genetic mapping and synteny analysis of common bean (Phaseolus vulgaris L.)

    PubMed Central

    2009-01-01

    Background Expressed sequence tags (ESTs) are an important source of gene-based markers such as those based on insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). Several gel based methods have been reported for the detection of sequence variants, however they have not been widely exploited in common bean, an important legume crop of the developing world. The objectives of this project were to develop and map EST based markers using analysis of single strand conformation polymorphisms (SSCPs), to create a transcript map for common bean and to compare synteny of the common bean map with sequenced chromosomes of other legumes. Results A set of 418 EST based amplicons were evaluated for parental polymorphisms using the SSCP technique and 26% of these presented a clear conformational or size polymorphism between Andean and Mesoamerican genotypes. The amplicon based markers were then used for genetic mapping with segregation analysis performed in the DOR364 × G19833 recombinant inbred line (RIL) population. A total of 118 new marker loci were placed into an integrated molecular map for common bean consisting of 288 markers. Of these, 218 were used for synteny analysis and 186 presented homology with segments of the soybean genome with an e-value lower than 7 × 10-12. The synteny analysis with soybean showed a mosaic pattern of syntenic blocks with most segments of any one common bean linkage group associated with two soybean chromosomes. The analysis with Medicago truncatula and Lotus japonicus presented fewer syntenic regions consistent with the more distant phylogenetic relationship between the galegoid and phaseoloid legumes. Conclusion The SSCP technique is a useful and inexpensive alternative to other SNP or Indel detection techniques for saturating the common bean genetic map with functional markers that may be useful in marker assisted selection. In addition, the genetic markers based on ESTs allowed the construction of a transcript map and

  16. DNA-based species delineation in tropical beetles using mitochondrial and nuclear markers.

    PubMed

    Monaghan, Michael T; Balke, Michael; Gregory, T Ryan; Vogler, Alfried P

    2005-10-29

    DNA barcoding has been successfully implemented in the identification of previously described species, and in the process has revealed several cryptic species. It has been noted that such methods could also greatly assist in the discovery and delineation of undescribed species in poorly studied groups, although to date the feasibility of such an approach has not been examined explicitly. Here, we investigate the possibility of using short mitochondrial and nuclear DNA sequences to delimit putative species in groups lacking an existing taxonomic framework. We focussed on poorly known tropical water beetles (Coleoptera: Dytiscidae, Hydrophilidae) from Madagascar and dung beetles (Scarabaeidae) in the genus Canthon from the Neotropics. Mitochondrial DNA sequence variation proved to be highly structured, with >95% of the observed variation existing between discrete sets of very closely related genotypes. Sequence variation in nuclear 28S rRNA among the same individuals was lower by at least an order of magnitude, but 16 different genotypes were found in water beetles and 12 genotypes in Canthon, differing from each other by a minimum of two base pairs. The distribution of these 28S rRNA genotypes in individuals exactly matched the distribution of mtDNA clusters, suggesting that mtDNA patterns were not misleading because of introgression. Moreover, in a few cases where sequence information was available in GenBank for morphologically defined species of Canthon, these matched some of the DNA-based clusters. These findings demonstrate that clusters of close relatives can be identified readily in the sequence variation obtained in field collected samples, and that these clusters are likely to correspond to either previously described or unknown species. The results suggest that DNA-assisted taxonomy will not require more than a short fragment of mtDNA to provide a largely accurate picture of species boundaries in these groups. Applied on a large scale, this DNA-based

  17. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity.

    PubMed

    Zhernakova, Alexandra; Kurilshikov, Alexander; Bonder, Marc Jan; Tigchelaar, Ettje F; Schirmer, Melanie; Vatanen, Tommi; Mujagic, Zlatan; Vila, Arnau Vich; Falony, Gwen; Vieira-Silva, Sara; Wang, Jun; Imhann, Floris; Brandsma, Eelke; Jankipersadsing, Soesma A; Joossens, Marie; Cenit, Maria Carmen; Deelen, Patrick; Swertz, Morris A; Weersma, Rinse K; Feskens, Edith J M; Netea, Mihai G; Gevers, Dirk; Jonkers, Daisy; Franke, Lude; Aulchenko, Yurii S; Huttenhower, Curtis; Raes, Jeroen; Hofker, Marten H; Xavier, Ramnik J; Wijmenga, Cisca; Fu, Jingyuan

    2016-04-29

    Deep sequencing of the gut microbiomes of 1135 participants from a Dutch population-based cohort shows relations between the microbiome and 126 exogenous and intrinsic host factors, including 31 intrinsic factors, 12 diseases, 19 drug groups, 4 smoking categories, and 60 dietary factors. These factors collectively explain 18.7% of the variation seen in the interindividual distance of microbial composition. We could associate 110 factors to 125 species and observed that fecal chromogranin A (CgA), a protein secreted by enteroendocrine cells, was exclusively associated with 61 microbial species whose abundance collectively accounted for 53% of microbial composition. Low CgA concentrations were seen in individuals with a more diverse microbiome. These results are an important step toward a better understanding of environment-diet-microbe-host interactions. PMID:27126040

  18. Use of urine-based markers for detection and monitoring of bladder cancer.

    PubMed

    Pirtskalaishvili, G; Getzenberg, R H; Konety, B R

    1999-12-01

    Diagnosis and monitoring of bladder cancer present a difficult clinical problem. Urine cytology with confirmatory cystoscopy form the cornerstone of diagnosis at the present time. The subjectivity and low sensitivity of cytology led to the development of numerous tests as adjuncts to cystoscopy for the diagnosis and follow-up of bladder cancer patients. These tests usually are objective, quantitative (NMP-22, BTA TRAK, BLCA-4, telomerase activity, etc.), or qualitative (BTA Stat and FDP) and have higher sensitivity than cytology, but some have lower specificity. We review the different, new urine-based tests that were developed recently for the diagnosis and monitoring of patients with bladder cancer. The advantages and disadvantages of these tests are discussed, as well as their possible future role in the management of patients with bladder cancer.

  19. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity.

    PubMed

    Zhernakova, Alexandra; Kurilshikov, Alexander; Bonder, Marc Jan; Tigchelaar, Ettje F; Schirmer, Melanie; Vatanen, Tommi; Mujagic, Zlatan; Vila, Arnau Vich; Falony, Gwen; Vieira-Silva, Sara; Wang, Jun; Imhann, Floris; Brandsma, Eelke; Jankipersadsing, Soesma A; Joossens, Marie; Cenit, Maria Carmen; Deelen, Patrick; Swertz, Morris A; Weersma, Rinse K; Feskens, Edith J M; Netea, Mihai G; Gevers, Dirk; Jonkers, Daisy; Franke, Lude; Aulchenko, Yurii S; Huttenhower, Curtis; Raes, Jeroen; Hofker, Marten H; Xavier, Ramnik J; Wijmenga, Cisca; Fu, Jingyuan

    2016-04-29

    Deep sequencing of the gut microbiomes of 1135 participants from a Dutch population-based cohort shows relations between the microbiome and 126 exogenous and intrinsic host factors, including 31 intrinsic factors, 12 diseases, 19 drug groups, 4 smoking categories, and 60 dietary factors. These factors collectively explain 18.7% of the variation seen in the interindividual distance of microbial composition. We could associate 110 factors to 125 species and observed that fecal chromogranin A (CgA), a protein secreted by enteroendocrine cells, was exclusively associated with 61 microbial species whose abundance collectively accounted for 53% of microbial composition. Low CgA concentrations were seen in individuals with a more diverse microbiome. These results are an important step toward a better understanding of environment-diet-microbe-host interactions.

  20. Relationship Between Markers of Insulin Resistance, Markers of Adiposity, HbA1c, and Cognitive Functions in a Middle-Aged Population–Based Sample: the MONA LISA Study

    PubMed Central

    Sanz, Caroline M.; Ruidavets, Jean-Bernard; Bongard, Vanina; Marquié, Jean-Claude; Hanaire, Hélène; Ferrières, Jean; Andrieu, Sandrine

    2013-01-01

    OBJECTIVE To determine the relationship between markers of insulin resistance (fasting insulin and homeostasis model assessment of insulin resistance), markers of adiposity (BMI, waist circumference, and body fat), HbA1c, and cognitive performances in a middle-aged population–based sample free of diabetes. RESEARCH DESIGN AND METHODS Our study sample consisted of 1,172 people aged 35–64 years (49% women), free of diabetes, and recruited between 2005 and 2007 in the MONA LISA survey. Cognitive functions (memory, attention, and processing speed) were evaluated by neuropsychological tests: word-list learning test, digit symbol substitution test (DSST), word fluency test, and Stroop Test. Multiple logistic regressions were used to estimate the relationship between cognitive performance and metabolic markers. We serially adjusted for age, sex, education, and occupational status (model A), additionally for income, smoking, alcohol consumption, sedentarity, and psychotropic substance use (model B), and finally, included variables linked to the metabolic syndrome (hypertension, dyslipidemia, vascular disease, and C-reactive protein) and depression (model C). RESULTS Elevated markers of adiposity were associated with poor cognitive performance in tests evaluating processing speed. The probability of being in the lowest quartile of each test was nearly doubled for participants in the upper quartile of BMI, compared with those in the lowest one [BMI, adjusted odds ratio (OR) 2.18, P = 0.003 (DSST), and OR 2.09, P = 0.005 (Stroop Test)]. High HbA1c was associated with poor cognitive performance in DSST (adjusted OR 1.75, P = 0.037). Waist circumference was linked to poor cognitive performance in men but not in women. CONCLUSIONS Poor cognitive performance is associated with adiposity and hyperglycemia in healthy middle-aged people. PMID:23275371

  1. Sequence-related amplified polymorphism (SRAP) markers: A potential resource for studies in plant molecular biology1

    PubMed Central

    Robarts, Daniel W. H.; Wolfe, Andrea D.

    2014-01-01

    In the past few decades, many investigations in the field of plant biology have employed selectively neutral, multilocus, dominant markers such as inter-simple sequence repeat (ISSR), random-amplified polymorphic DNA (RAPD), and amplified fragment length polymorphism (AFLP) to address hypotheses at lower taxonomic levels. More recently, sequence-related amplified polymorphism (SRAP) markers have been developed, which are used to amplify coding regions of DNA with primers targeting open reading frames. These markers have proven to be robust and highly variable, on par with AFLP, and are attained through a significantly less technically demanding process. SRAP markers have been used primarily for agronomic and horticultural purposes, developing quantitative trait loci in advanced hybrids and assessing genetic diversity of large germplasm collections. Here, we suggest that SRAP markers should be employed for research addressing hypotheses in plant systematics, biogeography, conservation, ecology, and beyond. We provide an overview of the SRAP literature to date, review descriptive statistics of SRAP markers in a subset of 171 publications, and present relevant case studies to demonstrate the applicability of SRAP markers to the diverse field of plant biology. Results of these selected works indicate that SRAP markers have the potential to enhance the current suite of molecular tools in a diversity of fields by providing an easy-to-use, highly variable marker with inherent biological significance. PMID:25202637

  2. Antioxidant markers based TLC-DPPH differentiation on four commercialized botanical sources of Shankhpushpi (A Medhya Rasayana): A preliminary assessment.

