scholarly journals IDENTIFICATION OF CDNA FRAGMENT TIGHTLY LINKED TO NV AND TM-2 LOCI IN TOMATO

Zuriat ◽  
2015 ◽  
Vol 16 (2) ◽  
Author(s):  
, Sobir ◽  
Fusao Motoyoshi
Keyword(s):  
Southern Blot Analysis ◽  
Heterochromatic Region ◽  
Tomato Mosaic Virus ◽  
Polymorphic Band ◽  
Northern Hybridization ◽  
Cdna Fragment ◽  
Arbitrary Primers ◽  
Tomato Line ◽  
Polymorphic Bands ◽  
Genetic Experiment

Tm-2 is a resistance gene in tomato to Tomato Mosaic Virus (ToMV), located in heterochromatic region of chromosome nine. Since map based cloning difficult to perform for identify the gene on that region, we apply differential display approach by using two near-isogenic tomato lines (NILs), one without Tm-2 and the other with Tm-2 to identify cDNAs of the transcripts from the region surrounding the Tm-2 locus. Among the 150 combinations of three anchor primers and fifty arbitrary primers, 10 combinations generated cDNA polymorphic bands. Out of them, only one combination of CA6, exhibited polymorphic band under southern blot analysis, subsequently a genetic experiment showed that the CA6 locus tightly linked to the Tm-2 locus. The CA6 fragment also hybridized to genomic DNA fragments from a tomato line carrying Tm-2a, a line of L. peruvianum from which Tm-2a originated, and a tomato line carrying another Tm-2-like gene. A northern hybridization blotting result suggested that the gene corresponding to CA6 fragment was constitutively transcribed.

scholarly journals Polymerase Chain Reaction Fingerprinting of Erwinia amylovora has a Limited Phylogenetic Value but Allows the Design of Highly Specific Molecular Markers

2008 ◽  
Vol 98 (3) ◽  
pp. 260-269 ◽  
Author(s):  
Arantza Rico ◽  
M. Elena Führer ◽  
Amaya Ortiz-Barredo ◽  
Jesús Murillo
Keyword(s):  
Polymerase Chain Reaction ◽  
Molecular Markers ◽  
Fire Blight ◽  
Erwinia Amylovora ◽  
Epidemiological Studies ◽  
Northern Spain ◽  
Chain Reaction ◽  
Arbitrary Primers ◽  
Polymerase Chain ◽  
Polymorphic Bands

Erwinia amylovora, the causal agent of fire blight, is genetically very homogeneous, and current methodologies provide insufficient or contradictory information about the probable dispersal routes of the pathogen. With the final aim to obtain specific and reliable molecular markers for different lineages of the pathogen, we studied the molecular basis of rep-polymerase chain reaction (PCR) polymorphism using seven different arbitrary primers to fingerprint 93 E. amylovora strains from different countries, including Spain. Polymorphism was very low, and was displayed by only 11 E. amylovora strains, which produced 22 polymorphic bands. Five of 11 polymorphic bands cloned contained DNA that was present in more than 85% of the strains, whereas six bands were due to DNA present exclusively in the strains producing the rep-PCR polymorphism. Also, five of the polymorphic bands were due to the possession of either the ubiquitous plasmid pEA29, of plasmid pEU30, which was exclusively found in strains from North America, or of a 35-kb cryptic plasmid, present only in 28 strains from Northern Spain. We designed primer pairs from several cloned polymorphic bands that allowed the specific identification of the strains producing the polymorphism. Our results indicate that rep-PCR is not adequate for constructing genealogies of E. amylovora, although the strategy illustrated here, as well as the designed primers, can be used effectively in epidemiological studies with this pathogen.

scholarly journals Genetic Relationship of Four Strains of Guppy (Poeciliareticulata Peters, 1859) Using RAPD-PCR Method

