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1
Artykuł dostępny w postaci pełnego tekstu - kliknij by otworzyć plik
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Phylogenetic inference of Ericales based on plastid genomes and implication of cp-SSRs

100%
Hazra A., Das S., Bhattacharya S., Sur S., Sengupta C., Das S.
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
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2021
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tom 102
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nr 3
2
Artykuł dostępny w postaci pełnego tekstu - kliknij by otworzyć plik
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Molecular identification of blast resistance genes in rice genotypes using gene-specific markers

86%
Al-Daej M. I., Ismail M., Rezk A. A., El-Malky M. M.
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
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2019
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tom 100
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nr 3
3
Artykuł dostępny w postaci pełnego tekstu - kliknij by otworzyć plik
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Genetic diversity of Pyricularia grisea, the causal agent of rice blast by SRR

86%
Motlagh M. R. S., Hbibi F., Ebadi A. A.
Acta Scientiarum Polonorum. Hortorum Cultus
|
2015
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tom 14
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nr 1
Pyricularia grisea, the rice blast fungus is the main pathological threats to rice crop in Iran and worldwide. In this research was evaluated the genetic diversity of P. grisea collected from different fields of Guilan province by using of 14 microsatellite primers. These primers produced 64 polymorphic bands by an average of 4.57 bands for each marker. An average of polymorphic information content in whole primers was 0.734, an average of effective number of alleles was 2.68, an average of Nei’s expected heterozygosity was 0.734 and an average of Shannon’s information index was 1.05. Primer SSR43,44 had the most polymorphic information content (PIC = 0.85), observed number of alleles (na = 8), effective number of alleles (ne = 3.76), Nei’s expected heterozygosity (Ne = 0.861) and Shannon’s information index (I = 1.38). This marker was the best primer between 14 used primers for evaluation the genetic diversity of P. grisea. Cluster analysis was done with simple matching similarity matrix and UPGMA method. The results showed that the studied isolates were classified into 3 lineages by cutting off the dendrogram at 0.76 similar linkage level. Number 1 was the major group and represented most of those isolates. Results of principal coordinate analysis also divided the isolates into three groups exactly similar to obtained with cluster analysis. Overall, our results confirmed that microsatellite primers were good and suitable markers for analyzing structure of P. grisea
4
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Alkaloid production and response to natural adverse conditions in Peganum harmala: in silico transcriptome analyses

86%
Jazayeri S. M., Pooralinaghi M., Torres-Navarrete Y., Oviedo-Bayas B., Guerra I. E., Jacome D. H., Moran C. Q., Macias C. S., Escobar K. M., Ghafoor S. M. H. A. S., Veiskarami G., Jandaghi P., Torres R. O. V.
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
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2022
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tom 103
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nr 4
5

Characteristics and a comparison of three classes of microsatellite-based markers and their application in plants

86%
Rakoczy-Trojanowska M., Bolibok H.
Cellular and Molecular Biology Letters
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2004
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tom 09
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nr 2
Microsatellites (SSR - simple sequence repeats, STR - short tandem repeats, SSLP - simple sequence length polymorphism, VNTR - variable number of tandem repeats) are the class of repetitive DNA sequences present in all living organisms. Particular characterstics of microsatellites, such as their presence in the genomes of all living organisms, high level of allelic variation, co-dominant mode of inheritance and potential for automated analysis make them an excellent tool for a number of approaches like genotyping, mapping and positional clonig of genes. The three most popular types of markers containing microsatellite sequences that are presently used are: (1) SSR (simple sequence repeats), generated by amplifying in a PCR reaction with the use of primers complementary to flanking regions; (2) ISSR (inter-simple sequence repeats), based on the amplification of regions between inversely oriented closely spaced microsatellites; and (3) SAMPL (selective amplification of microsatellite polymorphic loci), which utilises AFLP (amplified fragment-length polymorphism) methodology, with one exception - for the second amplification, one of the starters is complementary to the microsatellite sequence. The usefulness of the three above-mentioned markers for numerous purposes has been well documented for plants.
6

Assessment the genetic diversity of Bulgarian raspberry germplasm collection by microsatellite and RAPD markers

86%
Badjakov I., Todorovska E., Kondakova V., Boicheva R., Atanassov A.
Journal of Fruit and Ornamental Plant Research
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2006
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tom 14
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nr Suppl.1
7

A new diagnostic SSR marker for selection of the Rym4-Rym5 locus in barley breeding

