scholarly journals Characterization of new variety of Chrysanthemum by using ISSR markers

2011 ◽  
Vol 29 (4) ◽  
pp. 613-617 ◽  
Author(s):  
SK Palai ◽  
Gyana Ranjan Rout
Keyword(s):  
Large Scale ◽  
Ornamental Plants ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Flower Bud ◽  
New Variety ◽  
In Vitro Technique ◽  
Asteraceae Family

Chrysanthemum is the important cut flower after rose among the ornamental plants traded in the global flower market. It is propagated vegetatively and also has a strong sporophytic self-incompatibility system as shown by all members of Asteraceae family. Morphologically, the petal numbers and flower colours present maximum variation when compared to existing varieties. Twenty Inter Simple Sequence Repeat primers were used to detect the new variety of Chrysanthemum developed through spontaneous sporting. The results indicate that the rate of polymorphism showed significant differences as compared to other existing varieties. The average number of amplification products per primer was eight. The size of ISSR amplified fragments varied from 0.25 - 2.4 Kbp. Therefore, ISSR marker is a useful technique for the rapid and easy assessment of genetic variation among the variants. Morphological traits of new variants showed variation as compared to other parents. The 1st flower bud appearance and the height of 1st bud of the variant were less as compared to original mother variety. The new variants can be propagated in large scale commercially through in vitro technique.

ISSR Marker Based Genetic Diversity in Morinda Spp. For Its Enhanced Collection, Conservation and Utilization

2021 ◽  
Author(s):  
Lalit Arya ◽  
Ramya Kossery Narayanan ◽  
Anjali Kak ◽  
Chitra Devi Pandey ◽  
Manjusha Verma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Morinda Citrifolia ◽  
Species Differentiation ◽  
Information Index ◽  
Upgma Cluster Analysis ◽  
Simple Sequence

Abstract Morinda (Rubiaceae) is considerably recognized for its multiple uses viz. food, medicine, dyes, firewood, tools, oil, bio-sorbent etc. The molecular characterization of such an important plant would be very useful for its multifarious enhanced utilization. In the present study, 31 Morinda genotypes belonging to two different species Morinda citrifolia and Morinda tomentosa collected from different regions of India were investigated using Inter Simple Sequence Repeat (ISSR) markers. Fifteen ISSR primers generated 176 bands with an average of 11.7 bands per primer, of which (90.34%) were polymorphic. The percentage of polymorphic bands, mean Nei’s gene diversity, mean Shannon’s information index in Morinda tomentosa and Morinda citrifolia was [(69.89%, 30.68%); (0.21 ± 0.19, 0.12 ± 0.20); (0.32 ± 0.27 0.17 ± 0.28)] respectively, revealing higher polymorphism and genetic diversity in Morinda tomentosa compared to Morinda citrifolia. Structure, and UPGMA cluster analysis placed the genotypes into well-defined separate clusters belonging to two species Morinda tomentosa and Morinda citrifolia revealing the utility of ISSR markers in species differentiation. Distinct ecotypes within a particular species could also be inferred emphasizing the collection and conservation of Morinda genotypes from different regions, in order to capture the overall diversity of respective species. Further higher diversity of M. tomentosa must be advanced for its utilization in nutraceutical, nutritional and other nonfood purposes.

Characterization of Italian populations ofLoliumspp. resistant and susceptible to diclofop by inter simple sequence repeat

Weed Science ◽  
2004 ◽  
Vol 52 (4) ◽  
pp. 554-563 ◽  
Author(s):  
Giovanni Dinelli ◽  
Alessandra Bonetti ◽  
Ilaria Marotti ◽  
Maurizio Minelli ◽  
Pietro Catizone
Keyword(s):  
Potential Role ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Intergeneric Hybridization ◽  
Banding Patterns ◽  
Inter Simple Sequence Repeats ◽  
Range Of Variation ◽  
Simple Sequence