2021 ◽  
pp. 15-24
Author(s):  
Ine Triana Nuradha ◽  
Ayi Yustiati ◽  
Asep Agus Handaka ◽  
Ibnu Bangkit
Keyword(s):  
Experimental Design ◽  
Genetic Relationship ◽  
Polymorphic Band ◽  
Qualitative And Quantitative ◽  
Rapd Pcr ◽  
Fish Samples ◽  
Pcr Method ◽  
Polymorphic Bands ◽  
Relationship Of ◽  
Guppy Fish

This study aims to determine the genetic relationship between four strains of guppy, albino full platinum (AFP), albino german yellow (AGY), top sword (TS) and guppy yellow cobra (GYC) using the RAPD-PCR method. This study used explorative method without experimental design and analyzed by descriptive qualitative and quantitative. The obtained genetic relationship data could be used as data reference for hybridization between strains of guppy fish that have been researched. The research was conducted in October 2020-April 2021. The three fish samples (AFP, TS and GYC) obtained from fish breeder in Cilengkrang-Bandung and AGY sample obtained from fish breeder in Tanggerang-Banten. Based on the results of amplification using OPA-03 primer (AGTCAGCCAC), four strains of guppy fish showed 30 DNA bands that included polymorphic and monomorphic bands. The AFP strains had 19 monomorphic bands, AGY had 21 DNA bands (20 monomorphic bands and one polymorphic bands), TS had 19 DNA bands (17 monomorphic bands and two polymorphic bands) and GYC had 15 DNA bands (14 monomorphic bands and one polymorphic band). Phylogenetic tree analyzed by NTSys program. It is shown between AFP and AGY strains had 95% relationship index, then between TS and GYC strains had 82% relationship index and between AFP-AGY and TS-GYC had 50% relationship index.

scholarly journals Study genetic diversity between trichophyton rubrum isolates using ISSR and RAPD markers

2018 ◽  
Vol 12 (2) ◽  
pp. 5-13
Author(s):  
Milad A. Mezher ◽  
Sanaa Mohammad ◽  
Khalil Wahab ◽  
Zainab Salman ◽  
Suzan Rashid ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Trichophyton Rubrum ◽  
Issr Markers ◽  
Polymorphic Band ◽  
Main Band ◽  
The Third ◽  
Polymorphic Bands ◽  
The Relationship ◽  
Rapd And Issr

        The present study included detection of genetic variability, and identification of genetic relationship and finding a fingerprint of the ten clinical isolates related to Trichophyton rubrum using RAPD and ISSR markers. The experiment was carried out and the results performed using six primer of the RAPD markers  these primers showed 239 amplified  band , out of  these band 90 of them was considered as a main band, and 149 was Polymorphic band , the largest number of bands was 30 in the isolate TR6  and less number of bands in the isolate TR7.   The results clear the value of genetic diversity based on RAPD analysis the lowest value of genetic diversity (0.13005) between the isolate TR3 and TR9while the highest genetic diversity (0.55941) was between the isolates TR5 and TR8. The analysis of the relationship shows that there are three main groups: the first group include isolate TR8, while the second group included three isolates are isolate TR2, isolate TR10 and isolates TR3, The third group included three subgroups included the first isolate TR1,isolates TR4 and second isolate TR3 and isolate TR9 and the third included the isolate TR5 and isolates TR6.The results of ISSR experiments: the use six a primers in the of the ISSR showed 192 bands, in the isolate  of Trichophyton rubrum, two of these primers showed monomorphic bands (in number and location) and six primers showed monomorphic and polymorphic bands, while one showed only polymorphic bands among Trichophyton rubrum isolates. And the largest number of bands was 24 in the TR5 and less number of bands 16 in isolate TR3 and isolate TR8 were finding DNA fingerprint to isolate TR1, isolate TR5, and isolate TR3.    The ISSR markers showed lowest genetic polymorphism was (0.05561) between the isolates TR2 and isolate TR7 and the largest genetic distance was (0.40501) between the isolate TR4 and isolate TR8. The analysis of the relationship of genetic showed that there are three groups key first included isolates and only one isolate TR8 and the second involving isolates TR2 and isolate TR7, isolate TR4 and isolate TR3, while the group included three sub-groups, the first included isolate TR1 and isolate TR6, and the second involving isolate TR5, isolate TR10 and isolate TR9. The results confirmed the efficiency markers of the RAPD and ISSR in contrast, find a genetic fingerprint to the isolates of Trichophyton rubrum, and these markers differ in mechanical detection contrast, and coverage is Genome. Therefore Complementary to each other, although the ISSR markers were more efficient in terms of the number of binding  sites in each type of the isolates of Trichophyton rubrum and so can the initiator of the discovery of a much larger area from  Genome.