72%
Tyrka M., Perovic D., Wardynska A., Ordon F.
Journal of Applied Genetics
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2008
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tom 49
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nr 2
127-134
Genomic sequence AY661558, representing a part of the ВАС contig of the Rym4/Rym5 locus conferring resistance to the barley yellow mosaic virus complex (BaMMV/BaYMV), was exploited in order to develop SSR markers for practical barley breeding. Out of 57 SSR motifs found within this sequence, primers were designed and tested for the 5 SSRs with the highest repeat length. The polymorphic SSR marker QLB1 со-segregated with rym4 and rym5 phenotypes in respective high-resolution mapping populations developed for the construction of the original ВАС contig. The primers targeted 2 sites located 756 bp and 5173 bp downstream of the translation initiation factor 4E (Hv-eIF4E). Physical linkage of the QLB1 marker to the Rym4/Rym5 locus was confirmed experimentally on Morex ВАС 519J14, a seed ВAC of Hv-eIF4E, and ВAC 801A11, which is located proximally to Hv-eIF4E. QLB1 revealed 7 alleles in a set of 100 winter barley lines and cultivars. Five alleles were found within 673 advanced breeding lines derived from applied Polish winter barley breeding programmes, which corresponds to a PIC value of 0.684. No recombinants between Rym4/5 and QLB1 were detected, suggesting that QLB1 can be used efficiently in marker-assisted selection of the Hv-eIF4E-mediated bymovirus resistance.
8
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Production of intergeneric allotetraploid between autotetraploid non-heading Chinese cabbage (Brassica campestris ssp. chinensis Makino) and autotetraploid radish (Raphanus sativus L.)

72%
Sun C.-Z., Li Y., Zhang S.-N., Zheng J.-S.
Acta Societatis Botanicorum Poloniae
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2014
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tom 83
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nr 1
Intergeneric hybrids between non-heading Chinese cabbage (Brassica campestris ssp. chinensis Makino; 2n = 4x = 40) and radish (Raphanus sativus L.; 2n = 4x = 36) were obtained through ovary culture and embryo rescue. Some hybrid embryos (0.11 per ovary) were produced, but only 4 of them germinated. As most hybrid embryos failed to develop into plantlets directly, plants were regenerated by inducing shoots on the cultured cotyledon and inducing roots on the root induction medium. All hybrid plants were morphologically uniform. They resembled the non-heading Chinese cabbage in the long-lived habit, the plant status, the vernalization requirement and the petiole color, while the petiole shape, leaf venation pattern and flowers were more similar to those of radish. Upon examination of the flowers, these were found to have normal pistil, but rudimentary anthers with non-functional pollen grains. The somatic chromosome number of F1 plants was 38. Analysis of SSR banding patterns provided additional confirmation of hybridity.
9

Transferability, amplification quality, and genome specificity of microsatellites in Brassica carinata and related species

72%
Marquez-Lema A., Velasco L., Perez-Vich B.
Journal of Applied Genetics
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2010
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tom 51
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nr 2
123-131
No information is available on the transferability and amplification quality of microsatellite (SSR) markers of the public domain in Brassica carinata A. Braun. The objective of the presented research was to study the amplification of a set of 73 SSRs from B. nigra (L.) Koch and B. napus L. in B. carinata, and to compare the results with those obtained in the amplification of the same markers in other Brassica species of the U triangle. This set of SSRs from B. nigra (B genome) and B. napus (AC genome) allows the identification of the 3 basic genomes of the Brassica species tested. 94.3% of the SSR markers from B. nigra and 97.4% of those from B. napus amplified SSR-specific products in B. carinata. Very high-quality amplification with a strong signal and easy scoring in B. carinata was recorded for 52.8% of the specific loci from B. nigra SSRs and 59.3% of the specific loci from B. napus SSRs, compared to 66.7% in B. nigra and 62.8% in B. napus. Genome specificity and amplification quality of B. nigra and B. napus SSR markers in the 6 species under study is reported. High-quality transferable SSR markers provide an efficient and cost-effective platform to advance in molecular research in B. carinata.
10

QTL mapping of Fusarium moniliforme ear rot resistance in maize. 1. Map construction with microsatellite and AFLP markers

72%
Zhang F., Wan X. Q., Pan G. T.
Journal of Applied Genetics
|
2006
|
tom 47
|
nr 1
To map the QTLs of Fusarium moniliforme ear rot resistance in Zea mays L., a total of 230 F₂ individuals, derived from a single cross between inbred maize lines R15 (resistant) and Ye478 (susceptible), were genotyped for genetic map construction using simple sequence repeat (SSR) markers and amplified fragment length polymorphism (AFLP) markers. We used 778 pairs of SSR primers and 63 combinations of AFLP primers to detect the polymorphisms between parents, R15 and Ye478. From the polymorphic 30 AFLP primer combinations and 159 SSR primers, we scored 260 loci in the F₂ population, among which 8 SSR and 13 AFLP loci could not be assigned to any of the linkage groups. An integrated molecular genetic linkage map was constructed by the remaining 151 SSR and 88 AFLP markers, which distributed throughout the 10 linkage groups of maize and spanned the genome of about 3463.5 cM with an average of 14.5 cM between two markers. On 4 chromosomes, we detected 5 putative segregation distortion regions (SDRs), including 2 new ones (SDR₂ and SDR₇). The other 3 SDRs were located near the regions where gametophyte genes were mapped, indicating that segregation distortion could be partially caused by gametophytic factors.
11