    PubMed

    Sethiya, Neeraj K; Raja, M K Mohan Maruga; Mishra, Shri Hari

    2013-01-01

    Shankhpushpi is a cognition boosting traditional ayurvedic brain supplement. Convolvulus pluricaulis (Convolvulaceae), Evolvulus alsinoides (Convolvulaceae), Clitoria ternatea (Papilionaceae), and Canscora decussata (Gentianaceae) are botanical claimants of Shankhpushpi. This investigation is to focus the identification of the compound based on biological marker differentiation of four botanical claimants of Shankhpushpi for their antioxidant evaluation on thin layer chromatography (TLC) by 2,2-diphenyl-1-picrylhydrazyl (DPPH) method. A rapid TLC-DPPH method was developed to identify and differentiate four botanical claimants of Shankhpushpi in terms of presence of β-carotene, rutin, scopoletin, chlorogenic acid, and mangiferin. C. pluricaulis shows presence of scopoletin; E. alsinoides shows presence of β-carotene, scopoletin, and chlorogenic acid; C. ternatea shows presence of β-carotene, scopoletin, and rutin; and C. decussata shows presence of β-carotene, scopoletin, and mangiferin. The order, they followed, based on their antioxidant potential is β-carotene < mangiferin < rutin < scopoletin < chlorogenic acid. Antioxidants are attributed for their beneficial role in age-related cognition decline. The proposed method provides an edge in terms of identification and quantification of antioxidant constituents in a multi-component system. This method may also provide application for identification of correct plant sources used in the name of Shankhpushpi in marketed ayurvedic formulation, food supplement, and extracts. PMID:23662279

  3. Antioxidant markers based TLC-DPPH differentiation on four commercialized botanical sources of Shankhpushpi (A Medhya Rasayana): A preliminary assessment

    PubMed Central

    Sethiya, Neeraj K.; Raja, M. K. Mohan Maruga; Mishra, Shri Hari

    2013-01-01

    Shankhpushpi is a cognition boosting traditional ayurvedic brain supplement. Convolvulus pluricaulis (Convolvulaceae), Evolvulus alsinoides (Convolvulaceae), Clitoria ternatea (Papilionaceae), and Canscora decussata (Gentianaceae) are botanical claimants of Shankhpushpi. This investigation is to focus the identification of the compound based on biological marker differentiation of four botanical claimants of Shankhpushpi for their antioxidant evaluation on thin layer chromatography (TLC) by 2,2-diphenyl-1-picrylhydrazyl (DPPH) method. A rapid TLC-DPPH method was developed to identify and differentiate four botanical claimants of Shankhpushpi in terms of presence of β-carotene, rutin, scopoletin, chlorogenic acid, and mangiferin. C. pluricaulis shows presence of scopoletin; E. alsinoides shows presence of β-carotene, scopoletin, and chlorogenic acid; C. ternatea shows presence of β-carotene, scopoletin, and rutin; and C. decussata shows presence of β-carotene, scopoletin, and mangiferin. The order, they followed, based on their antioxidant potential is β-carotene < mangiferin < rutin < scopoletin < chlorogenic acid. Antioxidants are attributed for their beneficial role in age-related cognition decline. The proposed method provides an edge in terms of identification and quantification of antioxidant constituents in a multi-component system. This method may also provide application for identification of correct plant sources used in the name of Shankhpushpi in marketed ayurvedic formulation, food supplement, and extracts. PMID:23662279

  4. Molecular and functional diversity of PGPR fluorescent Pseudomonads based on 16S rDNA-RFLP and RAPD markers.

    PubMed

    Singh, Bhim Pratap

    2015-09-01

    The genetic and functional diversity of plant growth promoting rhizobacterial (PGPR) fluorescent pseudomonads associated with chickpea (Cicer arietinum L.) rhizosphere was analyzed. In total, 34 isolates along with two reference isolates were screened for various plant growth promoting traits (phosphorous solubilization, ACC deaminase, HCN, IAA and siderophore productions) and antagonist activity against four fungal phytopathogens and three bacterial pathogens. Most of the isolates, that showed PGPR activity, also showed antagonistic activity against all the three fungal pathogens. The genetic relationship was assessed by using random amplification of polymorphic DNA (RAPD) and PCR-restriction fragment length polymorphism (16S rDNA-RFLP). Relationship between both the markers was analyzed based on mantel test and a negative correlation was observed. The study concluded that PGPR traits appeared to be strain specific rather than specific to any phylogenetic group. The study also reported that 16S rDNA based profiling differentiated PGPR fluorescent Pseudomonas on the basis of location rather than biological trait. RAPD profiling could be useful to differentiate among the closely related isolates. The genetic and functional diversity of fluorescent pseudomonads, associated with the chickpea rhizosphere, has useful ecological role and potential utilization in sustainable agriculture.

  5. Differentiation of metallicolous and non-metallicolous Salix caprea populations based on phenotypic characteristics and nuclear microsatellite (SSR) markers.

    PubMed

    Puschenreiter, Markus; Türktaş, Mine; Sommer, Peter; Wieshammer, Gerlinde; Laaha, Gregor; Wenzel, Walter W; Hauser, Marie-Theres

    2010-10-01

    The Salicaceae family comprises a large number of high-biomass species with remarkable genetic variability and adaptation to ecological niches. Salix caprea survives in heavy metal contaminated areas, translocates and accumulates Zn/Cd in leaves. To reveal potential selective effects of long-term heavy metal contaminations on the genetic structure and Zn/Cd accumulation capacity, 170 S. caprea isolates of four metal-contaminated and three non-contaminated middle European sites were analysed with microsatellite markers using Wright's F statistics. The differentiation of populations North of the Alps are more pronounced compared to the Southern ones. By grouping the isolates based on their contamination status, a weak but significant differentiation was calculated between Northern metallicolous and non-metallicolous populations. To quantify if the contamination and genetic status of the populations correlate with Zn/Cd tolerance and the accumulation capacity, the S. caprea isolates were exposed to elevated Cd/Zn concentrations in perlite-based cultures. Consistent with the genetic data nested anova analyses for the physiological traits find a significant difference in the Cd accumulation capacity between the Northern and Southern populations. Our data suggest that natural populations are a profitable source to uncover genetic mechanisms of heavy metal accumulation and biomass production, traits that are essential for improving phytoextraction strategies. PMID:20444221

  6. Exploring the intrinsic differences among breast tumor subtypes defined using immunohistochemistry markers based on the decision tree

    PubMed Central

    Li, Yang; Tang, Xu-Qing; Bai, Zhonghu; Dai, Xiaofeng

    2016-01-01

    Exploring the intrinsic differences among breast cancer subtypes is of crucial importance for precise diagnosis and therapeutic decision-making in diseases of high heterogeneity. The subtypes defined with several layers of information are related but not consistent, especially using immunohistochemistry markers and gene expression profiling. Here, we explored the intrinsic differences among the subtypes defined by the estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 based on the decision tree. We identified 30 mRNAs and 7 miRNAs differentially expressed along the tree’s branches. The final signature panel contained 30 mRNAs, whose performance was validated using two public datasets based on 3 well-known classifiers. The network and pathway analysis were explored for feature genes, from which key molecules including FOXQ1 and SFRP1 were revealed to be densely connected with other molecules and participate in the validated metabolic pathways. Our study uncovered the differences among the four IHC-defined breast tumor subtypes at the mRNA and miRNA levels, presented a novel signature for breast tumor subtyping, and identified several key molecules potentially driving the heterogeneity of such tumors. The results help us further understand breast tumor heterogeneity, which could be availed in clinics. PMID:27786176

  7. Phylogenetic relationships of the Orang Asli and Iban of Malaysia based on maternal markers.

    PubMed

    Ang, K C; Leow, J W H; Yeap, W K; Hood, S; Mahani, M C; Md-Zain, B M

    2011-01-01

    Malaysia remains as a crossroad of different cultures and peoples, and it has long been recognized that studying its population history can provide crucial insight into the prehistory of Southeast Asia as a whole. The earliest inhabitants were the Orang Asli in Peninsular Malaysia and the indigenous groups in Sabah and Sarawak. Although they were the earliest migrants in this region, these tribes are divided geographically by the South China Sea. We analyzed DNA sequences of 18 Orang Asli using mitochondrial DNA extracted from blood samples, each representing one sub-tribe, and from five Sarawakian Iban. Mitochondrial DNA was extracted from hair samples in order to examine relationships with the main ethnic groups in Malaysia. The D-loop region and cytochrome b genes were used as the candidate loci. Phylogenetic relationships were investigated using maximum parsimony and neighbor joining algorithms, and each tree was subjected to bootstrap analysis with 1000 replicates. Analyses of the HVS I region showed that the Iban are not a distinct group from the Orang Asli; they form a sub-clade within the Orang Asli. Based on the cytochrome b gene, the Iban clustered with the Orang Asli in the same clade. We found evidence for considerable gene flow between Orang Asli and Iban. We concluded that the Orang Asli, Iban and the main ethnic groups of Malaysia are probably derived from a common ancestor. This is in agreement with a single-route migration theory, but it does not dismiss a two-route migration theory. PMID:21491374

  8. Molecular phylogeny of the tribe Sphodrini (Coleoptera: Carabidae) based on mitochondrial and nuclear markers.

    PubMed

    Ruiz, Carlos; Jordal, Bjarte; Serrano, José

    2009-01-01

    A phylogenetic analysis of 6.4 kb of nucleotide sequence data from seven genes (mitochondrial cox1-cox2 and tRNA(leu), and nuclear Ef-1alpha C0, Ef-1alpha C1, 28S, and 18S) was done to reconstruct the phylogenetic relationships of the ground-beetle tribe Sphodrini. Gene regions of variable nucleotide length were aligned using both a secondary structure model, Clustal W, and a combination of the two. Sensitivity analysis was performed in order to explore the effect of alignment methods. The ribosomal and protein-coding genes were largely congruent based on the ILD test and partitioned Bremer support measures. MtDNA analysis provided high resolution and high support for most clades. The tribe Sphodrini and the related tribes Platynini, Pterostichini and Zabrini made up monophyletic clades, but the relationship between them was weakly resolved and sensitive to alignment strategy. Previously suggested relationships between subtribes of Sphodrini were not corroborated, and only the subtribe Atranopsina revealed high support as the sister clade to the other subtribes. The analyses clearly demonstrated the importance of exploring effects of alignment methods that may become particularly important in resolving polytomies and nodes with low support.

  9. Urea Monitor Based on Chemiluminescence and Electrolysis as a Marker for Dialysis Efficiency

    NASA Astrophysics Data System (ADS)

    Ozaki, Masahiro; Okabayashi, Tohru; Ishimaru, Teppei; Hayashi, Kunihito; Hori, Jun'ya; Yamamoto, Isao; Nakagawa, Masuo

    We have developed a practical urea monitor based on a chemiluminescent (CL) reaction of urea and hypobromous acid produced by electrolysis of sodium bromide (NaBr) for measuring urea concentration in spent dialysate at set intervals. A reagent containing 4×10-2 M hypobromous acid is produced by electrolysis of an electrolyte containing 5.9 M NaBr and 0.2 M sodium hydroxide (NaOH). Chemiluminescence is emitted by injection of spent hemodialysis fluid (0.11 ml) into the reagent, and the CL-intensity is measured by a photomultiplier tube using the photon counting technique. The CL-intensity is proportional to the 0.9th power of the urea concentration between 7×10-4 and 2×10-2 M. The urea monitor can determine the urea concentration in spent dialysate samples collected from the waste line of a dialyzer, and the time for the intermittent measurements including the cleaning cycle of the reaction chamber is 3 min. The urea concentrations measured by the monitor are in close agreement with those measured by the conventional enzyme colorimetric method using urease for the spent dialysate collected during a hemodialysis treatment, and the correlation coefficient is 0.93.

  10. Molecular beacon-based quantitiation of epithelial tumor marker mucin 1.

    PubMed

    Shin, Seonmi; Nam, Hye Yeon; Lee, Eun Jeong; Jung, Woong; Hah, Sang Soo

    2012-10-01

    Mucin 1 (Muc1) is a glycoprotein expressed on most epithelial cell surfaces, which has been confirmed as a useful biomarker for the diagnosis of early cancers. In this study, we demonstrate that a quantum dot (QD)-aptamer beacon acts by folding-induced dissociation of a DNA intercalating dye, BOBO-3, in the presence of the target molecules, Muc1. Release of intercalated BOBO-3s from the QD-conjugated aptamers results in a decrease in QD fluorescence resonance energy transfer (FRET)-mediated BOBO-3 emission, allowing for label-free Muc1 detection and quantitation. We attain highly specific and wide-range detection (from 50nM to 20μM) of Muc1, suggesting that our QD-aptamer beacon can be a potential alternative to immuno-based assays for Muc1 detection. The detection methodology is expected to be improved for the early diagnosis of different types of epithelial cancers of large populations.

  11. Genetic diversity of Capsicum chinensis (Solanaceae) accessions based on molecular markers and morphological and agronomic traits.