DNA Markers Reveal Hybrids Between Two Diverse Background Genotypes in Australian Collections of the Bean Rust Fungus Uromyces appendiculatus

1994 ◽  
Vol 42 (3) ◽  
pp. 255 ◽  
Author(s):  
KS Braithwaite ◽  
JM Manners ◽  
JAG Irwin ◽  
DJ Maclean
Keyword(s):  
Comprehensive Evaluation ◽  
Genetic Recombination ◽  
Random Amplified Polymorphic Dna ◽  
Rust Fungus ◽  
Uromyces Appendiculatus ◽  
Rflp Markers ◽  
Clear Correlation ◽  
Bean Rust ◽  
Arbitrary Primers ◽  
Polymorphic Bands

Two classes of molecular markers, RFLPs (restriction fragment length polymorphisms) and RAPDs (random amplified polymorphic DNA) were used to assess genetic diversity among Australian bean rust isolates (Uromyces appendiculatus (Pers.) Unger var. appendiculatus) collected from diverse geographic locations spanning the period 1973-1990. Initially we screened 22 isolates using WLPs from five DNA probes. This was followed by analysis of a subset of 12 of these isolates using RFLPs from 10 cDNA probes and RAPDs from 10 arbitrary primers for a comprehensive evaluation of background genotype. Polymorphic bands revealed the existence of two divergent clusters of isolates, representing genotypes designated A and B. The RFLP markers showed 30% band dissimilarity between A and B, and RAPDs 16% dissimilarity. Isolates in a third cluster (genotype AB) exhibited most of the polymorphic bands present in A and B, but no unique polymorphic bands of their own, indicating that they had most probably arisen from recent hybridisation between isolates of genotype A and B. The subset of 12 isolates included 10 race phenotypes, but no clear correlation between background genotype (as assessed by RFLP and RAPD markers) and race phenotype was evident. We suggest that Australian races of bean rust have most probably evolved by a combination of mutation to virulence from common A and B background genotypes, and genetic recombination.

scholarly journals Random Amplified Polymorphic Markers as Indicator for Genetic Conservation Program in Iranian Pheasant (Phasianus colchicus)

2012 ◽  
Vol 2012 ◽  
pp. 1-5 ◽  
Author(s):  
Ghorban Elyasi Zarringhabaie ◽  
Arash Javanmard ◽  
Ommolbanin Pirahary
Keyword(s):  
Dna Markers ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Conservation Strategy ◽  
Phasianus Colchicus ◽  
Polymorphic Markers ◽  
Genetic Origin ◽  
Arbitrary Primers ◽  
Conservation Program ◽  
Polymorphic Bands