Three ItalianLoliumweed populations, one susceptible and two resistant to diclofop, were characterized by the technique of inter simple sequence repeats (ISSR). The goal of this study was to taxonomically identify theseLoliumpopulations as well as to evaluate evidence for introgression of ISSR fragments fromFestucaand the potential role of this introgression in the diclofop response. ISSR analysis confirmed the genomic background of the weed populations to be consistent with that ofLolium. However, the great range of variation in ISSR banding patterns highlighted that the three ryegrass accessions are mixed populations made up of individuals resulting presumably from intrageneric and intergeneric hybridization in theLolium–Festucacomplex. TwoFestucagenus-discriminating and 20Festucaspecies-discriminating ISSR markers were screened among all the three ryegrass populations. The resistant Tuscania population carried the highest percentage ofFestucagenome (16.8%) followed by the resistant Roma (13.6%) and susceptible Vetralla (7.6%) populations. On the basis of these data some influence ofFestucagenome in diclofop resistance levels of studied ryegrass populations could be hypothesized.

scholarly journals Cytotoxic, Genotoxic, and Polymorphism Effects on Vanilla planifolia Jacks ex Andrews after Long-Term Exposure to Argovit® Silver Nanoparticles

Nanomaterials ◽  
2018 ◽  
Vol 8 (10) ◽  
pp. 754 ◽  
Author(s):  
Jericó Bello-Bello ◽  
José Spinoso-Castillo ◽  
Samantha Arano-Avalos ◽  
Eduardo Martínez-Estrada ◽  
María Arellano-García ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Large Scale ◽  
Inter Simple Sequence Repeat ◽  
Metallic Silver ◽  
Vanilla Planifolia ◽  
Genotoxic Effects ◽  
Total Percentage ◽  
Long Time ◽  
Mexican Government

Worldwide demands of Vanilla planifolia lead to finding new options to produce large-scale and contaminant-free crops. Particularly, the Mexican Government has classified Vanilla planifolia at risk and it subject to protection programs since wild species are in danger of extinction and no more than 30 clones have been found. Nanotechnology could help to solve both demands and genetic variability, but toxicological concerns must be solved. In this work, we present the first study of the cytotoxic and genotoxic effects promoted by AgNPs in Vanilla planifolia plantlets after a very long exposure time of six weeks. Our results show that Vanilla planifolia plantlets growth with doses of 25 and 50 mg/L is favored with a small decrease in the mitotic index. A dose-dependency in the frequency of cells with chromosomal aberrations and micronuclei was found. However, genotoxic effects could be considered as minimum due to with the highest concentration employed (200 mg/L), the total percentage of chromatic aberrations is lower than 5% with only three micronuclei in 3000 cells, despite the long-time exposure to AgNP. Therefore, 25 and 50 mg/L (1.5 and 3 mg/L of metallic silver) were identified as safe concentrations for Vanilla planifolia growth on in vitro conditions. Exposure of plantlets to AgNPs increase the polymorphism registered by inter-simple sequence repeat method (ISSR), which could be useful to promote the genetic variability of this species.

scholarly journals Variability and Correlation Studies on Induced Mutants of Marigold (Tagetes erecta L.) for Different Traits and Assessing Them Using Molecular Markers

2018 ◽  
Vol 28 (2) ◽  
pp. 223-236
Author(s):  
Jayoti Majumder ◽  
SK Singh ◽  
Meenu Kumari ◽  
Manjusha Verma
Keyword(s):  
Large Scale ◽  
Field Evaluation ◽  
Issr Markers ◽  
Phenotypic Correlation ◽  
Induced Mutations ◽  
Single Marker ◽  
Tagetes Erecta L ◽  
Mutant Identification

Induced mutations are important for creating novel variabilities in marigold for different purposes. Distinct putative mutants of marigold var. Pusa Narangi Gainda generated through gamma irradiation (in vivo and in vitro), were studied for variability and correlation in M2 generation for 11 traits. The maximum heritability (h2) was noted for days to flower harvest (0.9982%). The highest positive phenotypic correlation (0.637) was noted for number of flowers per plant to the days to first flower harvest. The most positive genotypic correlation (0.915) was found for seed yield (g) to the number of flowers per plant. Furthermore, the putative mutants in M2 were assessed for their diversity using ISSR markers and the amplified DNA fragments were compared with their respective parent genotype maintained (in vivo and in vitro). Single marker regression analysis indicated that the ISSR 811 and ISSR 817 were highly efficient markers for mutant identification in marigold. On the basis of dendrogram, putative mutant No. 3 (pm3) showed the highest dissimilarity with the parent (0.58). The mutants, pm5 and pm6 were found to be similar to each other (0.65), though they were quite distinct from the parent genotype morphologically. These selected mutants were multiplied up to six generations to attain the desired level of homozygosity for their large scale field evaluation. Plant Tissue Cult. & Biotech. 28(2): 223-236, 2018 (December)

scholarly journals Morphological and Molecular Characterization of Selected Chilean Runner Bean (Phaseolus coccineus L.) Genotypes Shows Moderate Agronomic and Genetic Variability