    PubMed

    Finger, F L; Lannes, S D; Schuelter, A R; Doege, J; Comerlato, A P; Gonçalves, L S A; Ferreira, F R A; Clovis, L R; Scapim, C A

    2010-01-01

    We estimated the genetic diversity of 49 accessions of the hot pepper species Capsicum chinensis through analyses of 12 physicochemical traits of the fruit, eight multi-categorical variables, and with 32 RAPD primers. Data from the physicochemical traits were submitted to analysis of variance to estimate the genetic parameters, and their means were clustered by the Scott-Knott test. The matrices from the individual and combined distance were estimated by multivariate analyses before applying Tocher's optimization method. All physicochemical traits were examined for genetic variability by analysis of variance. The responses of these traits showed more contribution from genetic than from environmental factors, except the percentage of dry biomass, content of soluble solids and vitamin C level. Total capsaicin had the greatest genetic divergence. Nine clusters were formed from the quantitative data based on the generalized distance of Mahalanobis, using Tocher's method; four were formed from the multi-categorical data using the Cole-Rodgers coefficient, and eight were formed from the molecular data using the Nei and Li coefficient. The accessions were distributed into 14 groups using Tocher's method, and no significant correlation between pungency and origin was detected. Uni- and multivariate analyses permitted the identification of marked genetic diversity and fruit attributes capable of being improved through breeding programs. PMID:20882481

  12. Phylogenetic relationships of the Orang Asli and Iban of Malaysia based on maternal markers.

    PubMed

    Ang, K C; Leow, J W H; Yeap, W K; Hood, S; Mahani, M C; Md-Zain, B M

    2011-01-01

    Malaysia remains as a crossroad of different cultures and peoples, and it has long been recognized that studying its population history can provide crucial insight into the prehistory of Southeast Asia as a whole. The earliest inhabitants were the Orang Asli in Peninsular Malaysia and the indigenous groups in Sabah and Sarawak. Although they were the earliest migrants in this region, these tribes are divided geographically by the South China Sea. We analyzed DNA sequences of 18 Orang Asli using mitochondrial DNA extracted from blood samples, each representing one sub-tribe, and from five Sarawakian Iban. Mitochondrial DNA was extracted from hair samples in order to examine relationships with the main ethnic groups in Malaysia. The D-loop region and cytochrome b genes were used as the candidate loci. Phylogenetic relationships were investigated using maximum parsimony and neighbor joining algorithms, and each tree was subjected to bootstrap analysis with 1000 replicates. Analyses of the HVS I region showed that the Iban are not a distinct group from the Orang Asli; they form a sub-clade within the Orang Asli. Based on the cytochrome b gene, the Iban clustered with the Orang Asli in the same clade. We found evidence for considerable gene flow between Orang Asli and Iban. We concluded that the Orang Asli, Iban and the main ethnic groups of Malaysia are probably derived from a common ancestor. This is in agreement with a single-route migration theory, but it does not dismiss a two-route migration theory.

  13. [Serological markers of fibrosis].

    PubMed

    Fernández-Varo, Guillermo

    2012-12-01

    Liver biopsy has classically been considered the gold standard to evaluate the degree of fibrosis, since it allows direct measurement of this entity. However, this technique carries an inherent risk of complications and observer variability and technical limitations can provoke sampling errors, all of which has prompted the search for alternative, noninvasive methods. The use of routine clinical laboratory tests has been investigated and various indexes that combine indirect serological markers have been developed and validated. These indexes are useful, low-cost, noninvasive tests to detect significant fibrosis or cirrhosis. Direct serological markers are those that reflect changes in the composition of the extracellular matrix. Several studies have analyzed the utility of these markers (either individually or combined with other direct and indirect markers) in the detection of the severity and progression of liver fibrosis and in the follow-up of changes related to antiviral therapy. In the last few years, imaging tests based on the measurement of liver stiffness, such as FibroScan or acoustic radiation force impulse (ARFI), have been found to be rapid and reproducible methods to evaluate liver fibrosis. Recently, the results obtained by combining distinct serological markers and imaging techniques have shown a higher diagnostic yield and this strategy seems promising. The present article reviews the most widely discussed noninvasive markers, the most recent alternatives, and the perspectives for their use in clinical practice. PMID:23298654

  14. Genetic and metal analyses of fragmented populations of Betula papyrifera (Marsh) in a mining reclaimed region: identification of population–diagnostic molecular marker

    PubMed Central

    Theriault, Gabriel; Nkongolo, Kabwe K; Michael, Paul

    2014-01-01

    White birch (Betula papyrifera) is an open pollinate species that is, dominant in the Northern Ontario after land reclamation. In fact, this species represents 65% of all trees in the region. We hypothesized that the exchange of genetic information between fragmented populations by range-wide paternal introgression is possible in wind-pollinated species such as B. papyrifera. On the other hand, the effects of heavy metal contamination from the mining activities on plant growth and population dynamics are well documented. The main objectives of this study were (1) to assess the level of genetic variation, gene flow, and population sustainability of B. papyrifera after land reclamation; and (2) to determine the level of phytoavailable metals in soil and their accumulation in trees. We found that B. papyrifera is a Ni and Zn accumulator with a translocation factor of 6.4 and 81, respectively, and an indicator of Cu and Pb. The level of polymorphic loci, Shannon index, Nei's genetic diversity, observed number of alleles, and gene flow were determined for the fragmented populations within the targeted region. The percent of polymorphic loci ranged from 28% to 56%; the gene flow was also low with a value of 0.89, and the population differentiation was very high with a value of 0.36. Two population–diagnostic ISSR markers were identified. They were cloned, sequenced, and converted to SCAR markers. Overall, the fragmented populations of B. papyrifera in Northern Ontario are genetically sustainable based on the moderate level of intrapopulation variability. PMID:25535559

  15. Genetic and metal analyses of fragmented populations of Betula papyrifera (Marsh) in a mining reclaimed region: identification of population-diagnostic molecular marker.

    PubMed

    Theriault, Gabriel; Nkongolo, Kabwe K; Michael, Paul

    2014-09-01

    White birch (Betula papyrifera) is an open pollinate species that is, dominant in the Northern Ontario after land reclamation. In fact, this species represents 65% of all trees in the region. We hypothesized that the exchange of genetic information between fragmented populations by range-wide paternal introgression is possible in wind-pollinated species such as B. papyrifera. On the other hand, the effects of heavy metal contamination from the mining activities on plant growth and population dynamics are well documented. The main objectives of this study were (1) to assess the level of genetic variation, gene flow, and population sustainability of B. papyrifera after land reclamation; and (2) to determine the level of phytoavailable metals in soil and their accumulation in trees. We found that B. papyrifera is a Ni and Zn accumulator with a translocation factor of 6.4 and 81, respectively, and an indicator of Cu and Pb. The level of polymorphic loci, Shannon index, Nei's genetic diversity, observed number of alleles, and gene flow were determined for the fragmented populations within the targeted region. The percent of polymorphic loci ranged from 28% to 56%; the gene flow was also low with a value of 0.89, and the population differentiation was very high with a value of 0.36. Two population-diagnostic ISSR markers were identified. They were cloned, sequenced, and converted to SCAR markers. Overall, the fragmented populations of B. papyrifera in Northern Ontario are genetically sustainable based on the moderate level of intrapopulation variability. PMID:25535559

  16. Analysis of conservation priorities of Iberoamerican cattle based on autosomal microsatellite markers

    PubMed Central

    2013-01-01

    Background Determining the value of livestock breeds is essential to define conservation priorities, manage genetic diversity and allocate funds. Within- and between-breed genetic diversity need to be assessed to preserve the highest intra-specific variability. Information on genetic diversity and risk status is still lacking for many Creole cattle breeds from the Americas, despite their distinct evolutionary trajectories and adaptation to extreme environmental conditions. Methods A comprehensive genetic analysis of 67 Iberoamerican cattle breeds was carried out with 19 FAO-recommended microsatellites to assess conservation priorities. Contributions to global diversity were investigated using alternative methods, with different weights given to the within- and between-breed components of genetic diversity. Information on Iberoamerican plus 15 worldwide cattle breeds was used to investigate the contribution of geographical breed groups to global genetic diversity. Results Overall, Creole cattle breeds showed a high level of genetic diversity with the highest level found in breeds admixed with zebu cattle, which were clearly differentiated from all other breeds. Within-breed kinships revealed seven highly inbred Creole breeds for which measures are needed to avoid further genetic erosion. However, if contribution to heterozygosity was the only criterion considered, some of these breeds had the lowest priority for conservation decisions. The Weitzman approach prioritized highly differentiated breeds, such as Guabalá, Romosinuano, Cr. Patagonico, Siboney and Caracú, while kinship-based methods prioritized mainly zebu-related breeds. With the combined approaches, breed ranking depended on the weights given to the within- and between-breed components of diversity. Overall, the Creole groups of breeds were generally assigned a higher priority for conservation than the European groups of breeds. Conclusions Conservation priorities differed significantly according to the

  17. An international reference consensus genetic map with 897 marker loci based on 11 mapping populations for tetraploid groundnut (Arachis hypogaea L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Only a few genetic maps based on recombinant inbred line (RIL) and backcross (BC) populations have been developed for tetraploid groundnut. The marker density, however, is not very satisfactory especially in the context of large genome size (2800 Mb/1C) and 20 linkage groups (LGs). Therefore, using ...

  18. Anthropometric markers and their association with incident type 2 diabetes mellitus: which marker is best for prediction? Pooled analysis of four German population-based cohort studies and comparison with a nationwide cohort study

    PubMed Central

    Hartwig, Saskia; Kluttig, Alexander; Tiller, Daniel; Fricke, Julia; Müller, Grit; Schipf, Sabine; Völzke, Henry; Schunk, Michaela; Meisinger, Christa; Schienkiewitz, Anja; Heidemann, Christin; Moebus, Susanne; Pechlivanis, Sonali; Werdan, Karl; Kuss, Oliver; Tamayo, Teresa; Haerting, Johannes; Greiser, Karin Halina

    2016-01-01

    Objective To compare the association between different anthropometric measurements and incident type 2 diabetes mellitus (T2DM) and to assess their predictive ability in different regions of Germany. Methods Data of 10 258 participants from 4 prospective population-based cohorts were pooled to assess the association of body weight, body mass index (BMI), waist circumference (WC), waist-to-hip-ratio (WHR) and waist-to-height-ratio (WHtR) with incident T2DM by calculating HRs of the crude, adjusted and standardised markers, as well as providing receiver operator characteristic (ROC) curves. Differences between HRs and ROCs for the different anthropometric markers were calculated to compare their predictive ability. In addition, data of 3105 participants from the nationwide survey were analysed separately using the same methods to provide a nationally representative comparison. Results Strong associations were found for each anthropometric marker and incidence of T2DM. Among the standardised anthropometric measures, we found the strongest effect on incident T2DM for WC and WHtR in the pooled sample (HR for 1 SD difference in WC 1.97, 95% CI 1.75 to 2.22, HR for WHtR 1.93, 95% CI 1.71 to 2.17 in women) and in female DEGS participants (HR for WC 2.24, 95% CI 1.91 to 2.63, HR for WHtR 2.10, 95% CI 1.81 to 2.44), whereas the strongest association in men was found for WHR among DEGS participants (HR 2.29, 95% CI 1.89 to 2.78). ROC analysis showed WHtR to be the strongest predictor for incident T2DM. Differences in HR and ROCs between the different markers confirmed WC and WHtR to be the best predictors of incident T2DM. Findings were consistent across study regions and age groups (<65 vs ≥65 years). Conclusions We found stronger associations between anthropometric markers that reflect abdominal obesity (ie, WC and WHtR) and incident T2DM than for BMI and weight. The use of these measurements in risk prediction should be encouraged. PMID:26792214

  19. The construction of a genetic linkage map of red raspberry (Rubus idaeus subsp. idaeus) based on AFLPs, genomic-SSR and EST-SSR markers.