The objective of present study was identification of genetic similarity between wild Iran and captive Azerbaijan Pheasant using PCR-RAPD markers. For this purpose, in overall, 28 birds were taken for DNA extraction and subsequently 15 arbitrary primers were applied for PCR-RAPD technique. After electrophoresis, five primers exhibited sufficient variability which yielded overall 65 distinct bands, 59 polymorphic bands, for detalis, range of number of bands per primer was 10 to 14, and produced size varied between 200 to 1500 bp. Highest and lowest polymorphic primers were OPC5, OPC16 (100%) and OPC15 (81%), respectively. Result of genetic variation between two groups was accounted as nonsignificant (8.12%) of the overall variation. According to our expectation the wild Iranian birds showed higher genetic diversity value than the Azerbaijan captive birds. As general conclusion, two pheasant populations have almost same genetic origin and probably are subpopulations of one population. The data reported herein could open the opportunity to search for suitable conservation strategy to improve richness of Iran biodiversity and present study here was the first report that might have significant impact on the breeding and conservation program of Iranian pheasant gene pool. Analyses using more regions, more birds, and more DNA markers will be useful to confirm or to reject these findings.

EVALUATION OF PTYCHOBOTHRIDEAN CESTODES USING RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD) MARKERS FROM FRESH WATER FISHES IN GODAVARI BASIN (M.S.) INDIA

2017 ◽  
Vol 23 (2) ◽  
Author(s):  
SUNITA BORDE ◽  
ASAWARI FARTADE ◽  
AMOL THOSAR ◽  
RAHUL KHAWAL
Keyword(s):  
Fresh Water ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Band Pattern ◽  
Genomic Variation ◽  
Polymorphic Band ◽  
Rapd Profile ◽  
Band Size ◽  
Pcr Product ◽  
The Common

Ptychobothridean genera like Senga and Circumoncobothrium are the common parasites of fresh water fishes. The genotypic study of these parasites was taken by RAPD. The RAPD profile of these two parasites were not similar to each other as depicted by the band pattern in picture. These results suggest the presence of inter-specific polymorphism among cestode parasites of two different genera for RAPD analysis. The present study demonstrated that genetic differentiation of cestode parasites could be accomplished on the basis of genomic variation with polymorphic band pattern using RAPD. All the detected bands (PCR product) were polymorphic and band size ranged from 500-5000 bp in length. The RAPD of profiles using GBO-31, GBO-32, GBO-33, GBO-34, GBO-35 and GBO-36. Primers were able to characterize inter-specific polymorphism among the two genus ( Senga and Circumoncobothrium ). Genetic analysis suggests that Senga and Circumoncobothrium show genetic diversity with respect to RAPD patterns using all the six primers used for the present study. The genetic distance between the analyzed genuses ranged from 0.14 to 0.80. The differentiation of the two parasites on the basis of genetic markers could greatly facilitate study on the biology of these parasites.

Study of a collection of tomato hybrids with genetic resistance to the yellow leaf curl virus in Southern Russia

2020 ◽  
pp. 30-34
Author(s):  
С.Ф. Гавриш ◽  
Т.А. Редичкина ◽  
А.В. Буц ◽  
Г.М. Артемьева
Keyword(s):  
Resistance Genes ◽  
Molecular Genetic Analysis ◽  
Tomato Yellow Leaf ◽  
Tomato Mosaic Virus ◽  
Average Weight ◽  
Yellow Leaf ◽  
The South ◽  
Economically Valuable Traits ◽  
Leaf Curl Virus ◽  
Leaf Curl