The molecular diversity of different isolates of Beauveria bassiana [Bals.] Vuill. as assessed using inter-microsatellites [ISSRs]

72%
Estrada M. E., Camacho M. V., Benito C.
Cellular and Molecular Biology Letters
|
2007
|
tom 12
|
nr 2
Inter-microsatellite PCR (ISSR-PCR) markers were used to identify and to examine the genetic diversity of eleven Beauveria bassiana isolates with different geographic origins. The variability and the phylogenetic relationships between the eleven strains were analyzed using 172 ISSR-PCR markers. A high level of polymorphism (near 80%) was found using these molecular markers. Seven different isolates showed exclusive bands, and ISSR primer 873 was able to distinguish between all the strains. The dendrogram obtained with these markers is robust and in agreement with the geographical origins of the strains. All the isolates from the Caribbean region were grouped together in a cluster, while the other isolates grouped in the other cluster. The similarity exhibited between the two clusters was less than 50%. This value of homology shows the high genetic variability detected between the isolates from the Caribbean region and the other isolates. ISSR-PCR markers provide a quick, reliable and highly informative system for DNA fingerprinting, and allowed the identification of the different B. bassiana isolates studied.
12

Microsatellite polymorphism in intron 1 of the bovine myostatin gene

72%
De l. R.-R. X. F., Rodriguez P. M. A., Sifuentes-Rincon A. M.
Journal of Applied Genetics
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2006
|
tom 47
|
nr 1
Microsatellites within genes have become important because of their association with genetic diseases in humans. A novel microsatellite was identified in the first intron of the bovine myostatin gene. It is characterized by a mononucleotide core motif that exhibits polymorphic sequence variants (from 12 to 21 repeats) within and between some bovine breeds. Structural analysis of the microsatellite region in bovines as well as in closely related species permitted to trace the possible mechanisms for its structural evolution across the order Artiodactyla.
13

Generation and mapping of AFLP, SSRs and SNPs in Lycopersicon esculentum

58%
Suliman-Pollatschek S., Kashkush K., Shats H., Hillel J., Lavi U.
Cellular and Molecular Biology Letters
|
2002
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tom 07
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nr 2A
Amplified Fragment Length Polymorphism (AFLP), Simple Sequence Repeat (SSR) and Single Nucleotide Polymorphism (SNP), were applied to the tomato genome for assessment of polymorphism and for mapping. The polymorphism of AFLP was studied in twenty-one commercial tomato (L. esculentum) varieties. Four AFLP primer combinations produced 298 elear bands; an average of 75 bands per combination. SSR markers were generated from two sources: (1) size-selected genomic libraries screened with (AT)n, (CT)n, (GT)n, (ATT)n and (CTT)n probes. (2) GeneBank database. Primers were designed for 114 loci and used for genotyping 13 tomato varieties and three Lycopersicon species. Eighteen markers were used to evaluate the polymorphism among the commercial cultivars and were found to be a useful tool for cultivar identification. In-silico comparison of DNA sequences (ESTs and genes) of L. pennellii and L. esculentum, yielded 312 SNPs. Ten L. pennelli genomic fragments were sequenced and the comparison with L. esculentum yielded 22 SNPs. Another 19 SNPs were discovered by sequencing and comparing L. pennellii genomic DNA to L. esculentum DNA fragments containing SSRs. The average SNP frequency was found to be one in a few tens of base pairs. A total of 52 microsatellites, 159 polymorphic AFLP markers and six SNPs were mapped using the Introgression Lines generated by [1]. Map location and markers’ distribution are presented.
14
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Genetic diversity in tomato genotypes (Solanum lycopersicum) based on salinity responsive candidate gene using simple sequence repeats

58%
Ja'afar U., Aliero A. A., Shehu K., Abubakar L.
International Letters of Natural Sciences
|
2018
|
tom 72
Salinity inhibition of plant growth is the result of osmotic and ionic effect and different plant species have developed different mechanisms to cope with those effects. With the discovery of molecular markers and marker assisted selection technology, it is possible to develop markers that identify salt tolerance. The genetic diversity of tomato genotypes were analyzed using SSRs polymorphic markers and Unweighted Pair Group Method with Arithmetic Mean. Leaves of the twenty tomato genotypes (landraces/accessions in Nigeria) were used to isolate their DNA using Bioland Plant Genomic DNA protocols. Primers were designed from 15 different salt responsive candidate genes, using Vector NTI and the sequence of the genes were obtained from ncbi genomic web site. All 15 primers sets generated shows clear distinct polymorphic profiles as evident from the 6% agarose gel profile. Dendrogram generated shows three groups, none of the panel intermixed in a subgroup. The genetic distance information reported in this study might be used by breeders when planning future crosses among tomato genotypes. From the result obtained UC82B recorded the highest vegetative and yield parameters, therefore, adoption of this genotype could be help to increase the tomato production in Sokoto agro-climatic area.
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