    PubMed

    Graham, J; Smith, K; MacKenzie, K; Jorgenson, L; Hackett, C; Powell, W

    2004-08-01

    Breeding in raspberry is time-consuming due to the highly heterozygous nature of this perennial fruit crop, coupled with relatively long periods of juvenility. The speed and precision of raspberry breeding can be improved by genetic linkage maps, thus facilitating the development of diagnostic markers for polygenic traits and the identification of genes controlling complex phenotypes. A genetic linkage map (789 cM) of the red raspberry Rubus idaeus has been constructed from a cross between two phenotypically different cultivars; the recent European cultivar Glen Moy and the older North American cultivar Latham. SSR markers were developed from both genomic and cDNA libraries from Glen Moy. These SSRs, together with AFLP markers, were utilised to create a linkage map. In order to test the utility of the genetic linkage map for QTL analysis, morphological data based on easily scoreable phenotypic traits were collected. The segregation of cane spininess, and the root sucker traits of density and spread from the mother plant, was quantified in two different environments. These traits were analysed for significant linkages to mapped markers using MapQTL and were found to be located on linkage group 2 for spines and group 8 for density and diameter. The availability of co-dominant markers allowed heterozygosities to be calculated for both cultivars.

  20. Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker

    PubMed Central

    Knief, Claudia

    2015-01-01

    Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoA) as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences representing “unknown methanotrophic bacteria.” This limits data interpretation due to restricted information about these uncultured methanotrophs. A few groups of uncultivated methanotrophs are assumed to play important roles in methane oxidation in specific habitats, while the biology behind other sequence clusters remains still largely unknown. The discovery of evolutionary related monooxygenases in non-methanotrophic bacteria and of pmoA paralogs in methanotrophs requires that sequence clusters of uncultivated organisms have to be interpreted with care. This review article describes the present diversity of cultivated and uncultivated aerobic methanotrophic bacteria based on pmoA gene sequence diversity. It summarizes current knowledge about cultivated and major clusters of uncultivated methanotrophic bacteria and evaluates habitat specificity of these bacteria at different levels of taxonomic resolution. Habitat specificity exists for diverse lineages and at different taxonomic levels. Methanotrophic genera such as Methylocystis and Methylocaldum are identified as generalists, but they harbor habitat specific methanotrophs at species level. This finding implies that future studies should consider these diverging preferences at different taxonomic levels when analyzing methanotrophic communities. PMID:26696968

  1. Use of Moringa oleifera Flower Pod Extract as Natural Preservative and Development of SCAR Marker for Its DNA Based Identification.

    PubMed

    Gull, Iram; Javed, Attia; Aslam, Muhammad Shahbaz; Mushtaq, Roohi; Athar, Muhammad Amin

    2016-01-01

    The use of Moringa oleifera as natural food preservative has been evaluated in the present study. In addition, for quality assurance, the study has also been focused on the shelf life of product to authenticate the identification of plant by development of DNA based marker. Among the different extracts prepared from flower pods of Moringa oleifera, methanol and aqueous extract exhibited high antibacterial and antioxidant activity, respectively. The high phenolic contents (53.5 ± 0.169 mg GAE/g) and flavonoid contents (10.9 ± 0.094 mg QE/g) were also recorded in methanol and aqueous extract, respectively. Due to instability of bioactive compounds in aqueous extract, methanol extract is considered as potent natural preservative. The shelf life of methanol extract was observed for two months at 4°C under dark conditions. The developed SCAR primers (MOF217/317/MOR317) specifically amplified a fragment of 317 bp from DNA of Moringa oleifera samples collected from different regions of Punjab province of Pakistan. The methanol extract of Moringa oleifera flower pods has great potential to be used as natural preservative and nutraceutical in food industry. PMID:27471732

  2. Use of Moringa oleifera Flower Pod Extract as Natural Preservative and Development of SCAR Marker for Its DNA Based Identification

    PubMed Central

    Gull, Iram; Javed, Attia; Aslam, Muhammad Shahbaz; Mushtaq, Roohi; Athar, Muhammad Amin

    2016-01-01

    The use of Moringa oleifera as natural food preservative has been evaluated in the present study. In addition, for quality assurance, the study has also been focused on the shelf life of product to authenticate the identification of plant by development of DNA based marker. Among the different extracts prepared from flower pods of Moringa oleifera, methanol and aqueous extract exhibited high antibacterial and antioxidant activity, respectively. The high phenolic contents (53.5 ± 0.169 mg GAE/g) and flavonoid contents (10.9 ± 0.094 mg QE/g) were also recorded in methanol and aqueous extract, respectively. Due to instability of bioactive compounds in aqueous extract, methanol extract is considered as potent natural preservative. The shelf life of methanol extract was observed for two months at 4°C under dark conditions. The developed SCAR primers (MOF217/317/MOR317) specifically amplified a fragment of 317 bp from DNA of Moringa oleifera samples collected from different regions of Punjab province of Pakistan. The methanol extract of Moringa oleifera flower pods has great potential to be used as natural preservative and nutraceutical in food industry. PMID:27471732

  3. Use of Moringa oleifera Flower Pod Extract as Natural Preservative and Development of SCAR Marker for Its DNA Based Identification.

    PubMed

    Gull, Iram; Javed, Attia; Aslam, Muhammad Shahbaz; Mushtaq, Roohi; Athar, Muhammad Amin

    2016-01-01

    The use of Moringa oleifera as natural food preservative has been evaluated in the present study. In addition, for quality assurance, the study has also been focused on the shelf life of product to authenticate the identification of plant by development of DNA based marker. Among the different extracts prepared from flower pods of Moringa oleifera, methanol and aqueous extract exhibited high antibacterial and antioxidant activity, respectively. The high phenolic contents (53.5 ± 0.169 mg GAE/g) and flavonoid contents (10.9 ± 0.094 mg QE/g) were also recorded in methanol and aqueous extract, respectively. Due to instability of bioactive compounds in aqueous extract, methanol extract is considered as potent natural preservative. The shelf life of methanol extract was observed for two months at 4°C under dark conditions. The developed SCAR primers (MOF217/317/MOR317) specifically amplified a fragment of 317 bp from DNA of Moringa oleifera samples collected from different regions of Punjab province of Pakistan. The methanol extract of Moringa oleifera flower pods has great potential to be used as natural preservative and nutraceutical in food industry.

  4. Genetic Diversity and Population Structure of Broomcorn Millet (Panicum miliaceum L.) Cultivars and Landraces in China Based on Microsatellite Markers

    PubMed Central

    Liu, Minxuan; Xu, Yue; He, Jihong; Zhang, Shuang; Wang, Yinyue; Lu, Ping

    2016-01-01

    Broomcorn millet (Panicum miliaceum L.), one of the first domesticated crops, has been grown in Northern China for at least 10,000 years. The species is presently a minor crop, and evaluation of its genetic diversity has been very limited. In this study, we analyzed the genetic diversity of 88 accessions of broomcorn millet collected from various provinces of China. Amplification with 67 simple sequence repeat (SSR) primers revealed moderate levels of diversity in the investigated accessions. A total of 179 alleles were detected, with an average of 2.7 alleles per locus. Polymorphism information content and expected heterozygosity ranged from 0.043 to 0.729 (mean = 0.376) and 0.045 to 0.771 (mean = 0.445), respectively. Cluster analysis based on the unweighted pair group method of mathematical averages separated the 88 accessions into four groups at a genetic similarity level of 0.633. A genetic structure assay indicated a close correlation between geographical regions and genetic diversity. The uncovered information will be valuable for defining gene pools and developing breeding programs for broomcorn millet. Furthermore, the millet-specific SSR markers developed in this study should serve as useful tools for assessment of genetic diversity and elucidation of population structure in broomcorn millet. PMID:26985894

  5. Patterns of genetic structure and evidence of gene flow among Tunisian Citrus species based on informative nSSR markers.

    PubMed

    Ben Romdhane, Meriam; Riahi, Leila; Selmi, Ayet; Zoghlami, Nejia

    2016-01-01

    This study investigates the extent of genetic diversity, phylogenetic relationships and the amount of gene flow among Tunisian Citrus species based on a set of 15 informative nuclear SSR molecular markers. Genotyping data highlighted an allelic richness among Tunisian Citrus species and has allowed the detection of 168 alleles among them 104.19 were effective. The partition of the total genetic diversity (HT=0.832) showed that the highest amount of variation within the Citrus species is HS=0.550, while the relative amount of the between-species genetic diversity GST does not exceed 0.338. This pattern of genetic structure was supported by low-to-moderate FST pairwise values and the presence of a gene flow (Nm) among the eight Citrus species. The lowest genetic differentiation was revealed between the species C. sinensis and C. insitorum (FST=0.111, Nm=1.99), while the highest genetic differentiation was recorded between the species C. aurantifolia and C. paradisi (FST=0.367, Nm=0.43). The established Neighbor Joining analysis showed that all genotypes were widely discriminated and clearly pooled according to their species of origin, with minor exceptions. PMID:27522638

  6. The genetic diversity and evolution of field pea (Pisum) studied by high throughput retrotransposon based insertion polymorphism (RBIP) marker analysis

    PubMed Central

    2010-01-01

    Background The genetic diversity of crop species is the result of natural selection on the wild progenitor and human intervention by ancient and modern farmers and breeders. The genomes of modern cultivars, old cultivated landraces, ecotypes and wild relatives reflect the effects of these forces and provide insights into germplasm structural diversity, the geographical dimension to species diversity and the process of domestication of wild organisms. This issue is also of great practical importance for crop improvement because wild germplasm represents a rich potential source of useful under-exploited alleles or allele combinations. The aim of the present study was to analyse a major Pisum germplasm collection to gain a broad understanding of the diversity and evolution of Pisum and provide a new rational framework for designing germplasm core collections of the genus. Results 3020 Pisum germplasm samples from the John Innes Pisum germplasm collection were genotyped for 45 retrotransposon based insertion polymorphism (RBIP) markers by the Tagged Array Marker (TAM) method. The data set was stored in a purpose-built Germinate relational database and analysed by both principal coordinate analysis and a nested application of the Structure program which yielded substantially similar but complementary views of the diversity of the genus Pisum. Structure revealed three Groups (1-3) corresponding approximately to landrace, cultivar and wild Pisum respectively, which were resolved by nested Structure analysis into 14 Sub-Groups, many of which correlate with taxonomic sub-divisions of Pisum, domestication related phenotypic traits and/or restricted geographical locations. Genetic distances calculated between these Sub-Groups are broadly supported by principal coordinate analysis and these, together with the trait and geographical data, were used to infer a detailed model for the domestication of Pisum. Conclusions These data provide a clear picture of the major distinct gene

  7. Genomic analysis of cultivated barley (Hordeum vulgare) using sequence-tagged molecular markers. Estimates of divergence based on RFLP and PCR markers derived from stress-responsive genes, and simple-sequence repeats (SSRs).

    PubMed

    Maestri, E; Malcevschi, A; Massari, A; Marmiroli, N

    2002-04-01

    Three types of molecular markers have been compared for their utility in evaluating genetic diversity among cultivars of Hordeum vulgare. Restriction fragment length polymorphisms at 71 sites were scored with the aid of probes corresponding to stress-responsive genes from barley and wheat, coding for a low-molecular-weight heat shock protein, a dehydrin, an aldose reductase homolog, and a 18.9-kDa drought-induced protein of unknown function. Indexes of genetic diversity computed in the total sample and within groups of cultivars (two-rowed and six-rowed, winter and spring varieties) indicated high values of genetic differentiation ( F (ST) >15%). A second assessment of genetic diversity was performed by PCR amplification of genomic DNA using as primers 13 arbitrary oligonucleotides derived from sequences of the same stress-responsive genes. A high degree of polymorphism was uncovered using these markers also, but they yielded low values for F (ST) (<7%) among groups of cultivars. Finally, 15 different simple-sequence repeats (AC or AG) were amplified with primers based on unique flanking sequences. Levels of polymorphism and differentiation between groups of cultivars revealed by these markers were quite high. Ordination techniques applied to measures of genetic distance among cultivars demonstrated a remarkable ability of the RFLPs associated with stress-responsive genes to discriminate on the basis of growth habit. The correlation with production data for the cultivars in different environments was also significant. This "functional genomics" strategy was therefore as informative as the "structural genomics" (SSR-based) approach, but requires the analysis of fewer probes. PMID:11976962

  8. A RAD tag derived marker based eggplant linkage map and the location of QTLs determining anthocyanin pigmentation.

    PubMed

    Barchi, Lorenzo; Lanteri, Sergio; Portis, Ezio; Valè, Giampiero; Volante, Andrea; Pulcini, Laura; Ciriaci, Tommaso; Acciarri, Nazareno; Barbierato, Valeria; Toppino, Laura; Rotino, Giuseppe Leonardo

    2012-01-01

    Both inter- and intra-specific maps have been developed in eggplant (Solanum melongena L.). The former benefit from an enhanced frequency of marker polymorphism, but their relevance to marker-assisted crop breeding is limited. Combining the restriction-site associated DNA strategy with high throughput sequencing has facilitated the discovery of a large number of functional single nucleotide polymorphism (SNP) markers discriminating between the two eggplant mapping population parental lines '305E40' and '67/3'. A set of 347 de novo SNPs, together with 84 anchoring markers, were applied to the F(2) mapping population bred from the cross '305E40' x '67/3' to construct a linkage map. In all, 415 of the 431 markers were assembled into twelve major and one minor linkage group, spanning 1,390 cM, and the inclusion of established markers allowed each linkage group to be assigned to one of the 12 eggplant chromosomes. The map was then used to discover the genetic basis of seven traits associated with anthocyanin content. Each of the traits proved to be controlled by between one and six quantitative trait loci (QTL), of which at least one was a major QTL. Exploitation of syntenic relationships between the eggplant and tomato genomes facilitated the identification of potential candidate genes for the eggplant QTLs related to anthocyanin accumulation. The intra-specific linkage map should have utility for elucidating the genetic basis of other phenotypic traits in eggplant.