Дана информация об изучении коллекции гибридов F1томата (Solanum lycopersicum L.) зарубежной селекции различных фирм-оригинаторов, рекомендованных производителями семян как толерантные к вирусу желтой курчавости листьев томата. Все гибриды обладали комплексом хозяйственно ценных признаков и набором генов устойчивости к основным заболеваниям томата, в том числе к новому для юга России опасному патогену с максимальным потенциальным риском – вирусу желтой курчавости листьев томата (Tomato yellow leaf curl virus — TYLCV). Исследования проведены в 2017-2018 годах в лаборатории пасленовых культур ООО «НИИСОК» и в лаборатории молекулярной диагностики растений ООО «Семеновод». Всего было протестировано 34 гибрида F1 томата. Гибриды оценивали по совокупности хозяйственно ценных признаков, также проводили молекулярно-генетический анализ на наличие и аллельное состояние основных генов устойчивости: к вирусу табачной мозаики (Tm2а), фузариозному увяданию (I2), вертициллезному увяданию (Ve), к кладоспориозу (Cf9), нематодам (Mi1.2), вирусу бронзовости томата (Sw5), вирусу желтой курчавости листьев томата (Ty3a). Установлено, что все проанализированные гибриды томата с заявленной оригинаторами семян устойчивостью к вирусу желтой курчавости листьев были гетерозиготны по гену Ty3a. На основании проведенных исследований и с учетом требований рынка разработаны модели гибридов F1 томата юга России. Перспективный гибрид томата должен обладать индетерминантным типом роста с укороченными междоузлиями (4,5-5 см) а также хорошей облиственностью. Плоды томата должны быть с красной равномерной окраской без зеленого пятна у плодоножки, с плоскоокруглой или округлой формой плода и со средней массой 220-270 г. Для повышения транспортабельности томатов необходимо, чтобы плоды отличались высокой прочностью и характеризовались хорошей лежкостью. Урожайность гибрида томата должна быть более 30 кг/м2, а товарность - не менее 85%. Гибрид томата должен обладать следующим набором генов устойчивости в гетерозиготном состоянии: Ty3a, Mi1.2, Cf-9, а также в гомозиготном состоянии: Tm2a, I2, Ve. The article provides information on the study of the collection of F1 tomato hybrids (Solanum lycopersicumL.) of foreign breeding from various firms-originators recommended for cultivation in regions with a strong spread of tomato yellow leaf curl virus. All hybrids had a complex of economically valuable traits and a set of genes for resistance to the main diseases of tomato, including a new dangerous pathogen for the South of Russia with a maximum potential risk — the tomato yellow leaf curl virus (TYLCV). The studies were carried out in 2017-2018 in the Solanaceae Laboratory of LLC NIISOK and in the Molecular Diagnostics Laboratory of Plants of LLC Semenovod. A total of 34 F1 tomato hybrids were tested. The hybrids were assessed by a set of economically valuable traits. Molecular genetic analysis was also carried out for the presence and allelic state of the main resistance genes: Tomato mosaic virus (Tm2a), Fusarium wilt (I2), Werticillium wilt (Ve), Cladosporium fulvum (Cf9), Nematodes (Mi1.2), Tomato spotted wilt virus (Sw5), Tomato yellow leaf curl virus (Ty3a). It was found that all the analyzed tomato hybrids with the declared by seed originators resistance to yellow leaf curl virus were heterozygous for the Ty3a gene. Based on the conducted research and taking into account the market requirements, models of F1 tomato hybrids for protected ground for the South of Russia have been developed. A promising tomato hybrid should have an indeterminate growth type with shortened internodes (4.5-5 cm) and good foliage. Tomato fruits should have a uniform red color without green shoulders, with a flat-round or round shape of the fruit and with an average weight of 220-270 g. To increase the transportability of tomatoes, it is necessary that the fruits are highly firm and characterized by good shelf life. The yield of tomato hybrid should be more than 30 kg/m2, and marketability should be at least 85%. The tomato hybrid should have the following set of resistance genes in a heterozygous state: Ty3a, Mi1.2, Cf-9, and also in a homozygous state: Tm2a, I2, Ve.

scholarly journals Identification of Tomato Infecting Viruses That Co-Isolate with Nanovesicles Using a Combined Proteomics and Electron-Microscopic Approach

Nanomaterials ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1922
Author(s):  
Ramila Mammadova ◽  
Immacolata Fiume ◽  
Ramesh Bokka ◽  
Veronika Kralj-Iglič ◽  
Darja Božič ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Mosaic Virus ◽  
Protein Identification ◽  
Plant Viruses ◽  
Size Exclusion ◽  
Tomato Mosaic Virus ◽  
High Yield ◽  
Plant Resources ◽  
Electron Microscopic ◽  
Viral Particles