Plants ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1688
Author(s):  
Osvin Arriagada ◽  
Andrés R. Schwember ◽  
María Jesús Greve ◽  
Milan O. Urban ◽  
Ricardo A. Cabeza ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Agronomic Traits ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Small Scale ◽  
Central Chile ◽  
Runner Bean ◽  
Agronomic Potential ◽  
Phaseolus Species

The runner bean is the third most economically important Phaseolus species, which is cultivated on small-scale agriculture for the production of immature pods or to obtain dry seeds. However, despite the economic importance and agronomic potential of this species, the runner bean has been little studied from the genetic standpoint. Therefore, the main objective of this study was to characterize ten selected lines of runner bean obtained from Central (Santiago) and Southern (Valdivia and Villarica) Chile based on morphological and agronomic traits. In addition, the genetic variability of these lines was determined using 12 Inter-Simple Sequence Repeat (ISSR) markers to evaluate the potential of this germplasm for breeding and commercial purposes. As a result, the lines from Central Chile were characterized, and had a higher number of pods per plant compared to the Southern lines, although the size and weight of their seeds were lower. Moreover, a low level of genetic diversity (He = 0.251) was encountered in this population. Finally, this is one of the first studies that generate relevant and novel information on the morphological, agronomic and genetic characterization of the P. coccineus germplasm present in Chile.

scholarly journals A new variety of Plocama calabrica (Rubiaceae) from Denizli (Turkey) confirmed by morphological and molecular ISSR markers

2019 ◽  
Vol 78 (2) ◽  
pp. 142-146
Author(s):  
Ramazan Süleyman Göktürk ◽  
Olcay Düşen ◽  
Ergun Kaya ◽  
Betül Gürcan ◽  
Uygar Sarpkaya
Keyword(s):  
Conservation Status ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
New Variety ◽  
South West ◽  
Related Variety ◽  
Distribution And Ecology ◽  
Issr Pcr ◽  
Simple Sequence ◽  
Molecular Characters

Abstract Plocama calabrica (L.f.) M.Backlund & Thulin var. alba Göktürk, O.D.Düşen, B.Gürcan & U. Sarpkaya variety nova is described from South-West Anatolia. The new variety grows on limestone slopes between Akpınar and Yaylapınar villages in the Çameli district in Denizli. It is closely related to P. calabrica var. calabrica, and can be readily distinguished by morphological and molecular characters from the related variety. Taxonomic comments such as descriptive and diagnostic characters, distribution and ecology, phenology and proposed conservation status for this new variety are given in the current study. Morphological affinities and the inter-simple-sequence repeat (ISSR)-PCR based phylogenetic relationships between the new and the related variety are also discussed

scholarly journals Genetic diversity of Panax vietnamensis var. langbianensis populations in Lam Vien plateau - Vietnam detected by inter simple sequence repeat (ISSR) markers

2020 ◽  
Vol 17 (4) ◽  
pp. 651-661
Author(s):  
Le Ngoc Trieu ◽  
Nong Van Duy ◽  
Tran Van Tien
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Sequence Repeat ◽  
New Variety ◽  
Gene Differentiation ◽  
The Stability ◽  
Simple Sequence