  9. Evaluation of independence assumptions for PCR-based and protein-based genetic markers in New Jersey Caucasians.

    PubMed

    Budowle, B; Jankowski, L B; Corey, H W; Swec, N T; Freck-Tootell, S; Pino, J A; Schwartz, R; Kelley, C A; Tarver, M L

    1997-03-01

    Allele frequencies for six PCR-based loci and three protein-based (i.e., enzyme systems) loci were determined in a Caucasian sample population from New Jersey. The loci are LDLR, GYPA, HBGG, D7S8, Gc, HLA-DQA1, PGM1, ESD, and EAP. All loci meet Hardy-Weinberg expectations. In addition, there is little evidence for association of alleles among the nine loci. The allelic frequency data generally are similar to another Caucasian population database. PMID:9068180

  10. Highly efficient SERS-based detection of cerebrospinal fluid neopterin as a diagnostic marker of bacterial infection.

    PubMed

    Kamińska, Agnieszka; Witkowska, Evelin; Kowalska, Aneta; Skoczyńska, Anna; Gawryszewska, Iwona; Guziewicz, Elżbieta; Snigurenko, Dymitr; Waluk, Jacek

    2016-06-01

    A highly efficient recognition unit based on surface-enhanced Raman spectroscopy (SERS) was developed as a promising, fast, and sensitive tool for detection of meningococcal meningitis, which is an extremely serious and often fatal disease of the nervous system (an inflammation of the lining around the brain and spinal cord). The results of this study confirmed that there were specific differences in SERS spectra between cerebrospinal fluid (CSF) samples infected by Neisseria meningitidis and the normal CSF, suggesting a potential role for neopterin in meningococcal meningitis detection and screening applications. To estimate the best performance of neopterin as a marker of bacterial infection, principal component analysis (PCA) was performed in a selected region (640-720 cm(-1)) where the most prominent SERS peak at 695 cm(-1) arising from neopterin was observed. The calculated specificity of 95 % and sensitivity of 98 % clearly indicate the effective diagnostic efficiency for differentiation between infected and control samples. Additionally, the limit of detection (LOD) of neopterin in CSF clinical samples was estimated. The level of neopterin was significantly higher in CSF samples infected by N. meningitidis (48 nmol/L), compared to the normal (control) group (4.3 nmol/L). Additionally, this work presents a new type of SERS-active nanostructure, based on polymer mats, that allows simultaneous filtration, immobilization, and enhancement of the Raman signal, enabling detection of spectra from single bacterial cells of N. meningitidis present in CSF samples. This provides a new possibility for fast and easy detection of bacteria in CSF and other clinical body fluids on a time scale of seconds. This method of detection produces consistent results faster and cheaper than traditional laboratory techniques, demonstrates the powerful potential of SERS for detection of disease, and shows the viability of future development in healthcare applications. PMID

  11. The Swift Turbidity Marker

    ERIC Educational Resources Information Center

    Omar, Ahmad Fairuz; MatJafri, Mohd Zubir

    2011-01-01

    The Swift Turbidity Marker is an optical instrument developed to measure the level of water turbidity. The components and configuration selected for the system are based on common turbidity meter design concepts but use a simplified methodology to produce rapid turbidity measurements. This work is aimed at high school physics students and is the…

  12. Genetic differentiation induced by spaceflight treatment of Cistanche deserticola and identification of inter-simple sequence repeat markers associated with its medicinal constituent contents

    NASA Astrophysics Data System (ADS)

    Wu, Y.; Yang, D. Y.; Tu, P. F.; Tian, Y. Z.; Guo, Y. H.; Wang, X. M.; Li, X. B.

    2011-02-01

    The dried, fleshy stems of Cistanche deserticola (Orobanchaceae) are popular tonics in Traditional Chinese Medicine (TCM) to treat the inability of kidney in expelling extra fluid in the body, causing fluid retention, and reform reproductive system. However, the wild plants of C. deserticola have become endangered due to habitat downsizing and over-harvesting for its medicinal usages. The present research was carried out for the following purposes: (1) promoting the space-breeding research; (2) providing molecular evidence for agricultural selective breeding; and (3) protecting this endangered herbal medicine and conserving its genetic resources.In this study, plants were cultivated from seeds specifically treated in spaceflight for seven days, and sampled to screen positive mutants and identify ISSR markers associated with their medicinal constituents. As a result, nine out of the 94 ISSR primers were showed high polymorphism, and a total of 118 bands were generated, of which 80 were polymorphic, ranging from 250 to 2600 bp. The spaceflight mutants were found to have lower coefficient of gene differentiation (Gst = 0.0269), and higher gene flow (Nm = 18.0740) than those of the controls (Gst = 0.2067 and Nm = 1.9185). The results demonstrated that most of the genetic variation were harnessed within populations (>97%). The Analysis of Molecular Variance (AMOVA) revealed high genetic variation within populations (88.03%) and low genetic differentiation among regions (-18.83%) and populations (30.79%), respectively. The results also indicated a profound difference between spaceflight condition and that on the earth. The unique vacuum environment of spaceflight was suggested to induce DNA mutation and various variations of C. deserticola. In addition, six particular ISSR markers were identified, cloned and sequenced; one of them, CA41939-934, was found positively correlated with acteoside with correlation coefficient values of 0.264 (P < 0.05). Our work may provide a

  13. Glycomics and Disease Markers

    PubMed Central

    An, Hyun Joo; Kronewitter, Scott R.; de Leoz, Maria Lorna A.; Lebrilla, Carlito B.

    2009-01-01

    Summary of Recent Advances Glycomics is the comprehensive study of all glycans expressed in biological systems. The biosynthesis of glycan relies on a number of highly competitive processes involving glycosyl transferase. Glycosylation is therefore highly sensitive to the biochemical environment and has been implicated in many diseases including cancer. Recently, interest in profiling the glycome has increased due to the potential of glycans for disease markers. In this regard, mass spectrometry is emerging as a powerful technique for profiling the glycome. Global glycan profiling of human serum based on mass spectrometry has already led to several potentially promising markers for several types of cancer and diseases. PMID:19775929

  14. Development and Characterization of Simple Sequence Repeat (SSR) Markers Based on RNA-Sequencing of Medicago sativa and In silico Mapping onto the M. truncatula Genome

    PubMed Central

    Wang, Zan; Yu, Guohui; Shi, Binbin; Wang, Xuemin; Qiang, Haiping; Gao, Hongwen

    2014-01-01

    Sufficient codominant genetic markers are needed for various genetic investigations in alfalfa since the species is an outcrossing autotetraploid. With the newly developed next generation sequencing technology, a large amount of transcribed sequences of alfalfa have been generated and are available for identifying SSR markers by data mining. A total of 54,278 alfalfa non-redundant unigenes were assembled through the Illumina HiSeqTM 2000 sequencing technology. Based on 3,903 unigene sequences, 4,493 SSRs were identified. Tri-nucleotide repeats (56.71%) were the most abundant motif class while AG/CT (21.7%), AGG/CCT (19.8%), AAC/GTT (10.3%), ATC/ATG (8.8%), and ACC/GGT (6.3%) were the subsequent top five nucleotide repeat motifs. Eight hundred and thirty- seven EST-SSR primer pairs were successfully designed. Of these, 527 (63%) primer pairs yielded clear and scored PCR products and 372 (70.6%) exhibited polymorphisms. High transferability was observed for ssp falcata at 99.2% (523) and 71.7% (378) in M. truncatula. In addition, 313 of 527 SSR marker sequences were in silico mapped onto the eight M. truncatula chromosomes. Thirty-six polymorphic SSR primer pairs were used in the genetic relatedness analysis of 30 Chinese alfalfa cultivated accessions generating a total of 199 scored alleles. The mean observed heterozygosity and polymorphic information content were 0.767 and 0.635, respectively. The codominant markers not only enriched the current resources of molecular markers in alfalfa, but also would facilitate targeted investigations in marker-trait association, QTL mapping, and genetic diversity analysis in alfalfa. PMID:24642969

  15. [Use of morphological and physiological characters, and molecular markers to evaluate the genetic diversity of three clementine cultivars].

    PubMed

    Chahidi, Bouchra; El-Otmani, Mohamed; Jacquemond, Camille; Tijane, M'hamed; El-Mousadik, Abdelhamid; Srairi, Ikbal; Luro, François

    2008-01-01

    Originating from a natural crossing between mandarin and sweet orange at the end of the 19(th) century, clementine diversified through the selection of spontaneous mutations. Today, it seems almost impossible to distinguish one variety from another. The development of molecular tools for variety identification is thus necessary. Three clementine cultivars, representing distinct groups of fruit maturity, were evaluated. Identification criteria were searched at the phenotypical level (organoleptic characteristics, leaves morphology) as well as the DNA level (isozymes, RAPD, and ISSR). The phenotypical diversity observed is relatively high and contrasted with the low molecular polymorphism. In fact, only the cultivar 'Guerdane' presents profiles of genetic fingerprints different from those of the two other cultivars. The frequency of the genetic modifications would thus be variable from a cultivar to another. Moreover, the specific molecular markers of the cultivar 'Guerdane', added to the phenotypic markers, extend the possibilities of identification to the young nursery plants.

  16. [Analysis of genetic diversity of Russian regional populations based on common STR markers used in DNA identification].

    PubMed

    Pesik, V Yu; Fedunin, A A; Agdzhoyan, A T; Utevska, O M; Chukhraeva, M I; Evseeva, I V; Churnosov, M I; Lependina, I N; Bogunov, Yu V; Bogunova, A A; Ignashkin, M A; Yankovsky, N K; Balanovska, E V; Orekhov, V A; Balanovsky, O P

    2014-06-01

    We conducted the first genetic analysis of a wide a range of rural Russian populations in European Russia with a panel of common DNA markers commonly used in criminalistics genetic identification. We examined a total of 647 samples from indigenous ethnic Russian populations in Arkhangelsk, Belgorod, Voronezh, Kursk, Rostov, Ryazan, and Orel regions. We employed a multiplex genotyping kit, COrDIS Plus, to genotype Short Tandem Repeat (STR) loci, which included the genetic marker panel officially recommended for DNA identification in the Russian Federation, the United States, and the European Union. In the course of our study, we created a database of allelic frequencies, examined the distribution of alleles and genotypes in seven rural Russian populations, and defined the genetic relationships between these populations. We found that, although multidimensional analysis indicated a difference between the Northern gene pool and the rest of the Russian European populations, a pairwise comparison using 19 STR markers among all populations did not reveal significant differences. This is in concordance with previous studies, which examined up to 12 STR markers of urban Russian populations. Therefore, the database of allelic frequencies created in this study can be applied for forensic examinations and DNA identification among the ethnic Russian population over European Russia. We also noted a decrease in the levels of heterozygosity in the northern Russian population compared to ethnic populations in southern and central Russia, which is consistent with trends identified previously using classical gene markers and analysis of mitochondrial DNA.

  17. [Analysis of genetic diversity of Russian regional populations based on common STR markers used in DNA identification].