Plant-derived nanovesicles (NVs) have attracted interest due to their anti-inflammatory, anticancer and antioxidative properties and their efficient uptake by human intestinal epithelial cells. Previously we showed that tomato (Solanum lycopersicum L.) fruit is one of the interesting plant resources from which NVs can be obtained at a high yield. In the course of the isolation of NVs from different batches of tomatoes, using the established differential ultracentrifugation or size-exclusion chromatography methods, we occasionally observed the co-isolation of viral particles. Density gradient ultracentrifugation (gUC), using sucrose or iodixanol gradient materials, turned out to be efficient in the separation of NVs from the viral particles. We applied cryogenic transmission electron microscopy (cryo-TEM), scanning electron microscopy (SEM) for the morphological assessment and LC–MS/MS-based proteomics for the protein identification of the gradient fractions. Cryo-TEM showed that a low-density gUC fraction was enriched in membrane-enclosed NVs, while the high-density fractions were rich in rod-shaped objects. Mass spectrometry–based proteomic analysis identified capsid proteins of tomato brown rugose fruit virus, tomato mosaic virus and tomato mottle mosaic virus. In another batch of tomatoes, we isolated tomato spotted wilt virus, potato virus Y and southern tomato virus in the vesicle sample. Our results show the frequent co-isolation of plant viruses with NVs and the utility of the combination of cryo-TEM, SEM and proteomics in the detection of possible viral contamination.

scholarly journals The phylogeographic history of tomato mosaic virus in Eurasia

Virology ◽  
2021 ◽  
Vol 554 ◽  
pp. 42-47
Author(s):  
Yuting Xu ◽  
Shuling Zhang ◽  
Jianguo Shen ◽  
Zujian Wu ◽  
Zhenguo Du ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Tomato Mosaic Virus ◽  
Phylogeographic History ◽  
History Of

scholarly journals Mutations in nuclear gene cyt-4 of Neurospora crassa result in pleiotropic defects in processing and splicing of mitochondrial RNAs.

Genetics ◽  
1989 ◽  
Vol 123 (1) ◽  
pp. 97-108 ◽  
Author(s):  
K F Dobinson ◽  
M Henderson ◽  
R L Kelley ◽  
R A Collins ◽  
A M Lambowitz
Keyword(s):  
Neurospora Crassa ◽  
Mitochondrial Protein ◽  
Nuclear Gene ◽  
Northern Hybridization ◽  
Rrna Gene ◽  
Mitochondrial Rna ◽  
Group I Introns ◽  
Group I ◽  
Processing Pathways ◽  
Aberrant Rna

Abstract The nuclear cyt-4 mutants of Neurospora crassa have been shown previously to be defective in splicing the group I intron in the mitochondrial large rRNA gene and in 3' end synthesis of the mitochondrial large rRNA. Here, Northern hybridization experiments show that the cyt-4-1 mutant has alterations in a number of mitochondrial RNA processing pathways, including those for cob, coI, coII and ATPase 6 mRNAs, as well as mitochondrial tRNAs. Defects in these pathways include inhibition of 5' and 3' end processing, accumulation of aberrant RNA species, and inhibition of splicing of both group I introns in the cob gene. The various defects in mitochondrial RNA synthesis in the cyt-4-1 mutant cannot be accounted for by deficiency of mitochondrial protein synthesis or energy metabolism, and they suggest that the cyt-4-1 mutant is defective in a component or components required for processing and/or turnover of a number of different mitochondrial RNAs. Defective splicing of the mitochondrial large rRNA intron in the cyt-4-1 mutant may be a secondary effect of failure to synthesize pre-rRNAs having the correct 3' end. However, a similar explanation cannot be invoked to account for defective splicing of the cob pre-mRNA introns, and the cyt-4-1 mutation may directly affect splicing of these introns.

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