Panax vietnamensis var. langbianensis is a new variety from Lam Vien plateau of Vietnam. In this study, inter simple sequence repeat (ISSR) markers were employed to investigate the genetic diversity and variability of 115 individuals belonging to two naturally distributed populations of this variety, which classified by habitat. Genetic diversity at the taxon level was high (HeT = 0.284 and PPBT = 97.2 %).   The result showed lightly higher genetic diversity in population in Lac Duong region (HeLD= 0.228 and PPBLD = 81.5 %) as compared to those located in Dam Rong region (HeDR= 0.213 and PPBDR = 79.4 %). The interpopulation gene differentiation was high (GST Total = 0.221) with the genetic distance among populations was DLD-DR = 0.191. Gene flow within populations was Nm = 0.8793. In Lac Duong population, the genetic diversity of older group (HeLD O = 0.233; PPBLD O = 77.1%) was higher than of younger group (HeLD Y = 0.214; PPBLD Y = 72.4 %) and the intergroup gene differentiation was GSTDL = 0.0205 with the genetic distance between these two group was DLD O-Y  = 0.0061 showed the risk of reduction in genetic diversity. In Dam Rong population, the genetic diversity of older group (HeDR O = 0.204; PPBDR O = 75.2 %) was equal to younger group (HeDR Y = 0.209; PPBDR Y = 72.7 %) and the intergroup gene differentiation was GSTDR = 0.0304 with the genetic distance between them was DDR O-Y = 0.01393 showed the stability in genetic diversity. Data for genetic diversity and variation from this study can be used to further investigate and protect this variety for conservation and development purposes and for sustainable exploiting and use of these valuable natural resources.

scholarly journals Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Suwen Zhao ◽  
Ayano Sakai ◽  
Xinshuai Zhang ◽  
Matthew W Vetting ◽  
Ritesh Kumar ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Large Scale ◽  
Sequence Similarity ◽  
Gene Clusters ◽  
Enzymatic Activities ◽  
Or Gene ◽  
Enzyme Functions

Metabolic pathways in eubacteria and archaea often are encoded by operons and/or gene clusters (genome neighborhoods) that provide important clues for assignment of both enzyme functions and metabolic pathways. We describe a bioinformatic approach (genome neighborhood network; GNN) that enables large scale prediction of the in vitro enzymatic activities and in vivo physiological functions (metabolic pathways) of uncharacterized enzymes in protein families. We demonstrate the utility of the GNN approach by predicting in vitro activities and in vivo functions in the proline racemase superfamily (PRS; InterPro IPR008794). The predictions were verified by measuring in vitro activities for 51 proteins in 12 families in the PRS that represent ~85% of the sequences; in vitro activities of pathway enzymes, carbon/nitrogen source phenotypes, and/or transcriptomic studies confirmed the predicted pathways. The synergistic use of sequence similarity networks3 and GNNs will facilitate the discovery of the components of novel, uncharacterized metabolic pathways in sequenced genomes.

scholarly journals CloneSifter: enrichment of rare clones from heterogeneous cell populations

BMC Biology ◽  
2020 ◽  
Vol 18 (1) ◽  
Author(s):  
David Feldman ◽  
FuNien Tsai ◽  
Anthony J. Garrity ◽  
Ryan O’Rourke ◽  
Lisa Brenan ◽  
...  
Keyword(s):  
Large Scale ◽  
Molecular Mechanisms ◽  
Cancer Metastasis ◽  
Population Level ◽  
Fitness Assessment ◽  
Large Populations ◽  
Organismal Development ◽  
Insight Into

Abstract Background Many biological processes, such as cancer metastasis, organismal development, and acquisition of resistance to cytotoxic therapy, rely on the emergence of rare sub-clones from a larger population. Understanding how the genetic and epigenetic features of diverse clones affect clonal fitness provides insight into molecular mechanisms underlying selective processes. While large-scale barcoding with NGS readout has facilitated cellular fitness assessment at the population level, this approach does not support characterization of clones prior to selection. Single-cell genomics methods provide high biological resolution, but are challenging to scale across large populations to probe rare clones and are destructive, limiting further functional analysis of important clones. Results Here, we develop CloneSifter, a methodology for tracking and enriching rare clones throughout their response to selection. CloneSifter utilizes a CRISPR sgRNA-barcode library that facilitates the isolation of viable cells from specific clones within the barcoded population using a sequence-specific retrieval reporter. We demonstrate that CloneSifter can measure clonal fitness of cancer cell models in vitro and retrieve targeted clones at abundance as low as 1 in 1883 in a heterogeneous cell population. Conclusions CloneSifter provides a means to track and access specific and rare clones of interest across dynamic changes in population structure to comprehensively explore the basis of these changes.

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