    PubMed

    Pesik, V Yu; Fedunin, A A; Agdzhoyan, A T; Utevska, O M; Chukhraeva, M I; Evseeva, I V; Churnosov, M I; Lependina, I N; Bogunov, Yu V; Bogunova, A A; Ignashkin, M A; Yankovsky, N K; Balanovska, E V; Orekhov, V A; Balanovsky, O P

    2014-06-01

    We conducted the first genetic analysis of a wide a range of rural Russian populations in European Russia with a panel of common DNA markers commonly used in criminalistics genetic identification. We examined a total of 647 samples from indigenous ethnic Russian populations in Arkhangelsk, Belgorod, Voronezh, Kursk, Rostov, Ryazan, and Orel regions. We employed a multiplex genotyping kit, COrDIS Plus, to genotype Short Tandem Repeat (STR) loci, which included the genetic marker panel officially recommended for DNA identification in the Russian Federation, the United States, and the European Union. In the course of our study, we created a database of allelic frequencies, examined the distribution of alleles and genotypes in seven rural Russian populations, and defined the genetic relationships between these populations. We found that, although multidimensional analysis indicated a difference between the Northern gene pool and the rest of the Russian European populations, a pairwise comparison using 19 STR markers among all populations did not reveal significant differences. This is in concordance with previous studies, which examined up to 12 STR markers of urban Russian populations. Therefore, the database of allelic frequencies created in this study can be applied for forensic examinations and DNA identification among the ethnic Russian population over European Russia. We also noted a decrease in the levels of heterozygosity in the northern Russian population compared to ethnic populations in southern and central Russia, which is consistent with trends identified previously using classical gene markers and analysis of mitochondrial DNA. PMID:25715463

  18. Base deficit as a marker of survival after traumatic injury: Consistent across changing patient populations and resuscitation paradigms

    PubMed Central

    Hodgman, Erica I.; Morse, Bryan C.; Dente, Christopher J.; Mina, Michael J.; Shaz, Beth H.; Nicholas, Jeffrey M.; Wyrzykowski, Amy D.; Salomone, Jeffrey P.; Rozycki, Grace S.; Feliciano, David V.

    2016-01-01

    BACKGROUND Damage control resuscitation (DCR) has improved outcomes in severely injured patients. In civilian centers, massive transfusion protocols (MTPs) represent the most formal application of DCR principles, ensuring early, accurate delivery of high fixed ratios of blood components. Recent data suggest that DCR may also help address early trauma-induced coagulopathy. Finally, base deficit (BD) is a long-recognized and simple early prognostic marker of survival after injury. METHODS Outcomes of patients with admission BD data resuscitated during the DCR era (2007–2010) were compared with previously published data (1995–2003) of patients cared for before the DCR era (pre-DCR). Patients were considered to have no hypoperfusion (BD, >−6), mild (BD, −6 to −14.9), moderate (BD, −15 to −23.9), or severe hypoperfusion (BD, <−24). RESULTS Of 6,767 patients, 4,561 were treated in the pre-DCR era and 2,206 in the DCR era. Of the latter, 218 (9.8%) represented activations of the MTP. DCR patients tended to be slightly older, more likely victims of penetrating trauma, and slightly more severely injured as measured by trauma scores and BD. Despite these differences, overall survival was unchanged in the two eras (86.4% vs. 85.7%, p = 0.67), and survival curves stratified by mechanism of injury were nearly identical. Patients with severe BD who were resuscitated using the MTP, however, experienced a substantial increase in survival compared with pre-DCR counterparts. CONCLUSION Despite limited adoption of formal DCR, overall survival after injury, stratified by BD, is identical in the modern era. Patients with severely deranged physiology, however, experience better outcomes. BD remains a consistent predictor of mortality after traumatic injury. Predicted survival depends more on the energy level of the injury (stab wound vs. nonstab wound) than the mechanism of injury (blunt vs. penetrating). LEVEL OF EVIDENCE IV, therapeutic/prognostic study. PMID:22491595

  19. A scientific approach to the attribution problem of renaissance ceramic productions based on chemical and mineralogical markers

    NASA Astrophysics Data System (ADS)

    Padeletti, G.; Fermo, P.

    2010-09-01

    Renaissance lustred majolica shards from Gubbio and Deruta (Central Italy) were investigated in order to point out differences in chemical and mineralogical composition between these two very similar Italian potteries and furthermore to find correlations with the local raw clay materials probably used for their production. Chemical and mineralogical analysis on the ceramic body were performed by ICP-OES (inductively coupled plasma optical emission spectroscopy) and XRD (X-ray diffraction), respectively. Investigation of the ceramic body revealed significant differences on calcium content indicating that it could be used as a marker for the two different productions. A separation of the ceramic shards in groups, on the base of their provenance, has been achieved applying to the data set formed by the chemical compositional data some multivariate techniques, such as PCA (principal component analysis) and HCA (hierarchical cluster analysis). Even the mineralogical composition of the groups shows very interesting features, differing Gubbio production from Deruta one for the presence of several mineralogical species. The investigations carried out on clays that were collected in the two geographical places have confirmed these differences. In fact, the clay materials have a chemical composition coherent with that one found in the shards. Firing tests performed by heating these clay in different conditions (temperature and soaking time) have shown a different behaviour as concerns the formation of the minerals and it is compatible with the shard composition found. From the comparison between the fired clay and the ceramic shards, some assumptions about the firing conditions applied by the ancient potters have been drawn.

  20. Population Genetics of the Endemic Hawaiian Species Chrysodracon hawaiiensis and Chrysodracon auwahiensis (Asparagaceae): Insights from RAPD and ISSR Variation

    PubMed Central

    Lu, Pei-Luen; Yorkson, Mitsuko; Morden, Clifford W.

    2016-01-01

    The genus Chrysodracon has six endemic species in the Hawaii Islands. Chrysodracon hawaiiensis is endemic to Hawaii Island and was described as a distinct species in 1980. It was listed as an endangered species on the International Union for the Conservation of Nature and Natural Resources (IUCN) Red List in 1997. This woody plant species was, at one time, common in exposed dry forests, but it became very rare due to grazing pressure and human development. The tree species Chrysodracon auwahiensis (C. auwahiensis), endemic to Maui and Molokai, still has large adult populations in dry lands of the islands, but unfortunately no regeneration from seed has been reported in those areas for many years. The two endemic species were examined using the molecular technique of random amplified polymorphic DNA (RAPD) and inter simple sequence repeats (ISSR) to determine the genetic structure of the populations and the amount of variation. Both species possess similar genetic structure. Larger and smaller populations of both species contain similar levels of genetic diversity as determined by the number of polymorphic loci, estimated heterozygosity, and Shannon’s index of genetic diversity. Although population diversity of Chrysodracon hawaiiensis (C. hawaiiensis) is thought to have remained near pre-disturbance levels, population size continues to decline as recruitment is either absent or does not keep pace with senescence of mature plants. Conservation recommendations for both species are suggested. PMID:27537876

  1. Population Genetics of the Endemic Hawaiian Species Chrysodracon hawaiiensis and Chrysodracon auwahiensis (Asparagaceae): Insights from RAPD and ISSR Variation.

    PubMed

    Lu, Pei-Luen; Yorkson, Mitsuko; Morden, Clifford W

    2016-01-01

    The genus Chrysodracon has six endemic species in the Hawaii Islands. Chrysodracon hawaiiensis is endemic to Hawaii Island and was described as a distinct species in 1980. It was listed as an endangered species on the International Union for the Conservation of Nature and Natural Resources (IUCN) Red List in 1997. This woody plant species was, at one time, common in exposed dry forests, but it became very rare due to grazing pressure and human development. The tree species Chrysodracon auwahiensis (C. auwahiensis), endemic to Maui and Molokai, still has large adult populations in dry lands of the islands, but unfortunately no regeneration from seed has been reported in those areas for many years. The two endemic species were examined using the molecular technique of random amplified polymorphic DNA (RAPD) and inter simple sequence repeats (ISSR) to determine the genetic structure of the populations and the amount of variation. Both species possess similar genetic structure. Larger and smaller populations of both species contain similar levels of genetic diversity as determined by the number of polymorphic loci, estimated heterozygosity, and Shannon's index of genetic diversity. Although population diversity of Chrysodracon hawaiiensis (C. hawaiiensis) is thought to have remained near pre-disturbance levels, population size continues to decline as recruitment is either absent or does not keep pace with senescence of mature plants. Conservation recommendations for both species are suggested. PMID:27537876

  2. Development of Nested PCR-Based Specific Markers for Detection of Peach Rosette Mosaic Virus in Plant Quarantine.

    PubMed

    Lee, S; Kim, C S; Shin, Y G; Kim, J H; Kim, Y S; Jheong, W H

    2016-03-01

    The Peach rosette mosaic virus (PRMV) is a plant pathogen of the genus Nepovirus, and has been designated as a controlled quarantine virus in Korea. In this study, a specific reverse transcription (RT)-PCR marker set, nested PCR marker set, and modified-plasmid positive control were developed to promptly and accurately diagnose PRMV at plant-quarantine sites. The final selected PRMV-specific RT-PCR marker was PRMV-N10/C70 (967 bp), and the nested PCR product of 419 bp was finally amplified. The modified-plasmid positive control, in which the SalI restriction-enzyme region (GTCGAC) was inserted, verified PRMV contamination in a comparison with the control, enabling a more accurate diagnosis. It is expected that the developed method will continuously contribute to the plant-quarantine process in Korea. PMID:26843704

  3. Genetic diversity and population structure in Physalis peruviana and related taxa based on InDels and SNPs derived from COSII and IRG markers

    PubMed Central

    Garzón-Martínez, Gina A.; Osorio-Guarín, Jaime A.; Delgadillo-Durán, Paola; Mayorga, Franklin; Enciso-Rodríguez, Felix E.; Landsman, David

    2015-01-01

    The genus Physalis is common in the Americas and includes several economically important species, among them Physalis peruviana that produces appetizing edible fruits. We studied the genetic diversity and population structure of P. peruviana and characterized 47 accessions of this species along with 13 accessions of related taxa consisting of 222 individuals from the Colombian Corporation of Agricultural Research (CORPOICA) germplasm collection, using Conserved Orthologous Sequences (COSII) and Immunity Related Genes (IRGs). In addition, 642 Single Nucleotide Polymorphism (SNPs) markers were identified and used for the genetic diversity analysis. A total of 121 alleles were detected in 24 InDels loci ranging from 2 to 9 alleles per locus, with an average of 5.04 alleles per locus. The average number of alleles in the SNP markers was two. The observed heterozygosity for P. peruviana with InDel and SNP markers was higher (0.48 and 0.59) than the expected heterozygosity (0.30 and 0.41). Interestingly, the observed heterozygosity in related taxa (0.4 and 0.12) was lower than the expected heterozygosity (0.59 and 0.25). The coefficient of population differentiation FST was 0.143 (InDels) and 0.038 (SNPs), showing a relatively low level of genetic differentiation among P. peruviana and related taxa. Higher levels of genetic variation were instead observed within populations based on the AMOVA analysis. Population structure analysis supported the presence of two main groups and PCA analysis based on SNP markers revealed two distinct clusters in the P. peruviana accessions corresponding to their state of cultivation. In this study, we identified molecular markers useful to detect genetic variation in Physalis germplasm for assisting conservation and crossbreeding strategies. PMID:26550601

  4. Fusion of mature HIV-1 particles leads to complete release of a gag-GFP-based content marker and raises the intraviral pH.

    PubMed

    Padilla-Parra, Sergi; Marin, Mariana; Gahlaut, Nivriti; Suter, Rolf; Kondo, Naoyuki; Melikyan, Gregory B

    2013-01-01

    By imaging the release of a GFP-based viral content marker produced upon virus maturation, we have previously found that HIV-1 fuses with endosomes. In contrast, fusion at the cell surface did not progress beyond a lipid mixing stage (hemifusion). However, recent evidence suggesting that free GFP can be trapped within the mature HIV-1 capsid raises concerns that this content marker may not be released immediately after the formation of a fusion pore. To determine whether a significant portion of GFP is trapped in the mature capsid, we first permeabilized the viral membrane with saponin. The overwhelming majority of pseudoviruses fully released GFP while the remaining particles exhibited partial loss or no loss of content. The extent of GFP release correlated with HIV-1 maturation, implying that incomplete Gag processing, but not GFP entrapment by mature capsids, causes partial content release. Next, we designed a complementary assay for visualizing pore formation by monitoring the intraviral pH with an additional pH-sensitive fluorescent marker. The loss of GFP through saponin-mediated pores was associated with a concomitant increase in the intraviral pH due to equilibration with the pH of an external buffer. We next imaged single HIV-cell fusion and found that these events were manifested in a highly correlated loss of content and increase in the intraviral pH, as it equilibrated with the cytosolic pH. Fused or saponin-permeabilized pseudoviruses that partially lost GFP did not release the remaining content marker under conditions expected to promote the capsid dissociation. We were thus unable to detect significant entrapment of GFP by the mature HIV-1 capsid. Together, our results validate the use of the GFP-based content marker for imaging single virus fusion and inferring the sites of HIV-1 entry.

  5. Development of microsatellite markers for common bean (Phaseolus vulgaris L.) based on screening of non-enriched, small-insert genomic libraries.

    PubMed

    Blair, Matthew W; Torres, Monica Muñoz; Pedraza, Fabio; Giraldo, Martha C; Buendía, Hector F; Hurtado, Natalia

    2009-09-01

    Microsatellite markers are useful genetic tools for a wide array of genomic analyses although their development is time-consuming and requires the identification of simple sequence repeats (SSRs) from genomic sequences. Screening of non-enriched, small-insert libraries is an effective method of SSR isolation that can give an unbiased picture of motif frequency. Here we adapt high-throughput protocols for the screening of plasmid-based libraries using robotic colony picking and filter preparation. Seven non-enriched genomic libraries from common bean genomic DNA were made by digestion with four frequently cutting restriction enzymes, double digestion with a frequently cutting restriction enzyme and a less frequently cutting restriction enzyme, or sonication. Library quality was compared and three of the small-insert libraries were selected for further analysis. Each library was plated and picked into 384-well plates that were used to create high-density filter arrays of over 18 000 clones each, which were screened with oligonucleotide probes for various SSR motifs. Positive clones were found to have low redundancy. One hundred SSR markers were developed and 80 were tested for polymorphism in a standard parental survey. These microsatellite markers derived from non-SSR-enriched libraries should be useful additions to previous markers developed from enriched libraries.

  6. Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea.

    PubMed

    Bajaj, Deepak; Saxena, Maneesha S; Kujur, Alice; Das, Shouvik; Badoni, Saurabh; Tripathi, Shailesh; Upadhyaya, Hari D; Gowda, C L L; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K; Parida, Swarup K

    2015-03-01

    Phylogenetic footprinting identified 666 genome-wide paralogous and orthologous CNMS (conserved non-coding microsatellite) markers from 5'-untranslated and regulatory regions (URRs) of 603 protein-coding chickpea genes. The (CT)n and (GA)n CNMS carrying CTRMCAMV35S and GAGA8BKN3 regulatory elements, respectively, are abundant in the chickpea genome. The mapped genic CNMS markers with robust amplification efficiencies (94.7%) detected higher intraspecific polymorphic potential (37.6%) among genotypes, implying their immense utility in chickpea breeding and genetic analyses. Seventeen differentially expressed CNMS marker-associated genes showing strong preferential and seed tissue/developmental stage-specific expression in contrasting genotypes were selected to narrow down the gene targets underlying seed weight quantitative trait loci (QTLs)/eQTLs (expression QTLs) through integrative genetical genomics. The integration of transcript profiling with seed weight QTL/eQTL mapping, molecular haplotyping, and association analyses identified potential molecular tags (GAGA8BKN3 and RAV1AAT regulatory elements and alleles/haplotypes) in the LOB-domain-containing protein- and KANADI protein-encoding transcription factor genes controlling the cis-regulated expression for seed weight in the chickpea. This emphasizes the potential of CNMS marker-based integrative genetical genomics for the quantitative genetic dissection of complex seed weight in chickpea.

  7. Development of microsatellite markers for common bean (Phaseolus vulgaris L.) based on screening of non-enriched, small-insert genomic libraries.

    PubMed

    Blair, Matthew W; Torres, Monica Muñoz; Pedraza, Fabio; Giraldo, Martha C; Buendía, Hector F; Hurtado, Natalia

    2009-09-01

    Microsatellite markers are useful genetic tools for a wide array of genomic analyses although their development is time-consuming and requires the identification of simple sequence repeats (SSRs) from genomic sequences. Screening of non-enriched, small-insert libraries is an effective method of SSR isolation that can give an unbiased picture of motif frequency. Here we adapt high-throughput protocols for the screening of plasmid-based libraries using robotic colony picking and filter preparation. Seven non-enriched genomic libraries from common bean genomic DNA were made by digestion with four frequently cutting restriction enzymes, double digestion with a frequently cutting restriction enzyme and a less frequently cutting restriction enzyme, or sonication. Library quality was compared and three of the small-insert libraries were selected for further analysis. Each library was plated and picked into 384-well plates that were used to create high-density filter arrays of over 18 000 clones each, which were screened with oligonucleotide probes for various SSR motifs. Positive clones were found to have low redundancy. One hundred SSR markers were developed and 80 were tested for polymorphism in a standard parental survey. These microsatellite markers derived from non-SSR-enriched libraries should be useful additions to previous markers developed from enriched libraries. PMID:19935925

  8. Cultivar identification, pedigree verification, and diversity analysis among Peach (Prunus persica L. Batsch) Cultivars based on Simple Sequence Repeat markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genetic relationships and pedigree inferences among peach (Prunus persica (L.) Batsch) accessions and breeding lines used in genetic improvement were evaluated using 15 simple sequence repeat (SSR) markers. A total of 80 alleles were detected among the 37 peach accessions with an average of 5.53...

  9. A SPR biosensor based on signal amplification using antibody-QD conjugates for quantitative determination of multiple tumor markers

    PubMed Central

    Wang, Huan; Wang, Xiaomei; Wang, Jue; Fu, Weiling; Yao, Chunyan

    2016-01-01

    The detection of tumor markers is very important in early cancer diagnosis; however, tumor markers are usually present at very low concentrations, especially in the early stages of tumor development. Surface plasmon resonance (SPR) is widely used to detect biomolecular interactions; it has inherent advantages of being high-throughput, real-time, and label-free technique. However, its sensitivity needs essential improvement for practical applications. In this study, we developed a signal amplification strategy using antibody-quantum dot (QD) conjugates for the sensitive and quantitative detection of α-fetoprotein (AFP), carcinoembryonic antigen (CEA) and cytokeratin fragment 21-1 (CYFRA 21-1) in clinical samples. The use of a dual signal amplification strategy using AuNP-antibody and antibody-QD conjugates increased the signal amplification by 50-folds. The constructed SPR biosensor showed a detection limit as low as 0.1 ng/mL for AFP, CEA, and CYFRA 21-1. Moreover, the results obtained using this SPR biosensor were consistent with those obtained using the electrochemiluminescence method. Thus, the constructed SPR biosensor provides a highly sensitive and specific approach for the detection of tumor markers. This SPR biosensor can be expected to be readily applied for the detection of other tumor markers and can offer a potentially powerful solution for tumor screening. PMID:27615417

  10. Association mapping for yield and yield-contributing traits in barley under drought conditions with genome-based SSR markers.

    PubMed

    Abou-Elwafa, Salah Fatouh

    2016-01-01

    Drought negatively affects plant development, growth, yield, and ultimately production of crop species. Association analysis of yield and yield-contributing traits was conducted for a barley germplasm collection consisting 107 wild (Hordeum spontaneum L.) genotypes, originating from 12 countries using 76 SSR markers. Phenotypic evaluations were performed for days to heading, plant height, number of tillers/plant, spike length, thousand kernel weight, single plant yield under well-watered and drought-stress conditions. Highly significant differences between well-watered and drought-stress conditions were observed in all measured traits. Association analysis revealed a total of 83 significant marker-trait associations for all six measured traits. The results revealed that several chromosomal regions significantly influence more than one trait, suggesting a possible existence of pleiotropic or indirect effects. The phenotypic variation explained by individual marker-trait associations ranged from 5.08 to 27.84%. The results demonstrated that wild barley is a valuable source for improving yield and yield-contributing traits for drought tolerance. Our data provide a tool kit for the potential application of marker-assisted selection for drought tolerance in barley.

  11. A SPR biosensor based on signal amplification using antibody-QD conjugates for quantitative determination of multiple tumor markers.

    PubMed

    Wang, Huan; Wang, Xiaomei; Wang, Jue; Fu, Weiling; Yao, Chunyan

    2016-01-01

    The detection of tumor markers is very important in early cancer diagnosis; however, tumor markers are usually present at very low concentrations, especially in the early stages of tumor development. Surface plasmon resonance (SPR) is widely used to detect biomolecular interactions; it has inherent advantages of being high-throughput, real-time, and label-free technique. However, its sensitivity needs essential improvement for practical applications. In this study, we developed a signal amplification strategy using antibody-quantum dot (QD) conjugates for the sensitive and quantitative detection of α-fetoprotein (AFP), carcinoembryonic antigen (CEA) and cytokeratin fragment 21-1 (CYFRA 21-1) in clinical samples. The use of a dual signal amplification strategy using AuNP-antibody and antibody-QD conjugates increased the signal amplification by 50-folds. The constructed SPR biosensor showed a detection limit as low as 0.1 ng/mL for AFP, CEA, and CYFRA 21-1. Moreover, the results obtained using this SPR biosensor were consistent with those obtained using the electrochemiluminescence method. Thus, the constructed SPR biosensor provides a highly sensitive and specific approach for the detection of tumor markers. This SPR biosensor can be expected to be readily applied for the detection of other tumor markers and can offer a potentially powerful solution for tumor screening. PMID:27615417

  12. Improvement of marker-based predictability of Apparent Amylose Content in japonica rice through GBSSI allele mining

    PubMed Central

    2014-01-01

    Background Apparent Amylose Content (AAC), regulated by the Waxy gene, represents the key determinant of rice cooking properties. In occidental countries high AAC rice represents the most requested market class but the availability of molecular markers allowing specific selection of high AAC varieties is limited. Results In this study, the effectiveness of available molecular markers in predicting AAC was evaluated in a collection of 127 rice accessions (125 japonica ssp. and 2 indica ssp.) characterized by AAC values from glutinous to 26%. The analyses highlighted the presence of several different allelic patterns identifiable by a few molecular markers, and two of them, i.e., the SNPs at intron1 and exon 6, were able to explain a maximum of 79.5% of AAC variation. However, the available molecular markers haplotypes did not provide tools for predicting accessions with AAC higher than 24.5%. To identify additional polymorphisms, the re-sequencing of the Waxy gene and 1kbp of the putative upstream regulatory region was performed in 21 genotypes representing all the AAC classes identified. Several previously un-characterized SNPs were identified and four of them were used to develop dCAPS markers. Conclusions The addition of the SNPs newly identified slightly increased the AAC explained variation and allowed the identification of a haplotype almost unequivocally associated to AAC higher than 24.5%. Haplotypes at the waxy locus were also associated to grain length and length/width (L/W) ratio. In particular, the SNP at the first intron, which identifies the Wx a and Wx b alleles, was associated with differences in the width of the grain, the L/W ratio and the length of the kernel, most likely as a result of human selection. PMID:24383761

  13. Microfluidic single-cell transcriptional analysis rationally identifies novel surface marker profiles to enhance cell-based therapies.

    PubMed

    Rennert, Robert C; Januszyk, Michael; Sorkin, Michael; Rodrigues, Melanie; Maan, Zeshaan N; Duscher, Dominik; Whittam, Alexander J; Kosaraju, Revanth; Chung, Michael T; Paik, Kevin; Li, Alexander Y; Findlay, Michael; Glotzbach, Jason P; Butte, Atul J; Gurtner, Geoffrey C

    2016-01-01

    Current progenitor cell therapies have only modest efficacy, which has limited their clinical adoption. This may be the result of a cellular heterogeneity that decreases the number of functional progenitors delivered to diseased tissue, and prevents correction of underlying pathologic cell population disruptions. Here, we develop a high-resolution method of identifying phenotypically distinct progenitor cell subpopulations via single-cell transcriptional analysis and advanced bioinformatics. When combined with high-throughput cell surface marker screening, this approach facilitates the rational selection of surface markers for prospective isolation of cell subpopulations with desired transcriptional profiles. We establish the usefulness of this platform in costly and highly morbid diabetic wounds by identifying a subpopulation of progenitor cells that is dysfunctional in the diabetic state, and normalizes diabetic wound healing rates following allogeneic application. We believe this work presents a logical framework for the development of targeted cell therapies that can be customized to any clinical application. PMID:27324848

  14. Microfluidic single-cell transcriptional analysis rationally identifies novel surface marker profiles to enhance cell-based therapies.

    PubMed

    Rennert, Robert C; Januszyk, Michael; Sorkin, Michael; Rodrigues, Melanie; Maan, Zeshaan N; Duscher, Dominik; Whittam, Alexander J; Kosaraju, Revanth; Chung, Michael T; Paik, Kevin; Li, Alexander Y; Findlay, Michael; Glotzbach, Jason P; Butte, Atul J; Gurtner, Geoffrey C

    2016-06-21

    Current progenitor cell therapies have only modest efficacy, which has limited their clinical adoption. This may be the result of a cellular heterogeneity that decreases the number of functional progenitors delivered to diseased tissue, and prevents correction of underlying pathologic cell population disruptions. Here, we develop a high-resolution method of identifying phenotypically distinct progenitor cell subpopulations via single-cell transcriptional analysis and advanced bioinformatics. When combined with high-throughput cell surface marker screening, this approach facilitates the rational selection of surface markers for prospective isolation of cell subpopulations with desired transcriptional profiles. We establish the usefulness of this platform in costly and highly morbid diabetic wounds by identifying a subpopulation of progenitor cells that is dysfunctional in the diabetic state, and normalizes diabetic wound healing rates following allogeneic application. We believe this work presents a logical framework for the development of targeted cell therapies that can be customized to any clinical application.

  15. Candidate Gene Identification with SNP Marker-Based Fine Mapping of Anthracnose Resistance Gene Co-4 in Common Bean.

    PubMed

    Burt, Andrew J; William, H Manilal; Perry, Gregory; Khanal, Raja; Pauls, K Peter; Kelly, James D; Navabi, Alireza

    2015-01-01

    Anthracnose, caused by Colletotrichum lindemuthianum, is an important fungal disease of common bean (Phaseolus vulgaris). Alleles at the Co-4 locus confer resistance to a number of races of C. lindemuthianum. A population of 94 F4:5 recombinant inbred lines of a cross between resistant black bean genotype B09197 and susceptible navy bean cultivar Nautica was used to identify markers associated with resistance in bean chromosome 8 (Pv08) where Co-4 is localized. Three SCAR markers with known linkage to Co-4 and a panel of single nucleotide markers were used for genotyping. A refined physical region on Pv08 with significant association with anthracnose resistance identified by markers was used in BLAST searches with the genomic sequence of common bean accession G19833. Thirty two unique annotated candidate genes were identified that spanned a physical region of 936.46 kb. A majority of the annotated genes identified had functional similarity to leucine rich repeats/receptor like kinase domains. Three annotated genes had similarity to 1, 3-β-glucanase domains. There were sequence similarities between some of the annotated genes found in the study and the genes associated with phosphoinositide-specific phosphilipases C associated with Co-x and the COK-4 loci found in previous studies. It is possible that the Co-4 locus is structured as a group of genes with functional domains dominated by protein tyrosine kinase along with leucine rich repeats/nucleotide binding site, phosphilipases C as well as β-glucanases. PMID:26431031

  16. Candidate Gene Identification with SNP Marker-Based Fine Mapping of Anthracnose Resistance Gene Co-4 in Common Bean

    PubMed Central

    Burt, Andrew J.; William, H. Manilal; Perry, Gregory; Khanal, Raja; Pauls, K. Peter; Kelly, James D.; Navabi, Alireza

    2015-01-01

    Anthracnose, caused by Colletotrichum lindemuthianum, is an important fungal disease of common bean (Phaseolus vulgaris). Alleles at the Co–4 locus confer resistance to a number of races of C. lindemuthianum. A population of 94 F4:5 recombinant inbred lines of a cross between resistant black bean genotype B09197 and susceptible navy bean cultivar Nautica was used to identify markers associated with resistance in bean chromosome 8 (Pv08) where Co–4 is localized. Three SCAR markers with known linkage to Co–4 and a panel of single nucleotide markers were used for genotyping. A refined physical region on Pv08 with significant association with anthracnose resistance identified by markers was used in BLAST searches with the genomic sequence of common bean accession G19833. Thirty two unique annotated candidate genes were identified that spanned a physical region of 936.46 kb. A majority of the annotated genes identified had functional similarity to leucine rich repeats/receptor like kinase domains. Three annotated genes had similarity to 1, 3-β-glucanase domains. There were sequence similarities between some of the annotated genes found in the study and the genes associated with phosphoinositide-specific phosphilipases C associated with Co-x and the COK–4 loci found in previous studies. It is possible that the Co–4 locus is structured as a group of genes with functional domains dominated by protein tyrosine kinase along with leucine rich repeats/nucleotide binding site, phosphilipases C as well as β-glucanases. PMID:26431031

  17. MALDI based identification of soybean protein markers--possible analytical targets for allergen detection in processed foods.

    PubMed

    Cucu, Tatiana; De Meulenaer, Bruno; Devreese, Bart

    2012-02-01

    Soybean (Glycine max) is extensively used all over the world due to its nutritional qualities. However, soybean is included in the "big eight" list of food allergens. According to the EU directive 2007/68/EC, food products containing soybeans have to be labeled in order to protect the allergic consumers. Nevertheless, soybeans can still inadvertently be present in food products. The development of analytical methods for the detection of traces of allergens is important for the protection of allergic consumers. Mass spectrometry of marker proteolytical fragments of protein allergens is growingly recognized as a detection method in food control. However, quantification of soybean at the peptide level is hindered due to limited information regarding specific stable markers derived after proteolytic digestion. The aim of this study was to use MALDI-TOF/MS and MS/MS as a fast screening tool for the identification of stable soybean derived tryptic markers which were still identifiable even if the proteins were subjected to various changes at the molecular level through a number of reactions typically occurring during food processing (denaturation, the Maillard reaction and oxidation). The peptides (401)Val-Arg(410) from the G1 glycinin (Gly m 6) and the (518)Gln-Arg(528) from the α' chain of the β-conglycinin (Gly m 5) proved to be the most stable. These peptides hold potential to be used as targets for the development of new analytical methods for the detection of soybean protein traces in processed foods. PMID:22212959

  18. MALDI based identification of soybean protein markers--possible analytical targets for allergen detection in processed foods.

    PubMed

    Cucu, Tatiana; De Meulenaer, Bruno; Devreese, Bart

    2012-02-01

    Soybean (Glycine max) is extensively used all over the world due to its nutritional qualities. However, soybean is included in the "big eight" list of food allergens. According to the EU directive 2007/68/EC, food products containing soybeans have to be labeled in order to protect the allergic consumers. Nevertheless, soybeans can still inadvertently be present in food products. The development of analytical methods for the detection of traces of allergens is important for the protection of allergic consumers. Mass spectrometry of marker proteolytical fragments of protein allergens is growingly recognized as a detection method in food control. However, quantification of soybean at the peptide level is hindered due to limited information regarding specific stable markers derived after proteolytic digestion. The aim of this study was to use MALDI-TOF/MS and MS/MS as a fast screening tool for the identification of stable soybean derived tryptic markers which were still identifiable even if the proteins were subjected to various changes at the molecular level through a number of reactions typically occurring during food processing (denaturation, the Maillard reaction and oxidation). The peptides (401)Val-Arg(410) from the G1 glycinin (Gly m 6) and the (518)Gln-Arg(528) from the α' chain of the β-conglycinin (Gly m 5) proved to be the most stable. These peptides hold potential to be used as targets for the development of new analytical methods for the detection of soybean protein traces in processed foods.

  19. Exploration of genetic diversity among medicinally important genus Epimedium species based on genomic and EST-SSR marker.

    PubMed

    Yousaf, Zubaida; Hu, Weiming; Zhang, Yanjun; Zeng, Shaohua; Wang, Ying

    2015-01-01

    Epimedium species has gained prime importance due to their medicinal and economic values. Therefore, in this study, 26 genomic SSR and 10 EST-SSR markers were developed for 13 medicinal species of the Epimedium genus and one out-group species Vancouveria hexandra W. J. Hooker to explore the existing genetic diversity. A total of 100 alleles by genomic SSR and 65 by EST-SSR were detected. The genomic SSR markers were presented between 2-7 alleles per locus. The observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.00 to 4.5 and 0.0254 to 2.8108, respectively. Similarly, for EST-SSR, these values were ranged from 3.00 to 4.00 and 1.9650 to 2.7142. The number of alleles for EST-SSR markers ranged from 3 to 10 with an average of 3.51 per loci. It has been concluded that medicinally important species of the genus Epimedium possesses lower intraspecific genetic variation.

  20. Proof-of-Concept Studies for Marker-Based Ultrasound Doppler Analysis of Microvascular Anastomoses in a Modified Large Animal Model.

    PubMed

    Coon, Devin; Chen, Lei; Boctor, Emad M; Prince, Jerry L; Bojovic, Branko

    2016-05-01

    Background Despite attempts to solve the problem of flap monitoring, assessing the patency of vascular anastomoses postoperatively remains challenging. In addition, experimental data suggest that near-total vessel occlusion is necessary to produce significant changes in clinical appearance or monitoring devices. We sought to develop an ultrasound-based system that would provide definitive data on anastomotic function. Methods A system was developed consisting of a resorbable marker made from poly-lactic-co-glycolic acid (PLGA) implanted during the time of surgery coupled with ultrasound software to detect the anastomotic site and perform Doppler flow analysis. Surgical procedures consisting of microvascular free tissue transfer or femoral vessel cutdown were performed followed by marker placement, closure, and ultrasound monitoring. Transient vascular occlusion was produced via vessel-loop constriction. Permanent thrombosis was induced via an Arduino-controlled system applying current to the vessel intima. Results Four surgeries (one femoral vessel cutdown and three microvascular tissue transfer) were successfully performed in Yorkshire swine. The markers were readily visualized under ultrasound and provided a bounding area for Doppler analysis as well as orientation guidance. Transient spasm and partial occlusion were detected based on changes in Doppler data, while complete occlusion was evident as the total loss of color Doppler. Conclusion In this preliminary report, we have conceptualized and developed a novel system that enables the real-time visualization of vascular pedicle flow at the bedside using Doppler ultrasound and a surgically implanted marker. In a large animal model, use of the system allowed identification of the anastomosis, flow analysis, and real-time detection of flow loss. PMID:26645155

  1. A new set of rDNA-NTS-based multiple integrative cassettes for the development of antibiotic-marker-free recombinant yeasts.

    PubMed

    Moon, Hye Yun; Lee, Dong Wook; Sim, Gyu Hun; Kim, Hong-Jin; Hwang, Jee Youn; Kwon, Mun-Gyeong; Kang, Bo-Kyu; Kim, Jong Man; Kang, Hyun Ah

    2016-09-10

    The traditional yeast Saccharomyces cerevisiae has been widely used as a host system to produce recombinant proteins and metabolites of great commercial value. To engineer recombinant yeast that stably maintains expression cassettes without an antibiotic resistance gene, we developed new multiple integration cassettes by exploiting the non-transcribed spacer (NTS) of ribosomal DNA (rDNA) in combination with defective selection markers. The 5' and 3'-fragments of rDNA-NTS2 were used as flanking sequences for the expression cassettes carrying a set of URA3, LEU2, HIS3, and TRP1 selection markers with truncated promoters of different lengths. The integration numbers of NTS-based expression cassettes, ranging from one to ∼30 copies, showed a proportional increase with the extent of decreased expression of the auxotrophic markers. The NTS-based cassettes were used to construct yeast strains expressing the capsid protein of red-spotted grouper necrosis virus (RG-NNVCP) in a copy number-dependent manner. Oral administration of the reco